Modify trajectory

pytraj.rmsd(traj=None, mask='', ref=0, ref_mask='', nofit=False, mass=False, update_coordinate=True, frame_indices=None, top=None, dtype='ndarray')

compute rmsd

Parameters:

traj : Trajectory-like

mask : str or 1D array-like of string or 1D or 2D array-like

Atom mask/indices

ref : {Frame, int}, default=0 (first frame)

Reference frame or index.

ref_mask: str, optional

if given, use it instead of mask

nofit : bool, default False

if False, perform fitting (rotation and translation). if traj is mutable, its coordinates will be updated if True, not fitting.

mass : bool, default False

if True, compute mass-weighted rmsd

update_coordinate : bool, default True

if True, coordinates will be updated. But this only apply to mutable Trajectory if False (same as nomod in cpptraj), no modification

frame_indices : int 1D array-like, default None

if not None, only compute rmsd for given frame indices

top : {Topology, str}, default None, optional

dtype : return data type, default=’ndarray’

Notes

  • if traj and ref has diffrent n_atoms, make sure to update ref.top
  • you can use pytraj.rmsd to superpose structure (use update_coordinate=True)

Examples

>>> import pytraj as pt
>>> traj = pt.datafiles.load_trpcage()
>>> # all atoms, do fitting, using ref=traj[-3]
>>> data = pt.rmsd(traj, ref=-3)
>>> # rmsd for 3 maskes, do fitting, using ref=traj[0] (defaul)
>>> data = pt.rmsd(traj, mask=['@CA', '@C', ':3-18@CA'], dtype='dataset')
>>> # rmsd to first frame, use mass ':3-13' but do not perorm fitting
>>> data= pt.rmsd(traj, ref=traj[0], mask=':3-13', nofit=True)
>>> # use atom indices for mask
>>> data= pt.rmsd(traj, ref=traj[0], mask=range(40), nofit=True)
>>> # compute rmsd (and align) with reference having different atoms
>>> trpcage_traj = pt.datafiles.load_trpcage()[:]
>>> tz2_traj = pt.datafiles.load_tz2()[:1]
>>> data = pt.rmsd(trpcage_traj, mask='@1-10', ref=tz2_traj, ref_mask='@11-20')
>>> data
array([ 2.16203842,  2.28859396,  2.15817654, ...,  2.20767189,
        2.30087764,  1.92654945])
Notes
-----
if ``traj`` is mutable and update_coordinate=True, its coordinates will be updated.
pytraj.superpose(traj, *args, **kwd)
pytraj.center(traj=None, mask='', center='box', mass=False, top=None, frame_indices=None)

Center coordinates in mask to specified point.

Parameters:

traj : Trajectory-like or Frame iterator

mask : str, mask

center : str, {‘box’, ‘origin’, array-like}, default ‘box’

if ‘origin’, center on coordinate origin (0, 0, 0) if ‘box’, center on box center if array-like, center on that point

mass : bool, default: False

if True, use mass weighted

top : Topology, optional, default: None
Returns:

updated traj

See also

pytraj.translate

Examples

>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> # load all frames to memory so we can 'mutate' them
>>> traj = traj[:]
>>> # all atoms, center to box center (x/2, y/2, z/2)
>>> traj = pt.center(traj)

>>> # center at origin, use @CA
>>> traj = pt.center(traj, '@CA', center='origin')

>>> # center to box center, use mass weighted
>>> traj = pt.center(traj, mass=True)
>>> traj = pt.center(traj, ':1', mass=True)
pytraj.translate(traj=None, command='', frame_indices=None, top=None)

translate coordinate

Examples

>>> import pytraj as pt
>>> # load to mutable trajectory by `load` method
>>> from pytraj.testing import get_fn
>>> fn, tn = get_fn('tz2')
>>> traj = pt.load(fn, tn)
>>> # do transform traj and return itself
>>> traj = pt.translate(traj, '@CA x 120.')
pytraj.scale(traj=None, command='', frame_indices=None, top=None)

Examples

>>> import pytraj as pt
>>> # load to mutable trajectory by `load` method
>>> from pytraj.testing import get_fn
>>> fn, tn = get_fn('tz2')
>>> traj = pt.load(fn, tn)
>>> # do transform traj and return itself
>>> traj = pt.scale(traj, '@CA x 1.2')
pytraj.rotate(traj=None, command='', frame_indices=None, top=None)

Notes

rotate is an alias of do_rotation

Examples

>>> import pytraj as pt
>>> # load to mutable trajectory by `load` method
>>> from pytraj.testing import get_fn
>>> fn, tn = get_fn('tz2')
>>> traj = pt.load(fn, tn)
>>> # do transform traj and return itself
>>> traj = pt.rotate(traj, 'x 90')
pytraj.autoimage(traj, mask='', frame_indices=None, top=None)

perform autoimage and return the updated-coordinate traj

>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()[:]
>>> traj = pt.autoimage(traj)
pytraj.transform(traj, by, frame_indices=None)

transform pytraj.Trajectory by a series of cpptraj’s commands

Parameters:

traj : Mutable Trajectory

by : list of cpptraj commands

frame_indices : {None, array-like}, default None

if not None, perform tranformation for specific frames.
Returns:

transformed Trajectory. Trajectory’s coordinates will be inplace-updated

Examples

>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> # perform 'autoimage', then 'rms', then 'center'
>>> traj = pt.transform(traj[:], by=['autoimage', 'rms', 'center :1-5'])
pytraj.rotate_dihedral(traj=None, mask='', top=None)
Returns:updated traj

Notes

Syntax and method’s name might be changed

Examples

>>> import pytraj as pt
>>> traj = pt.datafiles.load_rna()[:]
>>> traj = pt.rotate_dihedral(traj, "3:chin:120") # rotate chin of res 3 to 120 deg
>>> traj = pt.rotate_dihedral(traj, "1:O4':C1':N9:C4:120") # rotate dihedral with given mask
pytraj.replicate_cell(traj=None, mask='', direction='all', frame_indices=None, top=None)

create a trajectory where the unit cell is replicated in 1 or more direction (up to 27)

Parameters:

traj : Trajectory-like or Frame iterator

mask : str, default: “”

if default, using all atoms else: given mask

direction: {‘all’, ‘dir’} or list/tuple of <XYZ> (below)

if ‘all’, replicate cell once in all possible directions if ‘dir’, need to specify the direction with format ‘dir <XYZ>’, where each X (Y, Z) is either 0, 1 or -1 (see example below)

top : Topology, optional, default: None
Returns:

traj : pytraj.Trajectory

Examples

>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> new_traj = pt.replicate_cell(traj, direction='all')
>>> new_traj = pt.replicate_cell(traj, direction='dir 001 dir 111')
>>> new_traj = pt.replicate_cell(traj, direction='dir 001 dir 1-10')
>>> new_traj = pt.replicate_cell(traj, direction='dir 001 dir 1-10')

>>> # similiar usage
>>> new_traj = pt.replicate_cell(traj, direction=('001', '0-10'))
>>> new_traj = pt.replicate_cell(traj, direction=['001', '0-10'])