[Open Babel] Weighted-rotor search

Is it possible to do a weighted rotor search in pybel? I have been using openbabel and the WeightedRotorSearch function. I couldn't find any simple example online and wanted to find out if the approach below is ok and if anyone would advise changes. Am I right in saying that the mol is updated to t

Re: [Open Babel] Weighted-rotor search

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)? Wha

Re: [Open Babel] Weighted-rotor search

Thanks for the reply but that doesn't seem to be working for me (code below). If I just want to get a rough set of coordinates, what should I do? I see that gen3d (see link below) does a weighted rotor search as part of the process of making 3d coords but I wanted to just get the 3d coords and spec

Re: [Open Babel] Weighted-rotor search

Thanks Chris, do you have a link for that? -- View this message in context: http://forums.openbabel.org/Weighted-rotor-search-tp4655264p4655277.html Sent from the General discussion mailing list archive at Nabble.com. --

Re: [Open Babel] Weighted-rotor search

Thanks Geoffrey, that helps alright but I am still stuck with zero coordinates when I write to an output file (say mol2 or com). What am I still missing? mol = openbabel.OBMol() cv = openbabel.OBConversion() cv.SetInAndOutFormats('smi', outfile_type) cv.ReadString(mol, smiles_string) mol.AddHydrog

Re: [Open Babel] Weighted-rotor search

Ok problems solved from last post, I was missing the OBBuilder part (see below for ethane from smiles). I think this should now be the same as what gen3d does but with the python openbabel commands. import openbabel mol = openbabel.OBMol() cv = openbabel.OBConversion() cv.SetInAndOutFormats('smi

Re: [Open Babel] Problem with gen3D

Gen3d does a steepest descent optimization, weighted rotor search and then a conjugate gradients optimization (see http://forums.openbabel.org/what-does-gen3d-do-under-the-hood-td3397296.html). You might want to try a simple forcefield optimization to start with (like steepest descent) and see how

[Open Babel] Adding Hydrogens not working

I have a problem with the following smiles [O][N][C]([C])[C] and related smiles. When I try to add hydrogens nothing happens. The correct formula is C3H7NO. It looks to be some problem with the square brackets but I don't know how to automatically adjust the smiles so that it will add the right amo

[Open Babel] Compare 3D strucuture of molecules?

Hi all, Does babel have any conformer comparison function like the molecular overlay that can be done in Mercury? I'm looking to get a quantitative measure of the similarity of two conformers. Cheers, Scott -- View this message in context: http://forums.openbabel.org/Compare-3D-strucuture-of

Re: [Open Babel] Compare 3D strucuture of molecules?

Hi, Fredrik- thanks, that's working for me now. I am using the following simple python script to run the rmsd calcs on two conformers from two files: import pybel file1 = 'conf1.mol2' file2 = 'conf2.mol2' ref = pybel.readfile('mol2', file1).next() tar = pybel.readfile('mol2', file2).next() align

[Open Babel] OBAlign() error

Dear all, I have been using OBAlign() to get rmsd values between conformers but just came across an erroneous value of 3.14 for the molecule N-Acryloyl glycine, the CSD function tormat gives a rmsd of 0 for the two conformers. Any idea what is going wrong here? I've attached the two mol2 files. T

[Open Babel] MMFF94s force field

Dear all, I can't find any information about the MMFF94s force field (as opposed to just MMFF94). Is this available in open babel? Also, is there a way to list available forcefields interactively within python? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/M

[Open Babel] Smiles conversion problems with Ion and Zwitterion

Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is C7H8N2O4 but this changes to C7H9N2O4, whic

[Open Babel] Generating a diverse set of conformers

This topic has been touched on in other posts but I can't find any explanation about producing multiple conformers with a particular diversity. For example: obabel input -O output --conformer --nconf 50 --score rmsd - I seem to only get one conformer written to the output file. How can you prod

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

Thanks for the comments. I am using Open Babel 2.3.1 on a mac. The command still doesn't ouptut multiple conformers, only the one file with one conformer in it. obabel input.sdf -O out.sdf --conformer --nconf 50 --score rmsd obabel input.sdf -O out.sdf --writeconformers --nconf 50 --score rmsd Al

[Open Babel] Indexing in OBmol and OBMolAtomIter

Why does the GetAtom indexing begin at 1 but the OBMolAtomIter indexing begin at 0? So atom=obmol.GetAtom(1) but atom.GetIndex() returns 0. -- View this message in context: http://forums.openbabel.org/Indexing-in-OBmol-and-OBMolAtomIter-tp4656060.html Sent from the General discussion mailing li

[Open Babel] Intramolecular Hydrogen bond detection

Can openbabel detect intramolecular Hydrogen bonds? If not, would it be worth including in OBMol? I put together the python function below which uses OBMol functions to find the number of intramolecular hydrogen bonds based on a user define angle and distance cutoff. def getHBondList(obmol): "

[Open Babel] Cannot set up forcefield for this molecule

Dear all, I get an error when trying to set up the MMFF94 forcefield with the following molecule: B(CP(C(C)(C)C)C(C)(C)C)(CP(C(C)(C)C)C(C)(C)C)C1=CC=CC=C1 Any ideas why this is happening? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/Cannot-set-up-forcefie

[Open Babel] Unable to set up forcefield for coordinates from mol file

Hi all, I am trying to extract the structure from the following strangely formatted mol file: BASIS cc-pVTZ PP EXCITATION DIAGNOSTIC Atomtypes=3 Nosymmetry Charge=6.0 Atoms=10 C 2.27062225854.77301732840.00 C -2.27062225854.7730173284

[Open Babel] Smiles for diphosphorus

Hi all, When I use gen3d with P#P I get a molecule with two hydrogens. Should it not be the diphosphorus molecule with chemical formula P2? Using [P]#[P] produces the desired result but I wanted to find out why gen3d does this. Best wishes, Scott -- View this message in context: http://forum

[Open Babel] Two smi conversion problems

Hi all, 1. When converting a sdf file (see attached) for carbon monoxide to smi format I get the following smi result: [C-]#[OH] 2. Hydrogens are inserted when converting the smiles P#P for the diphosphorus molecule to sdf format (see attached) using gen3d. Best wishes, Scott CO.sdf

[Open Babel] Conformer searching

Hi all, I would like to generate conformers for molecules such as C2H6 and N2H4, is this possible? The bonds in these molecules are not being detected as rotatable bonds, why is this? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/Conformer-searching-tp465731