https://github.com/vtlim/misc

Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.
https://github.com/vtlim/misc

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Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.

• Host: GitHub
• URL: https://github.com/vtlim/misc
• Owner: vtlim
• Created: 2017-03-07T06:43:04.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2020-05-01T08:09:05.000Z (over 4 years ago)
• Last Synced: 2024-10-17T05:33:19.844Z (2 months ago)
• Language: Python
• Homepage:
• Size: 1.17 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        

# Contents

This file last updated: Nov 9 2018  

* Directories

  * `examples/` 

  * `oechem/` 

  * `pca-viewer/` 

  * `vmd/`

  * `xmgrace/`

* Scripts

  * `awksed.py` - Example application to process GROMACS `.top` files to add lines for dihedral restraint.  

    * Example:  

      `python awksed.py -i $i.top -s '[ moleculetype ]' -c 1 -a $'[ dihedral_restraints ]\n; atom1 a2 a3 a4 type=1 phi(ref) dphi kfactor\n4 3 2 8 1 $i 0 300\n' -r '$i' -p -1 -o $i.top`

  * `column_avg.py` 

  * `column_sum.py` 

  * `plotBar.py` - Customizable bar plots.

  * `plotScatter.py`

  * `plotXY.py` - Generates XY line plots from input ASCII data file of one `x` column and one or more `y` columns. This script can:

    * Subsample based on correlation time

    * Subsample based on running averages

    * Take in file of uncertainties to plot error bars

    * Separate a long xy data series into many line plots

* High-level view of contents

```

.

├── awksed.py

├── column_avg.py

├── column_sum.py

├── examples

│   ├── column_avg

│   ├── column_sum

│   ├── plotBar

│   ├── plotScatter

│   └── plotXY

├── oechem

│   ├── am1wib.py

│   ├── charge_mols.py

│   ├── combineSDF.py

│   ├── examples

│   ├── plotMultSDF.py

│   ├── plotSDF.py

│   └── README.md

├── openTabs.sh

├── pca-viewer

├── plotBar.py

├── plotScatter.py

├── plotXY.py

├── README.md

├── vmd

│   ├── drawBox.tcl

│   ├── move_atoms.tcl

│   ├── pbchelp.tcl

│   ├── README.md

│   └── wrapXY.tcl

└── xmgrace

    ├── add2.com

    ├── hist.com

    ├── README.md

    ├── runavg2.com

    ├── view2.par

    └── view2runavg.par

```