Matrix

pytraj.analysis.matrix.dist(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.idea(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.correl(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.covar(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.mwcovar(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.distcovar(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array
pytraj.analysis.matrix.dihcovar(traj=None, mask='', top=None, dtype='ndarray', mat_type='full', frame_indices=None)

Compute matrix

Parameters:

traj : Trajectory-like

mask : cpptraj mask

top : Topology, optional, default None

mat_type : str, {‘full’, ‘half’, ‘cpptraj’}, default ‘full’

if ‘full’: 2D full matrix if ‘half’: triangular matrix if ‘cpptraj’: 1D array