Utils

A lightweight collection of scripts and small tools I use for data analysis, plotting, file handling, and other routine research tasks.
Nothing fancy - just a repo to keep useful scripts in one place, make them reusable, and avoid rewriting the same thing every few months.

Structure

utils/
├── quickplot/                       # plotting scripts, figure templates, quick visualization tools
│   ├── ir-raman/                    # main.m plots all ir/raman spectral data in './data'
│   └── uv/                          # main.m plots all uv spectral data in './data'
├── render/                          # molecular-graphics presets
│   ├── chimera/                     # UCSF Chimera presets (.cmd)
│   ├── chimerax/                    # ChimeraX ports of the same presets (.cxc)
│   └── axes.bild                    # XYZ reference-frame triad at the origin
├── misc/                            # one-off helpers
│   ├── top2charges/
│   │   └── top2vmdcharges.sh        # GROMACS .top/.itp -> '$sel set charge {...}' for VMD IR spectra
│   └── fchk2dipole/
│       └── fchk2dipole.py           # Gaussian .fchk -> geometry (.xyz) + dipole & axes (.bild)
└── workflow/                        # batch runners, automation helpers

quickplot

MATLAB spectra plotting, config-driven. uv/ and ir-raman/ each read every data file in their ./data folder and plot it - uv/main.m for UV-Vis, ir-raman/main.m for IR and Raman. Set the defaults in config.m, or use the quick toggles at the top of main.m (overlay vs stacked, normalization, colors, axis limits), then run main.m.

render

UCSF Chimera presets live in render/chimera/ (.cmd); their ChimeraX ports are in render/chimerax/ (.cxc, applied with open file.cxc). Both cover a ball-and-stick look (molecule-style), signed orbital/Fukui isosurfaces (orbital-style, and fukui-style at level 0.004) and a two-view snapshot macro (fukui-snapshots). axes.bild draws an XYZ reference triad (open axes.bild).

misc/top2charges

VMD computes the IR spectrum from the dipole autocorrelation, so the charge field of every atom has to be filled in by hand. The script reads the partial charges from the [ atoms ] section of a GROMACS topology and prints the Tcl lines to paste into the Tk Console:

./top2vmdcharges.sh spiral.top

set sel [atomselect top "all"]
$sel set charge {0.13111 -0.14150 -0.10535 ... 0.11360}
$sel delete

#include directives are followed recursively and the charges are expanded according to [ molecules ] (name + n_mol), so the order matches the coordinate file GROMACS writes. Without a [ molecules ] section - a bare .itp - every moleculetype is emitted once. On stderr it reports atoms per molecule and the total charge, warning if it is not an integer.

Everything goes on a single line by default, because the Tk Console chokes on multi-line braced lists. Useful flags: -s "not water" for a different selection, -m NAME to pick one moleculetype, -o file.tcl to save, -p for the bare list, -n N / -1 to wrap. -h for the rest.

misc/fchk2dipole

Pulls everything needed to draw a molecule's permanent dipole from a Gaussian formatted checkpoint. Given mol.fchk it writes, next to it:

• mol.xyz - geometry (input orientation, Angstrom)
• mol-dipole.bild - the dipole as a red arrow, tail at the center of mass
• mol-axes.bild - an XYZ reference triad parked outside the bounding box

python3 fchk2dipole.py mol.fchk

Coordinates, dipole and center of mass all come from the same fchk (its input orientation - the frame cubegen writes the .cube in), so the arrow overlays the molecule with no rotation. The dipole keeps the Gaussian convention (points from

• to +). Flags: -s arrow scale in Angstrom/Debye (default 1, a negative value flips the arrow), --tail origin|com (default com). Open the outputs in ChimeraX with open. Standard library only.

License

MIT