schrodinger.application.prime.residue_interaction module

A Python interface to Prime residue interaction data

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.prime.residue_interaction.InteractionReader(struc)

Bases: object

Read the Prime residue interaction data from a structure

Variables:
  • _available_res (set) – A set of residue names for which Prime interaction data has been read
  • _energy (dict) – A dictionary of the interaction energy, stored as [energy type][res1][res2]. Note that this dictionary is not symmetric: [energy type][res1][res2] is stored but [energy type][res2][res1] is not. In _buildEnergyDict and getEnergy, res1 is arbitrarily assigned to be less than res2.
BLOCK_NAME = 'm_psp_residue_interaction_energies'
__init__(struc)

Read the Prime residue interaction data

Parameters:struc (schrodinger.structure.Structure) – The structure to read interaction data from
Raises:ValueError – If the structure does not have any Prime residue interaction data
classmethod hasData(struc)

Check if the specified structure contains interaction data

Parameters:struc (schrodinger.structure.Structure) – The structure to check
Returns:True if the structure has interaction data. False otherwise.
Return type:bool
getEnergy(energy_type, res1, res2)

Get the interaction energy between the specified residues

Parameters:
  • energy_type (str) – The name of the energy to retrieve, such as “r_psp_Prime_Energy” or “r_psp_Prime_Covalent”
  • res1 (schrodinger.structure._Residue or str) – The first residue or residue key (i.e. the string value returned by resKey)
  • res2 (schrodinger.structure._Residue or str) – The second residue or residue key (i.e. the string value returned by resKey)
Returns:

The interaction energy between the specified residues

Return type:

float

Raises:

ValueError – If no data is found for the given energy type or residues

static resKey(res)

Get the Prime-formatted residue name for the specified residue

Parameters:res (schrodinger.structure._Residue) – The residue to get the name for
Returns:The formatted name
Return type:str