Class Ligand

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

• st (Structure) - Ligand structure.
• mol_num (int) - Molecular index identifier. Typically, the mol.n from the original structure from whence this ligand structure was derived. Note, depending on the nature of the ligand and the treatment of the original structure this mol.n index may not be valid.
• atom_indexes (list) - Atom index identifiers. Typically, the at.n from the original structure from whence this ligand structure was derived.
• lig_asl (str) - ASL identifier. Typically, the expression is defined in terms of the original structure from whence this ligand structure was derived.

Overrides: object.__init__

cmp(self,other).

Enable sorting for Ligand objects. Comparison criteria for sorting Ligands: total number of atoms, unique smiles string, centroid.

Parameters:

• other (Ligand) - An instance of this class.

Returns: int

0 if equal, -1 if right is greater, 1 if left is greater.

str(x)

Returns: str

the unique SMILES string for this ligand.

Overrides: object.__str__

is_covalently_bound

The Ligand.is_covalently_bound property returns True if this ligand has any bonds (including zero-order) to any other atoms, and returns False if the ligand spans a complete molecule.

Get Method:

unreachable.is_covalently_bound(self) - The Ligand.is_covalently_bound property returns True if this ligand has any bonds (including zero-order) to any other atoms, and returns False if the ligand spans a complete molecule.

mol_num

Ligand's molecule number as defined upon instantiation.

Get Method:

unreachable.mol_num(self) - Ligand's molecule number as defined upon instantiation.

Type:

int

atom_indexes

Indices of the Ligand atoms as defined upon instantiation.

Get Method:

unreachable.atom_indexes(self) - Indices of the Ligand atoms as defined upon instantiation.

Type:

list

pdbres

PDB residue name identifier. If the ligand is composed of multiple residues then the names are joined with a '-' separator.

Get Method:

unreachable.pdbres(self) - PDB residue name identifier.

Type:

str

centroid

Centroid of the Ligand as a 4-element numpy array: [x, y, z, 0.0]

Get Method:

unreachable.centroid(self) - Centroid of the Ligand as a 4-element numpy array: [x, y, z, 0.0]

Type:

4-element numpy array

unique_smiles

Unique SMILES string representing this ligand structure.

Get Method:

unreachable.unique_smiles(self) - Unique SMILES string representing this ligand structure.

Type:

str

st

Copy of the ligand Structure.

Get Method:

unreachable.st(self) - Copy of the ligand Structure.

Type:

Structure

ligand_asl

Ligand_asl used when searching for the ligand. The ASL defined the ligand in the context of its original structure.

Get Method:

unreachable.ligand_asl(self) - Ligand_asl used when searching for the ligand.

Type:

str

regularized_structure

A regularized, but possibly distorted, Structure. Regularization is achieve by converting the SMILES string. The Structure will have the same atom ordering as the unique SMILES for this Ligand.

Get Method:

unreachable.regularized_structure(self) - A regularized, but possibly distorted, Structure.

Type:

Structure