Hello,
I am trying to figure out how the forcefieldgaff.cpp file reads the
gaff.prm file to assign atom types. Given a molecular model where I know
the bonds connected between atoms (and I know their basic element name
C,N,O,H, etc.), how can I deduce their atom type? (e.g. n2,n1,cp,cd, etc.)
within bool OBForceFieldGaff::SetTypes()
//reads gaff.prm
So once the atom has been assigned a SMARTS string then I guess it becomes
pretty easy to make the atom type assignment by matching up the columns.
So I guess the question becomes: how do I obtain the SMARTS string for each
atom in GAFF? Again, all I know is which atoms are connected to each other
and the bond type (single, double).
Thank you!
- Eric
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