https://github.com/berquist/personal_scripts
Personal scripts, mostly for computational chemistry analysis.
https://github.com/berquist/personal_scripts
computational-chemistry python
Last synced: 5 months ago
JSON representation
Personal scripts, mostly for computational chemistry analysis.
- Host: GitHub
- URL: https://github.com/berquist/personal_scripts
- Owner: berquist
- Created: 2015-06-11T03:52:28.000Z (about 11 years ago)
- Default Branch: main
- Last Pushed: 2025-12-05T17:17:09.000Z (7 months ago)
- Last Synced: 2025-12-09T04:48:38.382Z (7 months ago)
- Topics: computational-chemistry, python
- Language: Python
- Homepage:
- Size: 634 KB
- Stars: 7
- Watchers: 3
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
All my scripts jumbled together. Subfolders are machine-specific.
With the `__init__.py`, the directory is a Python module, and the
functions in each Python script can be used elsewhere.
## Python Requirements
### Newish Python standard library modules:
```
argparse
```
### External modules:
```
docopt
matplotlib
numpy
pandas
```
### External quantum chemistry modules:
```
cclib
```
### Personal repositories:
```
orcaparse
```
# Plotting in VMD
Interactive/graphical:
``` bash
# in normal terminal:
vmd_pretty_cubes.py --nsurf=1
vmd -e vmd.load_all_plt.vmd
# in VMD terminal:
source vmd.plot_all.vmd
# shell command, in either terminal:
./vmd.convert.bash
```
Text-only with no repositioning of the scene:
``` bash
# in normal terminal:
vmd_pretty_cubes.py --nsurf=1
cat vmd.load_all_plt.vmd vmd.plot_all.vmd > vmd.do_all.vmd
echo "quit" >> vmd.do_all.vmd
vmd -e vmd.do_all.vmd -dispdev text
./vmd.convert.bash
```