Package schrodinger :: Package application :: Package bioluminate :: Module protein :: Class Consensus

Class Consensus

Access the atoms, residues, and molecules (or just their indices) that are considered to be consensus objects for a template structure and query structure. All properties are returned as an OrderedDict that maps the template objects to their consensus objects from the query structure.

Here is an example of how to get all the consensus waters between two protein structures. We define the cutoff here at 2 Angstroms:

 from schrodinger.structure import StructureReader
 from schrodinger.application.bioluminate import protein

 pt = maestro.project_table_get()

 # Create an ASL map for all ligands in the WS
 asl_map = []
 for row in pt.included_rows:
     st = row.getStructure()
     ligands = analyze.find_ligands(st)
     if not ligands:
         continue
     indices = []
     for ligand in ligands:
         indices.extend([str(i) for i in ligand.atom_indexes])

     asl = 'atom.n %s' % ','.join(indices)

     asl_map.append((st, asl))

 # Create a consensus of all ligands, specifying that at least three
 # structures must have a ligand atom within 2A from one another.
 consensus = protein.Consensus(asl_map, 3, dist_cutoff=2)

 # To get the atom objects
 consensus_atoms = consensus.atoms

 # To get the molecule objects
 molecules = consensus.molecules

Instance Methods

[hide private]

__init__(self, asl_map, minimum_number, dist_cutoff=2.0)

_setIndexMap(self)
Private method called in __init__.

getClosest(self, ref_atom, mob_atoms)
Gets the closest atom to the ref_atom from mob_atoms.

list of lists

_createByAtomProperty(self, attr, is_callable=False)
Private method to get an atom property.

OrderedDict of atom objects where the keys are the template atoms and their values are the consensus atoms from the query.

atoms(self)
Get the map of atom objects of consensus atoms.

OrderedDict of ints where the keys are the template atom indices and their values are the consensus atom indices from the query.

atom_indices(self)
Get the map of atom indices of consensus atoms.

list of unique consensus residue objects for each structure in self.asl_map. (Order is maintained)

residues(self)
Get the list of residue objects of consensus atoms for each structure in self.asl_map.

list of unique consensus residue indices for each structure in self.asl_map. (Order is maintained)

residue_indices(self)
Get the map of residue indices of consensus atoms.

list of unique consensus molecule objects for each structure in self.asl_map. (Order is maintained)

molecules(self)
Get the map of molecule objects of consensus atoms.

list of unique consensus molecule indices for each structure in self.asl_map. (Order is maintained)

molecule_indices(self)
Get the map of molecule indices of consensus atoms.

Class Variables

[hide private]

ASL_WATER = 'water and NOT (atom.ele H)'

ASL_IONS = 'ions'

ASL_LIGAND = '(((m.atoms 5-130)) and not ((ions) or '

Instance Variables

[hide private]

_consensus_atoms
Atom indices mapping template and query consensus

Method Details

[hide private]

init(self, asl_map, minimum_number, dist_cutoff=2.0)
(Constructor)

Parameters:

asl_map (tuple of (structure, ASL)) - List of structures and the ASL used to limit the atoms used when calculating the consensus
minimum_number (int) - The minimum number of matches within structures. An atom will be considered a "consensus" atom if it is within the dist_cutoff of at least minimum_number of structures in the list of passed in structures.
dist_cutoff (float) - Distance in Angstroms used to define a consensus match

Attention: The list of consensus atoms (or molecules, residues, indices, etc. depending on the property called, i.e. self.molecules) will all be unique and will depend on the ASL passed in. If the ASL is not specific enough you may end up with poor results.

_setIndexMap(self)

Private method called in __init__. Finds the consensus atom indices between the template and query.

_createByAtomProperty(self, attr, is_callable=False)

Private method to get an atom property.

Parameters:

attr (str) - The attribute to get from the consensus atoms
is_callable (bool) - Whether the prop arg is a callable

Returns: list of lists

A list of lists of the new entities created from the properties

atoms(self)

Get the map of atom objects of consensus atoms.

Returns: OrderedDict of atom objects where the keys are the template atoms and their values are the consensus atoms from the query.

Atoms of consensus atoms

Decorators:

@property

atom_indices(self)

Get the map of atom indices of consensus atoms.

Returns: OrderedDict of ints where the keys are the template atom indices and their values are the consensus atom indices from the query.

Atom indices of consensus atoms

Decorators:

@property

residues(self)

Get the list of residue objects of consensus atoms for each structure in self.asl_map.

Returns: list of unique consensus residue objects for each structure in self.asl_map. (Order is maintained)

Residues of consensus atoms

Decorators:

@property

residue_indices(self)

Get the map of residue indices of consensus atoms.

Returns: list of unique consensus residue indices for each structure in self.asl_map. (Order is maintained)

Residue indices of consensus atoms

Decorators:

@property

molecules(self)

Get the map of molecule objects of consensus atoms.

Returns: list of unique consensus molecule objects for each structure in self.asl_map. (Order is maintained)

Molecules of consensus atoms

Decorators:

@property

molecule_indices(self)

Get the map of molecule indices of consensus atoms.

Returns: list of unique consensus molecule indices for each structure in self.asl_map. (Order is maintained)

Molecule indices of consensus atoms

Decorators:

@property

Class Consensus

__init__(self, asl_map, minimum_number, dist_cutoff=2.0) (Constructor)

_setIndexMap(self)

_createByAtomProperty(self, attr, is_callable=False)

atoms(self)

atom_indices(self)

residues(self)

residue_indices(self)

molecules(self)

molecule_indices(self)

init(self, asl_map, minimum_number, dist_cutoff=2.0)
(Constructor)