[Open Babel] Assign UFF atom types to mol2 file

Hi Users, I was wondering if it is possible to read in a mol2 file, and output the UFF atom types? I'm not sure what information is needed so if the question is unclear, please let me know. Thanks ---

[Open Babel] Couting all substructures

Hello, I am trying to count how many times a given moiety can be found in a database. My interest is not the list of the molecules containing this substructure, but how many times it can be found. Let's say that in my Database.smi file I have a biphenyl (c1ccc(cc1)c2c2) and I want to count how

[Open Babel] Converting xyz file to a SMILES string in C++

Hello, I would like to convert a file File.xyz into a SMILES string in a C++ program. I have done the following (I am simplifying): ifstream input("File.xyz"); ostringstream streamOBabel; OpenBabel::OBConversion conv(&input, &streamOBabel); conv.SetInAndOutFormats("XYZ","SMI"); conv.Convert(); st

Re: [Open Babel] How to get PNG support in OpenBabel/Pybel in Centos?

Hi Noel I tried replacing pybel.readstring('smi', str(v_name)).draw(show=False, filename=img_path) with pybel.readstring('smi', str(v_name)).draw(show=False, filename=img_path, formatok=obConversion.SetOutFormat("_png2")) but I got the error "draw() got an unexpected keyword argument 'format

Re: [Open Babel] How to get PNG support in OpenBabel/Pybel in Centos?

Hi Carolina, Try making a change like shown in this commit to the draw function in pybel.py : https://github.com/openbabel/openbabel/commit/df59c4a630cf753723d1318c40479d48b7507e1c Then, your original python code will hopefully work. -David On Fri, Apr 11, 2014 at 6:58 PM, Carolina Román Sa