Re: [Open Babel] generate obMol from smiles

2013-09-13 Thread Noel O'Boyle
Looks fine, but probably best to avoid "new" and "delete". For example, see code at http://openbabel.org/docs/current/UseTheLibrary/CppExamples.html - Noel On 5 September 2013 12:16, Rafel Israels wrote: > Dear all, > > As a new Babel-user first of all I'd like to thank you for this great > sof

Re: [Open Babel] Convert a DImer pdb to Mol2

2013-09-13 Thread Pascal Muller
Hi, Hello, I have some problems with the babel, when I convert a protein that > have more than one monomer (dimer, tetramer and etc), the mol2 file mix the > monomers, and I can generate the cartoon view and I can't use the mol2 > output in another softwares, for this mixture problem. > In which

Re: [Open Babel] Convert a DImer pdb to Mol2

2013-09-13 Thread Craig James
You need to provide a detailed, exact description of the steps you are using, exactly what goes wrong, and include the files you are using. Are you using other programs besides OpenBabel? Is the problem with OpenBabel or the other programs? The more information you can give, the better your chan

Re: [Open Babel] generate obMol from smiles

2013-09-13 Thread Craig James
Rafel, Valgrind often reports uninitialized-variable errors and off-by-one array index errors in system libraries. In the valgrind output you provided, the error is in libz, the gzip-compression system library. This has nothing to do with OpenBabel, and is probably a harmless warning. Craig O

[Open Babel] problem with converting VASP files

2013-09-13 Thread Saeedeh Tafreshi
Dear all, I have downloaded Openbabel on my windows, but when I want to convert a VASP-CONTCAR or POSCAR file to pdb file, it doesn't work. Any help would be appreciated. Cheers Saeedeh -- How ServiceNow helps IT peopl

[Open Babel] Convert a DImer pdb to Mol2

2013-09-13 Thread fabiofima
Hello, I have some problems with the babel, when I convert a protein that have more than one monomer (dimer, tetramer and etc), the mol2 file mix the monomers, and I can generate the cartoon view and I can't use the mol2 output in another softwares, for this mixture problem. Someone can help me? Th

[Open Babel] Regardin export of other entries while converting a cdx file to mol2

2013-09-13 Thread shagun
Hi all.. I want to convert a dataset of cdx files into mol2 format.but at the same I am having some text entries in those cdx like their chemical name and their inventor and their activity. I want to know that how to convert those cdx files along with their text entries into mol2 format? And is it

[Open Babel] generate obMol from smiles

2013-09-13 Thread Rafel Israels
Dear all, As a new Babel-user first of all I'd like to thank you for this great software !! My question: what is the correct way (in c++) to generate an OBMol object from a smiles-code ? I know how to convert smiles e.g. to inchi directly using a conv->convert(), but I dont see yet how I can get