¶ Xponge.helper.rdkit
This module gives the interface to the package RDKit
¶ subpackages
¶ submodules
¶ functions
¶ assign_to_rdmol
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 |
¶ rdmol_to_assign
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 |
¶ insert_atom_type_to_rdmol
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 |
¶ find_equal_atoms
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 |
