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
andgetEnergy
, 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 fromRaises: 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 checkReturns: 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 byresKey
) - res2 (
schrodinger.structure._Residue
or str) – The second residue or residue key (i.e. the string value returned byresKey
)
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 forReturns: The formatted name Return type: str