schrodinger.protein.reliability module

schrodinger.protein.reliability.run_quick_check(ct, binding_site_atoms=None)

Runs a quick analysis of protein health.

Parameters

• ct (schrodinger.structure) – protein CT

• binding_site_asl (atom indices) – list of atom indices to define binding site. Limits checks to area around the binding site.

:rtype str

Returns a Results object of problems spotted in the protein.

schrodinger.protein.reliability.run_check(ct, params)

Returns a Results object of problems spotted in the protein.

schrodinger.protein.reliability.find_isolated_water_molecules(ct)

Finds water molecules that are isolated (greater than 4.6 A) from other water clusters.

Returns a list of tuples (water_molecule, distance). The water molecule is represented as a set() of atom indexes, and the distance is the minimum distance from another water molecule.

class schrodinger.protein.reliability.ProteinCheckParameters

Bases: object

__init__()

Initialize self. See help(type(self)) for accurate signature.

enableSidechainPacking()

disableSidechainPacking()

setBindingSiteASL(site_asl)

class schrodinger.protein.reliability.Results(model)

Bases: object

The Results object stores the results from a protein health check.

__init__(model)

Initialize self. See help(type(self)) for accurate signature.

getTextSummary()

Returns a summary of problems found in the protein. If no problems, returns an empty list.

:rtype list of str

schrodinger.protein.reliability.main()