Hi Antionio,
OpenBabel generates new labels, unless there are already OBResiude info on
that. You can set it to whatever you want with OBResiude.SetAtomID().
Checkout the script below:
import pybel
> ob = pybel.ob
> mol = pybel.readstring('smi', 'c1ccccc1')
> res = ob.OBResidue()
> for atom in ob.OBMolAtomIter(mol.OBMol):
> res.AddAtom(atom)
> res.SetAtomID(atom, '%s%i' %
> (ob.OBElementTable().GetSymbol(atom.GetAtomicNum()), atom.GetIdx()))
>
print(mol.write('mol2'))
Note that if you use the -xl option the residue will be ignored, but you
can name the residue to whatever you want via res.SetName('BLAH')
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2018-01-18 23:57 GMT+01:00 Antonio Jesus Banegas Luna <
ajbane...@alu.ucam.edu>:
> Hello all,
>
> I'm a newby in obabel and I need a bit of help.
> I use obabel to convert a file from sdf to mol2 format because another
> program requires such conversion.
> The conversion is fine, and I get something like this (I only show the
> ATOM block):
>
> @<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
>
> However, the third-party software requires something like this:
>
> @<TRIPOS>ATOM
> 1 C*1* 0.5825 -1.4943 0.8613 C.ar 1 LIG1
> 0.0063
> 2 C*2* -0.4113 -2.1197 1.6364 C.ar 1 LIG1
> 0.0421
> 3 C*3* -1.7701 -1.8708 1.3728 C.ar 1 LIG1
> 0.1957
> 4 O*1* -2.7253 -2.4643 2.1262 O.3 1 LIG1
> -0.2866
> 5 C*4* -2.1325 -1.0044 0.3248 C.ar 1 LIG1
> 0.0421
>
> Now, my question is: is there any way of forcing obabel to generate atom
> names in the required format?
> Maybe someone has some experience with this.
>
> Thanks in advance,
> Antonio
>
> --
> Antonio J. Banegas Luna
> Bioinformatics and High Performance Computing Research
> groupajbane...@alu.ucam.edu
> http://orcid.org/0000-0003-1158-8877http://www.researcherid.com/rid/O-7331-2016https://scholar.google.es/citations?user=EWtHIUMAAAAJhttps://www.researchgate.net/profile/Antonio_Jesus_Banegas_Luna
>
>
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