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Orient molecule Build Status

Provides a python script to perform routine manipulations of .xyz coordinate files used in quantum chemistry. This script started out as Python practice but ended up being quite useful.

Usage

Give the script a filename and a list of operations and it will operate on the file and print the results to the screen. For example

orient.py water.xyz -tx 2.0 -rz 90.0 -ty -0.2

will transform the molecule found in water.xyz by

  • translating by 2.0 Angstroms in the x direction
  • rotating 90 degrees about the z axis
  • translating by -0.2 Angstrom in the y direction

All operations are composed before applying to the molecule when possible, so the total operation count is kept down.

Capabilities

  • translations
    • by any specified vector
    • center of mass to origin
  • rotations
    • about a cartesian axis
    • about a user defined vector
    • about the vector defined by a pair of atoms
  • compound transformations:
    • orient:
      • translate center of mass to origin
      • principle axes along cartesian axes
    • align: given three atoms
      • translate midpoint of atoms 1 and 2 to origin
      • rotate so atoms 1 and 2 lie along x axis, and all three atoms define xy plane

Requirements

  • numpy

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Python script for command-line manipulation of molecules

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