Re: [Open Babel] Canonical SMILES with disconnected parts

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"

Re: [Open Babel] Tidying up files

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. I

Re: [Open Babel] Gen3D troubles

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 is

Re: [Open Babel] lattice from unit cell

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

Re: [Open Babel] Option to input net charge and to disable adding protons

On Oct 10, 2012, at 4:41 AM, David van der Spoel sp...@xray.bmc.uu.se 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

Re: [Open Babel] Option to input net charge and to disable adding protons

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

Re: [Open Babel] FP2 reference and description for fingerprints

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

Re: [Open Babel] OBConversion OUTOPTIONS characters

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 of the

Re: [Open Babel] Problems building OB 2.3.1 with static libs

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): In

Re: [Open Babel] Setting stereochemistry with Python openbabel

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

Re: [Open Babel] distgeom.cpp vs Eigen2

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

Re: [Open Babel] OBPointGroup in Python

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

Re: [Open Babel] File format

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

Re: [Open Babel] is there a torsion angle energy minimizer in openbabel?

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 parameter)

Re: [Open Babel] Adjust total moleculare charge

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

Re: [Open Babel] Conformer generation with openbabel trunk - problem...

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, this is

Re: [Open Babel] Anyone using the parallel implementation of MMFF94 forcefield (via OpenMP)

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

Re: [Open Babel] Anyone using the parallel implementation of MMFF94 forcefield (via OpenMP)

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

Re: [Open Babel] openbabel-2.3.1.tar.gz : false trojan alert?

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 source

Re: [Open Babel] Conformer generation using openbabel - take two

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 each

Re: [Open Babel] cis amide

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

Re: [Open Babel] Periodic boundaries and atom typing large systems

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

Re: [Open Babel] sd to mopin conversion: molecular charge?

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

Re: [Open Babel] Molecular Mechanics Start Up Time?

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,

Re: [Open Babel] generate 3D coordinates based on a scaffold

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

Re: [Open Babel] PHP binding

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

Re: [Open Babel] SMILES SMARTS

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 your

Re: [Open Babel] Sum of Gasteiger Partial Charges

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

Re: [Open Babel] GAFF atom assignments

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

Re: [Open Babel] GAFF atom assignments

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

Re: [Open Babel] Fwd: debug openbabel

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.

Re: [Open Babel] OpenBabel Conformer Search

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

Re: [Open Babel] OpenBabel Conformer Search

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 means

Re: [Open Babel] MMFF94 and RNA Quadruplexes

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 me

Re: [Open Babel] How do I know what's mean of atom type?

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

Re: [Open Babel] MAC installation: What directory the source codes have installed?

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

Re: [Open Babel] OBChemTsfm in Python

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. We

Re: [Open Babel] OBChemTsfm in Python

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