| name | pymol_viz |
| description | How kinase structure visualization works in this repo: the StructureConfig/StructureVisualizer/PyMOLGenerator pipeline, the generate_pymol_files CLI, and when to use generated scripts (licensed PyMOL) vs in-process pymol2/SASA. Use when generating or editing PyMOL files, structure highlighting configs, or SASA computation. |
PyMOL / structure visualization
Two distinct PyMOL paths — do not conflate
- Rendering / images → generate a standalone PyMOL script (+ PDB +
instructions) and run it in the user's licensed PyMOL GUI for image
quality. This is what
mkt.databases.pymol.PyMOLGenerator and the
generate_pymol_files CLI produce.
- Numeric/compute work (e.g. SASA in
mkt.databases.sasa) → use in-process
open-source pymol2 only. Open-source PyMOL is for computation, not
rendering.
Pipeline
SequenceAlignment → StructureConfig (mkt.databases.app.schema)
(kinase info, ├─ generate_list_idx() / generate_style_color_lists()
dict_align) └─ produces list_idx (1-indexed), list_color, list_style, list_label
↓
StructureVisualizer (mkt.databases.app.structures)
loads KinCore CIF → Bio.PDB Structure → PDB text; get_highlight_data()
↓
PyMOLGenerator (mkt.databases.pymol)
writes <gene>_<attr>_{structure.pdb, pymol_script.py, instructions.txt}
Config types are the StandardConfig / StandardConfigChoice enums
(KLIFS_IMPORTANT, PHOSPHOSITES, MUTATIONS_KLIFS, MUTATIONS_GROUP, KLIFS_CUSTOM,
…). To add a highlight mode, subclass StructureConfig and implement
generate_list_idx() + generate_style_color_lists().
CLI
generate_pymol_files --gene ABL1 --config KLIFS_IMPORTANT
generate_pymol_files --gene EGFR --config PHOSPHOSITES
generate_pymol_files --gene ABL1 --config MUTATIONS_KLIFS --json-mutations muts.json
generate_pymol_files --gene ABL1 --config KLIFS_CUSTOM --indices 315,317 --colors red,blue
MUTATIONS_* configs require --json-mutations; KLIFS_CUSTOM requires
matched --indices (1-indexed full-length UniProt) and --colors. Output lands
in <repo_root>/images/pymol_output/<gene>/<subdir>/ by default.
Label tuning — do NOT add CLI flags for it
Fine label placement (label_offset, label_min_dist, label_spring_strength,
connector lines) is tuned by the user in the PyMOL GUI, not exposed as new CLI
flags. Leave those as StructureConfig defaults.
