I was wondering if there was a way to wash molecules in RDKit?
By washing, the manual in MOE means (and I understand that your definition
might vary to some degree):
1.
Replace or recalculate the molecule name
2.
Disconnect simple metal salts drawn in covalent notation
3.
Remove minor components (e.g. counterions and solvent molecules),
optionally storing the removed components in an alternate field
4.
Rebalance protonation states by deprotonating strong acids and/or
protonating strong bases
5.
Add explicit hydrogen atoms, or remove safely-deletable explicit hydrogen
atoms
6.
Replace the atomic coordinates with an aesthetic 2D depiction layout
7.
Enumerate tautomers and possibly also protonation states
8.
Filter enumerated structures according to strong acid/base rules
How many of the above are possible using RDKit?
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
(+44 / 0) 1865 262 034
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