Module order_parameters

A modue of classes for calculating order parameters

Classes

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OrderParameter
Given the Direcator (local or global), and the descriptor (local or global),...

Functions

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numpy.array

get_dipole_direction(st)
Return unit vector of a structure's dipole

list

get_moment_direction(st)
Return the principle moment (of intertia) of a given structure

list

get_vectors(st, atom_pair)
Return a list of unit vectors that matches specific pair of atoms

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: C{schrodinger.structure} @param st: Structure object

Variables

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__package__ = 'schrodinger.trajectory'

Function Details

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get_dipole_direction(st)

Return unit vector of a structure's dipole

Parameters:

st (schrodinger.structure) - Structure object

Returns: numpy.array

unit vector of the dipole

get_moment_direction(st)

Return the principle moment (of intertia) of a given structure

Parameters:

st (schrodinger.structure) - Structure object

Returns: list

unit vector

get_vectors(st, atom_pair)

Return a list of unit vectors that matches specific pair of atoms

Parameters:

st (schrodinger.structure) - Structure object
st (schrodinger.structure) - List of two atom indices
atom_pair (list)

Returns: list

unit vector

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: C{schrodinger.structure}
@param st: Structure object

@type tail_type: str
@param tail_type: lipid tail type: 'all', 'sn1' or 'sn2'

@return: tuple of pdb carbon list and dictionary of hydrogen atoms attache
         the carbon
@rtype L{str}, dict{(carbon_pdb_idx, L{tuple(carbon_idx, hydrogen_idx)}}