ost.mol.alg.ligand_scoring Namespace Reference

Data Structures
class	LigandScorer
class	NoSymmetryError
class	TooManySymmetriesError
class	DisconnectedGraphError

Functions
def	SCRMSD

Variables
list	__all__

Function Documentation

def ost.mol.alg.ligand_scoring.SCRMSD	(		model_ligand,
			target_ligand,
			transformation = geom.Mat4(),
			substructure_match = False,
			max_symmetries = 1e6
	)

Calculate symmetry-corrected RMSD.

Binding site superposition must be computed separately and passed as
`transformation`.

:param model_ligand: The model ligand
:type model_ligand: :class:`ost.mol.ResidueHandle` or
                    :class:`ost.mol.ResidueView`
:param target_ligand: The target ligand
:type target_ligand: :class:`ost.mol.ResidueHandle` or
                     :class:`ost.mol.ResidueView`
:param transformation: Optional transformation to apply on each atom
                       position of model_ligand.
:type transformation: :class:`ost.geom.Mat4`
:param substructure_match: Set this to True to allow partial target
                           ligand.
:type substructure_match: :class:`bool`
:param max_symmetries: If more than that many isomorphisms exist, raise
  a :class:`TooManySymmetriesError`. This can only be assessed by
  generating at least that many isomorphisms and can take some time.
:type max_symmetries: :class:`int`
:rtype: :class:`float`
:raises: :class:`NoSymmetryError` when no symmetry can be found,
         :class:`DisconnectedGraphError` when ligand graph is disconnected,
         :class:`TooManySymmetriesError` when more than `max_symmetries`
         isomorphisms are found.

Definition at line 1723 of file ligand_scoring.py.

Variable Documentation

list __all__

Initial value:

= ["LigandScorer", "SCRMSD", "NoSymmetryError", 
           "TooManySymmetriesError", "DisconnectedGraphError"]

Definition at line 1905 of file ligand_scoring.py.