Package csb :: Package bio :: Package nmr :: Class RandomCoil

Class RandomCoil

object --+
         |
        RandomCoil

Utility class containing all necessary data and methods for computing secondary chemical shifts.

Note: You are supposed to obtain an instance of this object only via the dedicated factory (see RandomCoil.get). The factory ensures a "singleton with lazy instantiation" behavior. This is needed since this object loads static data from the file system.

Instance Methods

__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

secondary_shift(self, chain, residue, nucleus, value)
Compute a secondary shift given a raw shift value for a specific residue and its neighboring residues. source code

simple_secondary_shift(self, residue, nucleus, value)
Compute a secondary shift given a raw shift value. source code

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

Static Methods

get()
Get the current RandomCoil instance (and create it, if this method is called for the first time).

source code

Class Variables
	RESOURCES = `'/home/travis/build/csb-toolbox/CSB/csb/bio/nmr/re...`

Properties
Inherited from `object`: `__class__`

Method Details

init(self)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

secondary_shift(self, chain, residue, nucleus, value)

source code

Compute a secondary shift given a raw shift value for a specific residue and its neighboring residues.

Parameters:

chain (Chain) - the protein chain containing the nucleus
residue (Residue, str or int) - the residue containing the nucleus. This can be a residue object, id (sequence number + insertion code, string) or rank (integer, 1-based)
nucleus (str) - atom name (PDB format)
value (float) - raw chemical shift value

simple_secondary_shift(self, residue, nucleus, value)

source code

Compute a secondary shift given a raw shift value. Residue neighborhood is not taken into account.

Parameters:

residue (str or EnumItem) - residue type (amino acid code)
nucleus (str) - atom name (PDB format)
value (float) - raw chemical shift value

Returns:

float

Raises:

EntityNotSupportedError - on unsupported residue or nucleus

Class Variable Details

RESOURCES

Value:

'/home/travis/build/csb-toolbox/CSB/csb/bio/nmr/resources'

Class RandomCoil

__init__(self) (Constructor)

secondary_shift(self, chain, residue, nucleus, value)

simple_secondary_shift(self, residue, nucleus, value)

RESOURCES

init(self)
(Constructor)