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
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| __init__(self,
asl_map,
minimum_number,
dist_cutoff=2.0) |
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getClosest(self,
ref_atom,
mob_atoms)
Gets the closest atom to the ref_atom from
mob_atoms. |
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list of lists
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ASL_WATER = 'water and NOT (atom.ele H)' |
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ASL_IONS = 'ions' |
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ASL_LIGAND = '(((m.atoms 5-130)) and not ((ions) or (res.pt AC... |
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_consensus_atoms
Atom indices mapping template and query consensus
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OrderedDict of atom objects where the keys are the
template atoms and their values are the consensus atoms from the
query.
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atoms
Get the map of atom objects of consensus atoms.
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OrderedDict of ints where the keys are the template atom indices and
their values are the consensus atom indices from the query.
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atom_indices
Get the map of atom indices of consensus atoms.
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list of unique consensus residue objects for each structure in
self.asl_map. (Order is maintained)
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residues
Get the list of residue objects of
consensus atoms for each structure in self.asl_map.
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list of unique consensus residue indices for each structure in
self.asl_map. (Order is maintained)
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residue_indices
Get the map of residue indices of consensus atoms.
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list of unique consensus molecule objects for each structure in
self.asl_map. (Order is maintained)
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molecules
Get the map of molecule objects of
consensus atoms.
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list of unique consensus molecule indices for each structure in
self.asl_map. (Order is maintained)
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molecule_indices
Get the map of molecule indices of consensus atoms.
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__init__(self,
asl_map,
minimum_number,
dist_cutoff=2.0)
(Constructor)
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- Parameters:
asl_map (tuple of (structure, ASL)) - List of structures and the ASL used to limit the atoms used when
calculating the consensusminimum_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.
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Private method called in __init__. Finds the consensus atom indices
between the template and query.
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_createByAtomProperty(self,
attr,
is_callable=False)
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Private method to get an atom property.
- Parameters:
attr (str) - The attribute to get from the consensus atomsis_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
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ASL_LIGAND
- Value:
'(((m.atoms 5-130)) and not ((ions) or (res.pt ACE ACT ACY BCT BME BOG
CAC CIT CO3 DMS EDO EGL EPE FES FMT FS3 FS4 GOL HEC HED HEM IOD IPA M
ES MO6 MPD MYR NAG NCO NH2 NH3 NO3 PG4 PO4 POP SEO SO4 SPD SPM SUC SUL
TRS )))'
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atoms
Get the map of atom objects of consensus atoms.
- Get Method:
- unreachable.atoms(self)
- Get the map of atom objects of consensus atoms.
- Type:
- OrderedDict of atom objects where the keys are the
template atoms and their values are the consensus atoms from the
query.
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atom_indices
Get the map of atom indices of consensus atoms.
- Get Method:
- unreachable.atom_indices(self)
- Get the map of atom indices of consensus atoms.
- Type:
- OrderedDict of ints where the keys are the template atom indices and
their values are the consensus atom indices from the query.
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residues
Get the list of residue objects of consensus
atoms for each structure in self.asl_map.
- Get Method:
- unreachable.residues(self)
- Get the list of residue objects of consensus
atoms for each structure in
self.asl_map.
- Type:
- list of unique consensus residue objects for each structure in
self.asl_map. (Order is maintained)
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residue_indices
Get the map of residue indices of consensus atoms.
- Get Method:
- unreachable.residue_indices(self)
- Get the map of residue indices of consensus atoms.
- Type:
- list of unique consensus residue indices for each structure in
self.asl_map. (Order is maintained)
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molecules
Get the map of molecule objects of consensus
atoms.
- Get Method:
- unreachable.molecules(self)
- Get the map of molecule objects of consensus
atoms.
- Type:
- list of unique consensus molecule objects for each structure in
self.asl_map. (Order is maintained)
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molecule_indices
Get the map of molecule indices of consensus atoms.
- Get Method:
- unreachable.molecule_indices(self)
- Get the map of molecule indices of consensus atoms.
- Type:
- list of unique consensus molecule indices for each structure in
self.asl_map. (Order is maintained)
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