This module gives the interface to the package RDKit
This function is used to convert an Xponge.Assign to a RDKit.rdMol
parameters |
explanation |
assign |
the Assign instance |
ignore_bond_type |
set the bond type always to UNSPECIFIED |
return |
the RDKit.rdMol instance |
This function is used to convert a RDKit.rdMol to an Xponge.Assign
parameters |
explanation |
rdmol |
the RDKit.rdMol instance |
return |
the Xponge.Assign instance |
This function inserts the atom types in the force field to the RDKit.rdmol instance.
parameters |
explanation |
mol |
the RDKit.rdmol instance |
res |
the Residue instance corresponding to mol |
assign |
the Assign instance corresponding to mol |
atom_type_dict |
the dict mapping the atom type to the isotope number |
This function is used to find the chemical equivalent atoms in the molecule
parameters |
explanation |
assign |
the Assign instance |
return |
a list of equalvalent atom index lists |