ms-contactmap 0.1.0__py3-none-any.whl

ms_contactmap/__init__.py

@@ -0,0 +1,41 @@
+"""Maestro-style 2D protein-ligand interaction diagrams for PySide6.
+
+Public objects are imported lazily to reduce startup time and keep analysis,
+layout and Qt drawing independently usable.
+"""
+from __future__ import annotations
+
+from importlib import import_module
+
+_PUBLIC = {
+    "Diagram": ("model", "Diagram"),
+    "DiagramView": ("widget", "DiagramView"),
+    "Interaction": ("model", "Interaction"),
+    "InteractionDiagramWidget": ("widget", "InteractionDiagramWidget"),
+    "LayoutResult": ("layout", "LayoutResult"),
+    "LigandGeometry": ("chem", "LigandGeometry"),
+    "Residue": ("model", "Residue"),
+    "ResidueRef": ("model", "ResidueRef"),
+    "build_diagram": ("interactions", "build_diagram"),
+    "build_scene": ("render", "build_scene"),
+    "document_from_dict": ("json_io", "document_from_dict"),
+    "document_to_dict": ("json_io", "document_to_dict"),
+    "export_png": ("export", "export_png"),
+    "export_svg": ("export", "export_svg"),
+    "load_json": ("json_io", "load_json"),
+    "load_ligand": ("chem", "load_ligand"),
+    "save_json": ("json_io", "save_json"),
+    "solve_layout": ("layout", "solve_layout"),
+}
+
+__all__ = list(_PUBLIC)
+
+
+def __getattr__(name: str):
+    try:
+        module_name, attribute = _PUBLIC[name]
+    except KeyError as exc:
+        raise AttributeError(name) from exc
+    value = getattr(import_module(f".{module_name}", __name__), attribute)
+    globals()[name] = value
+    return value

ms_contactmap/__main__.py

@@ -0,0 +1,96 @@
+"""Command line entry point.
+
+    python -m ms_contactmap data/4ps5.pdb --ligand 2TA --smiles "..." --json out.json
+    python -m ms_contactmap --from-json out.json --png out.png
+    python -m ms_contactmap --from-json out.json --show
+"""
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(prog="ms_contactmap", description=__doc__)
+    parser.add_argument("pdb", nargs="?", type=Path, help="PDB file of the complex")
+    parser.add_argument("--from-json", type=Path, default=None,
+                        help="visualize a previously computed diagram JSON")
+    parser.add_argument("--ligand", help="ligand residue name, e.g. 2TA")
+    parser.add_argument("--chain", default=None, help="restrict to this chain")
+    parser.add_argument("--resnum", type=int, default=None, help="restrict to this residue number")
+    parser.add_argument("--smiles", default=None, help="ligand SMILES (required with a PDB input)")
+    parser.add_argument("--no-exposure", action="store_true",
+                        help="skip SASA halos for a faster first analysis")
+    parser.add_argument("--json", dest="json_output", type=Path, default=None,
+                        help="write reusable analysis and layout JSON here")
+    parser.add_argument("--png", type=Path, default=None, help="write a PNG here")
+    parser.add_argument("--svg", type=Path, default=None, help="write an SVG here")
+    parser.add_argument("--scale", type=float, default=2.0, help="PNG scale factor")
+    parser.add_argument("--transparent", action="store_true", help="PNG without white background")
+    parser.add_argument("--show", action="store_true", help="open the interactive window")
+    args = parser.parse_args(argv)
+
+    if not args.png and not args.svg and not args.json_output and not args.show:
+        parser.error("nothing to do: pass --json, --png, --svg or --show")
+    if args.from_json and args.pdb:
+        parser.error("choose either a PDB input or --from-json, not both")
+    if not args.from_json and not args.pdb:
+        parser.error("pass a PDB input or --from-json")
+    if not args.from_json and not args.ligand:
+        parser.error("--ligand is required with a PDB input")
+    if not args.from_json and not args.smiles:
+        parser.error("--smiles is required with a PDB input")
+
+    from .export import ensure_app
+    app = ensure_app()
+    from .widget import InteractionDiagramWidget
+
+    if args.from_json:
+        widget = InteractionDiagramWidget.from_json(args.from_json)
+        diagram = widget.diagram
+    else:
+        from .interactions import build_diagram
+
+        diagram = build_diagram(
+            args.pdb,
+            args.ligand,
+            args.smiles,
+            chain=args.chain,
+            resnum=args.resnum,
+            name=args.pdb.stem,
+            compute_exposure=not args.no_exposure,
+        )
+        # Batch exports need a solved scene immediately.  A show-only command
+        # displays the window first and solves in the responsive Qt thread.
+        widget = InteractionDiagramWidget(
+            diagram if (args.png or args.svg or args.json_output) else None
+        )
+    assert diagram is not None
+    print(
+        f"{diagram.name}: {diagram.ligand_name}, "
+        f"{len(diagram.residues)} residues, {len(diagram.interactions)} interactions",
+        file=sys.stderr,
+    )
+
+    if args.json_output:
+        widget.export_json(args.json_output)
+        print(f"wrote {args.json_output}", file=sys.stderr)
+    if args.png:
+        widget.export_png(args.png, scale=args.scale, background=None if args.transparent else "#ffffff")
+        print(f"wrote {args.png}", file=sys.stderr)
+    if args.svg:
+        widget.export_svg(args.svg)
+        print(f"wrote {args.svg}", file=sys.stderr)
+    if args.show:
+        widget.resize(1100, 780)
+        widget.setWindowTitle(f"{diagram.name} - {diagram.ligand_name}")
+        widget.show()
+        if widget.layout_result is None:
+            widget.set_diagram_async(diagram)
+        return app.exec()
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())