Package schrodinger :: Package application :: Package prime :: Module residue_interaction :: Class InteractionReader

Class InteractionReader

object --+
         |
        InteractionReader

Read the Prime residue interaction data from a structure

Instance Methods

[hide private]

__init__(self, struc)
Read the Prime residue interaction data

tuple

_readEnergyMetaData(self, struc)
Get metadata about the stored interaction data

tuple

_readEnergyData(self, data_names, ninteract, data_handle)
Read in the interaction data

float

getEnergy(self, energy_type, res1, res2)
Get the interaction energy between the specified residues

str

_getResKey(self, res)
Get the Prime-formatted residue name for the specified residue

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods

[hide private]

bool

hasData(cls, struc)
Check if the specified structure contains interaction data

int

_openDataHandle(cls, struc)
Open an m2io handle to the interaction data

Static Methods

[hide private]

str

resKey(res)
Get the Prime-formatted residue name for the specified residue

Class Variables

[hide private]

BLOCK_NAME = 'm_psp_residue_interaction_energies'

Instance Variables

[hide private]

set

_available_res
A set of residue names for which Prime interaction data has been read

dict

_energy
A dictionary of the interaction energy, stored as [energy type][res1][res2].

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struc)
(Constructor)

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

Overrides: object.__init__

hasData(cls, struc)
Class Method

Check if the specified structure contains interaction data

Parameters:

struc (schrodinger.structure.Structure) - The structure to check

Returns: bool

True if the structure has interaction data. False otherwise.

_readEnergyMetaData(self, struc)

Get metadata about the stored interaction data

Parameters:

struc (schrodinger.structure.Structure) - The structure to read interaction data from

Returns: tuple

A tuple of

The names of the stored data (i.e. column headers) (list)
The number of interactions (i.e. row count) (int)
An open m2io handle to the data (int)

_openDataHandle(cls, struc)
Class Method

Open an m2io handle to the interaction data

Parameters:

struc (schrodinger.structure.Structure) - The structure to read interaction data from

Returns: int

An open m2io handle to the data

Raises:

ValueError - If the structure does not have any Prime residue interaction data

_readEnergyData(self, data_names, ninteract, data_handle)

Read in the interaction data

Parameters:

data_names (list) - The names of the stored data (i.e. column headers)
ninteract (int) - The number of interactions (i.e. row count)
data_handle (int) - An open m2iohandle to the data

Returns: tuple

A tuple of

The residues for which data was read (set)
The interaction data (dict). See InteractionReader._energy documentation for an explanation of the data format.

getEnergy(self, 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: float

The interaction energy between the specified residues

Raises:

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

_getResKey(self, res)

Get the Prime-formatted residue name for the specified residue

Parameters:

res (schrodinger.structure._Residue or str) - The residue to get the name for or the residue key

Returns: str

The formatted name

resKey(res)
Static Method

Get the Prime-formatted residue name for the specified residue

Parameters:

res (schrodinger.structure._Residue) - The residue to get the name for

Returns: str

The formatted name

Instance Variable Details

[hide private]

_energy

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.

Type:: dict

Class InteractionReader

__init__(self, struc) (Constructor)

hasData(cls, struc) Class Method

_readEnergyMetaData(self, struc)

_openDataHandle(cls, struc) Class Method

_readEnergyData(self, data_names, ninteract, data_handle)

getEnergy(self, energy_type, res1, res2)

_getResKey(self, res)

resKey(res) Static Method

_energy

init(self, struc)
(Constructor)

hasData(cls, struc)
Class Method

_openDataHandle(cls, struc)
Class Method

resKey(res)
Static Method