Package csb :: Package bio :: Package nmr :: Class AtomConnectivity

Class AtomConnectivity

object --+
         |
        AtomConnectivity

Instance Methods

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

source code

boolean

connected(self, residue, atom1, atom2)
Return True if atom1 is covalently connected to atom2 in residue source code

tuple of str

connected_atoms(self, residue, atom)
Return all atoms covalently connected to atom in residue. source code

bool

contains(self, residue, atom)
Return True if atom name is contained in residue. source code

frozenset of str

get_atoms(self, residue, prefix='')
Get all atoms contained in residue. source code

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

Static Methods

AtomConnectivity

get()
Get the current AtomConnectivity instance (and create it if this method is invoked 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)

connected(self, residue, atom1, atom2)

source code

Return True if atom1 is covalently connected to atom2 in residue

Parameters:

residue (EnumItem) - residue type (a member of ProteinAlphabet)
atom1 (str) - first atom name (IUPAC)
atom2 (str) - second atom name (IUPAC)

Returns: boolean

connected_atoms(self, residue, atom)

source code

Return all atoms covalently connected to atom in residue.

Parameters:

residue (EnumItem) - residue type (a member of ProteinAlphabet)
atom (str) - source atom name (IUPAC)

Returns: tuple of str

contains(self, residue, atom)

source code

Return True if atom name is contained in residue.

Parameters:

residue (EnumItem) - residue type (a member of ProteinAlphabet)
atom (str) - atom name (IUPAC)

Returns: bool

get_atoms(self, residue, prefix=`''`)

source code

Get all atoms contained in residue.

Parameters:

residue (EnumItem) - residue type (a member of ProteinAlphabet)
prefix (str) - atom name prefix wildcard (IUPAC)

Returns: frozenset of str

set of atom names

Class Variable Details

RESOURCES

Value:

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

Class AtomConnectivity

__init__(self) (Constructor)

connected(self, residue, atom1, atom2)

connected_atoms(self, residue, atom)

contains(self, residue, atom)

get_atoms(self, residue, prefix='')

RESOURCES

init(self)
(Constructor)

get_atoms(self, residue, prefix=`''`)