schrodinger.protein.

Module _reliability

This module is for assessing protein reliability and fitness for various structure-based applications. This module is private and is present to support legacy scripts. Any user facing APIs should be set through schrodinger.protein.reliability These are the following properties we currently look at: Active site properties: Buried hydrogen bond acceptors Buried hydrogen bond donors Incomplete/Missing residues B-factor error Bond length Bond angle Steric clashes Tau Angle Torsion angles Backbone phi/psi Side chain rotamers Backbone (conformation) Incorrect water Waters with no hydrogen bonds Abnormal packing Entire Protein: Ramachandran outliers Twinning Abnormal packing Copyright Schrodinger, LLC. All rights reserved.

Classes

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Lattice
Class to more conveniently contain space group and unit cell information extracted from a structure.Structure.

RealSpaceFit

Packing
read in parameters for packing calculation report residue Z-score

ModelCheck

Functions

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error(text)

warning(text)

info(text)

debug(text)

find_isolated_water_molecules(ct)

connected_resID(resID1, resID2)
check if two residues are connected

Variables

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__doc__ = ...

CRYST1_SPACE_GRP = 's_pdb_PDB_CRYST1_Space_Group'

CRYST1_A = 'r_pdb_PDB_CRYST1_a'

CRYST1_B = 'r_pdb_PDB_CRYST1_b'

CRYST1_C = 'r_pdb_PDB_CRYST1_c'

CRYST1_ALPHA = 'r_pdb_PDB_CRYST1_alpha'

CRYST1_BETA = 'r_pdb_PDB_CRYST1_beta'

CRYST1_GAMMA = 'r_pdb_PDB_CRYST1_gamma'

PDB_RESOL = 'r_pdb_PDB_RESOLUTION'

PDB_RFREE = 'r_pdb_PDB_Rfree'

PDB_R = 'r_pdb_PDB_R'

PROTEIN_REPORT_LABEL = ['STERIC CLASHES', 'BOND LENGTHS', 'BON...

MAX_HBOND_DIST = 4.0

MIN_HBOND_ANGLE = 90.0

logger = log.get_output_logger('structure_reliability_driver.py')

__package__ = 'schrodinger.protein'

Variables Details

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doc

Value:

"""
This module is for assessing protein reliability and fitness for vario
us
structure-based applications. This module is private and is present to
support legacy scripts. Any user facing APIs should be set through
schrodinger.protein.reliability

These are the following properties we currently look at:
...

PROTEIN_REPORT_LABEL

Value:

['STERIC CLASHES',
 'BOND LENGTHS',
 'BOND ANGLES',
 'BACKBONE DIHEDRALS',
 'SIDECHAIN DIHEDRALS',
 'BFACTORS',
 'PEPTIDE PLANARITY',
 'SIDECHAIN PLANARITY',
...