> I am trying to use OBChemTsfm in Python 3.1 with OpenBabel 2.3 . I can access
> the basic parts of openbabel (OBMol) but not OBChemTsfm. My code is as
> follows:
The scripting bindings must "wrap" each class from C++. So we have a very large
subset in the Python bindings, but not OBChemTsfm.
On Aug 2, 2011, at 2:36 PM, Tom Lamar wrote:
> So for now if I want to access OBChemTsfm I should just code in C++?
It depends upon how fast you need a revised binding. We can try out adding
phmodel.h to the openbabel-python.i SWIG file and re-run.
I won't have time to try that today, but it's
On Aug 10, 2011, at 7:36 PM, Craig A. James wrote:
> Sometimes you get this problem if your file has a mixture of Windows (CRLF)
> line endings and Unix/Linix (LF only) line endings. The files look fine in a
> text editor, but actually have extra line endings that the editor suppresses.
In pr
> I just installed OpenBabel 2.30 package for Mac and can not find the source
> codes.
> I found binaries and libs in /usr/local/ but could not find source codes
> there.
Source code is available from http://sf.net/projects/openbabel or
http://sourceforge.net/projects/openbabel/files/openbabel
> for example, C3 may mean [#6^3]. So how do I know what's mean of the extra
> atoms; is there a list to explain them. I want to use them to match the
> atom type in opls-aa forcefield.
I don't think the atom types defined by Open Babel are anywhere precise enough
for OPLS-AA, which has speciali
> How do I know if Swig is actually being used?
The development version doesn't include any scripting modules, so if it's even
attempting to compile/link, then it's using swig.
-Geoff
--
BlackBerry® DevCon Americas, Oct.
> Hi! I am trying to run obenergy on the TERRA Quadruplex (PDB Code 3IBK) and I
> am having trouble getting MMFF94 force field to calculate the energy. I am
> not sure what is causing this problem (I have only basic knowledge in
> computational chemistry) and I was wondering if any of you can help
> However, calling:
>
> ff = OBForceField.FindForceField("MMFF94");
> returns null.
> Using OBPlugin.List("forcefields");
>
> returns: forcefields is not a recognized plugin type. Those with instances of
> sub-types loaded are:
If you are using one of the current 2.3.x versions, you will ne
> Furthermore, why do I get no co-ordinates?
I started from a 3D molecule. So you'll want to add a --gen3d to your
command-line. (I'd feel a bit better if it was in 2 steps: generate
coordinates, then conformer search, but it looks OK on one command-line.)
Hope that helps,
-Geoff
> Q: The weighted rotor conformer gives only one conformer (lowest energy)?
> What happens when you specify the num of conformers to say 50 ?
At the moment, the weighted search runs a stochastic search for the lowest
energy across some number of test conformers. So specifying 50 conformers mean
> Seems like the debugger is looking for files located on ghutchis's computer.
> How do I create and link the .o files myself? Do I need to make modifications
> to CMakeLists.txt file?
Are you trying to link against the binary install of libopenbabel.dylib? If so,
it's built for "-g -O2" flags.
> Where are kr, kth, vn_half, etc. defined? They don't seem to be explicitly
> stated in the gaff.dat file. For example, kr is defined as
These things are usually in the appropriate journal articles. So for example:
> bondcalc.kr = KCAL_TO_KJ * parameter->_dpar[0];
Since Open Babel uses kJ/mol
> So I guess the question becomes: how do I obtain the SMARTS string for each
> atom in GAFF? Again, all I know is which atoms are connected to each other
> and the bond type (single, double).
I'm not sure I understand your question. SMARTS is a pattern matching system.
So the Open Babel code
On Dec 19, 2011, at 7:48 PM, Eric Jang wrote:
> 1. Is the assignment of atom types somehow based on the SMARTS string of a
> molecule? It would make sense that each atom has some SMARTS string property
> that is compared to the gaff.prm file.
SMARTS is essentially a programming language. So a
> How are formal charges assigned in a molecule? I can't seem to find the code
> other than setPartialCharge and getPartialCharge accessors.
Formal charges or partial charges? Formal charges are, by default, assigned by
a format, or at the moment, by the Gasteiger partial charge assignment
oper
You don't have to use SMARTS -- you could program the atom types with a set of
if/else clauses. Essentially all of MMFF94 atom typing is done this way in Open
Babel. It's probably more tedious, though.
> Sorry, but my question remains as to how can element is assigned its atom
> type based sole
> My code snippet (based on the example from the OBChargeModel
> documentation) is as follows:
Have you created an OBConversion object? We changed the way plugins are loaded
in OB 2.3.x, and it currently requires that an OBConversion object is created
to find plugins. This will be fixed in 2.4,
> I am trying to assign the Gasteiger partial charges to all the atoms.
> However, when I implemented the algorithm in molchrg.cpp (separate from
> OpenBabel), the sum of my partial charges is always 0 whereas the sum of
> OpenBabel partial charges is sometimes 0, -1, or 1.
Open Babel has "seed
> Then I'm doubly confused as to why having that line changes the
> behaviour of the code beneath it. My guess was that, for whatever
> reason, OBConversion is not pulling in the charge models and that my
> botched line above is pulling in enough for
If you like, send me the code, and I'll take a
> I'm having trouble building the latest SVN release (trunk) of Openbabel (from
> scratch) on Linux (CentOS 5.6). The build fails when it tries to build the
> python bindings because of a -fPIC switch not present. Is there a cmake
> option to allow me to turn this on?
I think the biggest quest
> I am currently trying to generate SMARTS Patterns from an 'mol' or 'sdf' file
> using pybel. So far I haven't been able to succeed.
> Is it possible to convert Canonical-SMILES (which is possible) into SMARTS?
> Or can I use Canonical-SMILES with the pybel.smarts() module?
> I look forward to y
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 s
> alternative site (e.g. 4-amino-pyridine). Is this currently possible
> with OpenBabel? I couldn't quite find what I was looking for on the
> wiki...
You could probably code something like this using the OBBuilder code, but it
would take some work (i.e, it sounds like you'd need to remove or mut
> So my question is this: Is there anyway to speed-up this start up time,
> or at the very least a way to perform consecutive minimizations without a
> startup in between every one?
Keep in mind the "startup" involves assigning the molecular mechanics atom/bond
types, assigning aromaticity, det
> It would be nice to have the internal coordinate format for qchem included.
Sorry for the delay. I think you're asking to specify internal coordinates for
qchem input?
Thanks,
-Geoff
--
Live Security Virtual Conferen
> With a build from SVN 4747 that I compiled on OS X on Friday, I get a
> perfectly reasonable set of 3D coordinates from Ferenc's 2D input. So I
> wonder if this is a compilation problem rather than a software one.
I put in a fix -- there was an issue with generating coordinates when multiple
> Everything compiles without any errors. However, everytime I execute my
> application and run into the function SetInAndOutFormats, the API returns the
> following:
> "Formats not available"
Have you created an OBConversion object? The C++ constructor will load the
formats. You may also need
> Isn't there some way to turn down the VdW via a distance cutoff or so?
> (EnableCutOff and SetVdWCutoff) I've never used these but hopefully they will
> prevent the pairwise generation of all of the VdW terms.
Yes, exactly.
-Geoff
--
> To make the OB force fields work with large amounts of atoms,
> the non-bonded pairs should be detected dynamically.
Well, I'm not sure if that's really a performance win. Probably these need to
be *updated* every 10 steps or something.
> force field calculations. I noticed that periodic bound
I'm not sure what you mean by pybel or Python to convert to PDB. Do you use the
3D coordinate generation in Pybel? Do you use 2D coordinate generation in
Python?
If you're using 3D coordinate generation in Python, it's the same code as babel
--gen3d. In this case, I would suspect you have a ver
> Some of the generated conformers look really ugly (in terms of close
> atoms/steric clashes).
> I have placed a selected subset at: http://imgur.com/a/LgJqL
>
> Is that to be expected in RMSD scoring -- because I have not used --score
> energy? (I tried the energy scoring, and the molecules
On May 29, 2012, at 11:23 AM, JP wrote:
> This value of 1A in the steric filter is not available from the command line,
> correct?
No, there isn't (yet) a way to set that. The current SVN trunk now has an
improved filter. It considers hydrogens, and will also filter based on VdW
radii for eac
> I decided to try compiling OB for Cygwin but found that
> openbabel-2.3.1.tar.gz makes the firewall unhappy: "This request is blocked
> by the SonicWALL Gateway Anti-Virus Service. Name: FraudLoad.ZKTH_2 (Trojan)"
I can vouch that the md5sum matches that which I uploaded. The tar contains
sou
> This is from the time before OpenBabel moved to CMake. I look at the
> CMakeLists.txt and there is no OpenMP flags there (-fopenmp, -lgomp).
> Which is the preferred way to do it.
Either edit you CMakeCache.txt (e.g., "ccmake .") after setting up the cmake
build directory, or declare these as
> It is a protein, but the retrieved PDB was DNA structure.
You don't say what version of Open Babel you're using. Looking at the current
code for fastaformat.cpp, it should accept:
>protein
>peptide
>Protein
>Peptide
-Geoff
> Now my question is why this happens, even when I
> run obminimize and I explicitly ask to use MMFF94 (not MMFF94s)
The forcefieldmmff94.cpp file (and thus the resulting library) include global
objects for both MMFF94 and MMFF94s. If you split the code, you could obviously
do away with the "du
Hi Omar,
A few notes on the OpenMP code -- which is presently just for the MMFF94
implementation. I don't think Tim spent a whole lot of time trying to optimize
how the OpenMP blocks were arranged. So it works, and validates, but I suspect
with a bit of tweaking, better speed-ups could be found
> But when I try to generate conformers using:
>
> obabel ./astex_1g9v/ligand_babel3d.sdf -O/tmp/test.sdf --conformer --nconf 10
> --writeconformers --score rmsd
>
> I get:
>
> Initial conformer does not pass filter!
> Initial conformer count: 0
> Generation #1 0
> Generation #2 -nan
Yes, th
> E.g. if I want to convert 1-methyl-pyridine I get a non-aromatic ring
> with a carbon radical. This would be correct if the moleculare should be
> neutral. But when I could set the total charge to +1 I would expect a
> aromatic, non-radical pyridinium cation.
This is largely due to the input for
> Is there an torsion angle energy minimizer in open babel?
Not per-se. There are multiple general force fields with minimizers, and you
could set up constraints to just minimize torsions and not anything else.
Hope that helps,
-Geoff
---
> So, in a nutshell, I should find all rotatable bonds present in the molecule
> and then add "AddTorsionConstraint" from OBFFConstraints? But what I want to
> do is "relax" a structure at the rotatable bonds, doesn't
> "AddTorsionConstraint" require me to give it the torsion angle (fifth
> pa
> open-babel perhaps already supports it.
> The format is:
> t # methane (name of molecule or any other information you want to put such
> as number of atoms/bonds..etc)
Nope, it's not already in OB. Sorry. Seems like it should be easy to code.
-Geoff
---
> Indeed it is. I'm not very familiar with OB protocols as to reading/writing
> molecules. Can you point out somewhere I can to look before I start coding
> things from scratch
Look at src/formats/ghemicalformat.cpp. It's very similar.
Hope that helps,
-Geoff
> I've recently been writing some code to automatically write GAMESS input
> files for me. As these files require a point group it would be advantageous
> to determine this automatically from a geometry. Unfortunately I'm having
> some difficulty accessing the OBPointGroup class with the python
> I've just seen a demo of the impact of running applications on the GPU and it
> does seem for some operations you can get striking performance gains. Would
> it be worth considering porting openbabel to OpenCL?
Much like muti-threading, it's not clear how some operations in Open Babel
would w
> Thanks for the response. Is it not possible to rotate the molecule into the
> correct frame once you have determined its point group?
That could probably be done (but isn't implemented). Reducing to the symmetry
unique atoms would take a decent amount of implementation work, which I don't
pe
> anyone would advise changes. Am I right in saying that the mol is updated to
> the best conformer and this is what will be written to the output file?
Yup. This is very similar to my version of this -- I usually usually something
like:
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRo
> Thanks for the reply - this problem occurs in the builder.Build method
> before the force field optimization, where initial coordinates are
> given to each atom.
It's not so much an issue of the "constraints" as the fact that you have a
messy fused-ring system. The ring perception and particula
> When I build the most recent revision in SVN, 4965, with Eigen2
> installed, it fails to compile due to an ambiguous overloaded call to
> Matrix. But with Eigen3 installed, it works.
That's my mistake, since I only have Eigen3 installed on my machines. If you
can give me the compile error, I
> I am having some problems to compile OpenBabel on Ubuntu with static
> libs. The compiler is GNU (GCC/G++), Eigen3, Zlib, Cairo and XML2
> libraries were installed.
>
> The error message appears during the linking step:
>
> Linking CXX executable ../bin/babel
> ../src/libopenbabel.a(plugin.o):
Unfortunately, Noel (the best person to answer this) is on holiday and changing
jobs shortly. My best suggestion would be to start with SMILES (i.e., if you
have the molecule/bond info, generate SMILES). This should set the
stereochemistry correctly.
Using the stereo classes is possible, but I
We've deprecated the openbabel-scripting list because the overlap with
openbabel-discuss was quite high.
I'm happy to add whatever attributes might be useful. The DLL is compiled using
the Mono compiler on Linux, which doesn't implement that. If you like, we can
distribute the various .cs files
> Is it possible, with Open Babel to calculate the principle moment of inertia
> for a library of 3d compounds?
There's no formal API call, but it's fairly easy. There is, for example,
OBMol::ToInertialFrame() which will rotate a molecule to the inertial frame of
reference. You could adapt that
> I am using OpenBabels C++ API to minimize ligands and I was wondering if
> there's a possibility to minimize hydrogens only?
Not directly, but it's a nice idea. You could do this right now by freezing
every heavy atom:
OBForceField* pFF = OBForceField::FindForceField("MMFF94");
if (!pFF
> characters to complete the translation of the command line argument
> for what I am trying to do:
>
> obabel benzodiazepine.sdf.gz -O out.svg --filter "title=3016" -s
> "c1ccc2c(c1)C(=NCCN2)c3c3 red" -xu -d
Keep in mind that if you're doing it programmatically, you don't use the 'x'
part o
> page. However, I aways get the error message "Initial conformer does
> not pass filter! Initial conformer count: 0". I used methotrexate, as
I've found a few cases like this and am working on a fix. The biggest problem
is making sure there isn't an infinite loop.
If you are willing to send me
> There's a really fast way to find what you want with Google. Try
> these searches:
>
> openbabel obatom
> openbabel obatom iterator
> openbabel ring
Indeed, I gave up trying to optimize the Doxygen search system. Google won the
search race. :-)
Cheers,
-Geoff
-
> Apparently it did more than just that and fixed some issue
> along the way.
>
> Geoff, could this be considered for maintenance release?
Not as-is. It changes API / ABI, so it must be confined for trunk. There are
usually bugs like this which are fixed by 2.x releases which cannot be fixed by
On Oct 10, 2012, at 4:41 AM, David van der Spoel wrote:
> Geoff was mentioning that the API would have to change to support this,
No, I was saying that a bug fix you seem to need (i.e., SMARTS) is currently on
the development trunk, and that has slightly different ABI (binary interface)
than
> I have a small doubt regarding lattice preparation from unit cell of a
> molecule. Is there any command in Openbabel, which can generate lattice (3X3)
> If I will give the pdb file with CRYST1 record. I know fillUC can give unit
> cell.
Apologies for the delay -- I've been traveling. My sug
> I have some troubles with the --gen3D option. On some files, i have this
> warning : WARNING: damped steplength
> and i can't do anything else after.
There shouldn't be any concern about this. Basically, it's suggesting that the
initial geometry is a bit crude. Often the resulting 3D geometry i
> I often end up editing files using a text editor because they contain
> features that are not compatible with other programs. In particular removing
> salts and/or solvents and expanding fragment labels e.g TMS, t-butyl etc.
Sorry Chris -- a pile of things stopped me from getting back to this.
No, this is a known bug with disconnected fragments. The canonical algorithm
does not canonicalize the fragments.
Geoff
> On May 27, 2017, at 4:20 AM, Noel O'Boyle wrote:
>
> Should be the same. Can you provide the files?
>
>> On 27 May 2017 12:51 a.m., "xh s" wrote:
>> In my program I conve
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