schrodinger.application.bioluminate.interaction

Module interaction_calculator

This module defines the InteractionCalculator class, which can be used for finding interactions between two groups of atoms.

Classes

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InteractionParams
A class to store settings for interaction parameters

_ResTuple
_ResTuple(chain, resnum, inscode, pdbres)

ResTuple
A class to store a residue.

Interactions
Store data about all the interactions made by a single residue

InteractingResidue
Store information about a residue and the interactions it makes

InteractionCalculator
Calculate all interactions between two groups of atoms

PiStackFinder
Find pi-pi interactions in proteins

InteractionCalculatorError
An error that happens during InteractionCalculator calculations

Functions

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approx_eq(val1, val2)

float

lipophilic_ChemScore_value(atom1, atom2, distance=None, cutoff=None)
Calculates a lipophilic score between an atom pair utilizing their van der Waals radii.

Variables

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ORIG_ATOM_NUM_PROP = 'i_temp_orig_atom_num'

HBOND_MAX_DIST = 2.5

HBOND_MIN_A_ANGLE = 90

HBOND_MIN_D_ANGLE = 120

ALLOWABLE_VDW_OVERLAP = 0.4

SALT_BRIDGE_MAX_DIST = 4.0

NEIGHBOR_MAX_DIST = 4.0

MAX_STACK_DIST = 4.0

RESIDUE_HYDROPHOBIC_ATOMS = {'ALA': [' CB '], 'ILE': [' CB ', ...

HYDROPHOBIC_DIST_CUTOFF = 8.0

EP = 1e-05

__package__ = 'schrodinger.application.bioluminate'

Function Details

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lipophilic_ChemScore_value(atom1, atom2, distance=None, cutoff=None)

Calculates a lipophilic score between an atom pair utilizing their van der Waals radii. An optional argument is available to avoid computation of the iter-atom distance within the function. The empirical function form is adopted from ChemScore:

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. Eldridge, Murray, Auton, Paolini, and Mee. JCAMD, 1997 (11).

Parameters:

atom1 (structure.StructureAtom) - first atom (usually a lipophilic ligand atom)
atom2 (structure.StructureAtom) - second atom (usually a lipophilic receptor atom)
distance (float) - inter-atom distance
cutoff (float) - distance beyond which to always return 0.0

Returns: float

emperical function value

Variables Details

[hide private]

RESIDUE_HYDROPHOBIC_ATOMS

Value:

{'ALA': [' CB '],
 'ILE': [' CB ', ' CG1', ' CG2', ' CD1'],
 'LEU': [' CB ', ' CG ', ' CD1', ' CD2'],
 'MET': [' CB ', ' CG ', ' SD ', ' CE '],
 'PHE': [' CB ', ' CG ', ' CD1', ' CD2', ' CE1', ' CE2', ' CZ '],
 'PRO': [' CB ', ' CG ', ' CD '],
 'TRP': [' CB ',
         ' CG ',
...