Recent changes to file-format-support

pdb2

2026-04-13T21:52:10.429000Z

pdb

2026-04-13T21:50:49.827000Z

eman1

2025-01-09T12:41:40.967000Z

Defined partial charges in OBForceField

2019-11-25T22:03:23.261000Z

Hi,

I would like to know if it was possible to force the internal OBMol copy in OBForceField to have the same partial charges as defined in mol2 file? And also the same for the atom types (that are of course also defined in GAFF)?

I put some python codes below as an example. That's how far I can go... Also I am not restricted to Python only. The solution can be also in C++ (if there is one).

Thanks for your help!

Jerome.

from openbabel import openbabel as ob

obconv = ob.OBConversion()
obconv.SetInFormat("mol2")
OBMol = ob.OBMol()
obconv.ReadFile(OBMol, "molecule.mol2")

forcefield = ob.OBForceField.FindForceField("GAFF")
forcefield.Setup(OBMol)

forcefield.SetLogLevel(ob.OBFF_LOGLVL_HIGH)
forcefield.SetLogToStdErr()
forcefield.PrintFormalCharges()
forcefield.PrintTypes()

forcefield.GetAtomTypes(OBMol)
forcefield.GetPartialCharges(OBMol)

atom = OBMol.GetAtom(1)
pairdata = ob.toPairData(atom.GetData("FFAtomType"))
print(pairdata.GetAttribute(), pairdata.GetValue())
pairdata = ob.toPairData(atom.GetData("FFPartialCharge"))
print(pairdata.GetAttribute(), pairdata.GetValue())

Segmentation fault (core dumped) error while generating 3D coordinates from .sdf files

2019-07-03T15:45:16.567000Z

Hi,
I am trying to generate 3D coordinates from the Mechanistic Sets .sdf files downloaded from NCI. But I keep getting the error 'Segmentation fault (core dumped)'. However, it worked with the Diversity Sets .sdf files. So any help here? And I am using Linux Ubuntu. Thanks!
Ruben

#102 Enumerate atoms when converting sdf to mol2

2018-01-18T12:34:15.895000Z

Hi there. I thought it was no longer to post tickets here. It seems I was wrong. There was a notice at the top of the submission page with the following info:

The File Format Support tracker for Open Babel here at sourceforge.net
is in read-only mode. It presents the state of
Open Babel file format support tickets in March 2017. Tickets are now
managed at

https://github.com/openbabel/openbabel/issues

Go there to submit new tickets, comment on
existing tickets, or follow ongoing efforts
to service the tickets.

Enumerate atoms when converting sdf to mol2

2018-01-15T19:28:59.193000Z

Hello,

I'm a newby in obabel and I need some help. This is the issue I'm facing:

I have a file in SDF format and I use obabel to convert it to MOL2. The section ATOMS in the new file looks like this:

@<TRIPOS>ATOM
1 C 0.5825 -1.4943 0.8613 C.ar 1 LIG1 0.0063
2 C -0.4113 -2.1197 1.6364 C.ar 1 LIG1 0.0421
3 C -1.7701 -1.8708 1.3728 C.ar 1 LIG1 0.1957
4 O -2.7253 -2.4643 2.1262 O.3 1 LIG1 -0.2866
5 C -2.1325 -1.0044 0.3248 C.ar 1 LIG1 0.0421
6 C -1.1389 -0.3865 -0.4590 C.ar 1 LIG1 0.0063

The problem comes up when I want to use this file with another software which requires atoms to be enumerated. So that, the second software expects something like this:

@<TRIPOS>ATOM
1 C1 0.5825 -1.4943 0.8613 C.ar 1 LIG1 0.0063
2 C2 -0.4113 -2.1197 1.6364 C.ar 1 LIG1 0.0421
3 C3 -1.7701 -1.8708 1.3728 C.ar 1 LIG1 0.1957
4 O1 -2.7253 -2.4643 2.1262 O.3 1 LIG1 -0.2866
5 C4 -2.1325 -1.0044 0.3248 C.ar 1 LIG1 0.0421
6 C5 -1.1389 -0.3865 -0.4590 C.ar 1 LIG1 0.0063

Is there any option to force obabel to include the atom number automatically?

Thanks in advance

#40 KCF file format

2016-12-20T13:59:47.487000Z

mol2kcf source

ftp://ftp.genome.jp/pub/tools/simcomp/kcfco-1.1.2.tar.gz

c3xml

2016-07-27T20:43:49.881000Z

It would be nice to add c3xml format to the list of supported chemical formats.
Thank you,
Rafael Dolezal.

probelm with converting .res file

2015-08-31T16:50:33.056000Z

I cannot convert res files. I get error message "0 molecules converted" both inder Linux and Windows.