mdciao.utils.contact_matrix¶
Functions related to contact-map operations (WIP)
Functions
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Return a matrix with the contact frequency for all possible contacts over all available frames :param trajectories: :type trajectories: list of obj:mdtraj.Trajectory :param n_frames_per_traj: Stride the trajectories so that, on average, this number of frames is used to compute the contacts :type n_frames_per_traj: int, default is 20 :param mdcontacts_kwargs: |
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Return a matrix with the contact frequency for all possible contacts over all available frames :param trajectories: :type trajectories: list of obj:mdtraj.Trajectory :param n_frames_per_traj: Stride the trajectories so that, on average, this number of frames is used to compute the contacts :type n_frames_per_traj: int, default is 20 :param mdcontacts_kwargs: |
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Returns the full contact map of residue-residue contacts from a list of trajectory files |
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mdciao.utils.contact_matrix.
contact_matrix
(trajectories, cutoff_Ang=3, n_frames_per_traj=20, **mdcontacts_kwargs)¶ Return a matrix with the contact frequency for all possible contacts over all available frames :param trajectories: :type trajectories: list of obj:mdtraj.Trajectory :param n_frames_per_traj: Stride the trajectories so that, on average, this number of frames
is used to compute the contacts
- Parameters
mdcontacts_kwargs –
- Returns
ctc_freq
- Return type
square 2D np.ndarray
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mdciao.utils.contact_matrix.
contact_matrix_slim
(trajectories, cutoff_Ang=3, **mdcontacts_kwargs)¶ Return a matrix with the contact frequency for all possible contacts over all available frames :param trajectories: :type trajectories: list of obj:mdtraj.Trajectory :param n_frames_per_traj: Stride the trajectories so that, on average, this number of frames
is used to compute the contacts
- Parameters
mdcontacts_kwargs –
- Returns
ctc_freq
- Return type
square 2D np.ndarray
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mdciao.utils.contact_matrix.
xtcs2ctc_mat_dict
(xtcs, top, list_ctc_cutoff_Ang, stride=1, return_time=False, res_COM_cutoff_Ang=25, chunksize=100, n_jobs=1, progressbar=False, **mdcontacts_kwargs)¶ Returns the full contact map of residue-residue contacts from a list of trajectory files
- Parameters
xtcs (list of strings) – list of filenames with trajectory data. Typically xtcs, but can be any type of file readable by :obj:mdtraj
top (str or
mdtraj.Topology
) – Topology that matches :obj:xtcsstride (int, default is 1) – Stride the trajectory data down by this value
chunksize (integer, default is 100) – How many frames will be read into memory for computation of the contact time-traces. The higher the number, the higher the memory requirements
n_jobs (int, default is 1) – to how many processors to parallellize
- Returns
- Return type
ctc_mat