Package schrodinger :: Package protein :: Module _reliability

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

[hide private]

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

[hide private]

error(text)

warning(text)

info(text)

debug(text)

find_isolated_water_molecules(ct)

atom_to_resID(atom)
Generate a residue ID string from an atom object.

resID_to_asl(resID)
convert a residue ID string to an ASL string

resID_to_atoms(ct, resID)
get residue atoms from its ID

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

Variables

[hide private]

__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'

STERIC_CLASHES = 'STERIC CLASHES'

BOND_LENGTHS = 'BOND LENGTHS'

BOND_ANGLES = 'BOND ANGLES'

BACKBONE_DIHEDRALS = 'BACKBONE DIHEDRALS'

SIDECHAIN_DIHEDRALS = 'SIDECHAIN DIHEDRALS'

BFACTORS = 'BFACTORS'

PEPTIDE_PLANARITY = 'PEPTIDE PLANARITY'

SIDECHAIN_PLANARITY = 'SIDECHAIN PLANARITY'

IMPROPER_TORSIONS = 'IMPROPER TORSIONS'

MISSING_ATOMS = 'MISSING ATOMS'

MISSING_LOOPS = 'MISSING LOOPS'

NONSITE_PACKING = 'NONSITE PACKING'

SITE_PACKING = 'SITE PACKING'

OVERALL_PACKING = 'OVERALL PACKING'

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

MAX_HBOND_DIST = 4.0

MIN_HBOND_ANGLE = 90.0

PEPTIDE_BOND_LENGTH_CUTOFF = 2.2

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

__package__ = 'schrodinger.protein'

Function Details

[hide private]

atom_to_resID(atom)

Generate a residue ID string from an atom object. These residue IDs are visible to the user, so PDB residue names are added.

NOTE: These residue IDs are the same format as what is used in analysis.py for checking inclusion/exclusion of an atom set.

Variables Details

[hide private]

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',
...