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[, ...])

Parameters:

res_idxs_pair (iterable of len two) -- two integers representing the residue serial index (residxs)

Attributes

`anchor_index`	The index [0,1] of the anchor residue
`anchor_residue`	rtype: str, anchor residue if anchor residue index is provided else None
`anchor_residue_index`	rtype: int, anchor residue index if passed else None(default)
`consensus_labels`	Labels derived from GPCR, CGN or other type of consensus nomenclature.
`idxs_pair`	serial indices of the pair of residues
`names`	returns: * list, for each residue index in the residue contact pair, the corresponding residue name from the topology file. * example (['GLU30','VAL212'])
`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'])
`partner_index`
`partner_residue`	rtype: str, partner residue if partner residue index is provided else None
`partner_residue_index`	rtype: int, partner residue if passed else (default)

property anchor_index: The index [0,1] of the anchor residue

property anchor_residue: rtype: str, anchor residue if anchor residue index is provided else None

property anchor_residue_index: 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

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: rtype: str, partner residue if partner residue index is provided else None

property partner_residue_index: rtype: int, partner residue if passed else (default)