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
hash(x)

ALIGNED_STYLE = 3
hash(x)

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.

"""