Module rxn_path

Classes and functions for generating reaction paths.

Classes

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ParserWrapper
Manages the argparse module to parse user command line arguments.

CheckInput
Check user input.

Coord
Manage the properties of an internal coordinate.

InternalCoords
Manage the internal coordinates of a structure.

ReactionCoords
Manage reaction coordinates.

Point
Collect properties of reaction path points.

ReactionPath
Generate reaction path.

Functions

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int, int, float

max_pair_vdw_distance(astructure)
Find the largest atom-atom VDW distance in a structure.

int

add_temp_hydrogen(astructure, index)
To the given structure add a temporary hydrogen to the atom with the given index.

Variables

[hide private]

__doc__ = ...

_version = '$Revision 0.0 $'

__package__ = 'schrodinger.application.matsci'

Function Details

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max_pair_vdw_distance(astructure)

Find the largest atom-atom VDW distance in a structure.

Parameters:

astructure (schrodinger.structure.Structure) - the structure

Returns: int, int, float

atom1, atom2, maxdistance, atom1 and atom2 are the first and second atom indicies and maxdistance is the largest distance. If input structure is a single atom then just return that atom index twice followed by twice its VDW radius, i.e. the atomic diameter.

add_temp_hydrogen(astructure, index)

To the given structure add a temporary hydrogen to the atom with the given index. This function is more robust than structutils.build.add_hydrogens.

Parameters:

astructure (schrodinger.structure.Structure) - the structure containing the atom to which a hydrogen will be added
index (int) - the index of the atom to which to add the hydrogen

Returns: int

the index of the added temporary hydrogen

Variables Details

[hide private]

doc

Value:

"""
Classes and functions for generating reaction paths.

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