prolint2.computers.contacts#

Authors:

Daniel P. Ramirez & Besian I. Sejdiu

Year:

2022

Copyright:

MIT License

class prolint2.computers.contacts.SerialContacts(universe, query, database, cutoff=7.0, **kwargs)[source]#

Class to get the distance-based contacts starting from two AtomGroups using a serial approach.

It inherits from the MDAnalysis AnalysisBase class.

Parameters:

  • universe (MDAnalysis.Universe) – The MDAnalysis Universe object.

  • query (MDAnalysis.AtomGroup) – AtomGroup representing the query.

  • database (MDAnalysis.AtomGroup) – AtomGroup representing the database.

  • cutoff (float) – The distance cutoff (default from parameters_config).

  • kwargs (dict) – Additional keyword arguments.

prolint2.computers.distances#

Authors:

Daniel P. Ramirez & Besian I. Sejdiu

Year:

2022

Copyright:

MIT License

class prolint2.computers.distances.SerialDistances(universe, query, database, lipid_id, residue_id, frame_filter, **kwargs)[source]#

Class to get the distance-based contacts starting from two AtomGroups using a serial approach.

It inherits from the MDAnalysis AnalysisBase class.

Parameters:

  • universe (MDAnalysis.Universe) – The MDAnalysis Universe.

  • query (MDAnalysis.AtomGroup) – AtomGroup to query.

  • database (MDAnalysis.AtomGroup) – AtomGroup to use as the database.

  • lipid_id (int) – Residue ID for the lipid group.

  • residue_id (int) – Residue ID for the query group.

  • frame_filter (list) – List of frame indices to analyze.

  • kwargs (dict) – Additional keyword arguments.

class prolint2.computers.distances.TwoPointDistances(universe, query, database, lipid_id, residue_id, lipid_sel=None, residue_sel=None, unit='frame', **kwargs)[source]#

Initialize the TwoPointDistances analysis.

Parameters:

  • universe (MDAnalysis.Universe) – The molecular dynamics universe.

  • query (MDAnalysis.AtomGroup) – The query object for comparison.

  • database (MDAnalysis.AtomGroup) – The database object for comparison.

  • lipid_id (int) – The ID of the lipid to consider.

  • residue_id (int) – The ID of the residue to consider.

  • lipid_sel (str) – The optional selection for the lipid atom.

  • residue_sel (str) – The optional selection for the residue atom.

  • unit (str) – The unit for calculating distances (“frame” or “time”).

  • **kwargs –

    Additional keyword arguments.

This method sets up the analysis and initializes necessary attributes.

class prolint2.computers.payload.ServerPayload(contacts, ts)[source]#

Class that provides the data for the dashboard.

Parameters:

  • contacts (ContactsProvider) – The contacts provider object.

  • ts (Universe) – The universe object.

get_payload()[source]#

Return the payload.

property payload#

The payload.

residue_contacts(lipid_type: Optional[str] = None, metric='sum', dt=1, totaltime=1)[source]#

Compute residue contacts.