Package schrodinger :: Module structure :: Class _Residue

Class _Residue

     object --+    
              |    
_AtomCollection --+
                  |
                 _Residue

A class which is returned by the ResidueIterator and contains information about the residue including the atoms which make it up.

Important methods include extractStructure and getAtomList. The atom attribute can be used to iterate over all atoms in the molecule, and the number of atoms can be determined via len(molecule.atom).

Instance Methods

[hide private]

__init__(self, st, resnum, inscode, chain, atoms=[])
x.__init__(...) initializes x; see help(type(x)) for signature

__str__(self)
Return a string representation - chain:resnum[inscode].

_getPdbRes(self)

_setPdbRes(self, newvalue)

_getChain(self)

_setChain(self, newvalue)

_getResnum(self)

_setResnum(self, newvalue)

_getInscode(self)

_setInscode(self, newvalue)

_getBF(self)

_getMolNumber(self)

_getSecStruct(self)

getCode(self)
Return the one-letter residue code for this residue.

hasMissingAtoms(self)
Returns True is this residue doesn't have the expected number of heavy atoms.

isStandardResidue(self)
Returns True if this residue is on the list of standard PDB residues

isConnectedToResidue(self, other_res)
Returns True if the given residue is connected (C->N) to this residue.

applyStyle(self, atoms=3, bonds=3)
Applies the given display styles to the atoms and bonds of the residue.

Inherited from _AtomCollection: __len__, extractStructure, getAtomList

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

Properties

[hide private]

pdbres
PDB residue name

chain
Chain name

resnum
PDB residue number

inscode
PDB residue insertion code

temperature_factor
Residue B (temperature) factor

molecule_number
Molecule number

secondary_structure
Secondary structure

Inherited from _AtomCollection: atom

Inherited from object: __class__

Method Details

[hide private]

init(self, st, resnum, inscode, chain, atoms=`[]`)
(Constructor)

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

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

Return a string representation - chain:resnum[inscode]. Insertion code is included only it is present. If the residue has no chain ID, then underscore ("_") is used.

Overrides: object.__str__

hasMissingAtoms(self)

Returns True is this residue doesn't have the expected number of heavy atoms. Will return False is this residue has the correct number of heavy atoms or if it is of a type we don't know

isConnectedToResidue(self, other_res)

Returns True if the given residue is connected (C->N) to this residue.

If the "C" PDB atom of this residue is connected to the "N" PDB atom of the other_res, then the residues are connected. Otherwise, they are not considered connected.

applyStyle(self, atoms=3, bonds=3)

Applies the given display styles to the atoms and bonds of the residue.

Parameters:

atoms (int) - display style for atoms given by structure module constants ATOM_NOSTYLE, ATOM_CIRCLE, ATOM_CPK, ATOM_BALLNSTICK. Default is ATOM_BALLNSTICK.
atoms (int) - display style for bonds given by structure module constants BOND_NOSTYLE, BOND_WIRE, BOND_TUBE, BOND_BALLNSTICK. Default is BOND_BALLNSTICK.
bonds (int)

Property Details

[hide private]

pdbres

PDB residue name

Get Method:: _getPdbRes(self)
Set Method:: _setPdbRes(self, newvalue)

chain

Chain name

Get Method:: _getChain(self)
Set Method:: _setChain(self, newvalue)

resnum

PDB residue number

Get Method:: _getResnum(self)
Set Method:: _setResnum(self, newvalue)

inscode

PDB residue insertion code

Get Method:: _getInscode(self)
Set Method:: _setInscode(self, newvalue)

temperature_factor

Residue B (temperature) factor

Get Method:: _getBF(self)

molecule_number

Molecule number

Get Method:: _getMolNumber(self)

secondary_structure

Secondary structure

Get Method:: _getSecStruct(self)

Class _Residue

__init__(self, st, resnum, inscode, chain, atoms=[]) (Constructor)

__str__(self) (Informal representation operator)

hasMissingAtoms(self)

isConnectedToResidue(self, other_res)

applyStyle(self, atoms=3, bonds=3)

pdbres

chain

resnum

inscode

temperature_factor

molecule_number

secondary_structure

init(self, st, resnum, inscode, chain, atoms=`[]`)
(Constructor)

str(self)
(Informal representation operator)