#102 Enumerate atoms when converting sdf to mol2

[Anonymous]

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

[Noel O'Boyle]

Hi there. I thought it was no longer possible 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
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