Package schrodinger :: Package structutils :: Module sitealign
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Module sitealign

Perform a pairwise superposition of multiple structures using the C-alpha atoms of selected residues.

Classes [hide private]
  SiteMatchLookup
Lookup for any reference and mobile structures that have matching binding site atoms.
  BindingSiteAligner
Align structures by matching binding site atoms.
Functions [hide private]
str
get_ligand_asl(cutoff=5.0, molnum=None, fillres=True)
Returns an ASL expression defining binding site atoms based on the ligand molecule number and cutoff distance.
str
get_residue_asl(residues)
Returns an ASL expression defining binding site atoms based on the residue strings passed in.
Variables [hide private]
  __doc__ = ...
  BINDING_SITE_STYLE = 3
  ALIGNED_STYLE = 3
  ALIGNED_COLOR = 'green'
  __package__ = 'schrodinger.structutils'
Function Details [hide private]

get_ligand_asl(cutoff=5.0, molnum=None, fillres=True)

 

Returns an ASL expression defining binding site atoms based on the ligand molecule number and cutoff distance. This ASL specifically identifies the C-alpha atoms.

Parameters:
  • cutoff (float) - Cutoff from ligand used to asign binding site atoms
  • molnum (int) - The molecule number fo the ligand. If None the ligand will be automatically detected.
  • fillres (bool) - Use all atoms in a residue if any atom is found
Returns: str
ASL expression for binding site atoms

get_residue_asl(residues)

 

Returns an ASL expression defining binding site atoms based on the residue strings passed in. This ASL specifically identifies the C-alpha atoms.

Parameters:
  • residues (list of residue strings (<chain>:<resnum>)) - Residues used to define binding site atoms
Returns: str
ASL expression for binding site atoms

Variables Details [hide private]

__doc__

Value:
"""
Perform a pairwise superposition of multiple structures using the
C-alpha atoms of selected residues.

"""