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CSB v1.2.5.d7fd331
Package csb :: Package bio :: Package nmr :: Class ContactMap
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Class ContactMap

source code

object --+
         |
        ContactMap

Describes a protein contact map. Atoms positioned at distance below a given cutoff are considered to be in contact.

Instance Methods
 
__contains__(self, atom) source code
 
__init__(self, chain, cutoff=6.0, filter=None)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__iter__(self) source code
frozenset of Atom
atom_contacts(self, atom)
Return all atoms within self.cutoff angstroms of atom.		 source code
numpy.array (2D)
atom_matrix(self)
Build a 2D binary contact matrix (0=no contact, 1=contact).		 source code
 
build(self)
Extract all contacts from the chain using the current distance cutoff.		 source code
 
connect(self, atom1, atom2)
Define a contact between atom1 and atom2.		 source code
 
connected(self, atom1, atom2)
Return True if the specified atoms are in contact.		 source code
 
draw(self, plot, color='black')
Visualize this contact map.		 source code
float
position(self, rank, atom_name)
Compute the location of atom on the contact map.		 source code
frozenset of Residue
residue_contacts(self, residue)
Return all residues, having neighboring atoms within self.cutoff angstroms from any of the residue's atoms.		 source code

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

Static Methods
ContactMapComparisonInfo
compare(query, reference, min_distance=0)
Compare a query contact map against a reference.		 source code
 
load(filename)
Deserialize from a pickle.		 source code
Class Variables
  DISTANCE_CUTOFF = 6.0
Properties
tuple of Atom atoms
All atoms involved in this map, sorted by residue number
Chain chain
Source protein chain
iterator of 2-tuples contacts
All atom contacts: an iterator over all contacting (Atom, Atom) pairs.
float cutoff
Distance cutoff in Angstroms

Inherited from object: __class__

Method Details

__init__(self, chain, cutoff=6.0, filter=None)
(Constructor)

source code 

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

Parameters:
  • chain (csb.bio.structure.Chain) - source protein chain
  • cutoff (float) - distance cutoff in angstroms
  • filter (lambda) - a callable with signature 'bool def(csb.bio.structure.Atom)', invoked for every atom, which determines whether a given atom should be skipped (False) or considered (True). See Filters
Overrides: object.__init__
(inherited documentation)

atom_contacts(self, atom)

source code 

Return all atoms within self.cutoff angstroms of atom.

Parameters:
  • atom (Atom) - anchor atom
Returns: frozenset of Atom

atom_matrix(self)

source code 

Build a 2D binary contact matrix (0=no contact, 1=contact). The order of elements in each dimension will match the order of atoms in the contact map (see ContactMap.atoms and iter(ContactMap). That means, the atoms in each dimension are sorted by residue number first.

Returns: numpy.array (2D)

Deprecated: This method can be removed in future versions

compare(query, reference, min_distance=0)
Static Method

source code 

Compare a query contact map against a reference.

Parameters:
  • min_distance (int) - consider only contacts between atoms, separated by the given minimum number of residues
  • query (ContactMap)
  • reference (ContactMap)
Returns: ContactMapComparisonInfo
precision and coverage

connect(self, atom1, atom2)

source code 

Define a contact between atom1 and atom2.

Parameters:
  • atom1 (Atom) - first atom
  • atom2 (Atom) - second atom

connected(self, atom1, atom2)

source code 

Return True if the specified atoms are in contact.

Parameters:
  • atom1 (Atom) - first atom
  • atom2 (Atom) - second atom

draw(self, plot, color='black')

source code 

Visualize this contact map.

Parameters:
  • plot (matplotlib.AxesSubplot) - csb.io.plots.Chart's plot to draw on
  • color (str) - pixel color (must be a matplotlib color constant)

position(self, rank, atom_name)

source code 

Compute the location of atom on the contact map.

Parameters:
  • rank (int) - residue rank (1-based)
  • atom_name (str) - atom name
Returns: float

residue_contacts(self, residue)

source code 

Return all residues, having neighboring atoms within self.cutoff angstroms from any of the residue's atoms.

Parameters:
  • residue (Residue) - anchor residue
Returns: frozenset of Residue

Property Details

atoms

All atoms involved in this map, sorted by residue number

Get Method:
unreachable.atoms(self) - All atoms involved in this map, sorted by residue number
Type:
tuple of Atom

chain

Source protein chain

Get Method:
unreachable.chain(self) - Source protein chain
Type:
Chain

contacts

All atom contacts: an iterator over all contacting (Atom, Atom) pairs.

Get Method:
unreachable.contacts(self) - All atom contacts: an iterator over all contacting (Atom, Atom) pairs.
Type:
iterator of 2-tuples

cutoff

Distance cutoff in Angstroms

Get Method:
unreachable.cutoff(self) - Distance cutoff in Angstroms
Type:
float

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