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