mdciao.contacts.Residues¶
-
class
mdciao.contacts.
Residues
(res_idxs_pair, residue_names, anchor_residue_idx=None, consensus_labels=None, top=None)¶ Container for
mdtraj.Topology.Residues
objects-
__init__
(res_idxs_pair, residue_names, anchor_residue_idx=None, consensus_labels=None, top=None)¶ - Parameters
res_idxs_pair (iterable of len two) – two integers representing the residue serial index (residxs)
residue_names (iterable of len two) – two strings with the residue names
anchor_residue_idx –
consensus_labels –
top –
Methods
__init__
(res_idxs_pair, residue_names[, …])- param res_idxs_pair
two integers representing the residue serial index (residxs)
Attributes
The index [0,1] of the anchor residue
returns: :rtype: str, anchor residue if anchor residue index is provided else None
returns: :rtype: int, anchor residue index if passed else None(default)
Labels derived from GPCR, CGN or other type of consensus nomenclature.
serial indices of the pair of residues
returns: * list, for each residue index in the residue contact pair, the corresponding residue name from the topology file. * example ([‘GLU30’,’VAL212’])
returns: * list, for each residue name in the residue contact pair, the corresponding short residue name from the topology file. * example ([‘E30’, ‘V212’])
returns: :rtype: str, partner residue if partner residue index is provided else None
returns: :rtype: int, partner residue if passed else (default)
-
property
anchor_index
¶ The index [0,1] of the anchor residue
-
property
anchor_residue
¶ returns: :rtype: str, anchor residue if anchor residue index is provided else None
-
property
anchor_residue_index
¶ returns: :rtype: int, anchor residue index if passed else None(default)
-
property
consensus_labels
¶ Labels derived from GPCR, CGN or other type of consensus nomenclature. They were parsed at initialization
TODO
Warning
This property can be changed externally by the method
ContactGroup.relabel_consensus
. This is bad practice and probably anti-pattern but ATM there’s no way around it
-
property
idxs_pair
¶ serial indices of the pair of residues
- Returns
- Return type
list of residue index pair passed
-
property
names
¶ returns: * list, for each residue index in the residue contact pair, the corresponding residue name from the topology file. * example ([‘GLU30’,’VAL212’])
-
property
names_short
¶ returns: * list, for each residue name in the residue contact pair, the corresponding short residue name from the topology file. * example ([‘E30’, ‘V212’])
-
property
partner_index
¶
-
property
partner_residue
¶ returns: :rtype: str, partner residue if partner residue index is provided else None
-
property
partner_residue_index
¶ returns: :rtype: int, partner residue if passed else (default)
-