libio

Handle input and output general operations.

taurenmd.libs.libio.add_prefix_to_path(ipath, prefix)[source]

Add prefix to file path.

Example

>>> mk_frame_path('traj_output.xtc', prefix='my_prefix')
>>> my_prefixtraj_output.xtc

Mind the _ is not placed automatically.

>>> mk_frame_path('traj_output.xtc', prefix='my_prefix_')
>>> my_prefix_traj_output.xtc
Parameters

  • ipath (str or Path) – The file path to alter.

  • prefix (str) – The complete prefix for the file name.

Returns

taurenmd.core.Path() – The new file path.

taurenmd.libs.libio.add_suffix_to_path(ipath, suffix)[source]

Add suffix to file path.

If suffix has extention, updates the path extension, otherwise keeps the original extension.

Examples

>>> mk_frame_path('traj_output.xtc', suffix='my_suffix')
>>> traj_outputmy_suffix.xtc

Mind the underscore is not placed automatically:

>>> mk_frame_path('traj_output.xtc', suffix='_my_suffix')
>>> traj_output_my_suffix.xtc

Updating extensions:

>>> mk_frame_path('traj_output.xtc', suffix='_my_suffix.pdb')
>>> traj_output_my_suffix.pdb
Parameters

  • ipath (str or Path) – The file path to alter.

  • suffix (str) – The complete suffix for the file name, extension should be included in the suffix, extension of the ipath is ignored.

Returns

taurenmd.core.Path() – The new file path.

taurenmd.libs.libio.evaluate_to_slice(*, value=None, start=None, stop=None, step=None)[source]

Evaluate to slice.

If any of start, stop or step is given returns slice(start, stop, step). Otherwise tries to evaluate value to its representative slice form.

Examples

>>> evaluate_to_slice(value='1,100,2')
>>> slice(1, 100, 2)

>>> evaluate_to_slice(start=10)
>>> slice(10, None, None)

>>> evaluate_to_slice(value=(0, 50, 3))
>>> slice(0, 50, 3)

>>> evaluate_to_slice(value=(None, 100, None))
>>> slice(None, 100, None)

>>> #ATTENTION
>>> evaluate_to_slice(value='10')
>>> slice(10, None, None)
>>> # this is different from slice(10)
>>> #though
>>> evaluate_to_slice(value=10)
>>> slice(None, 10, None)
Parameters

  • value (list, tuple, str, None or int) – A human readable value that can be parsed to a slice object intuitively. Defaults to None.

  • start (None or int) – The starting index of the slice (inclusive). Defaults to None.

  • stop (None or int) – The final index of the slice (exclusive). Defaults to None.

  • step (None or int) – Slice periodicity. Defaults to None.

Returns

slice – Python slice object.

Raises

ValueError – If slice can not be computed.

taurenmd.libs.libio.export_data_to_file(xdata, *ydata, fname='results.csv', header='', fmt='{:.3f}', delimiter=',')[source]

Save data to file.

Following the format:

>>> # header
>>> x1,ya1,yb1,yc1
>>> x2,ya2,yb2,yc2
>>> x3,ya3,yb3,yc3

Where x are the elements in xdata, and y* are the elements in the different ydata series.

Parameters

  • xdata (list-like) – Contains the x axis data.

  • ydata (list of list-like) – Contains the y axis data series.

  • fname (str) – The output file path name.

  • header (str) – The commented header of the file. Comment character, like # is not placed, it should be already provided if desired.

  • fmt (str) – The float format. Defaults to {:.3f}.

  • delimiter (str) – The string delimiter between columns. Defaults to ,.

taurenmd.libs.libio.frame_list(len_traj, start=None, stop=None, step=None, flist=None)[source]

Create frame integer list from a length and slice parameters.

Examples

>>> frame_list(10)
>>> list(range(10)) # returns

>>> frame_list(10, start=2, stop=5)
>>> list(range(2, 5)) # returns

>>> frame_list(10, 2, 50)
>>> list(range(2, 10)) # returns

>>> frame_list(10, None, None, 2)
>>> list(range(0, 10, 2)) # returns

>>> frame_list(10, flist='1,2,45,65')
>>> [1, 2, 45, 65]

>>> frame_list(10, flist=[1, 2, 45, 65])
>>> [1, 2, 45, 65]

>>> frame_list(10, flist=['1', '2', '45', '65'])
>>> [1, 2, 45, 65]

>>> frame_list(None, flist=['1', '2', '45', '65'])
>>> [1, 2, 45, 65]
Parameters

  • len_traj (int) – The length to evaluate. Normally this is the length of the trajectory.

  • start (int or None, optional) – The start index for the frame list after length evaluation. Defaults to None.

  • stop (int or None, optional) – The stop index for the frame list after length evaluation. Defaults to None.

  • step (int or None, optional) – the step index for the frame list after length evaluation. Defaults to None.

  • flist (list-like, or comma-separated string, optional) – The list of specific frames. Defaults to None.

Returns

list – The resulting frame list.

taurenmd.libs.libio.frame_slice(start=None, stop=None, step=None)[source]

Create a slice object from parameters.

Logs the created slice object.

Returns

Slice Object – The slice object created from slice(start, stop, step)

taurenmd.libs.libio.get_number(path)[source]

Extract tail number from path.

Examples

>>> get_number('traj_1.dcd')
>>> 1

>>> get_number('traj_3.dcd')
>>> 3

>>> get_number('traj_1231.dcd')
>>> 1231

>>> get_number('traj_0011.dcd')
>>> 11

>>> get_number('traj_1_.dcd')
>>> 1

>>> get_number('traj_20200101_1.dcd')
>>> 1
Parameters

path (str or Path obj) – The path to evaluate.

Returns

int – The tail integer of the path.

taurenmd.libs.libio.mk_frame_path(ipath, frame=0, ext='.pdb', leading=0, suffix=None)[source]

Create the path name for a frame.

Given an input_path ipath (usually the name of the trajectory), create the corresponding frame file name.

Example

>>> mk_frame_path('traj_output.xtc')
>>> traj_output_frame0.pdb

>>> mk_frame_path('traj_output.xtc', frame=4, leading=4)
>>> traj_output_frame0004.pdb
Parameters

  • ipath (str or Path) – The file path. Normally, trajectory file path.

  • frame (int, optional) – The frame to label the new path. Defaults to 0.

  • ext (str, optional) – The returned file desired extension. Defaults to .pdb.

  • leading (int) – The leading zeros to left append to the frame number. Defaults to 0.

  • suffix (str) – Complete specifications of the desired suffix. If suffix is given, frame and ext and leading are ignored and add_suffix_to_path() is used directly.

Returns

taurenmd.core.Path() – The new file path.

taurenmd.libs.libio.parse_top_output(top_output, traj_output=None)[source]

Parse different output definitions for topology output file name.

If top_output startswith _ uses :py:func:add_suffix_to_path. If top_output endswith _ uses :py:func:add_prefix_to_path. Else: Return Path object of top_output.

Parameters

  • top_output (str or Path) – The string to evaluate.

  • traj_output (str or Path) – The trajectory output file name. Return value depends on this parameters.

Returns

taurenmd.core.Path() – The new topology file path.

taurenmd.libs.libio.report_input(topology, trajectories)[source]

Report on topology and trajectory file paths used as input.

taurenmd.libs.libio.sort_numbered_input(*inputs)[source]

Sort input paths to tail number.

If possible, sort criteria is provided by get_number(). If paths do not have a numbered tag, sort paths alphabetically.

Parameters

*inputs (str of Paths) – Paths to files.

Returns

list – The sorted pathlist.