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2015-3 Schrodinger Python API
Package schrodinger :: Package structutils :: Module analyze :: Class Ligand
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Class Ligand

A putative AslLigandSearcher ligand structure with read-only data and convenience methods.

Ligand items sort from smallest to largest, by total number of atoms, then by SMILES.

Instance Methods [hide private]
 
__init__(self, st, mol_num=None, atom_indexes=None, lig_asl=None, is_covalently_bound=None)
 
is_covalently_bound(self)
int
__cmp__(self, other)
cmp(self,other).
str
__str__(self)
Returns: the unique SMILES string for this ligand.
int
mol_num(self)
Ligand's molecule number as defined upon instantiation.
list
atom_indexes(self)
Indices of the Ligand atoms as defined upon instantiation.
str
pdbres(self)
PDB residue name identifier.
4-element numpy array
centroid(self)
Centroid of the Ligand as a 4-element numpy array: [x, y, z, 0.0]
str
unique_smiles(self)
Unique SMILES string representing this ligand structure.
Structure
st(self)
Copy of the ligand Structure.
str
ligand_asl(self)
Ligand_asl used when searching for the ligand.
Structure
regularized_structure(self)
A regularized, but possibly distorted, Structure.
Method Details [hide private]

__init__(self, st, mol_num=None, atom_indexes=None, lig_asl=None, is_covalently_bound=None)
(Constructor)

 
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.

is_covalently_bound(self)

 
Decorators:
  • @property

__cmp__(self, other)
(Comparison operator)

 

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__(self)
(Informal representation operator)

 
Returns: str
the unique SMILES string for this ligand.

mol_num(self)

 

Ligand's molecule number as defined upon instantiation.

Returns: int
Decorators:
  • @property

Warning: Depending on the nature of the ligand and the treatment of the original structure, e.g. zero-order bonds cut, this mol.n index may not be valid.

atom_indexes(self)

 

Indices of the Ligand atoms as defined upon instantiation.

Returns: list
Decorators:
  • @property

pdbres(self)

 

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

Returns: str
Decorators:
  • @property

centroid(self)

 

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

Returns: 4-element numpy array
Decorators:
  • @property

unique_smiles(self)

 

Unique SMILES string representing this ligand structure.

Returns: str
Decorators:
  • @property

st(self)

 

Copy of the ligand Structure.

Returns: Structure
Decorators:
  • @property

ligand_asl(self)

 

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

Returns: str
Decorators:
  • @property

regularized_structure(self)

 

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.

Returns: Structure
Decorators:
  • @property

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2015-3 Schrodinger Python API
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