pylipid.util.get_traj_info

pylipid.util.get_traj_info(traj, lipid=None, lipid_atoms=None, resi_offset=0, nprot=1, protein_ref=None, lipid_ref=None)[source]

Get trajectory information regarding atom/residue index and topologies.

Parameters

  • traj (mdtraj.Trajectory) – A mdtraj.Trajectory object.

  • lipid (str or None) – The residue name of the lipid to check.

  • lipid_atoms (a list of str; opt) – The names of lipid atoms that are used to define lipid interaction and lipid binding sites. Default is None, that is all the lipid atoms will be used for calculation.

  • resi_offset (int, optional, default=0) – Shift of residue index. The new residue index (i.e. the original index + resi_offset) will be used in all the generated data.

  • nprot (int, optional, default=1) – Number of protein copies in the systems. If nprot >= 2, the protein copies need to be identical, and the generated data will be the averages of the copies.

  • protein_ref (None or mdtraj.Trajectory, optional, default=None) – A mdtraj.Trajectory object that stores the topology and coordinates of a copy of the protein structure.

  • lipid_ref (None or mdtraj.Trajectory, optional, default=None) – A mdtraj.Trajectory object that stores the topology and coordinates of a lipid molecule structure.

Returns

  • traj_info (dict) – A dictionary that contains the topology information of traj.

  • protein_ref (mdtraj.Trajectory) – A mdtraj.Trajectory object that stores the topology and coordinates of a copy of the protein structure.

  • lipid_ref (mdtraj.Trajectory) – A mdtraj.Trajectory object that stores the topology and coordinates of a lipid molecule structure.