Package csb :: Package bio :: Package structure :: Class Chain

Class Chain

            object --+        
                     |        
core.AbstractContainer --+    
                         |    
  core.AbstractNIContainer --+
                             |
                object --+   |
                         |   |
            AbstractEntity --+
                             |
                            Chain

Represents a polymeric chain. Provides list-like and rank-based access to the residues in the chain:

>>> chain[0]
<ProteinResidue [1]: SER None>
>>> chain.residues[1]
<ProteinResidue [1]: SER None>

You can also access residues by their PDB sequence number:

>>> chain.find(sequence_number=5, insertion_code='A')
<ProteinResidue [1]: SER 5A>

Nested Classes
Inherited from `core.AbstractContainer`: `__metaclass__`

Instance Methods

__init__(self, chain_id, type=Protein, name='', residues=None, accession=None, molecule_id=None)
x.__init__(...) initializes x; see help(type(x)) for signature source code

__len__(self)

source code

__repr__(self)
repr(x)

source code

SuperimposeInfo

align(self, other, what=['CA'], how=Global)
Align other's alpha carbons over self in space and return SuperimposeInfo. source code

Chain

clone(self)
Make a deep copy of the chain.

source code

compute_torsion(self)
Iterate over all residues in the chain, compute and set their torsion property.

source code

Residue

find(self, sequence_number, insertion_code=None)
Get a residue by its original Residue Sequence Number and Insertion Code.

source code

float

rmsd(self, other, what=['CA'])
Compute the C-alpha RMSD against another chain (assuming equal length). source code

Chain

subregion(self, start, end, clone=False)
Extract a subchain defined by [start, end].

source code

SuperimposeInfo

superimpose(self, other, what=['CA'], how=Global)
Find the optimal fit between self and other. source code

float

tm_score(self, other, what=['CA'])
Compute the C-alpha TM-Score against another chain (assuming equal chain length and optimal configuration - no fitting is done). source code

SuperimposeInfo

tm_superimpose(self, other, what=['CA'], how=Global)
Find the optimal fit between self and other. source code

Inherited from core.AbstractNIContainer: __getitem__

Inherited from core.AbstractContainer: __bool__, __iter__, __nonzero__

Inherited from AbstractEntity: components, get_coordinates, transform

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

Static Methods

Chain

from_sequence(sequence, id='_')
Create a new chain from an existing sequence. source code

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
str	accession Accession number
csb.core.enum	alphabet Sequence alphabet corresponding to the current chain type
str	entry_id Accession number + chain ID
bool	has_torsion True if `Chain.compute_torsion` had been invoked
str	header FASTA header in PDB format
str	id Chain's ID
iterator of AbstractEntity	items Iterator over all immediate children of the entity
int	length Number of residues
int	molecule_id PDB MOL ID of this chain
str	name Chain name
ChainResiduesCollection	residues Rank-based access to Chain's Residues
SecondaryStructure	secondary_structure Secondary structure (if available)
str	sequence Chain sequence
TorsionAnglesCollection	torsion Torsion angles
enum item	type Chain type - any member of SequenceTypes
Inherited from `object`: `__class__`

Method Details

init(self, chain_id, type=Protein, name=`''`, residues=None, accession=None, molecule_id=None)
(Constructor)

source code

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

Parameters:

chain_id (str) - ID of the new chain
type (csb.core.EnumItem) - sequence type (a member of the SequenceTypes enum)
name (str) - name of the chain
residues (list) - initialization list of Residue-s
accession (str) - accession number of the chain
molecule_id - MOL ID of the chain, if part of a polymer

Overrides: object.__init__

(inherited documentation)

len(self)
(Length operator)

source code

Overrides: core.AbstractContainer.__len__

repr(self)
(Representation operator)

source code

repr(x)

Overrides: object.__repr__: (inherited documentation)

align(self, other, what=`['CA']`, how=Global)

source code

Align other's alpha carbons over self in space and return SuperimposeInfo. Coordinates of other are overwritten in place using the rotation matrix and translation vector in SuperimposeInfo. Alias for:

   R, t = self.superimpose(other, what=['CA'])
   other.transform(R, t)

Parameters:

other (Chain) - the subject (movable) chain
what (list) - a list of atom kinds, e.g. ['CA']
how (csb.core.EnumItem) - fitting method (global or local) - a member of the AlignmentTypes enum

Returns: SuperimposeInfo

superimposition info object, containing rotation matrix, translation vector and computed RMSD

clone(self)

source code

Make a deep copy of the chain. If this chain is part of a structure, detach from it.

Returns: Chain: a deep copy of self

compute_torsion(self)

source code

Iterate over all residues in the chain, compute and set their torsion property.

Raises:

Missing3DStructureError - when a 3D structure is absent
Broken3DStructureError - when a given atom cannot be retrieved from any residue

find(self, sequence_number, insertion_code=None)

source code

Get a residue by its original Residue Sequence Number and Insertion Code.

Parameters:

sequence_number (str) - PDB sequence number of the residue
insertion_code (str) - PDB insertion code of the residue (if any)

Returns: Residue

the residue object with such an ID

Raises:

EntityNotFoundError - if no residue with that ID exists

from_sequence(sequence, id=`'_'`)
Static Method

source code

Create a new chain from an existing sequence.

Parameters:

sequence (csb.bio.sequence.AbstractSequence) - source sequence

Returns: Chain

rmsd(self, other, what=`['CA']`)

source code

Compute the C-alpha RMSD against another chain (assuming equal length). Chains are superimposed with Least Squares Fit / Singular Value Decomposition.

Parameters:

other (Chain) - the subject (movable) chain
what (list) - a list of atom kinds, e.g. ['CA']

Returns: float

computed RMSD over the specified atom kinds

subregion(self, start, end, clone=False)

source code

Extract a subchain defined by [start, end]. If clone is True, this is a deep copy of the chain. Otherwise same as:

>>> chain.residues[start : end + 1]

but coordinates are checked and a Chain instance is returned.

Parameters:

start (int) - start position of the sub-region
end (int) - end position
clone (bool) - if True, a deep copy of the sub-region is returned, otherwise - a shallow one

Returns: Chain

a new chain, made from the residues of the extracted region

Raises:

IndexError - if start/end positions are out of range

superimpose(self, other, what=`['CA']`, how=Global)

source code

Find the optimal fit between self and other. Return SuperimposeInfo (RotationMatrix, translation Vector and RMSD), such that:

>>> other.transform(rotation_matrix, translation_vector)

will result in other's coordinates superimposed over self.

Parameters:

other (Chain) - the subject (movable) chain
what (list) - a list of atom kinds, e.g. ['CA']
how (csb.core.EnumItem) - fitting method (global or local) - a member of the AlignmentTypes enum

Returns: SuperimposeInfo

superimposition info object, containing rotation matrix, translation vector and computed RMSD

Raises:

AlignmentArgumentLengthError - when the lengths of the argument chains differ

tm_score(self, other, what=`['CA']`)

source code

Compute the C-alpha TM-Score against another chain (assuming equal chain length and optimal configuration - no fitting is done).

Parameters:

other (Chain) - the subject (movable) chain
what (list) - a list of atom kinds, e.g. ['CA']

Returns: float

computed TM-Score over the specified atom kinds

tm_superimpose(self, other, what=`['CA']`, how=Global)

source code

Find the optimal fit between self and other. Return SuperimposeInfo (RotationMatrix, translation Vector and TM-score), such that:

>>> other.transform(rotation_matrix, translation_vector)

will result in other's coordinates superimposed over self.

Parameters:

other (Chain) - the subject (movable) chain
what (list) - a list of atom kinds, e.g. ['CA']
how (csb.core.EnumItem) - fitting method (global or local) - a member of the AlignmentTypes enum

Returns: SuperimposeInfo

superimposition info object, containing rotation matrix, translation vector and computed TM-score

Raises:

AlignmentArgumentLengthError - when the lengths of the argument chains differ

Property Details

accession

Accession number

Get Method:: unreachable.accession(self) - Accession number
Set Method:: unreachable.accession(self, accession)
Type:: str

alphabet

Sequence alphabet corresponding to the current chain type

Get Method:: unreachable.alphabet(self) - Sequence alphabet corresponding to the current chain type
Type:: csb.core.enum

entry_id

Accession number + chain ID

Get Method:: unreachable.entry_id(self) - Accession number + chain ID
Type:: str

has_torsion

True if Chain.compute_torsion had been invoked

Get Method:: unreachable.has_torsion(self) - True if Chain.compute_torsion had been invoked
Type:: bool

header

FASTA header in PDB format

Get Method:: unreachable.header(self) - FASTA header in PDB format
Type:: str

id

Chain's ID

Get Method:: unreachable.id(self) - Chain's ID
Set Method:: unreachable.id(self, id)
Type:: str

items

Iterator over all immediate children of the entity

Get Method:: unreachable.items(self)
Type:: iterator of AbstractEntity

length

Number of residues

Get Method:: unreachable.length(self) - Number of residues
Type:: int

molecule_id

PDB MOL ID of this chain

Get Method:: unreachable.molecule_id(self) - PDB MOL ID of this chain
Set Method:: unreachable.molecule_id(self, value)
Type:: int

name

Chain name

Get Method:: unreachable.name(self) - Chain name
Set Method:: unreachable.name(self, value)
Type:: str

residues

Rank-based access to Chain's Residues

Get Method:: unreachable.residues(self) - Rank-based access to Chain's Residues
Type:: ChainResiduesCollection

secondary_structure

Secondary structure (if available)

Get Method:: unreachable.secondary_structure(self) - Secondary structure (if available)
Set Method:: unreachable.secondary_structure(self, ss)
Type:: SecondaryStructure

sequence

Chain sequence

Get Method:: unreachable.sequence(self) - Chain sequence
Type:: str

torsion

Torsion angles

Get Method:: unreachable.torsion(self) - Torsion angles
Type:: TorsionAnglesCollection

type

Chain type - any member of SequenceTypes

Get Method:: unreachable.type(self) - Chain type - any member of SequenceTypes
Set Method:: unreachable.type(self, type)
Type:: enum item

Class Chain

__init__(self, chain_id, type=Protein, name='', residues=None, accession=None, molecule_id=None) (Constructor)

__len__(self) (Length operator)

__repr__(self) (Representation operator)

align(self, other, what=['CA'], how=Global)

clone(self)

compute_torsion(self)

find(self, sequence_number, insertion_code=None)

from_sequence(sequence, id='_') Static Method

rmsd(self, other, what=['CA'])

subregion(self, start, end, clone=False)

superimpose(self, other, what=['CA'], how=Global)

tm_score(self, other, what=['CA'])

tm_superimpose(self, other, what=['CA'], how=Global)

accession

alphabet

entry_id

has_torsion

header

id

items

length

molecule_id

name

residues

secondary_structure

sequence

torsion

type

init(self, chain_id, type=Protein, name=`''`, residues=None, accession=None, molecule_id=None)
(Constructor)

len(self)
(Length operator)

repr(self)
(Representation operator)

align(self, other, what=`['CA']`, how=Global)

from_sequence(sequence, id=`'_'`)
Static Method

rmsd(self, other, what=`['CA']`)

superimpose(self, other, what=`['CA']`, how=Global)

tm_score(self, other, what=`['CA']`)

tm_superimpose(self, other, what=`['CA']`, how=Global)