Package Scientific :: Package IO :: Module PDB :: Class NucleotideResidue

Class NucleotideResidue

Group --+    
        |    
  Residue --+
            |
           NucleotideResidue

Nucleotide residue in a PDB file

Instance Methods

__init__(self, name, atoms=None, number=None)

addAtom(self, atom)
Add an atom to the group

bool

hasDesoxyribose(self)
Returns: True if the residue has no atom named O2*

bool

hasPhosphate(self)
Returns: True if the residue has a phosphate group

bool

hasRibose(self)
Returns: True if the residue has an atom named O2*

bool

hasTerminalH(self)
Returns: True if the residue has a 3-terminal H atom

isCompatible(self, residue_data)

writeToFile(self, file)
Write the group to a file

Inherited from Group: __getitem__, __len__, __repr__, __str__, changeName, deleteAtom, deleteHydrogens

Class Variables
	is_nucleotide = `1`

Method Details

init(self, name, atoms=None, number=None)
(Constructor)

Parameters:

name - the name of the group
atoms - a list of atoms (or None for no atoms)
number - the PDB residue number (or None)

Overrides: Group.__init__

(inherited documentation)

addAtom(self, atom)

Add an atom to the group

Parameters:

atom - the atom

Overrides: Group.addAtom

(inherited documentation)

hasDesoxyribose(self)

Returns: bool: True if the residue has no atom named O2*

hasPhosphate(self)

Returns: bool: True if the residue has a phosphate group

hasRibose(self)

Returns: bool: True if the residue has an atom named O2*

hasTerminalH(self)

Returns: bool: True if the residue has a 3-terminal H atom

isCompatible(self, residue_data)

Overrides: Group.isCompatible

writeToFile(self, file)

Write the group to a file

Parameters:

file - a PDBFile object or a file name

Overrides: Group.writeToFile

(inherited documentation)

Class NucleotideResidue

__init__(self, name, atoms=None, number=None) (Constructor)

addAtom(self, atom)

hasDesoxyribose(self)

hasPhosphate(self)

hasRibose(self)

hasTerminalH(self)

isCompatible(self, residue_data)

writeToFile(self, file)

init(self, name, atoms=None, number=None)
(Constructor)