Package schrodinger :: Package protein :: Module analysis :: Class Report

Class Report

A class to calculate properties of proteins.

To use this class in a script to compute a set of data:

   reporter = Report(struct, ['SIDECHAIN DIHEDRALS', 'GAMMA BFACTORS'])
   dihedrals = reporter.get_set('SIDECHAIN DIHEDRALS')
   for point in dihedrals.points:
       resnum = point.descriptor.split()[1]
       resid = point.descriptor.split(':')[0] + ':' + resnum
       for val in point.values:
           try:
               true_value = float(val)
           except ValueError:
               # Some angles will have '-' if they aren't defined for 
               # this residue type
               continue
           do_something_with_chi_angle(true_value)

Nested Classes

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data_set
Base class for all data sets.

steric_clash_data_set
Class to compute and hold data for Steric Clashes.

primex_steric_clash_data_set
A subclass of steric_clash_data_set that computes clashes using a different set of criteria used by PrimeX Polish.

bond_length_data_set
Class to compute and hold data for Bond Length Deviations

bond_angle_data_set
Class to compute and hold data for Bond Angle Deviations

backbone_dihedral_data_set
Class to compute and hold data for Backbone Dihedrals

sidechain_dihedral_data_set
Class to compute and hold data for Sidechain Dihedrals

Gfactor_summary_data_set
Class to compute and hold data for G-factor summaries of the Backbone and Sidechain dihedrals.

Bfactor_data_set
Class to compute and hold data for B-Factors

gamma_Bfactor_data_set
Class to compute and hold data for B-Factors of sidechain gamma atoms

peptide_planarity_data_set
Class to compute and hold data for Peptide Planarity

sidechain_planarity_data_set
Class to compute and hold RMS data for planarity of sidechains

improper_torsion_data_set
Class to compute and hold RMS data for improper torsions

chirality_data_set
Class to compute and hold C-alpha chirality data

missing_atoms_data_set
Class to compute and hold information on missing atoms

local_atom
Private class used to store atom information locally for speed

local_residue
Private class used to store residue information locally for convenience

local_protein
Private class used to store protein information locally for convenience

Instance Methods

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__init__(self, ct, sets_to_run=['ALL'])
Create a Report instance.

get_vdw_radius(self, atom, vdwr_mode=VDWR_MMAT_H)

setup_protein(self, ct)
An internal method used to set up the protein for Report calculations.

make_local_protein(self, ct, keep_hydrogens=False, vdwr_mode=VDWR_MMAT_H)

str

get_residue_name(self, iatom, protein=None)
Create a residue name for the atom iatom.

get_set(self, set_label)
Return a single set of data that was specified using the sets_to_run parameter when the class object was created.

write_to_stdout(self)
Write each of the computed sets of data to the terminal

Method Details

[hide private]

init(self, ct, sets_to_run=['ALL'])
(Constructor)

Create a Report instance.

Parameters:

ct (Structure) - The structure this Report operates on
sets_to_run (list) - Either ['ALL'] (default) or one or more of the following to compute:
- 'STERIC CLASHES'
- 'PRIMEX STERIC CLASHES'
- 'BOND LENGTHS'
- 'BOND ANGLES'
- 'BACKBONE DIHEDRALS'
- 'SIDECHAIN DIHEDRALS'
- 'GFACTOR SUMMARY'
- 'BFACTORS'
- 'GAMMA BFACTORS'
- 'PEPTIDE PLANARITY'
- 'SIDECHAIN PLANARITY'
- 'IMPROPER TORSIONS'
- 'CHIRALITY'
- 'MISSING ATOMS'

setup_protein(self, ct)

An internal method used to set up the protein for Report calculations. This method should be considered a private method of the Report class and need not be explicitly called by the user/calling script.

Parameters:

ct (Structure) - The structure this method operates on

make_local_protein(self, ct, keep_hydrogens=False, vdwr_mode=VDWR_MMAT_H)

Parameters:

ct (Structure) - The structure this method operates on
keep_hydrogens (bool) - Whether to include hydrogens in the local protein
vdwr_mode (int) - which VDWR source should be used

get_residue_name(self, iatom, protein=None)

Create a residue name for the atom iatom.

Parameters:

iatom (int) - the atom index to build a residue name for

Returns: str

A residue name of the form: Chain:PDB_residue_codeResidue_numberInsertion_code where PDB_residue_code is a 4 character field and Residue_number is a 3 character field

get_set(self, set_label)

Return a single set of data that was specified using the sets_to_run parameter when the class object was created.

Parameters:

set_label (str) - One of the sets specified at Report object creation time using the sets_to_run parameter. Valid values are:
- 'STERIC CLASHES'
- 'BOND LENGTHS'
- 'BOND ANGLES'
- 'BACKBONE DIHEDRALS'
- 'SIDECHAIN DIHEDRALS'
- 'GFACTOR SUMMARY'
- 'BFACTORS'
- 'GAMMA BFACTORS'
- 'PEPTIDE PLANARITY'
- 'SIDECHAIN PLANARITY'
- 'IMPROPER TORSIONS'
- 'CHIRALITY'
- 'MISSING ATOMS'
If the requested set was not specified at the Report object creation time, None will be returned.

Class Report

__init__(self, ct, sets_to_run=['ALL']) (Constructor)

setup_protein(self, ct)

make_local_protein(self, ct, keep_hydrogens=False, vdwr_mode=VDWR_MMAT_H)

get_residue_name(self, iatom, protein=None)

get_set(self, set_label)

init(self, ct, sets_to_run=['ALL'])
(Constructor)