Development branch to be merged to master

[JavierSanchez-Utges]

This branch includes several changes across 15 files. Minor changes on HTML templates and README. Major updates include:

1. Reading from new mmCIF assembly files superposed to representative segment structure
2. Edits to maintain the view when transitioning from superposition view to assembly and across assemblies. This includes fixing: water molecules, ligands, labels, surfaces, etc.

Changes should work for both LIGYSIS pre-computed results as well as user-submitted job results.

[Copilot]

Pull Request Overview

This PR merges the development branch into master, adding support for reading and transforming mmCIF assembly files and improving view persistence across superposition and assembly modes, as well as updating citations across templates and documentation.

• Added functions to parse custom matrix files and transform coordinate data for assemblies
• Updated 3DMol JS toggling logic to preserve styling for clicked residues
• Revised citation entries in HTML templates and README

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
templates/index.html, help.html, contact.html, about.html	Updated citation text and DOIs for new publications
static/js/charts.js	Cleared chart dataset labels and updated tooltips
static/js/chart_listeners.js	Removed stray whitespace
static/js/USER_3DMol_toggle_surfs.js / 3DMol_toggle_surfs.js	Enhanced toggle logic to exclude selected residues
static/js/USER_3DMol_applet.js / 3DMol_applet_DEV.js	Commented out initial zoom/render calls to avoid override
config.py	Pointed ASSEMBLY_FOLDER to per-protein split folder
app.py	Imported new MATS_FOLDER, added parse/transform funcs, updated routes
README.md	Added publication reference to README

Comments suppressed due to low confidence (5)

README.md:6

• [nitpick] Citation markup varies between <em>, <i> and plain text; consider standardizing tag usage and punctuation for consistency.

This is the repository for our ligand binding site analysis, **LIGYSIS**, [web server](https://www.compbio.dundee.ac.uk/ligysis/) published in [Nucleic Acids Research](https://doi.org/10.1093/nar/gkaf411). LIGYSIS is a Python [Flask](https://flask.palletsprojects.com/en/stable/) Web application.

app.py:281

• The new transform_coordinates() and parse_custom_matrix() functions lack unit tests; consider adding tests to ensure correct behavior and prevent regressions.

### TRANSFORMATION FUNCTIONS ###

static/js/USER_3DMol_toggle_surfs.js:399

• The selector variable protAtoms may be undefined or incorrect here; use the correct model selector (e.g., protAtomsModel) to avoid runtime errors.

{...protAtoms, model: activeModel, not: {or: siteAssemblyPDBResNums}},

static/js/3DMol_toggle_surfs.js:388

• The variable AssemblyClickedSiteResidues may not be defined in this scope; ensure the correct residue list variable is passed to not.

{...protAtoms, model: activeModel, not: {or: AssemblyClickedSiteResidues}},

[Copilot]

Removing the dataset label will leave an empty legend entry; consider specifying a meaningful label or disabling the legend if not needed.

Suggested change

	label: "",
	label: chartLab,

[Copilot]

Remove or replace this debug print statement to avoid noisy console output in production.

Suggested change

	print(full_ASSEMBLY_FOLDER, os.path.basename(filename))
	logger.debug("Assembly folder: %s, Filename: %s", full_ASSEMBLY_FOLDER, os.path.basename(filename))

[Copilot]

These debug print statements in get_contacts should be removed or replaced with proper logging.

[Copilot]

[nitpick] Consider removing this obsolete commented-out ASSEMBLY_FOLDER definition or add a comment explaining why it must remain.

Suggested change

#ASSEMBLY_FOLDER = os.path.join(DATA_FOLDER, "data", "structures", "assembly") # IN EXAMPLE & CLUSTER

[Copilot]

[nitpick] Remove this commented-out viewer.zoomTo() (and the subsequent render call) if they're no longer needed.

Suggested change

	// viewer.zoomTo();
	// viewer.render();

[Copilot]

[nitpick] Clean up the commented viewer.zoomTo() and viewer.render() calls to reduce dead code.

Suggested change

	// viewer.zoomTo();
	// viewer.render();