This adds support for a feature request from Syngenta. They have a set of chemical groups they are interested in, as a set of fragment SMILES, and would like to limit the cuts to those groups, rather than use a more general fragmentation pattern.
These fragment SMILES are rooted using a "" wildcard atom. For examples, `c1ccc(O)cc1for phenol and*C(C)C` for isopropyl.
The new code converts the fragment SMILES into a SMARTS pattern which matches that SMARTS exactly, for examples, *-!@[cH0v4]1:[cHv4]:[cHv4]:[cH0v4](-[OHv2]):[cHv4]:[cHv4]:1 and *-!@[CHv4](-[CH3v4])-[CH3v4] respectively. (The valence and hydrogen counts must match exactly.)
It then combines the SMARTS into a single recursive SMARTS, like *-!@[$([cH0v4]1:[cHv4]:[cHv4]:[cH0v4](-[OHv2]):[cHv4]:[cHv4]:1),$([CHv4](-[CH3v4])-[CH3v4])], which can be used by the normal mmpdb fragmentation algorithm. The fragmentation format and database schema are unchanged - this is a front-end modification only.
The fragment SMILES can be specified on the "mmpdb fragment" command-line either using one --cut-rgroup for each SMILES, or by putting the fragment SMILES into a file (one SMILES per line) and specifying the fragment name as --cut-rgroup-file.
There is also a new helper command, "mmpdb rgroup2smarts" to help users understand the conversion process from rgroup fragment SMILES to SMARTS.
This adds support for a feature request from Syngenta. They have a set of chemical groups they are interested in, as a set of fragment SMILES, and would like to limit the cuts to those groups, rather than use a more general fragmentation pattern.
These fragment SMILES are rooted using a "" wildcard atom. For examples, `c1ccc(O)cc1
for phenol and*C(C)C` for isopropyl.The new code converts the fragment SMILES into a SMARTS pattern which matches that SMARTS exactly, for examples,
*-!@[cH0v4]1:[cHv4]:[cHv4]:[cH0v4](-[OHv2]):[cHv4]:[cHv4]:1and*-!@[CHv4](-[CH3v4])-[CH3v4]respectively. (The valence and hydrogen counts must match exactly.)It then combines the SMARTS into a single recursive SMARTS, like
*-!@[$([cH0v4]1:[cHv4]:[cHv4]:[cH0v4](-[OHv2]):[cHv4]:[cHv4]:1),$([CHv4](-[CH3v4])-[CH3v4])], which can be used by the normal mmpdb fragmentation algorithm. The fragmentation format and database schema are unchanged - this is a front-end modification only.The fragment SMILES can be specified on the "
mmpdb fragment" command-line either using one--cut-rgroupfor each SMILES, or by putting the fragment SMILES into a file (one SMILES per line) and specifying the fragment name as--cut-rgroup-file.There is also a new helper command, "
mmpdb rgroup2smarts" to help users understand the conversion process from rgroup fragment SMILES to SMARTS.