rodolfoferro / mol_transform

Molecular transformations for graphic displaying using Cartesian coordinates.

mol_transform 💻⚗️

Molecular transformations for graphic displaying using Cartesian coordinates.

How to use it

Generalities:

The -f tag stands for file and will open the file named input.xyz, center the first position into the origin and translate the rest of positions to maintain the structure. The -o tag stands for output, meaning that you need to add the output path (in our example is output.xyz). Both tags (-f and -o) are needed.

• Centering

Simply run:

python mol_transform.py -f input.xyz -o output.xyz

PLEASE OBSERVE that we won't need need any extra parameters for a molecule translation to the center of our Cartesian space.

• Translating

To translate a molecule using a specific vector (a, b, c), we'll need to use the -t tag (that stands to translate) and run:

python mol_transform.py -f input.xyz -o output.xyz -t -a -b -c

For instance, we have the position (0.47050, -0.66520, -1.79270) in our file C20.xyz and if we want to translate it to the origin (and the rest of the positions to maintain the structure), we would have to run:

python mol_transform.py -f C20.xyz -o C20_translated.xyz -t -0.47050 0.66520 1.79270

PLEASE OBSERVE that we need the inverted signs of each value of the position, since we want a negative translation to that position. Also, in this example we will create the file C20_translated.xyz with the translated positions.

• Scaling

To scale the molecule along the 3-axis by a vector (a, b, c), we'll need to use the -s tag (that stands to scale) and run:

python mol_transform.py -f input.xyz -o output.xyz -s a b c

For instance in our file C20.xyz, if we want to scale it to the double of size we would have to run:

python mol_transform.py -f C20.xyz -o C20_scaled.xyz -s 2 2 2

---

LICENSE

MIT License

Copyright (c) 2017 Rodolfo Ferro

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.