Hi, I made the following observation in the tools directory:
% grep FindForceField *cpp
obconformer.cpp: OBForceField *pFF =
OBForceField::FindForceField("MMFF94");
obdistgen.cpp: OBForceField* pFF = OBForceField::FindForceField("mmff94");
obenergy.cpp: OBForceField* pFF = OBForceField::FindForceField(ff);
obgen.cpp: OBForceField* pFF = OBForceField::FindForceField(ff);
obminimize.cpp: OBForceField* pFF = OBForceField::FindForceField(ff);
obmm.cpp: OBForceField* pFF = OBForceField::FindForceField("MMFF94");
obmm.cpp: pFF = OBForceField::FindForceField(vs[1]);
obprobe.cpp: OBForceField* pFF = OBForceField::FindForceField("MMFF94");
In other words, in a number of tools the force field is hardcoded which
seems unnecessary. Would this be worthwhile to fix?
If so, this begs the question about whether command line processing,
which is rudimentary and duplicated between codes, should be fixed
first. I would think that OB should use the same command line flags for
the same variable in different codes.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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