Module _reliability

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)

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

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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

PEPTIDE_BOND_LENGTH_CUTOFF = 2.2

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

Function Details

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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

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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 P
LANARITY', 'IMPROPER TORSIONS', 'MISSING ATOMS']