Package csb :: Package bio :: Package nmr :: Class RandomCoil |
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# Class RandomCoil

source code

    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'