CompChemKit is an Android app for everyday work in computational chemistry and molecular modelling, organised in five suites and tied together by a control center. This guide gives a short tour of each part.
The suites are a lab notebook, a literature hub, an HPC workbench, a structure studio with a QM/MM region builder, and a paper kit. The app works offline apart from the online lookups (Crossref, OpenAlex, RCSB PDB, UniProt, AlphaFold DB and PubChem) and keeps all data on the phone, with no account and no tracking. The screenshots use made-up example data for a fictional researcher: the papers in the library are real publications, while the people, calculations, radar results, citation profile and journal figures are invented or illustrative.
I - Installation
CompChemKit needs Android 8.0 or newer. Download the compchemkit-X.Y.Z.apk file from the Releases page of the repository on the phone, open it and allow the install when Android asks. The app is signed by its author rather than distributed through the Play Store, so Android shows a warning and Play Protect may offer to scan it; you install it at your own risk. The only permission it asks for is Internet access, for the online lookups.
The launcher gets six icons: CompChemKit (the control center), Lab notebook, Literature hub, HPC workbench, Structure studio and Paper kit. Each opens in its own window, so you can switch between them from the recent apps screen, and all of them share the same data. To update, install the newer APK over the old one and your data stays.
In every suite the apps sit in a bar at the bottom of the screen, next to a Backup button. Most apps have a ⋮ menu with exports and Export backup / Import backup, and a + button to add something new. The back button closes an open sheet before leaving the page, and files the apps save (exports, scripts, figures) go to Download/CompChemKit/.
II - Control center
The place to start the day. Today shows what needs attention (passed deadlines, overdue action items, failed jobs, allocations running out early), an agenda for the next 14 days, running and queued calculations, and new papers and structures. Projects gathers everything linked to one project across all apps, Search looks through every app at once, Apps opens any suite at the right app, and Backup backs everything up or restores it.
The + button adds a log entry, idea, deadline, calculation, command or paper without opening the suite. Papers are looked up in Crossref by DOI or title words, and you pick the right one from the list of matches. Settings (the palette icon) holds the colour scheme, your name for My actions, and your OpenAlex key.
III - Lab notebook
Research log: dated entries (notes, results, problems, fixes, decisions) sorted by project, with #tags, pins and filters, plus meeting notes with people, decisions and action items. The Actions tab collects the open actions from every meeting, grouped by due date, and a follow-up meeting brings along whatever is still open.
Ideas: a board with four stages (sparks, exploring, doing, done), categories, tags and favourites.
Script plans: plan a Python or Bash script (inputs and outputs, command-line options, functions, steps and checks) and get a skeleton with a complete argument parser to start from.
Deadlines: grant calls, abstracts, reports and teaching, with countdowns, yearly repeats and export to a calendar file.
IV - Literature hub
Papers: your library, with collections and stars. Add papers by DOI or by searching Crossref, copy DOIs and citations, and export BibTeX, RIS or CSV.
Radar: follows topics such as PETase OR cutinase in OpenAlex and marks new papers until you have seen them, with filters for dates, paper types, open access and citations. One tap saves a paper to the library.
Citations: your OpenAlex author profile, with citations, h-index, i10-index, yearly charts and the citations each work gained since the last check.
V - HPC workbench
Tracker: every calculation with its cluster, resources, walltime and progress. It estimates progress and finishing time from the rate, warns when a walltime runs out and counts core-hours. Allocations get a projection of how fast you are using them.
Job scripts: SLURM or PBS scripts for Gaussian, ORCA, CP2K, GROMACS, AMBER or any command, with presets for your clusters and warnings about common mistakes.
Benchmarks: ns/day for each setup, the cost per ns, the fastest and cheapest options, and the wall time and cost of the run you are planning.
Commands: the commands you keep looking up, with blanks such as {tpr} that you fill in before copying; the last values are remembered.
VI - Structure studio
Viewer: a 3D viewer (3Dmol.js) for PDB, mmCIF, GRO, XYZ, SDF, MOL2 and PQR files. It opens PDB entries, AlphaFold models and PubChem compounds by ID, or searches all three by keyword. It has the usual styles and colourings, surfaces, ligand pockets, residue selections, distances and angles, trajectory frames and PNG snapshots.
QM/MM: pick the QM region on a protonated structure by tapping or typing residues, choose where each residue is cut, and follow a running count of QM atoms, link atoms, charge, electrons and multiplicity, with every boundary checked. It writes Gaussian ONIOM input, a CP2K QM/MM section, Amber, VMD and GROMACS selections, and an XYZ file of the QM region.
Watcher: saved searches (words, EC numbers, UniProt accessions or a sequence) that flag new structures in the PDB and new sequences in UniProt, ready to open in the viewer.
The viewer shows HIV-1 protease with its inhibitor (PDB 1HVR); the QM/MM example is the zinc site of a zinc finger (PDB 5A7U, with hydrogens added).
VII - Paper kit
Plot guide: 31 chart types, each with a tested Python script that draws it from example data and saves a 600 dpi PNG.
Schemes: an editor for reaction mechanisms with bonds, lone pairs, charges, curved arrows, reaction arrows and transition-state brackets, exported as SVG or 600 dpi PNG.
Journals: 37 journals to filter by scope, citation impact (OpenAlex 2-year mean citedness, close to but not the same as the Impact Factor), open access cost and speed. You can edit the values and add your own journals.
VIII - Backups, colours and privacy
Your data lives only on the phone, so keep copies. The app backs up each app automatically to dated files, a few seconds after its data changes, and copies them to Download/CompChemKit/backups/. These copies stay on the phone even if the app is uninstalled, which deletes the data kept inside the app. The Backup button in each suite shows the latest file for each app and restores any earlier one. The control center's Backup view can also restore from a file you pick, and its Download everything as one file saves all apps in a single file; use it to move to a new phone.
Settings offers dark, light or match device, in five palettes (Orchid, Ocean, Forest, Ember and Graphite). The choice applies at once to every suite, including windows that are already open, and to the status bar.
Nothing leaves the phone unless you use a lookup, and then the service receives only what the request needs. Papers come from Crossref; the radar, citations and journal figures from OpenAlex; structures from RCSB PDB, UniProt, AlphaFold DB and PubChem. OpenAlex needs a free API key: sign in at openalex.org/settings/api, copy the key and paste it in the control center's Settings. It stays on the phone and is never written into backup files.