Re: [Open Babel] Is it possible to change forcefield when using --gen3d?

Another unexpected issue. When I enter with clean 3d coordinates (generated by ChemAxon) wash them with OpenBabel and then use that seed conformation to start a conformational search I never get output. Most of the time (and this is with a batch of 25 molecules) I get through around 10% of the mo

Re: [Open Babel] Is it possible to change forcefield when using --gen3d?

Just a quick santity check, but does either obabel --gen3d or obgen work? In my hands both are giving seg faults starting from smiles. What is weird is that --gen2d is working fine. I should specify that I am using OpenBabel 2.3.2 and starting from smiles produced by OpenBabel and I had no is

[Open Babel] addFragment

Dear All, I'm trying to run a multiple fragment minimization. I found how to include the inter and intra-molecular interactions here: http://openbabel.org/api/2.3.0/classOpenBabel_1_1OBForceField.shtml The multiple fragments are coming from different OBMol objects already established where I'm a

[Open Babel] First official release of ACPC, a ligand-based virtual screening open source tool

Dear list, I am very pleased to announce the first official release of ACPC. ACPC is an open source tool for ligand-based virtual screening (a chemoinformatics task), using autocorrelation of partial charges. A very short documentation with some usage examples is available here: https://github.c

[Open Babel] how to set smiles write options programmatically

I'd like to know how to set smiles write options programmatically, e.g. -a Output atomclass like [C:2], if available thx., H -- View this message in context: http://forums.openbabel.org/how-to-set-smiles-write-options-programmatically-tp4657450.html Sent from the General discussion mailing li

[Open Babel] Error with inchi dependents

Please see attached: Compiled on OSX Mavericks cmake.out Description: Binary data make.out Description: Binary data -- "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium

[Open Babel] MACCS fingerprint

Greetings, My name is Pedro Reis and i am a student of Industrial Pharmaceutical Chemistry in Coimbra, Portugal. I am using OpenBabel program to calculate the 166 bits MACCS fingerprint for some coumponds and got a result with 256 bits in API after convert hexadecimal to binary. I wonder if it was

Re: [Open Babel] MACCS fingerprint

> I am using OpenBabel program to calculate the 166 bits MACCS fingerprint for > some coumponds and got a result with 256 bits in API after convert > hexadecimal to binary. By default, the fingerprints are "folded" to certain bit lengths. http://open-babel.readthedocs.org/en/latest/FileFormats/

Re: [Open Babel] Error with inchi dependents

I would suggest getting the latest development version from GitHub, e.g. https://github.com/openbabel/openbabel/archive/master.zip Hope that helps, -Geoff -- "Accelerate Dev Cycles with Automated Cross-Browser Testing -

Re: [Open Babel] addFragment

> The multiple fragments are coming from different OBMol objects already > established where I'm also doing some rotation and translation. What is the > best way to combine these multiple fragments to a single OBMol object for the > minimization? You'll want to make sure the coordinates of the

Re: [Open Babel] Is it possible to change forcefield when using --gen3d?

> Just a quick santity check, but does either obabel --gen3d or obgen work? > In my hands both are giving seg faults starting from smiles. What is weird > is that --gen2d is working fine. They work just fine for me, but if you're getting segfaults, I'd definitely like some example SMILES. >

Re: [Open Babel] Conversion to SVG

Noel, Did we ever get instructions on how to add 2D templates for the MCDL code? I'd think something like a c60 is destined to cause problems with programatic layout. (Indeed, I know that ChemDraw and other depiction codes have special cases for these.) Thanks, -Geoff On May 8, 2014, at 5:47

Re: [Open Babel] Couting all substructures

Sorry for the delayed reply.. my e-mail got confused and I didn't notice until now. obgrep -c http://openbabel.org/wiki/Obgrep Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison

Re: [Open Babel] MMFF94 forcefield phenol atom typing

Sorry for the delayed reply.. my interpretation is certainly "aromatic OH" for phenolic H, which is certainly how the code is written. The implementation validates against the MMFF94 test set, which does not have an OH on a heterocyclic aromatic. I think my question would be .. do you think the

Re: [Open Babel] Question about Conformer Search

> Glancing over the source I found "minenergy" and "minrmsd" to be > implemented but the respective command-line parameter ignored. Is > there any particular reason for this? They were crashing for me. Certainly if you're willing to test them, I'd be happy to try a patch. > "--converge #" ou