Module order_parameter_mod

Utilities for order parameter analysis.

Classes

AslException

DipoleDirector
Manage a dipole director.

MomentOfInertiaDirector
Manage a moment of inertia director.

UniqueSmartsDirector
Manage a unique SMARTS director.

SmartsDirector
Manage a SMARTS director.

Descriptor
Manage a descriptor.

Director
Manage a director.

OrderParameter
Manage order parameter analysis.

Functions

list

get_trj_from_cms_file(cms_file)
Return the trajectory from the given .cms file.

list

get_descriptors_from_file(descriptors_file)
Return a list of descriptors from the given descriptors file.

Variables

__doc__ = ...

ORDER_PARAMETER_OUTPUT_FILES_PROP = 's_matsci_order_parameter_...

ORDER_PARAMETER_OUTPUT_FILES_SEP = ','
hash(x)

RESULTS_FILE_EXT = 'csv'

OUT_FILE_TAG = 'op'

INDEX_NAME = 'Frame'

__package__ = 'schrodinger.application.matsci'

Function Details

Return the trajectory from the given .cms file.

Parameters:

Returns: list

contains the trajectory as a list of schrodinger.application.desmond.packages.traj.Frame

Return a list of descriptors from the given descriptors file.

Parameters:

descriptors_file (str) - .json file containing specifications for descriptors, i.e. ways to determine vectors used in computing the order parameters with respect to the director, a specification includes information like name, group, ASL, type, and SMARTS (can be a path)

Returns: list

contains Descriptor

Variables Details

Value:

"""
Utilities for order parameter analysis.

Copyright Schrodinger, LLC. All rights reserved.
"""

Value:

's_matsci_order_parameter_output_files'