Re: [Open Babel] Help to conversion format cif_to_pdb

Ok Thanks for the interest Now, i need to convert the format, only and it's necessary that it has the best fidelity possible with the original structure I think it's openbabel can't help me I'm going to research more 2014-04-15 19:09 GMT-03:00 Dimitri Maziuk : > On 04/15/2014 03:59 PM, Wellisson

[Open Babel] SMARTS charge descriptor

Dear OpenBabel community: I'm faced with a problem of selecting atoms by SMARTS patterns that include charge descriptor "+/-" such as '[O-][N+](=O)C'. In my tests the pattern matching does not work properly unless the molecular structure is given in the smile format. To localize the problem I have

[Open Babel] Spam holdup

For reasons I don't quite understand, the report of "held" messages to the mailing list ended up in my spam folder. So there's a backlog of about two weeks. I must state for the record.. if you are not a member of the mailing list, your messages will get flagged as potential spam. Subscribe to

[Open Babel] Charges in smarts

Dear OpenBabel community: I'm faced with a problem of selecting atoms by SMARTS patterns that include charge descriptor "+/-" such as '[O-][N+](=O)C'. The pattern matching does not work properly unless the molecular structure is given in the smile format. To localize the problem I have tested di

[Open Babel] OPENBABEL-2.3.2 compiles, passes all tests but shows no plugins

. . . 57/57 Test #57: pytest_kekule Passed0.66 sec 100% tests passed, 0 tests failed out of 57 Total Test time (real) = 55.10 sec Yet after “make install” obabel -L Ops Why can’t my install find more of its plugins? obabel -L mol2 mol2 is not a recogniz

[Open Babel] Issues with structures from "-p Add hydrogens appropriate for this pH"

Hello, This is my first email to the group so I hope my etiquette is correct. I am seeing an issue with some structures generated by the -p flag. For example... > obabel -V Open Babel 2.3.90 -- Mar 27 2014 -- 16:44:24 > echo "c1ccc(cc1)C1=NN=C(SC1)Nc1ccc(c(c1)Cl)Cl ZINC05859393" | obabel -ismi

[Open Babel] How to store fingerprints of mols to make it faster similarity calculation | Python

Hi, I want to calculate the similarity between a query molecule and a set of molecules which are stored in a database. I tried to store the SMILES in the database and it is too slow for pybel to calculate each fingerprint of the set of molecules. So I'd like to store the fingerprints of the set

[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

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

Hi I'm trying to get Pybel (OpenBabel 2.3.2) to export to PNG format in Centos 6.5. As I understood from the the docs, I just need to install Cairo; the packages for Centos are cairo and cairo-devel. I also installed libpng and libpng-devel. This is the compilation command and (relevant) outp

Re: [Open Babel] Help to conversion format cif_to_pdb

On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote: > Sorry but i don't understand your answer OpenBabel deals with molecules. PDB deals with studies of crystal structures, extended (with varying degree of success) to structures obtained from EM, NMR, and other methods. The "study" includes much

Re: [Open Babel] Help to conversion format cif_to_pdb

Sorry but i don't understand your answer What's OBMol and what can it do ? in fact babel in openbabel don't translate the file completely it's omits a lot of information. I don't worried about this The point is how different and reliable it is 2014-04-15 14:14 GMT-03:00 Dimitri Maziuk : > On 04/

Re: [Open Babel] obabel: Converting sdf with multi-line properties

On Wed, Aug 14, 2013 at 12:41 PM, Jeff Janes wrote: > On Wed, Jul 17, 2013 at 1:52 PM, Chris Morley > wrote: > > The fix is at Line 183 in obconversion.cpp: > > -static string title(_title); //potential problems in calling code > > with multiple molecules! > > +static string title; //sta

Re: [Open Babel] Help to conversion format cif_to_pdb

On 04/14/2014 08:51 AM, David Hall wrote: > Can you explain what parts of the file are not compatible that you are > looking at? Residue numbering? Temperature Factors? Testing briefly, it > appears the coordinates agree, so knowing that fields you are looking to > preserve would be useful. SEQRES

[Open Babel] Issues with structures from "-p Add hydrogens appropriate for this pH"

Hello, This is my first email to the group so I hope my etiquette is correct. I am seeing an issue with some structures generated by the -p flag. For example... > obabel -V Open Babel 2.3.90 -- Mar 27 2014 -- 16:44:24 > echo "c1ccc(cc1)C1=NN=C(SC1)Nc1ccc(c(c1)Cl)Cl ZINC05859393" | obabel -ismi