Hi, I have a thought about mol2 files form Dock program, which contain additional information in commentary (###). Those information is being lost during openbabel operations, which is a pity. I'd like to propose a in/out option for mol2 for Dock'ed mol2's to read/write compatible information from those files. Especially conformer ID is important for further anylisis. Simmilar approach is used with pdbqt's contained in Autodock's .dlg files.
Commentaru in each molecule has following information (the MOLECULE part
included for context reference:
########## Name: MOLNAME_babel_1
########## HA_RMSD: 7.6335
########## Grid Score: -33.058090
########## Grid_vdw: -30.147516
########## Grid_es: -2.910574
########## Int_energy: 1.057763
@<TRIPOS>MOLECULE
MOLNAME_babel
34 35 1 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
In my mind openbabel should read name from Dock's commentary (which is
suffixed - _1) and add RMSD, scores and internal energy information to
commentary and output them in compatible manner. These would surely made
life easier since UCSF Chimera uses those information in ViewDock.
Unfortuantelly I don't feel confident enough to propose a patch mol2 format
file.
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