Re: [Open Babel] Converting pdbqt to sdf
Hi Eduardo, As I understand - you are trying to read back Vina docked conformers of your small molecules. Maybe I can suggest a different approach, which I implemented in ODDT. Instead of reading back the molecules and recreating bonds, you could read back just the 3D conformer onto an original molecule (without touching the bond orders at all). See https://github.com/oddt/oddt/blob/master/oddt/docking/AutodockVina.py#L285 Additionally, you could use either OB and RDKit, the latter has some more boilerplate in ODDT, where you can write the RDKit molecules straight to PDBQT for Vina. https://github.com/oddt/oddt/blob/a3ff8b84b3abf986ad5bdbfebc9ef96cb8a84d8c/oddt/toolkits/extras/rdkit/__init__.py#L353 The bottom line is the same for both toolkits - you do not care what the BO are after docking as long as you have the original molecule in place. Best, Maciek Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl czw., 11 mar 2021 o 09:46 Eduardo Mayo napisał(a): > Hi OpenBabels users, > Nice to join the community. > I would like to convert pdbqt file to sdf file without using openbabel > itself. I mean why should my project has another dependency just to do a > single task. So I look into OpenBabel code and I finally found this ( > https://github.com/openbabel/openbabel/blob/4709b0752109db593f1bee6298ef3bfa718d260d/src/formats/pdbqtformat.cpp > ) > > I have some questions: > Where are defined these functions? > line:219 parseAtomRecord > line:295 resdat.AssignBonds(mol) > > > Bests, > Eduardo > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Access OBElementTable from C# binding OBDotNet.dll
Hi Chengxi, All methods of ElementsTable() class are right now in the openbabel.openbabel namespace. E.g. if you used to have "openbabel.OBElementTable().GetVdwRad(1)" you should change it to "openbabel.GetVdwRad(1)" now. Remember that openbabel and pybel are located both in openbabel namespace, so you need to import it as follows: > from openbabel import openbabel Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl niedz., 10 lis 2019 o 15:23 Yang, Chengxi napisał(a): > Hi Openbabel Team, > > I noticed that you have removed the OBElementTable class in 3.0.0. > In you documentation, you mentioned it is replaced by OBElement namespace. > I am wondering how can I access this namespace from the csharp binding. > > Thank, > Chengxi > > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Adding hydrogens before docking
Hi, This is highly dependent on docking software. Autodock Vina requires only polar hydrogens, but others will differ. Best, Maciek sob., 3 lis 2018, 11:28: Noel O'Boyle napisał(a): > You need to add all hydrogens. I have never understood why those options > are provided. > > On Thu, 1 Nov 2018, 19:41 Leif Peterson wrote: > >> Before performing ligand energy minimization then docking with receptors, >> I am adding hydrogens to ligands via the syntax: >> >> Addhydrogens(False, False); >> >> I am pretty sure this adds implicit H since polar-only is false. For >> docking, should I only add polar H, or is ...(False, False) the recommended >> choice for ligand prep? >> >> >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Help with generation of atom names in mol2 format
Hi Antionio,
OpenBabel generates new labels, unless there are already OBResiude info on
that. You can set it to whatever you want with OBResiude.SetAtomID().
Checkout the script below:
import pybel
> ob = pybel.ob
> mol = pybel.readstring('smi', 'c1c1')
> res = ob.OBResidue()
> for atom in ob.OBMolAtomIter(mol.OBMol):
> res.AddAtom(atom)
> res.SetAtomID(atom, '%s%i' %
> (ob.OBElementTable().GetSymbol(atom.GetAtomicNum()), atom.GetIdx()))
>
print(mol.write('mol2'))
Note that if you use the -xl option the residue will be ignored, but you
can name the residue to whatever you want via res.SetName('BLAH')
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2018-01-18 23:57 GMT+01:00 Antonio Jesus Banegas Luna <
ajbane...@alu.ucam.edu>:
> Hello all,
>
> I'm a newby in obabel and I need a bit of help.
> I use obabel to convert a file from sdf to mol2 format because another
> program requires such conversion.
> The conversion is fine, and I get something like this (I only show the
> ATOM block):
>
> @ATOM
> 1 C 0.5825 -1.49430.8613 C.ar1 LIG1
> 0.0063
> 2 C -0.4113 -2.11971.6364 C.ar1 LIG1
> 0.0421
> 3 C -1.7701 -1.87081.3728 C.ar1 LIG1
> 0.1957
> 4 O -2.7253 -2.46432.1262 O.3 1 LIG1
> -0.2866
> 5 C -2.1325 -1.00440.3248 C.ar1 LIG1
> 0.0421
>
> However, the third-party software requires something like this:
>
> @ATOM
> 1 C*1* 0.5825 -1.49430.8613 C.ar1 LIG1
> 0.0063
> 2 C*2* -0.4113 -2.11971.6364 C.ar1 LIG1
> 0.0421
> 3 C*3* -1.7701 -1.87081.3728 C.ar1 LIG1
> 0.1957
> 4 O*1* -2.7253 -2.46432.1262 O.3 1 LIG1
> -0.2866
> 5 C*4* -2.1325 -1.00440.3248 C.ar1 LIG1
> 0.0421
>
> Now, my question is: is there any way of forcing obabel to generate atom
> names in the required format?
> Maybe someone has some experience with this.
>
> Thanks in advance,
> Antonio
>
> --
> Antonio J. Banegas Luna
> Bioinformatics and High Performance Computing Research
> groupajbane...@alu.ucam.edu
> http://orcid.org/-0003-1158-8877http://www.researcherid.com/rid/O-7331-2016https://scholar.google.es/citations?user=EWtHIUMJhttps://www.researchgate.net/profile/Antonio_Jesus_Banegas_Luna
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Define origin for ECFP2 fingerprints
Hi Marcos, There is no straightforward way to do it OpenBabel, I've recentrly developed such fingerprint (Protein-Ligand Extended Connectivity FP) and presented it on RDKit UGM https://github.com/rdkit/UGM_2017/blob/master/Posters/Wojcikowski-PLEC_fingerprint.pdf PLEC Basically is what you've suggested - a collection of hashed contacts in the complex. There is an OpenBabel and RDKit's implementation of PLEC in ODDT, see https://oddt.readthedocs.io/en/latest/rst/oddt.html#oddt.fingerprints.PLEC and here https://github.com/oddt/oddt/blob/master/oddt/fingerprints.py#L616 If you wish to experiment with the function that you've asked for there it is (_ECFP_atom_hash): https://github.com/oddt/oddt/blob/master/oddt/fingerprints.py#L358 There is Noel's blog with ECFP that you can play with ( https://baoilleach.blogspot.com/2008/07/calculate-circular-fingerprints-with.html) although OBMolAtomBFSIter is buggy and does not work correctly with disconnected molecular parts, which will happen with proteins ( https://github.com/openbabel/openbabel/issues/1639). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-10-16 15:27 GMT+02:00 Marcos Vinicius Da Silva Santana < marcossant...@id.uff.br>: > Is it possible to calculate circular fingerprints around a predefined > atom/atom-pair? > > For example, I'm using a PDB file containing a ligand (LIG) showing a > nitrogen atom (e.g. N) that interacts with an oxygen atom of a serine > residue (let's call it OG). > What I want is to generate a circular fingerprint around this atom pair > (N-OG), while ignoring other ligand atoms. This would be similar to > protein-ligand interaction fingerprints. > Is it possible with OpenBabel? > > Best wishes, > > Marcos Vinicius Santana > M.Sc > Farmacêutico > Universidade Federal Fluminense > Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular > (LABiEMol) > Niterói, RJ - Brazil > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Submolecule from OBMol
I was wrong, the "F" option retains bonds' order and it even works for
aromatic atoms.
For future reference, to generate smiles of fragment by atom indices in
Python you can do:
> idxs = [1,2,3,4]
> mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip()
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 17:19 GMT+02:00 Maciek Wójcikowski :
> No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
> Chem.PathToSubMol() in RDKit, but the function you've suggested is also
> feasible.
>
> @Geoff - the smiles fragment does not perserve any bond information from
> what I've tested so far.
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-19 17:12 GMT+02:00 Andrew Dalke :
>
>> Me:
>> > Perhaps you want Chem.MolFragmentToSmiles(mol, atomsToUse=idxs)?
>> >
>> > http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-
>> module.html#MolFragmentToSmiles
>>
>> Err, umm, *blush*. Forgot which list I was reading.
>>
>> [Andrew! It says it right in the subject line! :]
>>
>> Andrew
>> da...@dalkescientific.com
>>
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Submolecule from OBMol
No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and Chem.PathToSubMol() in RDKit, but the function you've suggested is also feasible. @Geoff - the smiles fragment does not perserve any bond information from what I've tested so far. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 17:12 GMT+02:00 Andrew Dalke : > Me: > > Perhaps you want Chem.MolFragmentToSmiles(mol, atomsToUse=idxs)? > > > > http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-module.html# > MolFragmentToSmiles > > Err, umm, *blush*. Forgot which list I was reading. > > [Andrew! It says it right in the subject line! :] > > Andrew > da...@dalkescientific.com > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Submolecule from OBMol
I'm trying to get back the ECFP environments, most preferably as smiles. So it's literally a list of connected atoms. The dumb solution goes as follows: def submol(mol, idxs): > mol_clone = mol.clone > mol_clone.OBMol.BeginModify() > delete_atoms = [] > for i in reversed(range(len(mol.atoms))): > if i in idxs: > continue > delete_atoms.append(mol_clone.OBMol.GetAtomById(i)) > for atom in delete_atoms: > mol_clone.OBMol.DeleteAtom(atom) > mol_clone.OBMol.BeginModify() > return mol_clone Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 15:53 GMT+02:00 Noel O'Boyle : > This would be a useful API function. > > If it's a disconnected portion of the molecule, and you wanted to > write a smiles, there is a fragment option for the smiles writer that > you could use. > > - Noel > > On 17 June 2017 at 21:44, Maciek Wójcikowski > wrote: > > Hi all, > > > > Quick question: I have OBMol and want to create a sub-molecule from a > subset > > of atoms given by atom/bond indices. Is there a clever way to do it in > > OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms > ;) > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > -- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Submolecule from OBMol
The last BeginModify should be EndModify. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski : > I'm trying to get back the ECFP environments, most preferably as smiles. > So it's literally a list of connected atoms. > > The dumb solution goes as follows: > > def submol(mol, idxs): >> mol_clone = mol.clone >> mol_clone.OBMol.BeginModify() >> delete_atoms = [] >> for i in reversed(range(len(mol.atoms))): >> if i in idxs: >> continue >> delete_atoms.append(mol_clone.OBMol.GetAtomById(i)) >> for atom in delete_atoms: >> mol_clone.OBMol.DeleteAtom(atom) >> mol_clone.OBMol.BeginModify() >> return mol_clone > > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 2017-06-19 15:53 GMT+02:00 Noel O'Boyle : > >> This would be a useful API function. >> >> If it's a disconnected portion of the molecule, and you wanted to >> write a smiles, there is a fragment option for the smiles writer that >> you could use. >> >> - Noel >> >> On 17 June 2017 at 21:44, Maciek Wójcikowski >> wrote: >> > Hi all, >> > >> > Quick question: I have OBMol and want to create a sub-molecule from a >> subset >> > of atoms given by atom/bond indices. Is there a clever way to do it in >> > OpenBabel? I'm aware that I can make a copy and prune the unwanted >> atoms ;) >> > >> > >> > Pozdrawiam, | Best regards, >> > Maciek Wójcikowski >> > mac...@wojcikowski.pl >> > >> > >> -- >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > ___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > >> > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Submolecule from OBMol
Hi all, Quick question: I have OBMol and want to create a sub-molecule from a subset of atoms given by atom/bond indices. Is there a clever way to do it in OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms ;) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.
I've rebuilt the Python 2.7 packages for Windows (the rest is still
compiling), and the PNG should work now. Update openbabel package to 2.4.1
py27_3: `conda install -c openbabel openbabel`.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-05-31 13:16 GMT+02:00 Noel O'Boyle :
> That's a pity. In the meanwhile, you can still create SVG images if
> you choose this a write format, and pysvg might be able to convert to
> PNG (?).
>
> On 31 May 2017 at 10:21, Maciek Wójcikowski wrote:
> > Hi,
> >
> > PNG is not supported yet on Windows - Openbabel was not compiled with
> it, as
> > there is no cairo package on Anaconda main channel for windows (note
> you're
> > using conda-forge).
> >
> > Unfortunately this is also the case in bioconda, so for now there is no
> > better conda solution yet. I will revisit this issue and try to support
> PNG
> > files.
> >
> >
> > Pozdrawiam, | Best regards,
> > Maciek Wójcikowski
> > mac...@wojcikowski.pl
> >
> > 2017-05-31 11:06 GMT+02:00 Hongbin Yang :
> >>
> >> Hi，
> >>
> >> I installed openbabel via `conda install -c openbabel openbabel`.
> >>
> >> I wanted to draw the molecule like
> >> `pybel.readstring('smi','c1c1').draw()`
> >>
> >> Then the error was raised:
> >> C:\Users\yanya\Anaconda2\lib\site-packages\pybel.pyc in draw(self,
> show,
> >> filename, update, usecoords)
> >> 615 formatok = obconversion.SetOutFormat("_png2")
> >> 616 if not formatok:
> >> --> 617 raise ImportError("PNG depiction support not found. You should "
> >> 618 "compile Open Babel with support for Cairo. See "
> >> 619 "installation instructions for more "
> >>
> >> ImportError: PNG depiction support not found. You should compile Open
> >> Babel with support for Cairo. See installation instructions for more
> >> information.
> >>
> >> The installed packages includes:
> >> libpng 1.6.28 vc9_0 [vc9] conda-forge
> >> pillow 4.0.0 py27_0
> >> pycairo 1.10.0
> >> openbabel 2.4.1 py27_2 openbabel
> >> cairo 1.14.6 vc9_4 [vc9] conda-forge
> >>
> >> I have both pillow and (py)cairo. Why can't I draw the molecule ?
> >> I guess that if I followed the suggestion and compile it with suport
> cairo
> >> it will work. But I have to work with conda. Is there any better way?
> >>
> >> Sincerely,
> >>
> >>
> >> Hongbin Yang 杨弘宾
> >> Research: Toxicophore and Chemoinformatics
> >> Pharmaceutical Science, School of Pharmacy
> >> East China University of Science and Technology
> >>
> >>
> >>
> --
> >> Check out the vibrant tech community on one of the world's most
> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> ___
> >> OpenBabel-discuss mailing list
> >> OpenBabel-discuss@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >>
> >
> >
> >
> --
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.
Hi,
PNG is not supported yet on Windows - Openbabel was not compiled with it,
as there is no cairo package on Anaconda main channel for windows (note
you're using conda-forge).
Unfortunately this is also the case in bioconda, so for now there is no
better conda solution yet. I will revisit this issue and try to support PNG
files.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-05-31 11:06 GMT+02:00 Hongbin Yang :
> Hi，
>
> I installed openbabel via `conda install -c openbabel openbabel`.
>
> I wanted to draw the molecule like
> `pybel.readstring('smi','c1c1').draw()`
>
> Then the error was raised:
> C:\Users\yanya\Anaconda2\lib\site-packages\pybel.pyc in draw(self, show,
> filename, update, usecoords)
> 615 formatok = obconversion.SetOutFormat("_png2")
> 616 if not formatok:
> --> 617 raise ImportError("PNG depiction support not found. You should "
> 618 "compile Open Babel with support for Cairo. See "
> 619 "installation instructions for more "
>
> ImportError: PNG depiction support not found. You should compile Open
> Babel with support for Cairo. See installation instructions for more
> information.
>
> The installed packages includes:
> libpng 1.6.28 vc9_0 [vc9] conda-forge
> pillow 4.0.0 py27_0
> pycairo 1.10.0
> openbabel 2.4.1 py27_2 openbabel
> cairo 1.14.6 vc9_4 [vc9] conda-forge
>
> I have both pillow and (py)cairo. Why can't I draw the molecule ?
> I guess that if I followed the suggestion and compile it with suport cairo
> it will work. But I have to work with conda. Is there any better way?
>
> Sincerely,
>
> --
> Hongbin Yang 杨弘宾
> Research: Toxicophore and Chemoinformatics
> Pharmaceutical Science, School of Pharmacy
> East China University of Science and Technology
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] About pybel module installation
Hello, What you need is openbabel package not pybel: "pip install openbabel" See https://pypi.python.org/pypi/openbabel Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-04-06 1:23 GMT+02:00 Phuong Do : > Hello, > > I intend to use pybel module in python for my project. When I install > pybel by "pip install pybel" and "import pybel", there is no error. > However, now when I check for "modules installed in python", it is pyBEL > 0.4.4, not pybel that I want. > > Is there any way that I can install it properly. I am using macbook. > Thank you very much. > > Phuong Do > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3
Hello, Python 3.6 support is not there yet. It should be added soon. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-02-13 5:31 GMT+01:00 i4hashmi : > I am using Python for making a script to work with some chemical structures > in my PhD. I want to install openbabel libraries for python. I tried my > best > but I could not install it on Windows. I posted a question earlier about > installing it on Windows at > http://stackoverflow.com/questions/42151301/how-do-i- > install-openbabel-for-python-3-6-in-windows-10/42151551? > noredirect=1#comment71470260_42151551 > but could not find a solution. The solution installed the library but it > does not work and could not connect to SWIG. > No I am trying to install it on my office computer which is a mac for past > 5 > hours but I could not figure what is going on. > I tried to install it from source code of Openbabel and link it with > python3 > but it is making problem. > If I use the following command: > > `cmake ../ -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON` > > It successfully links it to Python 2.7 which I do not want. When I try the > following options, it gives the error shown below: > > `cmake ../ -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON > -DRUN_SWIG=ON` > > OR > > `cmake ../ -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 > -DPYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/ > Versions/3.5/include/python3.5m > -DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/ > Versions/3.5/lib/libpython3.5m.dylib > -DPYTHON_BINDINGS=ON` > > It gives the following error at the end after a lot of successful output: > > -- Found PythonInterp: /usr/bin/python3.6 (found version "1.4") > -- Found SWIG: /usr/local/bin/swig (found version "3.0.12") > -- Found SWIG: /usr/local/bin/swig (found suitable version "3.0.12", > minimum required is "2.0") > -- Found PythonLibs: > /usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/ > Versions/3.6/lib/libpython3.6m.dylib > (found version "3.6.0") > -- Python bindings will be compiled > CMake Error at scripts/CMakeLists.txt:120 (install): > install TARGETS given no LIBRARY DESTINATION for module target > "bindings_python". > CMake Error at scripts/CMakeLists.txt:123 (install): > install FILES given no DESTINATION! > CMake Error at scripts/CMakeLists.txt:126 (install): > install FILES given no DESTINATION! > -- Configuring incomplete, errors occurred! > See also > "/usr/local/Cellar/obabel/openbabel-master/ali/ > CMakeFiles/CMakeOutput.log". > See also > "/usr/local/Cellar/obabel/openbabel-master/ali/CMakeFiles/CMakeError.log". > > > I am not sure why It detects the Python as v1.4 `-- Found PythonInterp: > /usr/bin/python3.6 (found version "1.4") ` instead of finding v.3.5. > I tried all the procedure with python 3.6 as well but the same errors > occur. > I am also using the openbabel obtained from github which was said to be > working with these commands at the following post: > http://forums.openbabel.org/OpenBabel-for-Python-3-td4659432.html > But it doesn't work as well. > Please help me as I require this module for my research. > Thanks > > > > -- > View this message in context: http://forums.openbabel.org/ > How-to-Install-openbabel-for-Python-3-6-on-macOS-Sierra-10- > 12-3-tp4659726.html > Sent from the General discussion mailing list archive at Nabble.com. > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OpenBabel for Python 3?
Hi Sanjan, Since you've already have (Ana)conda, the easiest solution whould be installing it via conda: "conda install -c openbabel openbabel" Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-11-30 3:46 GMT+01:00 tpsanjan : > Hi, > > I have been trying install python bindings for openbabel 2.4.1 on > Ubunut16.04 with python 3.5.2 (installed via Anaconda) but haven't been > able > to get it working. Here's what I have tried so far: > > Based on David Hall's post in this thread: > > $ git clone https://github.com/openbabel/openbabel.git > $ cd openbabel > $ mkdir build > $ cd build > $ cmake .. -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_BINDINGS=ON > -DRUN_SWIG=ON > $ grep '^PYTHON' CMakeCache.txt > > And then followed the steps given on openbabel docs > (https://open-babel.readthedocs.io/en/latest/Installation/install.html# > compile-bindings) > > $ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON > $ make > # make install > $ export PYTHONPATH=/usr/local/lib:$PYTHONPATH > > All commands seemed to run smoothly (python3-dev is installed). But when I > use python shell through terminal: > > sgupta78@sgupta78:~$ python > imPython 3.5.2 |Anaconda 4.1.1 (64-bit)| (default, Jul 2 2016, 17:53:06) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux > Type "help", "copyright", "credits" or "license" for more information. > >>> import openbabel > >>> mol = openbabel.OBMol() > Traceback (most recent call last): > File "", line 1, in > AttributeError: module 'openbabel' has no attribute 'OBMol' > > import openbabel was successful *but none of the functions in openbabel > module are being recognized*. As shown above it's raising AttributeError. > Is > there something that I missed during installation steps shown above? > > Secondly, when I ran a simple script [just to test OBMol() ] stored in a > sub-folder of home directory, *even the import openbabel failed*. This > possibly means that the environment variables haven't been set. I assumed > that cmake and export steps above possibly take care of it. > > Any help would be appreciated. > > Thanks, > Sanjan > > > > > > > > -- > View this message in context: http://forums.openbabel.org/ > OpenBabel-for-Python-3-tp4659432p4659622.html > Sent from the General discussion mailing list archive at Nabble.com. > > > -- > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] MOPAC
Babel is deprecated in 2.4, maybe that's messing with your app? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-11-15 12:45 GMT+01:00 Chris Swain : > Hi, > > Thanks, that works fine. > > Chris > > On 15 Nov 2016, at 11:06, Pascal Muller > wrote: > > Hi, > > > A user of iBabel reported that they could not convert sdf files to MOPAC >> (.mop) . >> >> I checked using the command line >> >> /usr/local/bin/babel '/Users/Chris/Desktop/confs/temp1.sdf' -omop >> -xf '/Users/Chris/Desktop/confs/temp1.mop’ >> >> and >> >> /usr/local/bin/obabel '/Users/Chris/Desktop/confs/temp1.sdf' -omop >> -xf '/Users/Chris/Desktop/confs/temp1.mop’ >> >> and whilst output appears in the terminal window no output file is created >> >> Do I have the syntax wrong or something? >> > > Try using the -O option (-O) e.g. > obabel tmp.sdf -O tmp.mop > > Regards, > Pascal > > >> Cheers >> >> Chris >> >> >> -- >> >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > -- > > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem with Pybel installation for Anaconda
Hi,
Indeed for some reason InCHI is not built on windows. I'll have to fix it,
stay tuned for updates.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-10-15 9:30 GMT+02:00 Noel O'Boyle :
> I can't comment on the anaconda parts, but maybe Maciek can...
>
> Regarding pip, apologies, we're in the middle of releasing OB 2.4.1 and I
> haven't yet updated the "pip install" parts which need to be in synch with
> the OB install. Give me until Monday and it should be fine.
>
> Regarding uninstall, pip is lying. I guess it's a pip bug, but it doesn't
> uninstall when the pip package is a wheel. If you go to your site-packages
> directory you will see several openbabel files - I don't know if this is
> the problem though.
>
> - Noel
>
>
> On 14 Oct 2016 8:41 p.m., "Richard Marchese Robinson" <
> rmarcheserobin...@gmail.com> wrote:
>
>> Hi,
>>
>> I've been encountering difficulties getting Pybel to install for Anaconda.
>>
>> I would be grateful for any assistance you have time to provide.
>>
>> I managed to install Pybel via the following command:
>> conda install -c openbabel openbabel=2.4.1
>> [based on https://anaconda.org/openbabel/openbabel]
>>
>> However, it seems 'inchi' is not a recognised format, as shown below,
>> even though - when working with Pybel version 1.8 with Python 2.7.5
>> (vanilla Python installation) - the following sequence of commands worked
>> without error.
>>
>>
>> Python 2.7.12 |Anaconda 4.0.0 (32-bit)| (default, Jun 29 2016, 11:42:13)
>> [MSC v.1500 32 bit (Intel)] on win32
>> Type "help", "copyright", "credits" or "license" for more information.
>> Anaconda is brought to you by Continuum Analytics.
>> Please check out: http://continuum.io/thanks and https://anaconda.org
>> >>> import pybel
>> >>> mol = pybel.readstring('smi','c1c1')
>> >>> mol.write('inchi')
>> Traceback (most recent call last):
>> File "", line 1, in
>> File "C:\Anaconda2\lib\site-packages\pybel.py", line 527, in write
>> format)
>> ValueError: inchi is not a recognised Open Babel format
>> =
>>
>> Please note that I did previously try getting Pybel via the PyPi
>> openbabel package [pip install openbabel], for which import pybel failed
>> with the message ["ImportError: DLL load failed: The specified procedure
>> could not be found."]. I do hope I have not created a mess. However, as
>> "pip uninstall openbabel" reported "Cannot uninstall requirement openbabel,
>> not installed", I believe the old PyPi installation was cleared up?
>>
>>
>> Best regards,
>>
>> Richard
>>
>>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Question about file conversion
Hi, That is a wild guess, since you gave us near to zero information, but what is the first line of your .smi file? If it's not valid smiles, then the reader will give up, since it has finish reading the file on first line. Valid smiles file is: "smiles string, white-space and name", like "c1c1 benzene" Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-05-09 4:35 GMT+02:00 Brendan M. O'Boyle : > Hello, > > I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf > files for manipulation with Schrodinger software. > > I installed the OpenBabel first and then I am using iBabel. I put in the > SMILES string under the convert header and then use that to prepare an sdf > file. > > However, the file is zero bytes and there is something wrong with the > conversion even though a file is generated. > > Is this a common problem? > > Thank you, > Brendan > > -- > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] generating conformers with open babel
Hello, I think that Confab is available only in current development branch. Check "obabel -L confab" to see if it's there. If not then you'd have to use conda or compile it yourself. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-05-03 12:14 GMT+02:00 Francois Berenger : > Hello, > > I am running Open Babel 2.3.2. > > I naively thought that the command: > > obabel input.mol2 -O output.mol2 --confab --conf 50 > > Would give me in output.mol2 the 50 lowest energy conformers > of each molecule in input.mol2. > > Unfortunately not (output.mol2 is equal to input.mol2). > > What is the proper way to call confab ? > > Thanks, > F. > > > -- > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] set the atom type in python interface
Hi,
Here you go:
from openbabel import OBAtomAtomIter,OBTypeTable
# setup typetable to translate atom types
typetable = OBTypeTable()
typetable.SetFromType('INT')
typetable.SetToType('SYB')
lig = pybel.readfile('sdf', "xxx.sdf").next()
types = [typetable.Translate(a.type) for a in lig.atoms]
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-04-13 19:13 GMT+02:00 Yun Ding :
> Dear all,
>
>
> I would like to get the SYB type of the atom using the python interface,
> however, it always gives the INT type, how can I set it to be SYB type?
>
>
> By studying the C++ code I know how to do it in C++. But using python is
> much more convenient for me.
>
>
> So far my code is like
>
>
> ```
>
> import pybel
>
>
> lig = pybel.readfile('sdf', "xxx.sdf").next()
>
> types = [a.type for a in lig.atoms]
>
> ```
>
>
> Thanks!
>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] problem with residue detection
Hi, Add "-xl" to the command line (which ignores the residues for mol2). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-04-11 19:08 GMT+02:00 Fredy Quevedo : > Dear all: > > I am having some problem with the conversion of a .smi file to a .mol2 > structure. The .smi notation is: > > OC[C@@H]1CCCN1C(=O)[C@H](Cc1c[nH]c2c12)Nc1ccc(Nc2ccncc2)cc1 > > > after applying the following script: > > obabel -ismi file.smi -omol2 -O file.mol2 > > > I obtain a .mol2 file in which residues are named TRP and UNK, and it > seems like the molecule es detected as containing 2 residues. Is obable > recognizing a tryptophan residue in my organic molecule and it is > assignig it as a residue? > How can I skip this detection? > > thank you very much in advance for the help, > > best regards > > Alfredo > > > -- > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ > gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] PAINS filtering
Hi, There are improved SMARTS for PAINS in RDKit. https://github.com/rdkit/rdkit/tree/master/Data/Pains http://rdkit.blogspot.com/2015/08/curating-pains-filters.html You can also use ODDT to do the filtering http://oddt.readthedocs.org/en/latest/#oddt-command-line-interface-cli example #2. (although currently it uses Rajarshi's SMARTS definition). I have to update those to Greg's revised version. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-03-15 18:54 GMT+01:00 Stefano Forli : > About that, a while ago I had compiled an OB-compatible data file with the > three pattern > classes (L15, L150 and M150) from Raj Gua [1]. > > Dirt cheap implementation with Pybel works fine, but the main issue is > timing. Processing > a Mol2 file with 1000 random molecules from the ZINC database takes about > 13 seconds. > Not bad, but not even fast: to process a pretty large library for virtual > screning (e.g, > ChemBridge library, 1.5M compounds) would take about 5.4 hours. > > I'm not sure if there's a way to speed up the process, but if so, it > should be definitely > considered. > > Anyway, let me know what would be the best way to share the files, and > I'll do it. > > Cheers, > > S > > > [1] http://blog.rguha.net/?p=850 > > > On 03/15/2016 08:21 AM, mirix wrote: > > There you go: > > > > http://pastebin.ca/raw/3401877 <http://pastebin.ca/raw/3401877> > > > > This comes from here: > > > > http://blog.rguha.net/?p=850 > > > > > > > > > > -- > > View this message in context: > http://forums.openbabel.org/PAINS-filtering-tp4659223p4659226.html > > Sent from the General discussion mailing list archive at Nabble.com. > > > > > -- > > Transform Data into Opportunity. > > Accelerate data analysis in your applications with > > Intel Data Analytics Acceleration Library. > > Click to learn more. > > http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140 > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > -- > > Stefano Forli, PhD > > Assistant Professor of Integrative > Structural and Computational Biology, > Molecular Graphics Laboratory > > Dept. of Integrative Structural >and Computational Biology, MB-112A > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > fax: +1 (858)784-2860 > email: fo...@scripps.edu > http://www.scripps.edu/~forli/ > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] pdf export
If you need this badly there is na option to write CSV file in ODDT's
virtual screening module. You can choose a delimiter and quotation signs,
but unfortunately it does not write smiles to CSV. If you need it badly i
can add parameter to include smiles in CSV. Sorry for off-OpenBabel mail.
from oddt.virtualscreening import virtualscreening as vs
pipeline = vs()
pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
pipeline.write_csv('ampc_docked.csv')
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-22 14:17 GMT+01:00 Chris Swain :
> Apologies the title should be sdf export.
>
> A couple of additional comments.
>
> It would be useful to have options for the delimiter. It is possible the
> content may contain commas, so options for tab or pipe might be useful
> and/or putting quotes around text.
>
> Not every record in a sdf will have all fields so the usual strategy is to
> first scan the sdf file to identify all fields and then go back to the
> start to do the export.
>
> Cheers,
>
> Chris
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] pdf export
Hi Chris, There is not such thing, as far as I know. Although a hack comes to my mind: smi + --append in CLI: obabel -ismi -:'c1c1 title_here' -osmi --append logp The only issue is that smiles and title is separated by tab (\t) and properties in title append after spaces. Plus you have to enumerate all the columns you'd like to include. I would also second a CSV output format to write all the properties. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-01-21 22:43 GMT+01:00 Chris Swain : > Hi, > > Is there an output format that can be used to convert an sdf file to > delimited text, such that the output contains SMILES, molecule name and any > fields within the sdf? Ideally with the first row of the file being the > titles off the fields? > > Cheers, > > Chris > > > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] azoxy
Hi Stefano,
I might suggest trying VS module in oddt (https://github.com/oddt/oddt)
which is based on Pybel (DISCLAIMER: I'm the author of oddt). To overcome
the connectivity problem it just copy the coordinates of docked
conformationson the input molecules. This way you should retain the
connectivity.[
https://github.com/oddt/oddt/blob/master/oddt/docking/AutodockVina.py#L199]
Sample docking pipeline is below. Note that comments (which allow you to
save scores) in mol2 files are available in development version of
OpenBabel. If you use stable, then use SDF.
from oddt.virtualscreening import virtualscreening as vs
# Initiate virtual screening pipeline using 8 CPUs
pipeline = vs(n_cpu=8)
# Load ligands from a mol2 file
pipeline.load_ligands('mol2', 'ampc/actives_final.mol2.gz')
# Dock entire library to receptor, autocenter docking box on ligand
pipeline.dock('autodock_vina', 'ampc/receptor.pdbqt',
'ampc/crystal_ligand.mol2')
# Write docked ligands conformations to a file (including scores)
pipeline.write('mol2', 'ampc_docked.mol2', overwrite=True, opt={'c':None})
The arguments for dock method:
http://oddt.readthedocs.org/en/latest/rst/oddt.docking.html#module-oddt.docking.AutodockVina
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-05 12:14 GMT+01:00 Stefano Forli :
> Hi Stefano,
> the problem with the PDBQT format is that connectivity is implicit and
> bond order is lost.
> If your atom coordinates are close to ideal (i.e., bond lengths are
> optimal, non-distorted) you have a good chance of OB to be able to re-build
> the correct bond order.
> Although, there's been some discussion in the mailing list about similar
> problems using PDB files as well.
> My advice is to manually correct the issues, hoping you don't have too
> many files to process.
>
> Best,
>
> S
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor of Integrative
> Structural and Computational Biology,
> Molecular Graphics Laboratory
>
> Dept. of Integrative Structural
> and Computational Biology, MB-112F
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
> From: Stefano Guglielmo [stefano.guglie...@unito.it]
> Sent: Monday, January 04, 2016 4:12 PM
> To: openbabel-discuss@lists.sourceforge.net
> Subject: [Open Babel] azoxy
>
> Dear opnebabel users,
>
> I've made docking with autodock of some molecules containing an azoxy
> function; I need to generate sdf file from pdbqt, but openbabel seems to
> manage the molecules not so well as it adds hydrogens to the azoxy group.
> Any suggestion about generating a correct sdf file?
>
> Thanks a lot
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678
>
>
>
>
>
> --
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
FYI The obabel -m option you've used separates molecules in multi-mol2 file
- the molecules must already be in separate molecule blocks.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 19:54 GMT+01:00 Filip Stefaniak :
> Hi Maciek,
>
> Maciek Wójcikowski pisze:
> > Hi Filip,
> >
> > OBMol has a Separate method, which does exactly what you'd
> > like.
> http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
> >
> > import pybel
> > mol = pybel.readfile('mol2', 'ligand.mol2').next()
> > for m in mol.OBMol.Separate():
> > print m
> >
> >
> > Note that m is an OBMol object, so to get pybel molecule you need to
> > initiate it via Molecule class:
> >
> > for m in mol.OBMol.Separate():
> > print pybel.Molecule(m)
>
> Thanks for that tip. I will try it.
>
> best regards,
> Filip
>
>
> --
> Filip Stefaniak
> Uptime: 13079 dni 19 godzin
> W lodówce ma 10.8stC, na działce w sadku 16.7stC
>
>
> --
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] splitting molecule file - the hard case
Hi Filip,
OBMol has a Separate method, which does exactly what you'd like.
http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
import pybel
> mol = pybel.readfile('mol2', 'ligand.mol2').next()
> for m in mol.OBMol.Separate():
> print m
Note that m is an OBMol object, so to get pybel molecule you need to
initiate it via Molecule class:
for m in mol.OBMol.Separate():
> print pybel.Molecule(m)
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-11-10 16:59 GMT+01:00 Filip Stefaniak :
> Hi,
> I have a mol2 file:
> https://gist.github.com/filipsPL/0b936f4d416bdc45ebea
>
> There are three apparently separate molecules inside. But I'm not able
> to separate them. obabel -m doesn't solve the problem.
>
> I've tried to do it in python with pybel, but I don't know how to
> exactly code it (it is not the simple case as described here:
>
> https://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html#split-an-sdf-file-using-the-molecule-titles
> )
>
> In pybel I can see that the molecules are actually separated somehow:
>
> from pybel import *
> mol = readfile("mol2", "ligand.mol2").next()
> print mol
>
> result is:
> [Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N.[Rh](N)(N)(N)(N)(N)N
>
> so my question is: how to separate this mol2 file into separate
> components? python or shell methods are acceptable.
>
> thank you for any tips,
> Filip
>
>
> --
> Filip Stefaniak
> Uptime: 13185 dni 16 godzin
> W lodówce ma 8.8stC, na działce w sadku 12.2stC
>
>
> --
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obabel -L conformer
Hello, What version od OB are you using? I would recommend checking latest master branch on github. Actually it has confab bundled, which was suggested by Pascal, while confab on itself also uses ancient version (2.3.1 as I remember correctly). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-05-29 10:02 GMT+02:00 Pascal Muller : > Hi, > > > >> According to "obabel -L conformer" there is an option that will carry out >> an exhaustive systematic search for the lowest energy conformer. When I >> execute "obabel --conformer --systematic", my output structure is identical >> to the input structure. For example: >> >> $ obabel in.xyz -O out.xyz --conformer --systematic >> 1 molecule converted >> >> $ diff in.xyz out.xyz >> 2c2 >> < >> --- >> > in.xyz >> >> Am I executing the program incorrectly? >> >> > --systematic doesn't output conformers for me too. > But e.g. --nconf 20 --writeconformers, instead of --systematic, does > output 20 conformers (starting from a 3D sdf). > obabel in.sdf -Oout.sdf --conformer --nconf 20 --writeconformers > > > Did you try confab? > > http://open-babel.readthedocs.org/en/latest/3DStructureGen/multipleconformers.html > > http://forums.openbabel.org/Confab-algorithm-for-openbabel-conformer-search-td4658039.html > > Regards, > Pascal > > > -- > > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] access all properties from mol2 file
Got it. OpenBabel currently does not support @COMMENT, where the
data sit from Gold. You can save docked conformations as SDF file and
normalize them. There is no other solution, as Gold embeds SDF style
variables in @COMMENT.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-30 18:45 GMT+02:00 Hitesh Patel :
> Hi Maciek,
> Attached is an example file. It is GOLD output file, and I want to
> normalize > .
>
> Regards,
> Hitesh Patel
>
> On Thu, Apr 30, 2015 at 6:24 PM, Maciek Wójcikowski > wrote:
>
>> Hi,
>>
>> Currently only UCSF Dock-style data fields are supported in mol2 files,
>> and you have to specify -ac or -xc option to read/write it from/to a file.
>> Can you give example of such mol2?
>>
>>
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>> 2015-04-30 17:16 GMT+02:00 Hitesh Patel :
>>
>>> Hi,
>>>
>>> I want to read a mol2 file containing thousands of molecules. Each
>>> molecule has some additional information specified by tags like below.
>>>
>>> >
>>> 31.8104
>>>
>>> I tried to read file using pybel But, I can access only Formula. There
>>> are no additional information from above tags.
>>>
>>> mol.data
>>> Out[80]: {'Formula': 'C27H37N2O4'}
>>>
>>> I want to modify the value and re-write the mol2 file
>>> without any more changes. Kindly suggest how to do that?
>>>
>>>
>>> Regards,
>>> Hitesh Patel
>>>
>>>
>>>
>>> --
>>> One dashboard for servers and applications across Physical-Virtual-Cloud
>>> Widest out-of-the-box monitoring support with 50+ applications
>>> Performance metrics, stats and reports that give you Actionable Insights
>>> Deep dive visibility with transaction tracing using APM Insight.
>>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] access all properties from mol2 file
Hi,
Currently only UCSF Dock-style data fields are supported in mol2 files, and
you have to specify -ac or -xc option to read/write it from/to a file. Can
you give example of such mol2?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-30 17:16 GMT+02:00 Hitesh Patel :
> Hi,
>
> I want to read a mol2 file containing thousands of molecules. Each
> molecule has some additional information specified by tags like below.
>
> >
> 31.8104
>
> I tried to read file using pybel But, I can access only Formula. There are
> no additional information from above tags.
>
> mol.data
> Out[80]: {'Formula': 'C27H37N2O4'}
>
> I want to modify the value and re-write the mol2 file without
> any more changes. Kindly suggest how to do that?
>
>
> Regards,
> Hitesh Patel
>
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Compressed pybel.Outputfile output
Hi Matthew,
In latest version of OB (master branch on github) automatically detects .gz
extensions and compresses the output - adds "-z" option to converter.
https://github.com/openbabel/openbabel/blob/master/scripts/python/pybel.py#L253
If you're using newest OB it should work out of the box. Otherwise
Stefano's solution is the one you go for.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-25 0:45 GMT+02:00 Matthew Lardy :
> Hi Stefano,
>
> That worked! Thanks!
> Matthew
>
> On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli wrote:
>
>> Hi Matthew,
>> I guess something like this could do the trick:
>> -
>> import gzip
>> import pybel
>>
>> mol = pybel.readfile('sdf', 'filename.sdf').next()
>> outfilename = 'example.sdf.gz'
>> output = gzip.open(outfilename, 'wb')
>> molString = mol.write(format='sdf')
>> output.write(molString)
>> output.close()
>> -
>> I didn't tested but I don't see why it shouldn't work(TM)
>>
>> S
>>
>>
>>
>> On 04/24/2015 03:12 PM, Matthew Lardy wrote:
>>
>>> Hi all,
>>>
>>> Does anyone have a route to write compressed sdf.gz files that are
>>> compatible with
>>> pybel.Outputfile?
>>>
>>> Thanks in advance!
>>> Matthew
>>>
>>
>> --
>> Stefano Forli, PhD
>>
>> Staff Scientist
>> Molecular Graphics Laboratory
>> Dept. of Integrative Structural
>> and Computational Biology, MB-112F
>> The Scripps Research Institute
>> 10550 North Torrey Pines Road
>> La Jolla, CA 92037-1000, USA.
>>
>> tel: +1 (858)784-2055
>> fax: +1 (858)784-2860
>> email: fo...@scripps.edu
>> http://www.scripps.edu/~forli/
>>
>
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] MACCS key 44
Hello Andrew,
I created pull request on github [
https://github.com/openbabel/openbabel/pull/96]
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-10-20 15:14 GMT+02:00 Andrew Dalke :
> Hi all,
>
> Open Babel's MACCS definitions derive from RDKit's. As such, it doesn't
> define key 44 because Greg didn't know what "OTHER" meant.
>
> You can see that in
> https://github.com/openbabel/openbabel/blob/master/data/MACCS.txt
> with
> 44:('?',0), # OTHER
>
> Since that time, Accelrys has published a white paper which clarifies
> a few things, including what "other" means. See my essay at
>
>
> http://www.dalkescientific.com/writings/diary/archive/2014/10/17/maccs_key_44.html
>
> for details.
>
> As a result, I proposed and Greg agreed that that definition be
> added to RDKit's implementation. The issues report is at
>
> https://github.com/rdkit/rdkit/issues/352
>
> the commit message is at
>
>
> https://github.com/rdkit/rdkit/commit/f48812238d6e7eb89cdb62920b176a242e1561d9
>
> and the pattern is
>
>[!#1;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#35;!#53]
>
> My argument for making a change is that so many people expect that
> a MACCS keys implementation means one thing (at least up to
> chemistry perception differences), and key 44 will affect the
> a chemical similarity measure, in a non-trivial and chemically
> relevant way (the other missing key, "isotope", doesn't have a real
> chemical difference in the same way).
>
> I think Open Babel should also make that change.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
>
> --
> Comprehensive Server Monitoring with Site24x7.
> Monitor 10 servers for $9/Month.
> Get alerted through email, SMS, voice calls or mobile push notifications.
> Take corrective actions from your mobile device.
> http://p.sf.net/sfu/Zoho
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Hello again, I also found out that there is problem with atom typing, which is bypassed while converting molecules (as in my previous reply). The nitrogen should be planar (N.pl3 as in mol2) and its' conformation in sdf file which you've provided is sp3. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-13 14:06 GMT+02:00 Maciek Wójcikowski : > We've received the input file. Of course there is problem with it, when > you pass it through mol2 file, then your fine. Also obabel reports "-nan" > scores for original molecule, which is bad. > > obabel crystal_ligand_flex.sdf -omol2 | obabel -imol2 --conformer --nconf > 2 --writeconformers -o smi > > Above command will output 2 conformets. I can't pin-point the problem with > this molecule yet,but still there is a solution. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2014-05-13 13:38 GMT+02:00 Douglas Houston : > > Can I just check people received the input file? I used the Nabble forum to >> attach it ... >> >> >> >> -- >> View this message in context: >> http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657429.html >> Sent from the General discussion mailing list archive at Nabble.com. >> >> >> -- >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. >> Get unparalleled scalability from the best Selenium testing platform >> available >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > -- "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
We've received the input file. Of course there is problem with it, when you pass it through mol2 file, then your fine. Also obabel reports "-nan" scores for original molecule, which is bad. obabel crystal_ligand_flex.sdf -omol2 | obabel -imol2 --conformer --nconf 2 --writeconformers -o smi Above command will output 2 conformets. I can't pin-point the problem with this molecule yet,but still there is a solution. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-13 13:38 GMT+02:00 Douglas Houston : > Can I just check people received the input file? I used the Nabble forum to > attach it ... > > > > -- > View this message in context: > http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657429.html > Sent from the General discussion mailing list archive at Nabble.com. > > > -- > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform > available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Hi, Is the input molecule flexible? It would be much easier to test if you could sent it to the list. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-07 11:19 GMT+02:00 Fredrik Wallner : > Continue by running > obabel -L formats > and > obabel -L ops > > Kind regards, > Fredrik > > Skickat från min iPhone > > > 7 maj 2014 kl. 11:06 skrev Douglas Houston >: > > > > /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L > > > > outputs: > > > > charges > > descriptors > > fingerprints > > forcefields > > formats > > loaders > > ops > > > > How do I tell? > > > > > > > > -- > > View this message in context: > http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657397.html > > Sent from the General discussion mailing list archive at Nabble.com. > > > > > -- > > Is your legacy SCM system holding you back? Join Perforce May 7 to find > out: > > • 3 signs your SCM is hindering your productivity > > • Requirements for releasing software faster > > • Expert tips and advice for migrating your SCM now > > http://p.sf.net/sfu/perforce > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- > Is your legacy SCM system holding you back? Join Perforce May 7 to find > out: > • 3 signs your SCM is hindering your productivity > • Requirements for releasing software faster > • Expert tips and advice for migrating your SCM now > http://p.sf.net/sfu/perforce > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] running Open Babel in parallel / distributed mode
Francois, could you please elaborate on the "log" argument? Because, that might be the only difference here. Using either gnu parallel or xargs standard output and error are "FIFO", which makes them useless. Other than that I cant see any advantage, since parallel line would be: cat commands.sh | parallel -P 8 > log 2> error.log (or 2>&1 if someone prefers joint log) ---- Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-02-04 11:58 GMT+01:00 Francois Berenger : > On 2/4/14, 6:28 PM, Noel O'Boyle wrote: > >> It would be nice to see some explicit examples of how Open Babel might >> be used in this way, using one or all of these tools. >> > > Let's say you have a file commmands.sh: > --- > obabel some_file1 -Osome_other_file1.other_format > ... > obabel some_file2 -Osome_other_file2.other_format > --- > > With PAR, you run them like this in parallel: > > par -i commands.sh -v -o log # all your cores will be used by default > > to check the logs (in case you are really careful about > what you are doing, e.g. when preparing datasets for scientific use), > I recommend: > > sort -u log | less > > > - Noel >> >> On 4 February 2014 00:52, Francois Berenger wrote: >> >>> On 02/04/2014 12:14 AM, Maciek Wójcikowski wrote: >>> >>>> You can also use xargs. >>>> >>> >>> Yes, xargs with the -P option, but the command lines are not trivial >>> then. >>> >>> >>>> Pozdrawiam, | Best regards, >>>> Maciek Wójcikowski >>>> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> >>>> >>>> >>>> 2014-02-03 16:10 GMT+01:00 Igor Filippov >>> <mailto:igor.v.filip...@gmail.com>>: >>>> >>>> How is it different from GNU parallel? >>>> http://www.gnu.org/software/bash/manual/html_node/GNU- >>>> Parallel.html >>>> >>> >>> It should be quite similar in functionality. >>> >>> Igor >>>> >>>> >>>> On Mon, Feb 3, 2014 at 1:37 AM, Francois Berenger < >>>> beren...@riken.jp >>>> <mailto:beren...@riken.jp>> wrote: >>>> >>>> Hello, >>>> >>>> I do this almost everyday so I think I should share it with >>>> this >>>> list. >>>> >>>> In case you need to execute many Open Babel commands >>>> and don't want to wait, you can execute them in parallel >>>> on a multi-core computer. >>>> Of course, the commands should be independent, for example >>>> processing different datasets. >>>> >>>> Let's say the commands are in a file called for_par.sh. >>>> I developped a tool called PAR years ago that can do this: >>>> >>>> par -i for_par.sh -v -o log >>>> >>>> It will use all cores of the computer, display a completion >>>> percentage and store all output messages in the file log. >>>> >>>> If your user can connect to several computers e.g. via >>>> SSH then you can even run commands in a distributed manner. >>>> I use it daily on Linux but know some people used it on Mac OS >>>> X >>>> as well. >>>> >>>> The project is there: >>>> >>>> https://savannah.nongnu.org/projects/par >>>> >>>> The paper is freely available there: >>>> >>>> http://bioinformatics.oxfordjournals.org/content/26/ >>>> 22/2918.long >>>> >>>> -- >>>> Best regards, >>>> Francois Berenger. >>>> >>>> >>>> -- >>>> Managing the Performance of Cloud-Based Applications >>>> Take advantage of what the Cloud has to offer - Avoid Common >>>> Pitfalls. >>>> Read the Whitepaper. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&; >>>> iu=/4140/ostg.clktrk >>>> ___ >>>> OpenBabel-discuss mailing list >>>> OpenBabel-di
Re: [Open Babel] running Open Babel in parallel / distributed mode
You can also use xargs. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-02-03 16:10 GMT+01:00 Igor Filippov : > How is it different from GNU parallel? > http://www.gnu.org/software/bash/manual/html_node/GNU-Parallel.html > > Igor > > > On Mon, Feb 3, 2014 at 1:37 AM, Francois Berenger wrote: > >> Hello, >> >> I do this almost everyday so I think I should share it with this list. >> >> In case you need to execute many Open Babel commands >> and don't want to wait, you can execute them in parallel >> on a multi-core computer. >> Of course, the commands should be independent, for example >> processing different datasets. >> >> Let's say the commands are in a file called for_par.sh. >> I developped a tool called PAR years ago that can do this: >> >> par -i for_par.sh -v -o log >> >> It will use all cores of the computer, display a completion >> percentage and store all output messages in the file log. >> >> If your user can connect to several computers e.g. via >> SSH then you can even run commands in a distributed manner. >> I use it daily on Linux but know some people used it on Mac OS X >> as well. >> >> The project is there: >> >> https://savannah.nongnu.org/projects/par >> >> The paper is freely available there: >> >> http://bioinformatics.oxfordjournals.org/content/26/22/2918.long >> >> -- >> Best regards, >> Francois Berenger. >> >> >> -- >> Managing the Performance of Cloud-Based Applications >> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. >> Read the Whitepaper. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > > -- > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > > http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] missing obabel executable when compiling by sources on HPC
I think you should build with SHARED = True and append correct directory to LD_LIBRARY_PATH, which probably should look like: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/openbabel/openbabel-2.3.2-install/lib Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014/1/15 Vedat Durmaz > > > > Am 14.01.2014 19:10, schrieb Dimitri Maziuk: > > On 01/14/2014 11:21 AM, Vedat Durmaz wrote: > ... > > i really don't > understand, why obabel building is deactivated by default in the static > case. however, i also don't have that much experience with that > cmake/configure stuff. > > Looks like a braino to me, perhaps the endif(BUILD_SHARED) was supposed > to be about 10 lines above where it is now? > > > but then still no obabel executable would have been compiled/linked in > case of a static build. maybe i haven't explained (and understood) well > enough. i don't know whether this will work, but i'll try to attach the > CMakeLists.txt file from the ./tools directory before and after > modification (concerning the last 1-15 lines only) .. > > vedat > > > > -- > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > > > > ___ > OpenBabel-discuss mailing > listOpenBabel-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > -- > CenturyLink Cloud: The Leader in Enterprise Cloud Services. > Learn Why More Businesses Are Choosing CenturyLink Cloud For > Critical Workloads, Development Environments & Everything In Between. > Get a Quote or Start a Free Trial Today. > > http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Bindings - first and last molecule option
Hello again,
I've fixed the issue here: https://github.com/openbabel/openbabel/pull/52
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/12 Maciek Wójcikowski
> I think, I've pin-pointed the issue in the source - OBConversion class.
> The first and last molecule is set by SetStartAndEnd method. It's being
> called only by Convert method, not by Read nor ReadFile, hence the binding
> dont use -f and -l. I figure if i't called SetStartAndEnd in Read or
> ReadFile, then it should work. Unfortunately I struggle to find the spot.
> Tried to add it to ReadFile, but it does not work.
>
> Any better ideas?
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> 2013/12/5 Geoffrey Hutchison
>
>> This only proves, that I really want to use it. Is the proof.py script
>> working correctly for anybody (attached in previous mail)? It should ouptut
>> molecules no. 5-10 out of 100 in proof.sdf
>>
>>
>> No, it doesn't work.
>>
>> % python proof.py | wc
>> 100 1001300
>>
>> Hmm. Chris, any idea why this wouldn't work from Python?
>>
>> obconversion = OBConversion()
>> obconversion.SetInFormat("sdf")
>> obconversion.AddOption('f', obconversion.GENOPTIONS, "5")
>> obconversion.AddOption('l', obconversion.GENOPTIONS, "10")
>> obmol = OBMol()
>>
>> notatend = obconversion.ReadFile(obmol,"proof.sdf")
>> while notatend:
>> print obmol.GetTitle()
>> obmol = OBMol()
>> notatend = obconversion.Read(obmol)
>>
>>
>>
>
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Bindings - first and last molecule option
I think, I've pin-pointed the issue in the source - OBConversion class. The
first and last molecule is set by SetStartAndEnd method. It's being called
only by Convert method, not by Read nor ReadFile, hence the binding dont
use -f and -l. I figure if i't called SetStartAndEnd in Read or ReadFile,
then it should work. Unfortunately I struggle to find the spot. Tried to
add it to ReadFile, but it does not work.
Any better ideas?
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/12/5 Geoffrey Hutchison
> This only proves, that I really want to use it. Is the proof.py script
> working correctly for anybody (attached in previous mail)? It should ouptut
> molecules no. 5-10 out of 100 in proof.sdf
>
>
> No, it doesn't work.
>
> % python proof.py | wc
> 100 1001300
>
> Hmm. Chris, any idea why this wouldn't work from Python?
>
> obconversion = OBConversion()
> obconversion.SetInFormat("sdf")
> obconversion.AddOption('f', obconversion.GENOPTIONS, "5")
> obconversion.AddOption('l', obconversion.GENOPTIONS, "10")
> obmol = OBMol()
>
> notatend = obconversion.ReadFile(obmol,"proof.sdf")
> while notatend:
> print obmol.GetTitle()
> obmol = OBMol()
> notatend = obconversion.Read(obmol)
>
>
>
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Bindings - first and last molecule option
This only proves, that I really want to use it. Is the proof.py script working correctly for anybody (attached in previous mail)? It should ouptut molecules no. 5-10 out of 100 in proof.sdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/12/3 Chris Morley > > On 2013-12-03 04:28, Maciek Wójcikowski wrote: > >> You're probably right, C also has to read therm, but other than > recognizing > the beginning and the end of the molecule it wouldn't do anything > especially > kekulization and bonding etc. > > > On 03/12/2013 18:11, Geoffrey Hutchison wrote: > > Actually no. Indeed this would be a useful "lazy" optimization, but is > not > > currently implemented this way. The C++ library does in fact read the > file, > > but the molecules go through the parsers, which means that things like > > kekulization, bond perception, etc. are generally done. > > In fact it is implemented this way for most common multi-molecule file > formats. The molecules before the one specified by the -f option are > skipped without being parsed. (The format's virtual SkipObjects() > function is used.) > > Chris > > > -- > Sponsored by Intel(R) XDK > Develop, test and display web and hybrid apps with a single code base. > Download it for free now! > > http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Bindings - first and last molecule option
Hi Dimitri, Try to do that for 20mln molecules, I guarantee you it'll kill your machine. The point is to skip n molecules at the beginning of the file, and do it efficiently(aka, read only desired range on n-m molecules). You're probably right, C also has to read therm, but other than recognizing the beginning and the end of the molecule it wouldn't do anything especially kekulization and bonding etc. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/12/3 Dimitri Maziuk > On 2013-12-03 04:28, Maciek Wójcikowski wrote: > > Hello, > > > > I'd like to ask, if it's somehow possible to use first [-f] and last > > [-l] options via python bindings? > > last = list(mols)[-1] ? -- I haven't tried myself. I suspect even in c++ > you still have to actually read them all in to get random access... > > Dima > > > > > -- > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Bindings - first and last molecule option
Hello, I'd like to ask, if it's somehow possible to use first [-f] and last [-l] options via python bindings? I've looked at pybel._operations, but there is no such option there. Setting it via OBConverter's methods AddOption() and SetOptions() does't seem to work either. My first instinct is that it's yet another options that relay on C streams, therefore is not supported via bindings, but correct me if I'm wrong. I'd be glad if you could help me figure this out, or point me to a solution avoiding reads to OBMol objects for molecules that I want to skip, as in example in Wiki [ http://openbabel.org/docs/current/UseTheLibrary/PythonExamples.html] ---- Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] baPHPel
Hello, I'd like to share with you my work involving PHP OpenBabel bindings: baPHPel. Basically it's pybel for php, and was intended to be as close API-wise as possible. So now you can do in php: https://github.com/mwojcikowski/openbabel/commit/288011f9b0672fb53e83423235dfa87580be442b There are few things missing which I intend to fix asap (mainly involving forcefields and fingerprints) due to SWIG errors. Any thoughts/ideas? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Openbabel and Lone Pairs
Hi, Currently I'm working on GOLD docking results, and try to process them through OB. Unfortunately OB doesn't understand GOLD's explicit lone pair pseudo atoms (atom type: Lp). For mol2 -> mol2 conversion it changes it to Xx type atoms, for sdf (sdf defines them as * type) -> mol2 they are changed as dummy atoms (Du). There is probably no way to remove them at conversion, unless I didn't found one, but maybe it should be fixed? From brief code analysis the lone pairs are defined implicitly, but maybe OB should also understand explicit representations as valid, or at least recognise Lp/*, as in mol2/sdf, atom types and ignore them. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Can we just copy the compiled files to another account ?
Hi,
You also have to copy the bash variables you've set. Have you done that?
There is no reason it shouldn't work, unless you've configured it right.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/10/30 Zhengyh
> Greetings,
>
> I compiled openbabel with python binding and I have 3 account on a HPC
> cluster.
> So I just copy the compiled files to the other 2 account and make the
> environment correct.
> But I got the same error in the 2 account when I was running a python
> program imported pybel:
> > Traceback (most recent call last):
> > File "/public/home/xzren/zhengyh/bin/st", line 201, in ?
> > mola = pybel.readfile('g09', 'a.log').next()
> > File
> >
> "/public/home/xzren/zhengyh/usr/openbabel/lib64/python2.4/site-packages/pybel.py",
> > line 84, in readfile
> > raise ValueError("%s is not a recognised OpenBabel format" % format)
> > ValueError: g09 is not a recognised OpenBabel format
>
> Why can't we just copy the compiled files to another account of the same
> system?
>
>
> Regards!
> Abruzzi
>
>
> --
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
Hi, Have you tried mol1 += mol2? I use it for joining proteins with ligands, but should work in any case. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/10/25 Zhengyh > Hello, > > Thank you all who are helping me with this openbabel. > We use --join to join all input molecules into a single output > moleculeentry. > But which is the right function to do this in the pybel or openbable API? > I just can't find it... > > Regards! > > > > -- > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Can't make it work on a Redhat X64 platform!
Hi,
Besides PYTHON_PATH please try adding the directory with openbabel.so.4
to $LD_LIBRARY_PATH
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/10/25 Zhengyh
> Greetings,
> I was compiling the openbabel 2.3.1 version with binding for Python on
> 'Red Hat Enterprise Linux Server release 5.6 (Tikanga)' .
> I installed openbabel locally and this is the path below:
> *
> *
>
> *babel: '/public/home/zhengyh/usr/openbabel/bin/babel'*
> *Python binding:
> '/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/'*
>
>
>
> I appended the Python binding path to $PYTHONPATH as the doc tells but it
> did not work when I imported openbabel in Python:
>
> In .bashrc :*
> *
>
> *
> PYTHONPATH="/public/home/zhengyh/usr/openbabel/lib:/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages:$PYTHONPATH"
> *
>
> But:
>
> *>>> import openbabel*
> *Traceback (most recent call last):*
> * File "", line 1, in ?*
> *ImportError: No module named openbabel*
> *>>> *
>
> *
> *And again I did this in another scheme:
>
> *>>> import sys,pprint**
> **>>> pprint.pprint(sys.path)**
> **['',**
> ** '/usr/lib64/python24.zip',**
> ** '/usr/lib64/python2.4',**
> ** '/usr/lib64/python2.4/plat-linux2',**
> ** '/usr/lib64/python2.4/lib-tk',**
> ** '/usr/lib64/python2.4/lib-dynload',**
> ** '/usr/lib64/python2.4/site-packages',**
> ** '/usr/lib64/python2.4/site-packages/Numeric',**
> ** '/usr/lib64/python2.4/site-packages/PIL',**
> ** '/usr/lib64/python2.4/site-packages/gtk-2.0',**
> ** '/usr/lib/python2.4/site-packages']**
> **>>>
> sys.path.append('/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages')
> **
> **>>> import openbabel**
> **Traceback (most recent call last):**
> ** File "", line 1, in ?**
> ** File
> "/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/openbabel.py",
> line 47, in ?**
> **import _openbabel**
> **ImportError: libopenbabel.so.4: cannot open shared object file: No such
> file or directory**
> **>>> sys.path.append('/public/home/zhengyh/usr/openbabel/lib')**
> **>>> import openbabel**
> **Traceback (most recent call last):**
> ** File "", line 1, in ?**
> ** File
> "/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages/openbabel.py",
> line 47, in ?**
> **import _openbabel**
> **ImportError: libopenbabel.so.4: cannot open shared object file: No such
> file or directory**
> **>>> pprint.pprint(sys.path)**
> **['',**
> ** '/usr/lib64/python24.zip',**
> ** '/usr/lib64/python2.4',**
> ** '/usr/lib64/python2.4/plat-linux2',**
> ** '/usr/lib64/python2.4/lib-tk',**
> ** '/usr/lib64/python2.4/lib-dynload',**
> ** '/usr/lib64/python2.4/site-packages',**
> ** '/usr/lib64/python2.4/site-packages/Numeric',**
> ** '/usr/lib64/python2.4/site-packages/PIL',**
> ** '/usr/lib64/python2.4/site-packages/gtk-2.0',**
> ** '/usr/lib/python2.4/site-packages',**
> ** '/public/home/zhengyh/usr/openbabel/lib64/python2.4/site-packages',**
> ** '/public/home/zhengyh/usr/openbabel/lib']**
> *
>
> It seems that openbabel.py could not find libopenbabel.so.4 in the
> convention place.
>
>
>
>
> --
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
> from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] DiSCuS [pre-release] - Database System for Compound Selection
Dear users and developers, I'm pleased to present the pre-release version of DiSCuS, an open-source tool based among others on Openbabel and JSmol. DiSCuS is designed to help you with analysis of docking results. More information about the features could be found on my G+ post here: https://plus.google.com/112020264806576764678/posts/WPy6PBF9qgr The pre-release version is also available online, but please contact me for login credentials, so you could try it for yourself. As usual every feedback is very welcome. So If you have comments or ideas how to change/improve DiSCuS, please write me an email or comment on G+. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] create a database with openbabel
Hello, The other choice, if you prefer MySQL, is Mychem http://mychem.sourceforge.net/. But I'd say neither of them is easy to use for unexperienced user (unless you have at least some DB knowledge). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/8/22 Steffen Neumann > Hi, > > you could check out > https://github.com/ergo70/pgchem_tigress > > Also check out the blog at > http://theplateisbad.blogspot.de/ > > Yours, > Steffen > > > On Sat, 2013-06-29 at 15:06 -0700, Juan F Sánchez wrote: > > Hello, my name is Juan Francisco Sánchez > > > > > > I am a professor of the university of Mèxico > > > > > > I'm interested in knowing how to build a database of chemical > > structures with openbabel, (file. SDF) but I do not know how to do it > > I'd like you to help me: > > Where do I find instructions or tutorial for building a database of > > chemical structures with openbabel, (file. SDF)? > > > > Thanks > > > > > > > > > > > > > > > -- > > This SF.net email is sponsored by Windows: > > > > Build for Windows Store. > > > > http://p.sf.net/sfu/windows-dev2dev > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- > IPB HalleAG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 http://msbi.bic-gh.de > 06120 Halle Tel. +49 (0) 345 5582 - 1470 > +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > -- > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Count Molecules
Hello, For sets that are not extremly big (as it could get quite long), I'd suggest converting to smiles and counting the lines: obabel input.mol2 -o smi | wc -l Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/8/20 Dimitri Maziuk > On 08/20/2013 12:32 PM, Noel O'Boyle wrote: > > I usually use grep too, but I understand what you're saying - it's a > > common task we should automate (e.g. "-ocount"). In the meanwhile, you > > could speed it up quite a bit by turning off some of the perception, > > i.e. -aT (read title only). > > python: > cnt = 0 > for mol in readfile( ... ) : cnt += 1 > print cnt, "molecules" > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > > -- > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
You could also look into ProDy, if you use PDB files. http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Maciek Wójcikowski > I think you need custom code. For python, you could use pybel. There are > three lines that do what you want ( > http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall). > You only miss one or two lines to get the atoms by their indices. > > Although searching pdb files with it could be a demanding and time > consuming task. It's really made for small molecules, i guess. I'd > personally would loop through atoms check if they are HETATOMs and then > check SMARTS pattern. Alternatively, you can filter them by name, if you > can suspect what's your residues name could be (although it's the most > error prone). > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2013/7/8 Brett Hannigan > >> Unfortunately, I don't think that's quite what I need. The obabel filter >> command will look at the given pdb and then output the entire pdb if it >> matches the given SMARTS query, right? What I would like to do is only get >> the atoms that match the SMARTS query. >> >> For example, let's say I have a pdb with a single phospho-serine residue. >> What I would like to do is get only the phosphate atoms from the pdb, and >> not get the rest of the residue atoms. >> >> Really what I am going for here is I'd like specify some groups that I >> find interesting, say a phosphate group, a phenyl group, etc. And then I >> have a database of protein + ligand pdbs. I'd like to loop through those >> pdbs and look for my groups that I am interested in. Rather than just >> identify the pdbs that have the sub-structure I am interested in (i.e. >> identify all pdbs with phosphates), I want to know which atoms in the pdb >> constitute the interesting sub-structure. That way I could then align all >> phosphate groups and look at the residues surrounding the phophates to see >> if I see common modes of binding etc. Phosphate would just be one example, >> you can imagine identifying many other interesting sub-structures. >> >> -Brett >> >> -- >> *From:* Maciek Wójcikowski >> *To:* Brett T. Hannigan >> *Cc:* openbabel-discuss@lists.sourceforge.net >> *Sent:* Saturday, July 6, 2013 6:21 AM >> *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB >> >> Hello, >> >> You can "convert" from PDB to PDB using filter option ( >> http://openbabel.org/wiki/--filter_option) >> obabel input.pdb -O output.pdb --filter "s='CN'" >> >> If your database is really large, or you want to search multiple times, >> then I'd suggest using FastSearch for performance reasons. For further >> lecture: http://openbabel.org/wiki/FastSearch >> >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> 2013/7/5 Brett T. Hannigan >> >> I have a database of molecules in pdb files. I'd like to go through each >> molecule and see if it has certain substructures, and if they do identify >> which atoms are part of that substructure. So it's easy enough to read the >> pdb file in, convert it to SMILES representation, and then do a SMARTS >> query to look for my substructures. However, if the SMARTS query reports >> that the substructure is present in the molecule, I'm not sure how to >> identify the atoms in the pdb file which make up the match. Any ideas? >> >> -- >> ** >> Brett T. Hannigan >> 8011 Ardleigh St. >> Philadelphia, PA 19118 >> brett.hanni...@gmail.com >> ** >> >> >> -- >> This SF.net <http://sf.net/> email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> >> >> >> > -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
I think you need custom code. For python, you could use pybel. There are three lines that do what you want ( http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall). You only miss one or two lines to get the atoms by their indices. Although searching pdb files with it could be a demanding and time consuming task. It's really made for small molecules, i guess. I'd personally would loop through atoms check if they are HETATOMs and then check SMARTS pattern. Alternatively, you can filter them by name, if you can suspect what's your residues name could be (although it's the most error prone). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Brett Hannigan > Unfortunately, I don't think that's quite what I need. The obabel filter > command will look at the given pdb and then output the entire pdb if it > matches the given SMARTS query, right? What I would like to do is only get > the atoms that match the SMARTS query. > > For example, let's say I have a pdb with a single phospho-serine residue. > What I would like to do is get only the phosphate atoms from the pdb, and > not get the rest of the residue atoms. > > Really what I am going for here is I'd like specify some groups that I > find interesting, say a phosphate group, a phenyl group, etc. And then I > have a database of protein + ligand pdbs. I'd like to loop through those > pdbs and look for my groups that I am interested in. Rather than just > identify the pdbs that have the sub-structure I am interested in (i.e. > identify all pdbs with phosphates), I want to know which atoms in the pdb > constitute the interesting sub-structure. That way I could then align all > phosphate groups and look at the residues surrounding the phophates to see > if I see common modes of binding etc. Phosphate would just be one example, > you can imagine identifying many other interesting sub-structures. > > -Brett > > -- > *From:* Maciek Wójcikowski > *To:* Brett T. Hannigan > *Cc:* openbabel-discuss@lists.sourceforge.net > *Sent:* Saturday, July 6, 2013 6:21 AM > *Subject:* Re: [Open Babel] SMILES, SMARTS, and PDB > > Hello, > > You can "convert" from PDB to PDB using filter option ( > http://openbabel.org/wiki/--filter_option) > obabel input.pdb -O output.pdb --filter "s='CN'" > > If your database is really large, or you want to search multiple times, > then I'd suggest using FastSearch for performance reasons. For further > lecture: http://openbabel.org/wiki/FastSearch > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2013/7/5 Brett T. Hannigan > > I have a database of molecules in pdb files. I'd like to go through each > molecule and see if it has certain substructures, and if they do identify > which atoms are part of that substructure. So it's easy enough to read the > pdb file in, convert it to SMILES representation, and then do a SMARTS > query to look for my substructures. However, if the SMARTS query reports > that the substructure is present in the molecule, I'm not sure how to > identify the atoms in the pdb file which make up the match. Any ideas? > > -- > ** > Brett T. Hannigan > 8011 Ardleigh St. > Philadelphia, PA 19118 > brett.hanni...@gmail.com > ** > > > -- > This SF.net <http://sf.net/> email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMILES, SMARTS, and PDB
Hello, You can "convert" from PDB to PDB using filter option ( http://openbabel.org/wiki/--filter_option) obabel input.pdb -O output.pdb --filter "s='CN'" If your database is really large, or you want to search multiple times, then I'd suggest using FastSearch for performance reasons. For further lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan > I have a database of molecules in pdb files. I'd like to go through each > molecule and see if it has certain substructures, and if they do identify > which atoms are part of that substructure. So it's easy enough to read the > pdb file in, convert it to SMILES representation, and then do a SMARTS > query to look for my substructures. However, if the SMARTS query reports > that the substructure is present in the molecule, I'm not sure how to > identify the atoms in the pdb file which make up the match. Any ideas? > > -- > ** > Brett T. Hannigan > 8011 Ardleigh St. > Philadelphia, PA 19118 > brett.hanni...@gmail.com > ** > > > -- > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Atom numbers again, this time from python
There is an undocumented option in molecule.write() and .readfile() which
allows of passing options to reading/writing. You must pass opt with
dictionary of options. For line you gave: opt = {'b' : None, 'i' : None,
'a' : None} although I believe that 'b' : None should be 'b' : '' if you
wish to pass empty value, since None is reserved for options without value.
You could look into that in pybel.py file.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> Hi everyone,
>
> one more python question: I'm trying to do
>
> obabel -h --canonical -xb none -xi -xa -xP1000 -osvg ...
>
> All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way
> to get to the rest? Specifically, "-xa" and "-xi", as I can
> post-process the SVG to change the size and the background.
>
> TIA
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
>
> --
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
How ServiceNow helps IT people transform IT departments:
1. A cloud service to automate IT design, transition and operations
2. Dashboards that offer high-level views of enterprise services
3. A single system of record for all IT processes
http://p.sf.net/sfu/servicenow-d2d-j___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] python api question
Yes. etab = ob.OBElementTable() etab.GetSymbol(6) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Dimitri Maziuk > On 2013-06-05 02:54, Maciek Wójcikowski wrote: > > If you realy need symbol of an element in automated fassion, then there > > is OBElementTable.GetSymbol( atomicnum ) that you can use. > > > > > http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405 > > So it's exported as openbabel.OBElementTable, right? The Fine Manual is > a bit sketchy. > > Thanks > Dimitri > > > > > -- > How ServiceNow helps IT people transform IT departments: > 1. A cloud service to automate IT design, transition and operations > 2. Dashboards that offer high-level views of enterprise services > 3. A single system of record for all IT processes > http://p.sf.net/sfu/servicenow-d2d-j > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] python api question
If you realy need symbol of an element in automated fassion, then there is OBElementTable.GetSymbol( atomicnum ) that you can use. http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405 Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Maciek Wójcikowski > Hello, > > Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It > returns atomic number of element (fe. C - 6). > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2013/6/5 Dimitri Maziuk > >> Hi all, >> >> I'm after the atom (element) type letter. What I get from pybel's >> atom.type or atom.OBAtom.GetType() are O3, O2, C3, C2, etc. Is there a >> function or property that returns just O's and C's? >> >> TIA, >> -- >> Dimitri Maziuk >> Programmer/sysadmin >> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu >> >> >> >> -- >> How ServiceNow helps IT people transform IT departments: >> 1. A cloud service to automate IT design, transition and operations >> 2. Dashboards that offer high-level views of enterprise services >> 3. A single system of record for all IT processes >> http://p.sf.net/sfu/servicenow-d2d-j >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] python api question
Hello, Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It returns atomic number of element (fe. C - 6). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Dimitri Maziuk > Hi all, > > I'm after the atom (element) type letter. What I get from pybel's > atom.type or atom.OBAtom.GetType() are O3, O2, C3, C2, etc. Is there a > function or property that returns just O's and C's? > > TIA, > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > > -- > How ServiceNow helps IT people transform IT departments: > 1. A cloud service to automate IT design, transition and operations > 2. Dashboards that offer high-level views of enterprise services > 3. A single system of record for all IT processes > http://p.sf.net/sfu/servicenow-d2d-j > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OpenMP in bindings
It turned out they work, as they should. For future reference: using opcode caching in PHP (like APC, xCache, etc) prevents it from using OpenMP. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/5/17 Geoffrey Hutchison > > Does anybody know, if MMFF94 with OpenMP works in any bindings? It works > fine in CLI, but bindings ignore that. > > I suspect you may need to check the environment variables, etc. Certainly > the bindings would just be calling the C++ library anyway. > > -Geoff > > -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] OpenMP in bindings
Hi, Does anybody know, if MMFF94 with OpenMP works in any bindings? It works fine in CLI, but bindings ignore that. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl> -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] PHP bindings
Hello, Since it seam, that pull requests are not read by everybody, I decided to post also here. I've included PHP bindings into my branch on github and would kindly ask anybody to test it on their environment. There is example PHP file which should depict one molecule. Here is the pull request: https://github.com/openbabel/openbabel/pull/7 and the branch I'm talking about: https://github.com/mwojcikowski/openbabel/tree/php-binding With this binding writing webapps for cheminformatics should be easier and more accessible to web developers. It can also by highly useful for importing data and molecules depiction. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl> -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
Try cherry-picking a commit. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/3/18 Noel O'Boyle > Hi David, > > Can you put all of the Confab-related code on a branch so I can get at > them without pulling the other unrelated code on your master? > Alternatively I can just copy+paste the files locally or if you know > some other way I can get these changes using Git I'm happy to hear it. > > - Noel > > On 15 March 2013 20:10, Noel O'Boyle wrote: > > Looks good, but not all the Confab code is in there. If it going to be > > called Confab I want to make sure it works the same as the original. > > So...what do you think about merging this onto a branch? I hereby > > commit to sorting it out :-) > > > > - Noel > > > > On 15 March 2013 19:26, Geoffrey Hutchison > wrote: > >>> I dug up old versions of tree.hh from Cadabra . Luckily, it actually > >>> has the exact same files as Confab, but with a GPLv2-compliant > >>> license. Since the author of Cadabra is the same person as the author > >>> of tree.hh, I think these files should be considered cleanly under > >>> GPLv2. > >> > >> If the file header is labeled as GPLv2, the file is released (to the > wild) under GPLv2. Thanks for the investigation. > >> > >>> changeset at > https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb > >> > >> If Noel gives the go-ahead, I'd be happy to merge this into openbabel > master. I think it's much better to avoid an unmaintained confab fork. > >> > >> Thanks! > >> -Geoff > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
According to current webpage of tree.hh it's released on GPL3 OR 2 [ http://tree.phi-sci.com/] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/3/12 Geoffrey Hutchison > > For some internal purposes, I wanted a combined openbabel/confab code > > base, so I merged them. > > Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind > me the differences that went into confab? I seem to remember that Noel > thought I might have some issues with certain changes and I'd prefer to > review them before the merge. > > I do see one clear issue, with tree.hh, which is covered under the GPL v3. > Despite the naming, Open Babel (GPv2) is not compatible with GPLv3 code. > > If there's a version of tree.hh covered under Boost (as suggested by the > comments) I think we'd be OK. > > Thanks very much, > -Geoff > > > Additionally, if you want openbabel-2.3.2 with confab, I put that > version here: > > http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 > > > > -David > > > > > -- > > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > > endpoint security space. For insight on selecting the right partner to > > tackle endpoint security challenges, access the full report. > > http://p.sf.net/sfu/symantec-dev2dev > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > -- > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obminimize
Try: obminimize -ff MMFF94 -sd source.sdf > target.sdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/2/27 Оги Боги > Hi guys, > > I am trying to use obminimize under 64bit windows 7 in order to minimize > geometry of molecules inside multimolecule sdf file. I'm using the > following command: > > obminimize -ff MMFF94 -sd > > The problem is that obminimize prints results from minimization procedure > in console but nothing happens with atom coordinates in sdf file. Is that > normal or I've made some mistake? > > > > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Residue support in Pybel
Hi, I've added few lines to pybel to make life easier while working with files containing proteins, f.e. PDB structures. With this capability you could do something like that: for residue in protein.residues: print residue.name for atom in residue: print atom.name If you think it's a good idea would it be possible to add it to trunk? PS. How is github/git integration going? Github repo seams to be forgotten since initial sync somewhere in October 2012... Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl> pybel.diff Description: Binary data -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Version 2.3.2: --AddPolarH with --gen3D
Gen3d is calling addhydrogen before forcefield calculation, So you might want to delete some hydrogens afterwards. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/21 David García Aristegui > Hello, i'm unable to generate the 3D coordinates and at the same time add > the polar hydrogens only. > > With this command the program adds all hydrogens, polar and non-polar > > obabel --AddPolarH --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 > > With or without the --AddPolarH flag i retrieve the same output. > > And with obabel -d --AddPolarH --gen3D -ismi 3.3_30.smi -omol2 -O > 3.3_30.mol2 no hydrogens (polar o non-polar) are added. > > Could somebody help me to find the correct syntax to generate the 3D > coordinates adding the polar hydrogens only? > > Best regards. > > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. SALE $99.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122412 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
470 -3.5196 H 1 LIG10.0625 63 H 8.7236 -2.60070.3194 H 1 LIG10.1030 64 H 10.6816 -1.8859 -6.7791 H 1 LIG10.1451 65 H 10.4817 -0.4112 -6.0074 H 1 LIG10.1451 @BOND 1 1 21 2 2 32 3 2 41 4 2 51 5 5 61 6 6 71 7 7 81 8 7 91 9 9101 1010121 1112131 1212141 1314151 14 7141 1514161 1612171 1717181 1818191 1919202 2019211 212122 ar 222223 ar 232324 ar 242425 ar 252526 ar 262627 ar 272728 ar 282829 ar 292429 ar 302930 ar 313031 ar 322231 ar 333132 ar 343233 ar 353334 ar 362134 ar 373536 ar 383637 ar 393738 ar 403839 ar 4139402 423941 ar 4341421 444143 ar 4543441 464345 ar 474546 ar 483546 ar 493846 ar 5010351 5110111 52 1471 53 4481 54 6491 55 6501 5616511 5718521 5818531 5923541 6025551 6126561 6227571 6328581 6430591 6532601 6633611 6734621 6836631 6944641 7044651 1 molecule converted Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui > OK, in the News section of the Openbabel main page is announced > "2011-10-17 Open Babel 2.3.1 Released only", i'm downloading the 2.3.2 > release. > > I will try to do the conversion with the new release, but the bug is > "Milestone: 2.3.x". > > By the way, would you be so kind to try to do the conversion, if you have > a 2.3.2 version available? > > Best regards. > > > Have you tried it with OB 2.3.2? > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > > 2013/1/20 David García Aristegui > > > >> OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > >> > >> > Hello, i'm trying to assign 3D coordinates to this SMILES structure > >> > > >> > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@ > >> @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 > >> > > >> > obabel is unable to resolve the structure > >> > > >> > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 > >> > 1 molecule converted > >> > > >> > real 6m8.107s > >> > user 6m7.947s > >> > sys 0m0.020s > >> > > >> > But the mol2 files looks like... > >> > > >> > @MOLECULE > >> > * > >> > 65 70 0 0 0 > >> > SMALL > >> > GASTEIGER > >> > > >> > @ATOM > >> > 1 O -nan -nan -nan O.3 1 LIG1 > >> > -0.3026 > >> > 2 P -nan -nan -nan P.3 1 LIG1 > >> > 0.4724 > >> > 3 O -nan -nan -nan O.2 1 LIG1 > >> > -0.2275 > >> > (...) > >> > > >> > Any ideas, is this a known bug? > >> > Best > >> > > >> > regards.-- > >> > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > >> > much more. Get web development skills now with LearnDevNow - > >> > 350+ hours of step-by-step video tutorials by Microsoft MVPs and > >> experts. > >> > SALE $99.99 this month only -- learn more at: > >> > > >> > http://p.sf.net/sfu/learnmore_122812___ > >> > OpenBabel-discuss mailing list > >> > OpenBabel-discuss@lists.sourceforge.net > >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >> > > >> > >> > >> >
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
Have you tried it with OB 2.3.2? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui > OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > > > Hello, i'm trying to assign 3D coordinates to this SMILES structure > > > > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@ > @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 > > > > obabel is unable to resolve the structure > > > > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 > > 1 molecule converted > > > > real 6m8.107s > > user 6m7.947s > > sys 0m0.020s > > > > But the mol2 files looks like... > > > > @MOLECULE > > * > > 65 70 0 0 0 > > SMALL > > GASTEIGER > > > > @ATOM > > 1 O -nan -nan -nan O.3 1 LIG1 > > -0.3026 > > 2 P -nan -nan -nan P.3 1 LIG1 > > 0.4724 > > 3 O -nan -nan -nan O.2 1 LIG1 > > -0.2275 > > (...) > > > > Any ideas, is this a known bug? > > Best > > > regards.-- > > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > > much more. Get web development skills now with LearnDevNow - > > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. > > SALE $99.99 this month only -- learn more at: > > > http://p.sf.net/sfu/learnmore_122812___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnmore_123012 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_123012___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] OB binginds segfault on EL5
Hi, Does anybody have a problem with bindings (both perl and python) have problems - segfault - on CentOS 5? I'm building latest SVN, with latest swig, eigen 2 & 3 (but also tried without eigen) and latest cmake. Is it possible that old gcc is the problem here? Same build on CentOS 6 works fine on the same set of compounds. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl> -- Keep yourself connected to Go Parallel: VERIFY Test and improve your parallel project with help from experts and peers. http://goparallel.sourceforge.net___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Copy format in Pybel
That was just a "proof of concept" piece of code. I wanted to process some molecules and try to leave them intact. Thanks for information. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/11/8 Geoffrey Hutchison > > Is pybel suppose to support 'copy' format? I try to make it work, but it > generates empty string. > > No, the copy format relies on the C++ stream code. But why would you need > it? In Python, you *have* the original file or string. > > So I'm a bit confused. > > -Geoff > > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_nov___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Copy format in Pybel
Is pybel suppose to support 'copy' format? I try to make it work, but it
generates empty string.
Proof of concept:
>>> mol = pybel.readstring("smi", "c1=CC=CC=c1")
>>> mol.write('copy')
''
I'm on latest SVN openbabel + CentOS 6.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<https://mail.google.com/mail/u/0/?view=cm&fs=1&tf=1&to=mac...@wojcikowski.pl>
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_nov___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OpenBabel to split multimol2 file but without changing bond types?
Have you tried "copy" output format? -ocopy Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/10/4 Juliette Pradon > Hello, > > I am using OpenBabel to split a multimol2 file into separate mol2 files > (i.e. one mol2 file per compound). I use the following command: > > babel my_ligands.mol2 ligandPart.mol2 -m > > such that each single ligand mol2 file will be called ligandPart1.mol2, > ligandPart2.mol2, etc > > The issue is that for some compounds, I have noticed that some bond types > have been changed in the process, particularly aromatic bonds appearing > where there should not be any. > > Is there another option to add to the command above that would tell > OpenBabel not to modify the bond types? > > Thank you in advance for any help! > > Juliette > > LEGAL NOTICE > Unless expressly stated otherwise, information contained in this > message is confidential. If this message is not intended for you, > please inform postmas...@ccdc.cam.ac.uk and delete the message. > The Cambridge Crystallographic Data Centre is a company Limited > by Guarantee and a Registered Charity. > Registered in England No. 2155347 Registered Charity No. 800579 > Registered office 12 Union Road, Cambridge CB2 1EZ. > > > -- > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] PHP binding
Hi, Is it possible to set up those PHP bindings in SVN branch? I'm willing to make some testing and write some example/test files. Unfortunately I have little experience with CMake to make it by my own... Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/4/3 Maciek Wójcikowski > If you set that up it would be nice. What kind of test scripts do you need? > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > W dniu 3 kwietnia 2012 02:40 użytkownik Geoff Hutchison < > ge...@geoffhutchison.net> napisał: > > >> On Apr 2, 2012, at 5:34 PM, mwojcikowski wrote: >> >> > Since web-interfaces are incredibly popular it would be a nice feature >> to >> > have openbabel built in PHP. I guess it would not be so hard, since we >> need >> > to create just php interface file for SWIG. >> >> The security implications scare me, but as you say, it would be fairly >> easy to run SWIG to generate PHP bindings. My only problem is that I have >> no idea how you'd test that. >> >> If you'd like to serve as guinea pig and will write some examples and >> tests, we can set that up in the development branch. It's been requested -- >> but no one has been willing to serve as tester. :-) >> >> Thanks, >> -Geoff > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Openbabel in Python in concurrent processes
Oh, I forgot to mention that. I use CentOS and ScientificLinux 6, both HVM. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/7/20 Craig James > Did you see this article? You didn't say what Linux you are using, but if > it's Ubuntu, this may be of interest. > > http://blog.xen.org/index.php/2011/11/29/baremetal-vs-xen-vs-kvm-redux/ > > Craig > > > On Fri, Jul 20, 2012 at 1:01 PM, Maciek Wójcikowski > wrote: > >> I also thought about L1 and L2 caches. But underlying problem seams to be >> much simpler. The server is VM on modern AMD server (4x 12 core opteron + >> 96gigs of DDR3 ECC ram). Due to virtualisation heavy memory IO (memory >> usage was less tan 50% including caches) minimization was running so slow. >> I've done same test on Intel Desktop (i7-2600) and process execution time >> changed from 18 min (single proc.) to 21 min (8 concurrent proc.). I'd say >> that the bias is due to Intel Turbo technology and HT (4 physical cores). >> >> The bottom line should be: don't use virtualisation (at least Xen) for >> memory intensive computing. I must say that I'm pretty disappointed with >> those results, although it's quite obvious... >> >> Out of curiosity I'm going to rerun the tests on KVM and probably on >> OpenVZ to see how it goes there. >> ---- >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> 2012/7/20 Craig James >> >>> >>> >>> On Fri, Jul 20, 2012 at 2:16 AM, Maciek Wójcikowski < >>> mac...@wojcikowski.pl> wrote: >>> >>>> Hi, >>>> I'm doing some scripting in Python to minimize ligands and want to run >>>> them concurrently on SMP server (many processes, one core per proc.). The >>>> problem that I hit is that when I run one instance, process take 100% CPU >>>> and runs for ~25min. For the same set if I run 32 concurrent processes it >>>> runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD >>>> Opteron) so there is no turbo mode, like in intel, to produce such power >>>> increase. Script is not doing any IO (at least I don't know of it, it gets >>>> data from MySQL, doing only SELECTs). >>>> >>>> How can I debug this issue? Any thoughts? >>>> >>> >>> There are many reasons why this might happen. You should do an >>> experiment starting with two process, then four, eight, etc ... and see >>> where it starts to slow down. >>> >>> You say 32 CPUs, but now many CPU chips? Is this 4x8-core CPUs, >>> 8x4core, or something else? >>> >>> When you run each process, how much memory does it use? How much memory >>> do you have? >>> >>> My first guess is that you are running into problems with memory >>> contention -- processors fighting each other for memory. This can be >>> either cache memory (for small processes) or main memory (if the ligand >>> minimization is a very large process). >>> >>> Modern CPUs are *much* faster than modern memory, which is why they have >>> multi-level (L1 and L2) caches (see >>> http://en.wikipedia.org/wiki/CPU_cache), and also have "NUMA" memory >>> architecture (see http://en.wikipedia.org/wiki/Non-Uniform_Memory_Access). >>> When you run a single process, it gets full access to all cache memory and >>> all main memory. When you run up to N processes where N is the number of >>> CPU chips (not cores), then each CPU has full access to its caches, but >>> there may be contention for main memory. When you run N processes where N >>> is the total number of CPUs (in your case, 32), then each CPU has to share >>> access to both main memory and to the on-chip memory caches and data >>> channels. >>> >>> The only time a process will scale from 1 to 32 on a 32-CPU system is if >>> each process is compute-bound and uses so little memory that all 32 >>> processors are mostly working from their internal caches and don't ever >>> have to wait for memory access. >>> >>> If you want to read a long but fascinating article about how this >>> affects other projects, check this one out. It's about MySQL running very >>> slowly on very fast CPUs because of memory contention. >>> >>> >>> http://blog.jcole.us/2010/09/28/mysql-swap-insanity-and-the-numa-arc
Re: [Open Babel] Openbabel in Python in concurrent processes
I also thought about L1 and L2 caches. But underlying problem seams to be much simpler. The server is VM on modern AMD server (4x 12 core opteron + 96gigs of DDR3 ECC ram). Due to virtualisation heavy memory IO (memory usage was less tan 50% including caches) minimization was running so slow. I've done same test on Intel Desktop (i7-2600) and process execution time changed from 18 min (single proc.) to 21 min (8 concurrent proc.). I'd say that the bias is due to Intel Turbo technology and HT (4 physical cores). The bottom line should be: don't use virtualisation (at least Xen) for memory intensive computing. I must say that I'm pretty disappointed with those results, although it's quite obvious... Out of curiosity I'm going to rerun the tests on KVM and probably on OpenVZ to see how it goes there. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/7/20 Craig James > > > On Fri, Jul 20, 2012 at 2:16 AM, Maciek Wójcikowski > wrote: > >> Hi, >> I'm doing some scripting in Python to minimize ligands and want to run >> them concurrently on SMP server (many processes, one core per proc.). The >> problem that I hit is that when I run one instance, process take 100% CPU >> and runs for ~25min. For the same set if I run 32 concurrent processes it >> runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD >> Opteron) so there is no turbo mode, like in intel, to produce such power >> increase. Script is not doing any IO (at least I don't know of it, it gets >> data from MySQL, doing only SELECTs). >> >> How can I debug this issue? Any thoughts? >> > > There are many reasons why this might happen. You should do an experiment > starting with two process, then four, eight, etc ... and see where it > starts to slow down. > > You say 32 CPUs, but now many CPU chips? Is this 4x8-core CPUs, 8x4core, > or something else? > > When you run each process, how much memory does it use? How much memory > do you have? > > My first guess is that you are running into problems with memory > contention -- processors fighting each other for memory. This can be > either cache memory (for small processes) or main memory (if the ligand > minimization is a very large process). > > Modern CPUs are *much* faster than modern memory, which is why they have > multi-level (L1 and L2) caches (see http://en.wikipedia.org/wiki/CPU_cache), > and also have "NUMA" memory architecture (see > http://en.wikipedia.org/wiki/Non-Uniform_Memory_Access). When you run a > single process, it gets full access to all cache memory and all main > memory. When you run up to N processes where N is the number of CPU chips > (not cores), then each CPU has full access to its caches, but there may be > contention for main memory. When you run N processes where N is the total > number of CPUs (in your case, 32), then each CPU has to share access to > both main memory and to the on-chip memory caches and data channels. > > The only time a process will scale from 1 to 32 on a 32-CPU system is if > each process is compute-bound and uses so little memory that all 32 > processors are mostly working from their internal caches and don't ever > have to wait for memory access. > > If you want to read a long but fascinating article about how this affects > other projects, check this one out. It's about MySQL running very slowly > on very fast CPUs because of memory contention. > > > http://blog.jcole.us/2010/09/28/mysql-swap-insanity-and-the-numa-architecture/ > > > Craig > > > >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> -- >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Openbabel in Python in concurrent processes
Hi, I'm doing some scripting in Python to minimize ligands and want to run them concurrently on SMP server (many processes, one core per proc.). The problem that I hit is that when I run one instance, process take 100% CPU and runs for ~25min. For the same set if I run 32 concurrent processes it runs from 60-130 min. Why is that? Server has 32 phisical cores (AMD Opteron) so there is no turbo mode, like in intel, to produce such power increase. Script is not doing any IO (at least I don't know of it, it gets data from MySQL, doing only SELECTs). How can I debug this issue? Any thoughts? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Weighted-rotor search
Hello,
You should use:
ff.GetCoordinates(mol)
Where ff is your OBForceField class and mol is OBMol.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/7/13 scott_m
> That's great, many thanks for the help. One other thing, I mentioned pybel
> because I haven't got the OBMol conversion from input smiles string to
> output file with 3D coordinates. Would you mind giving a quick example of
> this (or directing me to online documentation, I couldn't find much here)?
>
> What I have been trying:
>
> mol = openbabel.OBMol()
> conversion = openbabel.OBConversion()
> conversion.SetInAndOutFormats('smi', 'com')
> conversion.ReadString(mol, 'cc')
> mol.AddHydrogens()
>
> #Next step is what I'm not sure of, how do I get the coordinates so that I
> can optimize and write to file??
>
> cv.GetCoordinates()
> cv.WriteFile(mol, 'test.com')
>
> # But this just gives the coordinates as 0
>
> With pybel I found the make3d() and localopt() functions very handy for
> this
> but can't get a similar setup going with openbabel.
>
> Apologies if this is a bit of a new thread.
>
> Cheers,
>
> Scott
>
> --
> View this message in context:
> http://forums.openbabel.org/Weighted-rotor-search-tp4655264p4655272.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
Tried newest cmake, no success either. Actually it is not even looking for ptherad.h. I also found out in CMake file in tools/ directory that the check is made while you build OB staticly, Have you tried build_shared=off and on? Which variable exactly should contain -lpthreads? My perllibs='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc'; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle > Yes - I doublechecked. The latest SWIG still fails. > > What I can do is add in the output of perl -V:perllibs. This solves > the problem at the moment. I still don't understand the underlying > problem though. > > - Noel > > On 31 May 2012 13:43, Maciek Wójcikowski wrote: > > I was wrong. something went wrong and SWIG wasnt recognized at all. I'm > > looking for another problem. Do you have any Idea where first to look? > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > > 2012/5/31 Maciek Wójcikowski > >> > >> Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. > >> Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note > about > >> that in wiki, since that could potentially lead to some other > undiscovered > >> errors. > >> > >> Curiously cmake calls for SWIG in version 2.0 and > loads successfully 1.x. > >> > >> > >> Pozdrawiam, | Best regards, > >> Maciek Wójcikowski > >> mac...@wojcikowski.pl > >> > >> > >> 2012/5/31 Maciek Wójcikowski > >>> > >>> It worked. > >>> > >>> The failing line was: > >>> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags > >>> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc > -shared > >>> -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so > >>> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o > >>> -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl > -lz > >>> -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib > >>> > >>> Adding -lpthread leads to succesful compilation. > >>> > >>> > >>> Pozdrawiam, | Best regards, > >>> Maciek Wójcikowski > >>> mac...@wojcikowski.pl > >>> > >>> > >>> 2012/5/31 Noel O'Boyle > >>>> > >>>> We changed to compiling the bindings directly rather than use Perl's > >>>> build system. It seems to work fine on some Linux OSes but not on > >>>> others. I haven't tracked down the problem but you could try > >>>> "VERBOSE=1 make" to see the command that we are using to compile, and > >>>> repeating it manually but adding -lpthread to see what happens. > >>>> > >>>> - Noel > >>>> > >>>> On 31 May 2012 09:56, Maciek Wójcikowski > wrote: > >>>> > Hi, > >>>> > > >>>> > I have trouble building Perl bindings in openbabel SVN branch. My > >>>> > system is > >>>> > running 64bit CentOS 6. > >>>> > > >>>> > To compile i use following command: > >>>> > > >>>> > cmake ../openbabel \ > >>>> > -DRUN_SWIG=ON \ > >>>> > -DPERL_BINDINGS=ON \ > >>>> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > >>>> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > >>>> > -DPERL_PREFIX=/usr/lib64/perl5/ \ > >>>> > -DPYTHON_BINDINGS=ON \ > >>>> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > >>>> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > >>>> > > >>>> > Which leads to error: > >>>> > Linking CXX shared module ../lib/OpenBabel.so > >>>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > >>>> > `_wrap_resdat_get': > >>>> > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > >>>> > undefined reference to `pthread_getspecific' > >>>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > >>>> > `_wrap_chainsparser_get': > >>>> > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > >>>> >
Re: [Open Babel] Perl bindings in current SVN
I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski > Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. > Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about > that in wiki, since that could potentially lead to some other undiscovered > errors. > > Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Maciek Wójcikowski > >> It worked. >> >> The failing line was: >> /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags >> -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared >> -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so >> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o >> -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz >> -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib >> >> Adding -lpthread leads to succesful compilation. >> >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl >> >> >> 2012/5/31 Noel O'Boyle >> >>> We changed to compiling the bindings directly rather than use Perl's >>> build system. It seems to work fine on some Linux OSes but not on >>> others. I haven't tracked down the problem but you could try >>> "VERBOSE=1 make" to see the command that we are using to compile, and >>> repeating it manually but adding -lpthread to see what happens. >>> >>> - Noel >>> >>> On 31 May 2012 09:56, Maciek Wójcikowski wrote: >>> > Hi, >>> > >>> > I have trouble building Perl bindings in openbabel SVN branch. My >>> system is >>> > running 64bit CentOS 6. >>> > >>> > To compile i use following command: >>> > >>> > cmake ../openbabel \ >>> > -DRUN_SWIG=ON \ >>> > -DPERL_BINDINGS=ON \ >>> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ >>> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ >>> > -DPERL_PREFIX=/usr/lib64/perl5/ \ >>> > -DPYTHON_BINDINGS=ON \ >>> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ >>> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ >>> > >>> > Which leads to error: >>> > Linking CXX shared module ../lib/OpenBabel.so >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_resdat_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_chainsparser_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_atomtyper_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_aromtyper_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: >>> > undefined reference to `pthread_getspecific' >>> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >>> > `_wrap_isotab_get': >>> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: >>> > undefined reference to `pthread_getspecific' >>> > >>> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: >>> > more undefined references to `pthread_getspecific' follow >>> > collect2: ld returned 1 exit status >>> > make[2]: *** [lib/OpenBabel.so] Błąd 1 >>> > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 >>> > >>> > To clarify, given cmake command build 2.3.1 version without problem. >>> > >>> > >>> > Pozdrawiam, | Best regards, >>> > Maciek Wójcikowski >>>
Re: [Open Babel] Perl bindings in current SVN
Apparently it seams to be SWIG's fault. CentOS has SWIG in version 1.x. Compiling latest SWIG 2.x fixed the issue. Maybe we should ad a note about that in wiki, since that could potentially lead to some other undiscovered errors. Curiously cmake calls for SWIG in version 2.0 and loads successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski > It worked. > > The failing line was: > /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags > -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared > -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o > -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz > -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib > > Adding -lpthread leads to succesful compilation. > > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2012/5/31 Noel O'Boyle > >> We changed to compiling the bindings directly rather than use Perl's >> build system. It seems to work fine on some Linux OSes but not on >> others. I haven't tracked down the problem but you could try >> "VERBOSE=1 make" to see the command that we are using to compile, and >> repeating it manually but adding -lpthread to see what happens. >> >> - Noel >> >> On 31 May 2012 09:56, Maciek Wójcikowski wrote: >> > Hi, >> > >> > I have trouble building Perl bindings in openbabel SVN branch. My >> system is >> > running 64bit CentOS 6. >> > >> > To compile i use following command: >> > >> > cmake ../openbabel \ >> > -DRUN_SWIG=ON \ >> > -DPERL_BINDINGS=ON \ >> > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ >> > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ >> > -DPERL_PREFIX=/usr/lib64/perl5/ \ >> > -DPYTHON_BINDINGS=ON \ >> > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ >> > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ >> > >> > Which leads to error: >> > Linking CXX shared module ../lib/OpenBabel.so >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_resdat_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_chainsparser_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_atomtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_aromtyper_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: >> > undefined reference to `pthread_getspecific' >> > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function >> > `_wrap_isotab_get': >> > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: >> > undefined reference to `pthread_getspecific' >> > >> CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: >> > more undefined references to `pthread_getspecific' follow >> > collect2: ld returned 1 exit status >> > make[2]: *** [lib/OpenBabel.so] Błąd 1 >> > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 >> > >> > To clarify, given cmake command build 2.3.1 version without problem. >> > >> > >> > Pozdrawiam, | Best regards, >> > Maciek Wójcikowski >> > mac...@wojcikowski.pl >> > >> > >> -- >> > Live Security Virtual Conference >> > Exclusive live event will cover all the ways today's security and >> > threat landscape has changed and how IT managers can respond. >> Discussions >> > will include endpoint security, mobile security and the latest in >> malware >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> > ___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > >> > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Perl bindings in current SVN
It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -shared -Wl,-soname,OpenBabel.so -o ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -L/usr/lib64/perl5/CORE -lperl ../lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-rpath,/usr/lib64/perl5/CORE:/home/maciek/openbabel/build/lib Adding -lpthread leads to succesful compilation. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle > We changed to compiling the bindings directly rather than use Perl's > build system. It seems to work fine on some Linux OSes but not on > others. I haven't tracked down the problem but you could try > "VERBOSE=1 make" to see the command that we are using to compile, and > repeating it manually but adding -lpthread to see what happens. > > - Noel > > On 31 May 2012 09:56, Maciek Wójcikowski wrote: > > Hi, > > > > I have trouble building Perl bindings in openbabel SVN branch. My system > is > > running 64bit CentOS 6. > > > > To compile i use following command: > > > > cmake ../openbabel \ > > -DRUN_SWIG=ON \ > > -DPERL_BINDINGS=ON \ > > -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ > > -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ > > -DPERL_PREFIX=/usr/lib64/perl5/ \ > > -DPYTHON_BINDINGS=ON \ > > -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ > > -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ > > > > Which leads to error: > > Linking CXX shared module ../lib/OpenBabel.so > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_resdat_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_chainsparser_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_atomtyper_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_aromtyper_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: > > undefined reference to `pthread_getspecific' > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function > > `_wrap_isotab_get': > > /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: > > undefined reference to `pthread_getspecific' > > > CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: > > more undefined references to `pthread_getspecific' follow > > collect2: ld returned 1 exit status > > make[2]: *** [lib/OpenBabel.so] Błąd 1 > > make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 > > > > To clarify, given cmake command build 2.3.1 version without problem. > > > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > -- > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Perl bindings in current SVN
Hi, I have trouble building Perl bindings in openbabel SVN branch. My system is running 64bit CentOS 6. To compile i use following command: cmake ../openbabel \ -DRUN_SWIG=ON \ -DPERL_BINDINGS=ON \ -DPERL_LIBRARY=/usr/lib64/perl5/CORE/libperl.so \ -DPERL_INCLUDE_PATH=/usr/lib64/perl5/CORE/ \ -DPERL_PREFIX=/usr/lib64/perl5/ \ -DPYTHON_BINDINGS=ON \ -DPYTHON_LIBRARY=/usr/lib64/libpython2.6.so \ -DPYTHON_INCLUDE_PATH=/usr/include/python2.6/ Which leads to error: Linking CXX shared module ../lib/OpenBabel.so CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_resdat_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2641: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_chainsparser_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2633: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_atomtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2625: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_aromtyper_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2617: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o: In function `_wrap_isotab_get': /home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2609: undefined reference to `pthread_getspecific' CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o:/home/maciek/openbabel/openbabel/scripts/perl/openbabel-perl.cpp:2601: more undefined references to `pthread_getspecific' follow collect2: ld returned 1 exit status make[2]: *** [lib/OpenBabel.so] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] pybel + ouput options
Hello everyone, Is it possible to set conversion options in pybel? I couldn't find any information about it. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Energy Minimization of complex of two molecules
Have you tried "H1 + H2"? Actually this wasn't working for me in perl, but
it's supposed to be working in Python.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 23 kwietnia 2012 13:52 użytkownik Чугунов Антон
napisał:
>
> Dear Open Babel users,
> I'm writing a script to reconstruct a complex of two peptides. I employ OB
> python interface and also Pybel to make necessary transformations of both
> peptides, but finally I have to perform energy minimization of the whole
> complex to avoid bumping of side chains.
> It seems to be possible, since when I load two molecules from one PDB
> file, OB can optimize them. But here I don't know how to combine two
> molecules into one object that I could apply energy-minimization routine
> for the system.
> Can you help, please?
>
> PS. Let's say, molecules are defined as the following:
> H1 = pybel.readfile('pdb', 'pep1.pdb').next()
> H2 = pybel.readfile('pdb', 'pep2.pdb').next()
>
>
> --
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
>
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] 2D or 3D
Fingerprints are 1D therefore similarity search is 1D. To my knowledge there is no shape similarity search in OB. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 23 kwietnia 2012 09:20 użytkownik Jochen Schreiber < joc...@googlemail.com> napisał: > Hello guys, > > i need a fast answer. > > Is the similarity search in babel 2D or 3D? > > Greetz, > > Jochen Schreiber > > > -- > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] [Chimera-users] UCSF Dock mol2 files
Maybe @COMMENT would be a better place for them? http://tripos.com/data/support/mol2.pdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang napisał: > Our approach to file formats in Chimera is to support the "native" form > from the developers. The use of ## for Dock mol2 format is > obviously easiest for us since it is in use and already works in Chimera, > but we're happy to accommodate a more broadly useful format. > > Conrad > > > On 4/3/12 2:22 PM, Maciek Wójcikowski wrote: > >> For Chimera reference check out file >> UCSF-Chimera-XXX/share/**ViewDock/Compound.py You can see many versions >> of >> Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the >> same comment method. This comments are only used by ViewDock module, as >> far as I know. >> >> For Dock reference you can see dock6/src/dock/library_file.**cpp it seams >> fairy simple and always uses ##. >> >> Pozdrawiam, | Best regards, >> Maciek Wójcikowski >> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> >> >> >> >> W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell >> > <mailto:sbrozell@rci.rutgers.**edu>> >> napisał: >> >> >>Hi, >> >>This is a good suggestion. >> >>But before implementation, >>1) do the DOCK developers or users have any comments ? >>2) do the Chimera developers or users have any comments ? >> In particular, does Chimera use ## as the lexeme for the >>DOCK token ? >> It might be useful to have a consistent lexeme across programs. >> Or maybe the Babel folks have comments on what would be a more >>general tag ? >> >>thanks, >>scott >> >>On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: >> > Here you have two example files >> > >> http://dl.dropbox.com/u/**6846289/1afk_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2> >> > >> http://dl.dropbox.com/u/**6846289/3h78_ligand_**conformers.mol2<http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2> >> > >> > What OB should do (in my mind) is to take "Name:" value as target >>molecule >> > name and pass all 3 grid scores (total, vdw and ele) somehow (i >> guess >> > comment is a right place, since there is not much choice), so >>that it can >> > output it in simmilar manner. >> > >> > Maybe it would be easier to have an option "d" (aka. dock) which >>would copy >> > ALL the ## data, and some other one, such as "s" (aka. sufix) >>to take >> > suffixed name into account. Disadvantage of above is that it >>wouldn't work >> > for other formats. >> > >> > Pozdrawiam, | Best regards, >> > Maciek Wójcikowski >> > mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> >> >> > >> > >> > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < >> > ge...@geoffhutchison.net >> <mailto:geoff@geoffhutchison.**net>> >> napisał: >> >> > >> > > > I have a thought about mol2 files form Dock program, which >>contain >> > > > additional information in commentary (###). Those information >>is being >> > > lost >> > > > during openbabel operations, which is a pity. I'd like to >>propose a >> > > in/out >> > > > option for mol2 for Dock'ed mol2's to read/write compatible >>information >> > > from >> > > > those files. Especially conformer ID is important for further >>anylisis. >> > > > Simmilar approach is used with pdbqt's contained in >>Autodock's .dlg >> > > files. >> > > >> > > >> > > If you can give us a selection of example files and a list of what >> > > information you'd like retained, it's fairly easy to patch the >>parsers. >> > > >> > > Cheers, >> > > -Geoff >> >> >> >> >> __**_ >> Chimera-users mailing list >> chimera-us...@cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> > -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] UCSF Dock mol2 files
For Chimera reference check out file UCSF-Chimera-XXX/share/ViewDock/Compound.py You can see many versions of Dock, I reckon latest is the one we need. Anyhow since 4, dock uses the same comment method. This comments are only used by ViewDock module, as far as I know. For Dock reference you can see dock6/src/dock/library_file.cpp it seams fairy simple and always uses ##. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell < sbroz...@rci.rutgers.edu> napisał: > Hi, > > This is a good suggestion. > > But before implementation, > 1) do the DOCK developers or users have any comments ? > 2) do the Chimera developers or users have any comments ? > In particular, does Chimera use ## as the lexeme for the DOCK > token ? > It might be useful to have a consistent lexeme across programs. > Or maybe the Babel folks have comments on what would be a more general > tag ? > > thanks, > scott > > On Tue, Apr 03, 2012 at 05:40:46PM +0200, Maciek Wójcikowski wrote: > > Here you have two example files > > http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 > > http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 > > > > What OB should do (in my mind) is to take "Name:" value as target > molecule > > name and pass all 3 grid scores (total, vdw and ele) somehow (i guess > > comment is a right place, since there is not much choice), so that it can > > output it in simmilar manner. > > > > Maybe it would be easier to have an option "d" (aka. dock) which would > copy > > ALL the ## data, and some other one, such as "s" (aka. sufix) to take > > suffixed name into account. Disadvantage of above is that it wouldn't > work > > for other formats. > > > > Pozdrawiam, | Best regards, > > Maciek Wójcikowski > > mac...@wojcikowski.pl > > > > > > W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < > > ge...@geoffhutchison.net> napisał: > > > > > > I have a thought about mol2 files form Dock program, which contain > > > > additional information in commentary (###). Those information is > being > > > lost > > > > during openbabel operations, which is a pity. I'd like to propose a > > > in/out > > > > option for mol2 for Dock'ed mol2's to read/write compatible > information > > > from > > > > those files. Especially conformer ID is important for further > anylisis. > > > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > > > files. > > > > > > > > > If you can give us a selection of example files and a list of what > > > information you'd like retained, it's fairly easy to patch the parsers. > > > > > > Cheers, > > > -Geoff > -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] UCSF Dock mol2 files
Here you have two example files http://dl.dropbox.com/u/6846289/1afk_ligand_conformers.mol2 http://dl.dropbox.com/u/6846289/3h78_ligand_conformers.mol2 What OB should do (in my mind) is to take "Name:" value as target molecule name and pass all 3 grid scores (total, vdw and ele) somehow (i guess comment is a right place, since there is not much choice), so that it can output it in simmilar manner. Maybe it would be easier to have an option "d" (aka. dock) which would copy ALL the ## data, and some other one, such as "s" (aka. sufix) to take suffixed name into account. Disadvantage of above is that it wouldn't work for other formats. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 3 kwietnia 2012 17:23 użytkownik Geoffrey Hutchison < ge...@geoffhutchison.net> napisał: > > I have a thought about mol2 files form Dock program, which contain > > additional information in commentary (###). Those information is being > lost > > during openbabel operations, which is a pity. I'd like to propose a > in/out > > option for mol2 for Dock'ed mol2's to read/write compatible information > from > > those files. Especially conformer ID is important for further anylisis. > > Simmilar approach is used with pdbqt's contained in Autodock's .dlg > files. > > > If you can give us a selection of example files and a list of what > information you'd like retained, it's fairly easy to patch the parsers. > > Cheers, > -Geoff -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] PHP binding
If you set that up it would be nice. What kind of test scripts do you need? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 3 kwietnia 2012 02:40 użytkownik Geoff Hutchison < ge...@geoffhutchison.net> napisał: > > On Apr 2, 2012, at 5:34 PM, mwojcikowski wrote: > > > Since web-interfaces are incredibly popular it would be a nice feature to > > have openbabel built in PHP. I guess it would not be so hard, since we > need > > to create just php interface file for SWIG. > > The security implications scare me, but as you say, it would be fairly > easy to run SWIG to generate PHP bindings. My only problem is that I have > no idea how you'd test that. > > If you'd like to serve as guinea pig and will write some examples and > tests, we can set that up in the development branch. It's been requested -- > but no one has been willing to serve as tester. :-) > > Thanks, > -Geoff -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Difficulty appending OBMols in Perl (Was OBForceField in Perl)
I've wrote short script to replicate that problem.
#!/usr/bin/perl
use Chemistry::OpenBabel;
my $mol1 = new Chemistry::OpenBabel::OBMol;
my $mol2 = new Chemistry::OpenBabel::OBMol;
#my $mol3 = new Chemistry::OpenBabel::OBMol; # should not be necesary
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInFormat("smi");
$obConversion->ReadString($mol1, "C1=CC=CS1");
$obConversion->ReadString($mol2, "CCO");
print "Mol1: ".$mol1->NumAtoms()."\n";
print "Mol2: ".$mol2->NumAtoms()."\n";
$mol3 = $mol2;
print "Mol3 step one: ".$mol3->NumAtoms()."\n";
### there you go
#$mol3 += $mol1; # doesn't work, throws error
$mol3 -> add($mol1); # this does what above should.
###
print "Mol3 step two: ".$mol3->NumAtoms()."\n";
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 28 marca 2012 16:48 użytkownik Noel O'Boyle
napisał:
> Can you provide a short script that reproduces the problem? For
> example, with SMILES strings.
>
> - Noel
>
> On 26 March 2012 11:28, mwojcikowski wrote:
> > I've done some extra testing, when I wanted to write the simplest script
> to
> > recreate that problem. It seams it was my fault, and Setup does work
> > (although the weird error). I found out by the way that += operator on
> OBmol
> > class doesn't work resulting empty value. How would you recommend to
> append
> > ligand to pocket structure in perl instead of:
> > $mol = $mol_pocket;
> > $mol += $mol_ligand;
> > where every variable is initialized OBmol object and both prefixed ones
> are
> > read from files.
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/OBForceField-in-Perl-tp4503052p4505342.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
> --
> > This SF email is sponsosred by:
> > Try Windows Azure free for 90 days Click Here
> > http://p.sf.net/sfu/sfd2d-msazure
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OBForceField in Perl
I used all samples that i could. I also based my coding on samples on
OBForceField class. Here is a part on FF, you can se some parts that are
hashed - this means that I tried to used them, but it didnt help much. Also
ANY other class that I used before was throwing qite nice info if misused
or had bad arguments.
$pFF = Chemistry::OpenBabel::OBForceField::FindForceField("MMFF94");
#$OBForceField :: IsSetupNeeded($mol);
#$OBForceField -> FindForceField("MMFF94");
#$pFF = $pFF -> MakeNewInstance();
# check if correctly initialized
if(!$pFF) {
exit;
}
print "OK\n";
$pFF -> AddIntraGroup($bit_ligand); # bonded interactions in the ligand
$pFF -> AddInterGroup($bit_ligand); # non-bonded between ligand-ligand atoms
$pFF -> AddInterGroups($bit_ligand, $bit_pocket); # non-bonded between
ligand and pocket atoms
#$pFF -> SetLogFile('aaa.out');
#$pFF -> SetLogLevel('OBFF_LOGLVL_NONE');
#$pFF -> SetLogToStdOut(1);
$pFF -> SetLogLevel(2);
# We pass the constraints as argument for Setup()
$pFF -> Setup($mol, $constraints);
# Perform the actual minimization, maximum 1000 steps
$pFF->SteepestDescent(1000);
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
W dniu 26 marca 2012 02:58 użytkownik Matthew Ketterer <
mkett...@umail.iu.edu> napisał:
> Looking at the API, there is no Setup() method that takes no arguments,
> which might be why it is crashing. I'm not sure why or if you need to
> setup before you run or not once you initialize the forcefield using
> FindForcefield(Type).
>
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBForceField.shtml
>
>
>
>
> On Thu, Mar 22, 2012 at 5:08 PM, Maciek Wójcikowski <
> mac...@wojcikowski.pl> wrote:
>
>> Hello everyone,
>>
>> Is anybody here using OB perl bindings to do minimizationof any kind? I'm
>> trying to set it up, but I'm stuck on one problem - Setup() seams not to
>> run properly from perl:
>>
>> No matching function for overloaded 'OBForceField_Setup' at ./
>> minimizer_rm.pl line 68.
>>
>> It might be due to not initializing Forcefield properly, but I've did my
>> best and failed to do so. Can anyone post an example of correct part of
>> perl script with FF?
>>
>> Pozdrawiam, | Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>>
>> --
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
--
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] OBForceField in Perl
Hello everyone, Is anybody here using OB perl bindings to do minimizationof any kind? I'm trying to set it up, but I'm stuck on one problem - Setup() seams not to run properly from perl: No matching function for overloaded 'OBForceField_Setup' at ./ minimizer_rm.pl line 68. It might be due to not initializing Forcefield properly, but I've did my best and failed to do so. Can anyone post an example of correct part of perl script with FF? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
