schrodinger.trajectory.order_parameters module

A modue of classes for calculating order parameters

Copyright Schrodinger Inc. All rights reserved. Contributores: Dmitry Lupyan

class schrodinger.trajectory.order_parameters.OrderParameter(director_type, descriptor_type, atomsel, *args, **kwargs)

Bases: schrodinger.trajectory.analysistool.AnalysisTool

Given the Direcator (local or global), and the descriptor (local or global), calculate the order parameter

|S_k| = | 1/N sum( ((3 * M dot m)^2 -1) / 2) |

Where ‘M’ is the director vector and ‘m’ is the descriptor vectors

director_dict = {'Y': [0.0, 1.0, 0.0], 'Z': [0.0, 0.0, 1.0], 'moment_of_intertia': <function get_moment_direction>, 'system_dipole': <function get_dipole_direction>, 'X-axis': [1.0, 0.0, 0.0], 'X': [1.0, 0.0, 0.0], 'Y-axis': [0.0, 1.0, 0.0], 'dipole': <function get_dipole_direction>, 'Z-axis': [0.0, 0.0, 1.0]}

doFrameInit(frame)

Initialize analysis. this only runs once.

getFrameResults()

getLabel()

plot(*args, **kwargs)

A generic matplotlib 2D plot implementation.

processFrame(frame)

smarts_dict = {'CH': '([CX3,CX4][#1])'}

schrodinger.trajectory.order_parameters.get_CH_dict(st, tail_type)

Given the lipid tail type (sn1 or sn2) get back the connonical lipid carbon atom names and the dictionary of all the hydrogens that attached to them :type st: schrodinger.structure :param st: Structure object

Parameters:tail_type (str) – lipid tail type: ‘all’, ‘sn1’ or ‘sn2’ Returns:tuple of pdb carbon list and dictionary of hydrogen atoms attache the carbon

:rtype str, dict{(carbon_pdb_idx, tuple(carbon_idx, hydrogen_idx)}

schrodinger.trajectory.order_parameters.get_dipole_direction(st)

Return unit vector of a structure’s dipole :type st: schrodinger.structure :param st: Structure object

Returns:unit vector of the dipole Return type:numpy.array

schrodinger.trajectory.order_parameters.get_moment_direction(st)

Return the principle moment (of intertia) of a given structure :type st: schrodinger.structure :param st: Structure object

Returns:unit vector Return type:list

schrodinger.trajectory.order_parameters.get_vectors(st, atom_pair)

Return a list of unit vectors that matches specific pair of atoms :type st: schrodinger.structure :param st: Structure object

Parameters:st – List of two atom indices Returns:unit vector Return type:list