Module analysis

A class for diagnosing and reporting common structural problems of protein complexes.

Usage:

instance = Report(ct) instance.write_to_stdout()

Classes

[hide private]

Report
A class to calculate properties of proteins.

Variables

[hide private]

__doc__ = ...

ideal_bond_lengths = {'ALA ': {' C ': {' N ': (490.0, 1.329)...
Dictionary containing ideal bond lengths for some bonds in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are tuples of (G-factor coefficient, ideal bond length.

ideal_bond_angles = {'ALA ': {' C ': {' N ': {' CA ': (50.0,...
Dictionary containing ideal bond angles for some bond angles in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are dictionary D; dictionary D keys are atom types and values are tuples of (G-factor coefficient, ideal bond angle.

sidechain_dihedral_atomnames = {'ARG ': [[' N ', ' CA ', ' CB...
Dictionary containing atom names for amino acid sidechains, keys are residue names and values are lists of lists of atom names, one list for each sidechain.

planar_groups = {'ARG ': [' CD ', ' NE ', ' CZ ', ' NH1', ' NH...
Dictionary containing lists of groups that should be planar; keys are residue names and values are lists of atom names.

improper_torsions = {'ARG ': [[' HE ', ' CZ ', ' NE ', ' CD ']...
Dictionary containing lists of improper torsions; keys are residue names and values are lists of lists of atom names, one for each improper torsion in the residue.

backbone_dihedrals = {'ALA ': {'-100.0,-0.0': 0.001506, '-100....
Dictionary containing G-Factors for backbone_dihedral values, keys are residue names and values are dictionaries B; dictionary B keys are phi/psi dihedral values rounded to nearest 10 as strings ("60.0,30.0"), values are X, where G-factor = log(X).

sidechain_dihedrals = {'ARG ': {'-10.0,-170.0': 0.000163, '-10...
Dictionary containing G-factors for sidechain dihedral values, keys are residue names and values are dictionaries B; dictionary B keys are chi1/chi2 dihedral values rounded to nearest 10 as strings ("60.0,30.0"), values are X, where G-factor = log(X).

use_gfactors = False
Use gfactors instead of deviations.

kT = 0.5925
Value of kT at room temperature.

__package__ = 'schrodinger.protein'

Variables Details

[hide private]

doc

Value:

"""
A class for diagnosing and reporting common structural problems of pro
tein
complexes.

Usage:

instance = Report(ct)
...

ideal_bond_lengths

Dictionary containing ideal bond lengths for some bonds in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are tuples of (G-factor coefficient, ideal bond length.

Value:

{'ALA ': {' C  ': {' N  ': (490.0, 1.329), ' O  ': (570.0, 1.231)},
          ' CA ': {' C  ': (317.0, 1.525), ' CB ': (268.0, 1.521)},
          ' N  ': {' CA ': (337.0, 1.458)}},
 'ARG ': {' C  ': {' N  ': (490.0, 1.329), ' O  ': (570.0, 1.231)},
          ' CA ': {' C  ': (317.0, 1.525), ' CB ': (268.0, 1.53)},
          ' CB ': {' CG ': (268.0, 1.52)},
          ' CD ': {' NE ': (337.0, 1.46)},
          ' CG ': {' CD ': (268.0, 1.52)},
...

ideal_bond_angles

Dictionary containing ideal bond angles for some bond angles in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are dictionary D; dictionary D keys are atom types and values are tuples of (G-factor coefficient, ideal bond angle.

Value:

{'ALA ': {' C  ': {' N  ': {' CA ': (50.0, 121.7)}},
          ' CA ': {' C  ': {' N  ': (70.0, 116.2)}},
          ' CB ': {' CA ': {' C  ': (63.0, 110.5)}},
          ' N  ': {' C  ': {' O  ': (80.0, 123.0)}}},
 'ARG ': {' C  ': {' N  ': {' CA ': (50.0, 121.7)}},
          ' CA ': {' C  ': {' N  ': (70.0, 116.2)},
                   ' CB ': {' CG ': (58.35, 114.1)}},
          ' CB ': {' CA ': {' C  ': (63.0, 110.1)}, ' CG ': {' CD ': (
...

sidechain_dihedral_atomnames

Dictionary containing atom names for amino acid sidechains, keys are residue names and values are lists of lists of atom names, one list for each sidechain.

Value:

{'ARG ': [[' N  ', ' CA ', ' CB ', ' CG '],
          [' CA ', ' CB ', ' CG ', ' CD ']],
 'ASN ': [[' N  ', ' CA ', ' CB ', ' CG '],
          [' CA ', ' CB ', ' CG ', ' OD1']],
 'ASP ': [[' N  ', ' CA ', ' CB ', ' CG '],
          [' CA ', ' CB ', ' CG ', ' OD1']],
 'CYS ': [[' N  ', ' CA ', ' CB ', ' SG ']],
 'GLN ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', '
...

planar_groups

Dictionary containing lists of groups that should be planar; keys are residue names and values are lists of atom names.

Value:

{'ARG ': [' CD ', ' NE ', ' CZ ', ' NH1', ' NH2'],
 'ASN ': [' CB ', ' CG ', ' OD1', ' ND2'],
 'ASP ': [' CB ', ' CG ', ' OD1', ' OD2'],
 'GLN ': [' CG ', ' CD ', ' OE1', ' NE2'],
 'GLU ': [' CG ', ' CD ', ' OE1', ' OE2'],
 'HIS ': [' CB ', ' CG ', ' ND1', ' CD2', ' CE1', ' NE2'],
 'PHE ': [' CB ', ' CG ', ' CD1', ' CD2', ' CE1', ' CE2', ' CZ '],
 'TRP ': [' CB ', ' CG ', ' CD1', ' CD2', ' NE1', ' CE3', ' CE2', ' CZ
...

improper_torsions

Dictionary containing lists of improper torsions; keys are residue names and values are lists of lists of atom names, one for each improper torsion in the residue.

Value:

{'ARG ': [[' HE ', ' CZ ', ' NE ', ' CD '],
          [' NE ', ' NH2', ' CZ ', ' NH1'],
          ['1HH1', '2HH1', ' NH1', ' CZ '],
          ['2HH2', ' CZ ', ' NH2', '1HH2'],
          ['HH11', 'HH12', ' NH1', ' CZ '],
          ['HH22', ' CZ ', ' NH2', 'HH21']],
 'ASN ': [[' CB ', ' ND2', ' CG ', ' OD1'],
          ['2HD2', ' CG ', ' ND2', '1HD2'],
...

backbone_dihedrals

Dictionary containing G-Factors for backbone_dihedral values, keys are residue names and values are dictionaries B; dictionary B keys are phi/psi dihedral values rounded to nearest 10 as strings ("60.0,30.0"), values are X, where G-factor = log(X).

Value:

{'ALA ': {'-100.0,-0.0': 0.001506,
          '-100.0,-10.0': 0.001789,
          '-100.0,-100.0': 9.4e-05,
          '-100.0,-110.0': 9.4e-05,
          '-100.0,-20.0': 0.00113,
          '-100.0,-30.0': 0.000847,
          '-100.0,-40.0': 0.000565,
          '-100.0,-50.0': 0.000188,
...

sidechain_dihedrals

Dictionary containing G-factors for sidechain dihedral values, keys are residue names and values are dictionaries B; dictionary B keys are chi1/chi2 dihedral values rounded to nearest 10 as strings ("60.0,30.0"), values are X, where G-factor = log(X).

Value:

{'ARG ': {'-10.0,-170.0': 0.000163,
          '-10.0,160.0': 0.000163,
          '-10.0,170.0': 0.000163,
          '-100.0,-10.0': 0.000163,
          '-100.0,-140.0': 0.000163,
          '-100.0,-150.0': 0.000163,
          '-100.0,-160.0': 0.000163,
          '-100.0,-170.0': 0.000326,
...