Dear all,
I observed an erroneus parsing of /pqr/ files by openbabel.
Even while reading files created by openbabel itself, atom charges are lost.
I am not a C programmer, but I think the problem is in the file:
src/formats/pqrformat.cpp
at the functions /parseAtomCharge/ (line 186) and /parseAtomRadius/ (line
206)
the atom line should be:
Field name, atom number, atom name, residue name, residue number, x, y, z,
charge, radius, *element*
// OR
Field, atom number, atom name, chain id, residue number, X, Y, Z, chg, rad,
* element*
The element field is actually expected in the function /parseAtomRecord/
so I think that at line 198-201:
if (vs.size() == *10*)
return atof(vs[8].c_str());
else if (vs.size() == *11*)
return atof(vs[9].c_str());
should be:
if (vs.size() == *11*)
return atof(vs[8].c_str());
else if (vs.size() == *12*)
return atof(vs[9].c_str());
similar fix should be applied at /line 213 and 215/.
I would be very glad if you could confirm this bug and in case fix it.
Thank you in advance,
Luigi
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