schrodinger.application.bioluminate.interaction_calculator module¶
This module defines the InteractionCalculator class, which can be used for finding interactions between two groups of atoms.
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schrodinger.application.bioluminate.interaction_calculator.
approx_eq
(val1, val2)¶
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schrodinger.application.bioluminate.interaction_calculator.
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: emperical function value
Return type: float
- atom1 (
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class
schrodinger.application.bioluminate.interaction_calculator.
InteractionParams
¶ Bases:
object
A class to store settings for interaction parameters
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paramDict
()¶ Return a dictionary of all interaction parameters. Note that changes to this dictionary will change the instance variables as well.
Returns: A dictionary of all interaction parameters Return type: dict
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class
schrodinger.application.bioluminate.interaction_calculator.
ResTuple
¶ Bases:
schrodinger.application.bioluminate.interaction_calculator._ResTuple
A class to store a residue. Unlike schrodinger.structure._Residue, two ResTuple objects that describe the same residue are equal (and their hashes are equal). This class will also strip spaces from inscode and pdbres.
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class
schrodinger.application.bioluminate.interaction_calculator.
Interactions
¶ Bases:
object
Store data about all the interactions made by a single residue
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H_BOND
= 'hb'¶
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PI_STACK
= 'pi stack'¶
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SALT_BRIDGE
= 'salt bridge'¶
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CLASH
= 'clash'¶
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DISULFIDE
= 's-s'¶
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classmethod
init
(**kwargs)¶ Initialize a class instance from existing interaction dictionaries. This function allows for the output of __repr__() to be evaluated and is intended for use in testing.
Returns: The initialized instance Return type: Interactions
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numHbonds
()¶ Return the number of hydrogen bonds
Returns: The number of hydrogen bonds Return type: int
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numPiStacks
()¶ Return the number of pi stacks
Returns: The number of pi stacks Return type: int
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numSaltBridges
()¶ Return the number of salt bridges
Returns: The number of salt bridges Return type: int
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numDisulfides
()¶ Return the number of disulfide bonds
Returns: The number of disulfide bonds Return type: int
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numClashs
()¶ Return the number of steric clashes
Returns: The number of steric clashes Return type: int
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numSpecificInteractions
()¶ Return the total number of specific interactions (i.e. ignoring non- specific interactions such as buried SASA)
Returns: The total number of specific interactions Return type: int
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allInteractingResidues
()¶ Return a list of all residues that this one interacts with (not counting nearby residues)
Returns: A set of ResTuple objects Return type: set
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interactionSummary
()¶ Create the interaction summary to display in the specific interactions column.
Returns: The interaction summary Return type: str
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nearbyRes
()¶ Return the nearby residues
Returns: A tuple of - The nearby residues (as strings), sorted by distance - The sorted residue distances (floats) Return type: tuple
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class
schrodinger.application.bioluminate.interaction_calculator.
InteractingResidue
(res, interactions)¶ Bases:
object
Store information about a residue and the interactions it makes
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class
schrodinger.application.bioluminate.interaction_calculator.
InteractionCalculator
(interaction_params=<schrodinger.application.bioluminate.interaction_calculator.InteractionParams object>, ignore_backbone=False)¶ Bases:
object
Calculate all interactions between two groups of atoms
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calculate
(struc, asl_expressions)¶ Calculate all interactions
Parameters: - struc (
schrodinger.structure.Structure
) – The structure to analyze - asl_expressions (list of string) – A list of [asl_expresion for group 1, asl expression for group2]
- struc (
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compileResults
()¶ Compile all of the calculated interactions into a list of InteractingResidue objects
Returns: A list of InteractingResidue objects, sorted by residue Return type: list
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classmethod
run
(struc, asl_expressions, interaction_params=<schrodinger.application.bioluminate.interaction_calculator.InteractionParams object>, ignore_backbone=False)¶ A convenience function to initialize this class, calculate all interactions, and return the compiled results.
Parameters: - struc (
schrodinger.structure.Structure
) – The structure to analyze - asl_expressions (list of string) – A list of [asl_expresion for group 1, asl expression for group2]
- interaction_params (
interaction_calculator.InteractionParams
) – The interaction parameters - ignore_backbone (bool) – Should the calculations ignore backbone-backbone interactions?
Returns: A list of InteractingResidue objects describing all calculated interactions, sorted by residue
Return type: list
- struc (
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class
schrodinger.application.bioluminate.interaction_calculator.
PiStackFinder
(max_stack_dist=4.0)¶ Bases:
object
Find pi-pi interactions in proteins
Variables: NON_AROMATIC_RES (set) – A set of residue types that don’t contain aromatic side chains -
NON_AROMATIC_RES
= {'LEU', 'PRO', 'ARG', 'LYS', 'SER', 'THR', 'ASP', 'GLU', 'GLY', 'ASN', 'GLN', 'CYS', 'ILE', 'ALA', 'MET', 'VAL'}¶
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classmethod
createIter
(struc, group_strucs, max_stack_dist=4.0)¶ A convenience function to initalize the class and return an iterator
Parameters: - struc (
schrodinger.structure.Structure
) – The structure being analyzed - group_strucs (list) – A list of [Structure object for group 1, Structure object for group 2]
- max_stack_dist (float) – The maximum distance between two ring centroids allowed for face-face interactions.
Returns: An iterator that produces tuples of two atom number lists, representing (the ring atoms from group 1 involved in the stacking, the ring atoms from group 2 involved in the stacking
Return type: iter
- struc (
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piStacksIterator
(struc, group_strucs)¶ Create an iterator that iterates through all pi stacking between two groups of atoms
Parameters: - struc (
schrodinger.structure.Structure
) – The structure being analyzed - group_strucs (list) – A list of [Structure object for group 1, Structure object for group 2]
Returns: An iterator that produces tuples of two atom number lists, representing (the ring atoms from group 1 involved in the stacking, the ring atoms from group 2 involved in the stacking
Return type: iter
- struc (
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exception
schrodinger.application.bioluminate.interaction_calculator.
InteractionCalculatorError
¶ Bases:
Exception
An error that happens during InteractionCalculator calculations