Re: [Open Babel] Open Babel compilation to add Python bindings fails

d what the variable names are. Something like "cmake .. > -DPYTHON_INCLUDE_DIR=whatever -DPYTHON_LIBRARY=whatever > -DPYTHON_EXECUTABLE=whatever" (check the variable names) will cover > all of the bases. If this is not clear, let us know. > > And as I always say on this list,

[Open Babel] Open Babel compilation to add Python bindings fails

Hi all, I am trying to install a Pymol plugin and it requires my Open Babel to be re-installed, this time including the Python bindings: Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2 Type "help", "copyright", "credits" or "license" for

[Open Babel] Open Babel compilation to add Python bindings fails

Hi all, I am trying to install a Pymol plugin and it requires my Open Babel to be re-installed, this time including the Python bindings: Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2 Type "help", "copyright", "credits" or "license" for

Re: [Open Babel] [openbabel:bugs] #710 Gasteiger partial charges and the -p option

ted with the previous code. > > # pH model test > import pybel > from sys import argv > """patterns from phmodel.txt""" > pre = 'O=C[OD1-0:1]' > post = 'O=C[O-:1]' > transform = pybel.ob.OBChemTsfm() > success = transf

Re: [Open Babel] Generating a diverse set of conformers

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.

Re: [Open Babel] Generating a diverse set of conformers

Actually that input file isn't the most flexible, here is a different one that is more flexible and also only generates one conformer. crystal_ligand_flex.sdf -- View this message in context: http://forums.openbabel.org/Gene

Re: [Open Babel] Generating a diverse set of conformers

Sorry, I missed the request for the input file (still can't see it to be honest). Anyway, I have attached the file. obabel -V gives "Open Babel 2.3.2 -- May 7 2014 -- 09:05:30" i.e. the expected compilation date crystal_ligand.sdf

Re: [Open Babel] Generating a diverse set of conformers

The only message I got during the recompilation was: CMake Error at cmake_install.cmake:88 (FILE): file Internal CMake error when trying to open file: /usr/people/douglas/programs/openbabel-2.3.2_witheigen/openbabel-2.3.2/build/install_manifest.txt for writing. make: *** [install] Error 1

Re: [Open Babel] Generating a diverse set of conformers

It's gone worryingly quiet ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657420.html Sent from the General discussion mailing list archive at Nabble.com. ---

Re: [Open Babel] Generating a diverse set of conformers

obconformer with arguments: /usr/local/bin/obconformer 10 10 crystal_ligand.sdf outputs: The conformers appear to be generated - how do I get them written out? The input structure is in 3D by the way. -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-o

Re: [Open Babel] Generating a diverse set of conformers

obconformer when run outputs: Usage: obconformer NSteps GeomSteps -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657404.html Sent from the General discussion mailing list archive at Nabble.com. -

Re: [Open Babel] Generating a diverse set of conformers

So I've recompiled obabel with eigen, but the output of obabel -L ops has not changed: 0xout Additional file output addfilenameAppend input filename to title AddInIndexAppend input index to title AddPolarHAdds hydrogen to polar atoms only canonicalCanonicalize the atom order en

Re: [Open Babel] Generating a diverse set of conformers

OK will do. Just out of curiosity, what is my install of Babel doing when I specify those options? Just ignoring them, without informing the user? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657402.html Sent from the General di

Re: [Open Babel] Generating a diverse set of conformers

itiwks-> /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L ops 0xout Additional file output addfilenameAppend input filename to title AddInIndexAppend input index to title AddPolarHAdds hydrogen to polar atoms only canonicalCanonicalize the atom order energyFo

Re: [Open Babel] Generating a diverse set of conformers

/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 G

Re: [Open Babel] Generating a diverse set of conformers

Anyone have any comment on this? I am observing the same problem as OP. I am using the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --conformer --nconf 50 --writeconformers I only get 1 conformer in the 1 output file. I have also tried

Re: [Open Babel] Generating a diverse set of conformers

This doesn't work either: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -oconfbareport -xf tmp.sdf -xr 1.0 I get: obabel: cannot write output format! Open Babel 2.3.2 -- Mar 20 2013 -- 08:59:03 Usage: obabel [-i] [-o] -O [Options] Try -H option for more in

Re: [Open Babel] chemdraw bond lenghts

I should point out that the --gen3D workaround doesn't work in all cases. See the attached 2D SDF for an example - converting it to 3D results in 'nan' coordinates. What is the official stance on this? On the one hand Babel can't be expected to fix files that other software has screwed up.

Re: [Open Babel] erroneous structures when the option "-p" is activated

ly) > Tel: +39 011 670 7680 | Mob: +39 348 5537206 > Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it > http://open3dqsar.org | http://open3dalign.org > ========== > > > > On 30 Aug 2012, at 11:33, Douglas Houston >

Re: [Open Babel] erroneous structures when the option "-p" is activated

Hi, I don't know if this is related, but I've found another example of what appears to be an "erroneous structure" with the -p option in 2.3.1. I noticed it when converting to PDBQT format, but there's also a problem when I convert to PDB. The files in question are attached. babel -isdf i

[Open Babel] Fwd: OB writing non-standard atom types?

Just to follow up on this, can someone please try to replicate the problem for me using the attached files? - Forwarded message from dhous...@staffmail.ed.ac.uk - Date: Fri, 29 Jun 2012 16:50:03 +0100 From: Douglas Houston Subject: [Open Babel] OB writing non-standard atom

Re: [Open Babel] OpenCL

This seems like a good compromise to me, especially if it means we see it sooner ... Quoting JP on Thu, 12 Jul 2012 19:07:06 +0100: > A sidepoint from GPU development - and directly related to Geoff's > earlier point. > > Perhaps multicore awareness is the way to go... > > In the most reducti

[Open Babel] OB writing non-standard atom types?

Hi all, I've been trying to convert the attached in.pdb file to .mol2 format. I happened to be using the -p option: babel -ipdb in.pdb -omol2 out_p.mol2 -p 7.4 This produces a file that babel chokes on if used as input: babel -imol2 out_p.mol2 -opdb == *** Open

[Open Babel] Cleaning up structures

Hi all, I'm having problems "cleaning up" the structure of a small molecule. I was hoping to use obminimize to fix the distorted bond lengths/angles in the nitro group of the attached file obmin_in.mol. However, the program does not appear to be paying attention to the bond order information in t

Re: [Open Babel] erroneous structures when the option "-p" is activated

This may be related to a longstanding bug that has yet to be fixed. See: http://sourceforge.net/tracker/index.php?func=detail&aid=3203137&group_id=40728&atid=428740 This essentially makes the -p option unusable if you are expecting charges in the output format. Quoting green69 on Fri, 15 Ju

Re: [Open Babel] chemdraw bond lenghts

will be of tremendous help, and eventually be a fast patch > > > On 6/3/12 12:52 PM, Douglas Houston wrote: >> Yes, this is a serious problem in Chemdraw. I found that using >> OpenBabel to convert to 3D then back to 2D adjusted the bonds to the >> correct dimens

Re: [Open Babel] chemdraw bond lenghts

Yes, this is a serious problem in Chemdraw. I found that using OpenBabel to convert to 3D then back to 2D adjusted the bonds to the correct dimensions. Quoting cadeddu on Tue, 6 Mar 2012 03:06:02 -0800 (PST): > seems that files converted from the cdx or cdxml have wrong bond lenght (I've >

[Open Babel] Open Babel Warning in ReadMolecule Open Babel Warning in ReadMolecule: This Mol2 file is non-standard. Cannot interpret atom types correctly

Hi all, I wonder if anyone can help me work out what's going on here. I'm trying to convert a PDB file of ADP (from structure 3ATV) to mol2 format and add hydrogens. The first step seems to work fine: babel -ipdb 3ATV_ADP.pdb -omol2 3ATV_ADP1.mol2 -p 7.4 however as a check I thought I'd tr

Re: [Open Babel] problems with make test on centos 5.5

Thankyou Peter and Noel, I was having the exact same problem. Quoting Peter Schmidtke on Thu, 15 Dec 2011 08:12:11 +0100: > Ah ok, I'll try that then. > > Thanks. > > Peter > > On Wed, 14 Dec 2011 23:50:58 +0100, "Noel O'Boyle" > wrote: >> I'm sure it's fine. If you really want "make test" t

Re: [Open Babel] Gasteiger partial charges and the -p option

On 23 November 2011 19:33, Douglas Houston > wrote: >> I just checked and it is. Do you think this bug is related to this post?: >> >> http://forums.openbabel.org/Wrong-gasteiger-atomic-partial-charges-BUG-tp4096059p4096059.html >> >> >> >> >> Quo

Re: [Open Babel] explicit hydrogens in smiles

ption? Quoting Noel O'Boyle : > babel -H smi gives the "h" output option. See the docs for more info. > > - Noel > > On 24 March 2011 16:10, Douglas Houston wrote: >> Hi, >> >> Can anyone tell if if there's a way to get OpenBabel to output

[Open Babel] explicit hydrogens in smiles

Hi, Can anyone tell if if there's a way to get OpenBabel to output explicit hydrogens in smiles strings? I'm trying to define a hydroxymate group, which has a hydroxyl group, but the smiles I'm getting from OB at the moment doesn't seem to differentiate between a hydroxyl and an ether, i.e.

Re: [Open Babel] Gasteiger partial charges and the -p option

e this > don't fall between the cracks... > > On 3 March 2011 10:50, Douglas Houston wrote: >> OK, just to follow up on this, if no-one has any objections I will >> submit a bug report. >> >> >> Quoting "Mathias W." : >> >>> Ye

Re: [Open Babel] Gasteiger partial charges and the -p option

OK, just to follow up on this, if no-one has any objections I will submit a bug report. Quoting "Mathias W." : > Yeah, thats because I'm stupid - I didn't recognize that all these > numbers were recognized as text :-( > > 2010/12/3 Douglas Houston : >>

Re: [Open Babel] Gasteiger partial charges and the -p option

That's strange, if I sum everything in the charge column in your molecule_H.mol2 file, I get -9.0 ... Quoting "Mathias W." : > Servus, > > I get both times over all charge zero (with ob-2.2.3) > > (molecule_H2.mol2 was produced with -h) > > >

Re: [Open Babel] Gasteiger partial charges and the -p option

Hi all, Just wondering if anyone got a chance to test this molecule? I want to make sure it's not just my installation ... cheers, Doug Quoting Douglas Houston : > Hi, > > I have observed something curious about variations in the way > OpenBabel assigns Gasteiger

[Open Babel] Gasteiger partial charges and the -p option

Hi, I have observed something curious about variations in the way OpenBabel assigns Gasteiger charges. For example, babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h produces a molecule with an overall charge that is essentially 0. However, the command babel -isdf molecule.sdf -omol2 m

Re: [Open Babel] Error in DoTransformations

Thanks a lot for your reply Geoff, I can wait until the release of 2.3.1 as Hans De Winter has very kindly provided me with a similar fix in Sieve that provides this functonality (v. 3.0.4), cheers, Doug Quoting Geoffrey Hutchison : >> babel -isdf test1000.sdf -osdf test1000_nofrags

[Open Babel] Error in DoTransformations

Hi, I am trying to strip all salts from an SDF. Presumably the -r option should be able to do this? However, when I try the following command: babel -isdf test1000.sdf -osdf test1000_nofrags.sdf -r I get 997 of the following errors, and only 3 molecules converted: *** Open Babel Error in Do

Re: [Open Babel] Problem installing Sieve

Hi Pascal, I tried: setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/local/lib/ and that worked a treat. Thanks a lot! Doug Quoting Pascal Muller : > Hi, > > /usr/local/bin/sieve: error while loading shared libraries: >> libopenbabel.so.4: cannot open shared object file: No such file or >> d

Re: [Open Babel] "make test" fails

usr/local/sieve-3.0.3/CMakeCache.txt with various alternatives, to no avail. cheers, Doug Quoting Noel O'Boyle : > It's all fine. I will reply in more detail about a workaround later... > > On 2 November 2010 10:37, Douglas Houston > wrote: >> Hi, >> >&

[Open Babel] "make test" fails

Hi, I am trying to compile the new version of Openbabel. Here are the commands I used: mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/usr/people/douglas/programs/openbabel-2.3.0/ ../ make -j2 Everything seems to be OK up to this point. Then I try: make test Everything passes right up to

Re: [Open Babel] Release candidates available for testing

is a benzene ring in SMILES format but according to the following link will not match benzene if it's used as a SMARTS string. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html cheers, Doug Quoting Chris Morley : > On 08/09/2010 13:17, Douglas Houston wrote: >>

Re: [Open Babel] Release candidates available for testing

Hi, According to this page: http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints.html#fingerprints I can use the -s option with the name of a file, e.g.: babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf will write out all the compounds in mymols.sdf that contain t