icsel

This module contains the get_sets method as well as symmetry functions for selecting internal coordinates

icsel.Kemalian_metric(matrix, Diag_elements, counter, intfreq_penalty, intfc_penalty, args) → float

Given a matrix calculates the metric implemented in Nomodeco

icsel.are_two_elements_same(tup1, tup2) → bool

For two given tuples checks if they are the same and return True/False

icsel.get_different_elements(tup1, tup2) → list

Given two tuples calculates the difference in elements and outputs as list

icsel.get_sets(idof, out, atoms, bonds, angles, linear_angles, out_of_plane, dihedrals, specification) → dict

get_sets is the decicion tree of nomodeco where for a given molecular topology all possible sets are generated

Attributes:

idof:

a integer with the vibrational degrees of freedom

out:

the output file of nomodeco

atoms:

a object of the molecule class

bonds:

a list of tuples containing bonds

angles:

a list of tuples containing angles

linear_angles:

a list of tuples containing linear angles

out_of_plane:

a list of tuples containing oop’s

dihedrals:

a list of tuples containing dihedrals

specficiation:

the specification dictionary of nomodeco

Returns:

a dictionary of all the possible IC sets this is generated using the Topology module