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Audit follow-ups: bug fix, doc refresh, exception taxonomy, test hardening
Bug fix: - PrincipalMomentsDescriptor.clampNonNegative now also clamps NaN. The v<0 check was false for NaN, so a NaN eigenvalue (possible if a future code path bypasses GridGenerator.isFiniteBox) would have propagated to the CSV output. Doc refresh: - breaking-changes.md: 2.6 entry for the multi-column descriptor migration + the -vis_pocket_grid / pocket_grid_vis_* renames. - export-pocket-descriptors.md: step 4 rewrites a self-contradicting rationale — adding to the default list IS a breaking change for index-based parsers; recommends parse-by-name + breaking-changes.md note for future additions. - export-pocket-grid.md: added "Adding a new per-grid-point descriptor" recipe (parallel to the per-pocket one); unified √3/2 precision to 0.866 across docs and Params.groovy. - README.md: added an "Opt-in tabular exports" subsection mentioning -export_pocket_descriptors, -export_pocket_grid, -vis_pocket_grid. - testsets.sh "Full descriptor menu" now lists all seven shipped descriptors (was six). Exception taxonomy: - PocketDescriptorsRows.groovy and PocketGridBuilder.java now throw PrankException (was IllegalArgumentException) for user-facing config errors, matching the rest of the codebase. Registry hardening: - Both PocketDescriptorRegistry and PocketGridPointDescriptorRegistry now assert columnNames.size() == columnTypes.size() in register(). A future descriptor with mismatched lists fails fast at class-load. Quality fixes: - PocketGridRows.getColumn uses BASE_COLS-1 instead of literal 3 for the pocket column. Removed dead 2-arg PocketGridRows constructor (only 3 test sites used it; now inlined). - PocketGridPointContext gets a compact-constructor validator that rejects negative pointIndex/pocketRank, limiting blast radius of an int-arg swap. Test hardening: - VolsiteSmoothGridPointDescriptorTest + VolsiteGridPointDescriptorTest now pin sigma/radius in @BeforeEach AND restore in @AfterEach, so the Params singleton is clean for subsequent test classes. - New tests: HIS ND1 double-flag (single atom setting donor+acceptor), PrincipalMoments at cardinality=2, PrincipalMoments two coincident points, GridGenerator NaN-box throw, PocketDescriptorRegistry register/unregister round-trip, MorphologicalCloser maxIters=1. - Renamed respectsMaxIters → maxItersZeroIsNoOp (the test only covered the maxIters=0 case despite the general name); added maxIters=1 companion that verifies one iteration of fill actually runs. - Extracted RendererTestFixtures.tinyGrid (was byte-identical in both renderer test files); unified the volsite atomAt signatures so the parameter order can't get swapped between the two volsite tests.
This commit is contained in:
rdk
@@ -121,6 +121,10 @@ prank predict -c alphafold test.ds # use alphafold config and model (confi
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* **SAS points data**: coordinates and ligandability scores for solvent-accessible surface (SAS) points are saved in `visualizations/data/{protein_file}_points.pdb.gz`. Here:
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* Residue sequence number (position 23-26) represents the pocket rank (0 indicates no pocket).
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* B-factor column contains predicted ligandability score.
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* **Opt-in tabular exports** (off by default):
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* `-export_pocket_descriptors 1` → per-pocket geometric descriptors (volume, sphericity, radius of gyration, residue/atom counts, principal moments) in CSV/Arrow/Parquet. See [`documentation/export-pocket-descriptors.md`](documentation/export-pocket-descriptors.md).
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* `-export_pocket_grid 1` → per-pocket 3D grid of points covering the empty space around predicted pockets, with optional per-grid-point descriptors (e.g. `volsite` pharmacophore indicators). See [`documentation/export-pocket-grid.md`](documentation/export-pocket-grid.md).
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* `-vis_pocket_grid 1` → additional PyMOL/ChimeraX overlays of the grid for visualization.
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### Configuration
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@@ -27,6 +27,18 @@ All changes of that type should be rare and should be all listed here.
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* For additional internal evaluation-criterion fixes during the 2.6 dev cycle see
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[`documentation/dev/evaluation-metric-fixes-2.6.md`](documentation/dev/evaluation-metric-fixes-2.6.md).
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###### Pocket-descriptors export (opt-in feature)
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* Per-pocket descriptors `-export_pocket_descriptors` underwent a multi-column interface migration. The shipped default
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list now contains **seven** descriptors (previously six), adds `principal_moments` (a 3-column descriptor emitting
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`principal_moments.lambda1/lambda2/lambda3`), and reorders the existing six so `num_*` come first.
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Scripts parsing the descriptors CSV/Arrow/Parquet output by **column name** are unaffected;
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scripts parsing by **column index** need updating. See [`documentation/export-pocket-descriptors.md`](documentation/export-pocket-descriptors.md).
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* New opt-in `-vis_pocket_grid` (renamed from `-export_pocket_grid_pml`) emits both PyMOL `.pml` and ChimeraX `.cxc`
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overlay scripts. The two viz-tuning knobs were renamed for namespace consistency:
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`pocket_grid_vis_volume_radius` → `vis_pocket_grid_volume_radius` and
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`pocket_grid_vis_gaussian_iso` → `vis_pocket_grid_gaussian_iso`. Old names hard-fail at startup with no aliases.
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### 2.5.1
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none
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@@ -124,10 +124,15 @@ Implementations live under
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4. **To include it in the default output**, also add the name to the
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`pocket_descriptors` default list in `Params.groovy`. The default is
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declared explicitly rather than derived from `Registry.knownNames()`
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so that adding a descriptor doesn't silently change every existing
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user's output schema — that's intentional; skip step 4 if the new
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descriptor is opt-in only.
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declared explicitly (rather than derived from `Registry.knownNames()`)
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so each addition to the default schema is a conscious choice — but
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adding to the default IS a user-visible breaking change for anyone
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parsing the output by column index. Two recommendations:
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- Parse the descriptors file by column **name**, not by column index.
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- When you add a descriptor to the default list, note it in
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[`breaking-changes.md`](../breaking-changes.md).
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Skip step 4 if the new descriptor is opt-in only.
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INT columns return their value as a `double` that the writer downcasts at
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output time, matching the existing `TableData` convention. Implementations
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@@ -96,6 +96,36 @@ Descriptor params:
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| `pocket_grid_volsite_radius` | `4.0` Å | Cutoff radius for the `volsite` indicator. Standard VolSite pharmacophore search distance. |
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| `pocket_grid_volsite_sigma` | `2.0` Å | Gaussian σ for `volsite_smooth`. Kernel truncated at `4σ`. |
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### Adding a new per-grid-point descriptor
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Implementations live under
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`src/main/groovy/cz/siret/prank/program/routines/predict/output/grid/descriptors/`.
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1. Implement the `PocketGridPointDescriptor` interface (`name`, `columnNames`,
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`columnTypes`, `compute`). The shape mirrors the per-pocket
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`PocketDescriptor` (see
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[`export-pocket-descriptors.md`](export-pocket-descriptors.md#adding-a-new-descriptor)
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for the full recipe), with two differences:
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- **No `needsGrid()` method.** Every grid-point descriptor needs the grid
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by definition — the grid is the substrate that defines what a grid point
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is. The orchestrator always builds the grid when any grid-point
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descriptor is selected.
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- **No `AbstractScalarPocketDescriptor`-style adapter.** Both shipped
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descriptors (`volsite`, `volsite_smooth`) are multi-column; if you add
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the first scalar grid-point descriptor and it's the only one, implement
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`columnNames()` as a single-element list and rely on the bare `name()`
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output convention. If a second arrives, factor out an adapter then.
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2. Register in `PocketGridPointDescriptorRegistry`'s static initializer. The
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registry rejects descriptors with duplicate `columnNames` at registration
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time.
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3. Users opt in by name: `-pocket_grid_point_descriptors "volsite,my_new_descriptor"`.
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4. Default-empty is deliberate — adding a per-grid-point descriptor to the
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default would expand the row count by columns × rows, which is materially
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non-free (see cost rationale above). New descriptors should ship opt-in.
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## Parameters
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| Parameter | Default | Notes |
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@@ -151,7 +181,7 @@ The volume surface is rendered as a vdW-style surface (solvent probe = 0)
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of radius `vis_pocket_grid_volume_radius` (Å, auto-scaled to
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`0.85 × spacing` when the param is left at its `-1` sentinel; ≈ 1.02 Å
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at default spacing) around each grid point. The default sits just above
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the 3D-diagonal merge threshold (`spacing × √3 / 2 ≈ 0.87 × spacing`),
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the 3D-diagonal merge threshold (`spacing × √3 / 2 ≈ 0.866 × spacing`),
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so neighbors overlap in every direction and the surface reads as one
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clean continuous blob per pocket. Going much below `~spacing/2` leaves
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the spheres too disconnected for PyMOL's surface algorithm — most of
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@@ -561,8 +561,8 @@ pocket_grid() {
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format arrow.zst -out_subdir TEST/POCKET_GRID
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format parquet -out_subdir TEST/POCKET_GRID
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# Full descriptor menu
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -pocket_descriptors 'volume,sphericity,radius_of_gyration,num_residues,num_surface_atoms,num_grid_points' -out_subdir TEST/POCKET_GRID
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# Full descriptor menu (all seven shipped, including principal_moments)
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -pocket_descriptors 'volume,sphericity,radius_of_gyration,num_residues,num_surface_atoms,num_grid_points,principal_moments' -out_subdir TEST/POCKET_GRID
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# Grid-free descriptors only — exercises the grid-build short-circuit (no
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# "PocketGrid built" log line should appear for these invocations).
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@@ -78,7 +78,7 @@ final class PocketDescriptorsRows implements TableData {
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if (grid == null) {
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for (PocketDescriptor d : descriptors) {
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if (d.needsGrid()) {
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throw new IllegalArgumentException(
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throw new cz.siret.prank.program.PrankException(
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"Descriptor '${d.name()}' declares needsGrid()=true but a null " +
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"PocketGrid was passed to PocketDescriptorsRows. Either build the " +
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"grid upstream or drop this descriptor from -pocket_descriptors.")
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@@ -40,10 +40,6 @@ final class PocketGridRows implements TableData {
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/** [rowIndex][descriptorColumn] — flat across all descriptors; null when no descriptors. */
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private final double[][] descriptorValues
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PocketGridRows(PocketGrid grid, boolean includeUnassigned) {
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this(grid, includeUnassigned, null, null, Collections.<String> emptyList())
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}
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PocketGridRows(PocketGrid grid, boolean includeUnassigned,
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Protein protein, List<? extends Pocket> pockets,
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List<String> descriptorNames) {
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@@ -178,7 +174,7 @@ final class PocketGridRows implements TableData {
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double[] getColumn(int colIndex) {
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int n = rowPointIdx.length
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double[] out = new double[n]
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if (colIndex == 3) {
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if (colIndex == BASE_COLS - 1) { // pocket column — INT
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for (int i = 0; i < n; i++) out[i] = rowPocket[i]
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return out
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}
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@@ -45,6 +45,12 @@ public final class PocketDescriptorRegistry {
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*/
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public static void register(PocketDescriptor d) {
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List<String> cols = d.columnNames();
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List<?> types = d.columnTypes();
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if (cols.size() != types.size()) {
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throw new IllegalStateException(
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"Descriptor '" + d.name() + "' has columnNames.size()=" + cols.size()
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+ " but columnTypes.size()=" + types.size() + "; they must be parallel.");
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}
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if (cols.size() > 1 && new HashSet<>(cols).size() != cols.size()) {
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throw new IllegalStateException(
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"Descriptor '" + d.name() + "' declares duplicate columnNames: " + cols);
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@@ -107,9 +107,15 @@ public final class PrincipalMomentsDescriptor implements PocketDescriptor {
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return new double[] { l1, l2, l3 };
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}
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/** PSD eigenvalues should be ≥ 0; numerical noise can push them slightly negative. */
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/**
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* PSD eigenvalues should be ≥ 0; numerical noise can push them slightly negative.
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* NaN is also clamped to 0 as defense-in-depth: {@code NaN < 0} is false, so a NaN
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* eigenvalue would otherwise slip through and propagate to the CSV. The upstream
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* {@code GridGenerator.isFiniteBox} guard already rejects non-finite inputs, but
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* a future code path could bypass it.
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*/
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private static double clampNonNegative(double v) {
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return v < 0d ? 0d : v;
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return (v < 0d || !Double.isFinite(v)) ? 0d : v;
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}
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}
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@@ -120,7 +120,7 @@ public final class PocketGridBuilder {
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case "morph_closing": return new MorphologicalCloser();
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case "none": return new NoOpFiller();
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default:
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throw new IllegalArgumentException(
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throw new cz.siret.prank.program.PrankException(
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"Unknown pocket_grid_fill strategy: '" + strategy
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+ "'. Expected one of: morph_closing, none.");
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}
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@@ -23,4 +23,17 @@ public record PocketGridPointContext(
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@Nullable Pocket pocket,
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Protein protein,
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PocketGrid grid) {
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// Compact validator — limits the blast radius of an int-arg swap. Doesn't catch
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// pointIndex ↔ pocketRank swapped when both happen to be non-negative, but does
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// catch the common cases (negative index or rank from a misuse).
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public PocketGridPointContext {
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if (pointIndex < 0) {
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throw new IllegalArgumentException("pointIndex must be >= 0 (got " + pointIndex + ")");
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}
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if (pocketRank < 0) {
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throw new IllegalArgumentException(
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"pocketRank must be >= 0 (0 = unassigned; got " + pocketRank + ")");
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}
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}
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}
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@@ -36,6 +36,12 @@ public final class PocketGridPointDescriptorRegistry {
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*/
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public static void register(PocketGridPointDescriptor d) {
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List<String> cols = d.columnNames();
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List<?> types = d.columnTypes();
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if (cols.size() != types.size()) {
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throw new IllegalStateException(
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"Descriptor '" + d.name() + "' has columnNames.size()=" + cols.size()
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+ " but columnTypes.size()=" + types.size() + "; they must be parallel.");
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}
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if (cols.size() > 1 && new HashSet<>(cols).size() != cols.size()) {
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throw new IllegalStateException(
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"Descriptor '" + d.name() + "' declares duplicate columnNames: " + cols);
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@@ -117,6 +117,24 @@ class GridGeneratorBetweenTest {
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}
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}
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@Test
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void nanCoordInSasPointsThrowsClearError() {
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// GridGenerator's (Box, edge) ctor guards against NaN/Inf input — without it,
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// IEEEremainder(NaN, edge) silently produces NaN origins and a NaN-everywhere
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// lattice. This test pins the throw so a future refactor that drops the guard
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// can't reintroduce silent NaN propagation.
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Atoms atoms = new Atoms([carbonAt(0d, 0d, 0d)])
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Atoms sasWithNaN = new Atoms([
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new Point(0d, 0d, 0d) as Atom,
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new Point(Double.NaN, 0d, 0d) as Atom
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])
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IllegalArgumentException e = assertThrows(IllegalArgumentException.class) {
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GridGenerator.sampleGridPointsBetween(atoms, sasWithNaN, 1.0d, 3.0d, 0.5d)
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} as IllegalArgumentException
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assertTrue(e.message.toLowerCase().contains('non-finite'),
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"expected non-finite-box error, got: ${e.message}")
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}
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@Test
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void returnedOriginMatchesGridShift() {
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// Sampler exposes the lattice origin it picked so downstream callers don't
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@@ -45,7 +45,7 @@ class PocketGridRowsTest {
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@Test
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void multiPocketMembershipProducesMultipleRows() {
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// Point b is in both pockets → it appears twice (once per pocket).
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false)
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false, null, null, [] as List<String>)
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assertEquals(4, data.rowCount) // 2 + 2 assignments
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assertEquals(['x', 'y', 'z', 'pocket'], data.header)
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}
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@@ -62,16 +62,16 @@ class PocketGridRowsTest {
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assigned.put(1, bits(0))
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PocketGrid grid = new PocketGrid(new Atoms([a, unassigned]), 1.0d, 0d, 0d, 0d, idx, assigned)
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PocketGridRows included = new PocketGridRows(grid, true)
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PocketGridRows included = new PocketGridRows(grid, true, null, null, [] as List<String>)
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assertEquals(2, included.rowCount) // 1 assigned + 1 unassigned
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PocketGridRows omitted = new PocketGridRows(grid, false)
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PocketGridRows omitted = new PocketGridRows(grid, false, null, null, [] as List<String>)
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assertEquals(1, omitted.rowCount)
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}
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@Test
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void sortOrderIsPocketThenCoords() {
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false)
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false, null, null, [] as List<String>)
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// Expected sort: (pocket=1, x=1,2), then (pocket=2, x=2,3).
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double[] r0 = data.getRow(0); assertEquals(1.0d, r0[0], 0.0d); assertEquals(1, (int) r0[3])
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double[] r1 = data.getRow(1); assertEquals(2.0d, r1[0], 0.0d); assertEquals(1, (int) r1[3])
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@@ -81,7 +81,7 @@ class PocketGridRowsTest {
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@Test
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void columnTypes() {
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false)
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PocketGridRows data = new PocketGridRows(buildTwoPocketGrid(), false, null, null, [] as List<String>)
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assertEquals(TableData.ColumnType.DOUBLE, data.getColumnType(0))
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assertEquals(TableData.ColumnType.DOUBLE, data.getColumnType(1))
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assertEquals(TableData.ColumnType.DOUBLE, data.getColumnType(2))
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@@ -270,6 +270,33 @@ class PocketDescriptorsTest {
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||||
}
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||||
}
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||||
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/**
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* Round-trip the register/unregister API: register a fixture, see it land in
|
||||
* get/knownNames, unregister it, see it gone. Exercises the unregister code
|
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* path that production callers never touch (it exists for tests + future
|
||||
* descriptor plugins).
|
||||
*/
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@Test
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||||
void registryUnregisterRemovesAddedDescriptor() {
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String fixtureName = "__test_unregister_fixture__"
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||||
PocketDescriptor fixture = new AbstractScalarPocketDescriptor() {
|
||||
@Override String name() { fixtureName }
|
||||
@Override protected ColumnType scalarType() { ColumnType.DOUBLE }
|
||||
@Override protected double computeScalar(PocketGridContext ctx) { 0d }
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||||
}
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||||
PocketDescriptorRegistry.register(fixture)
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||||
try {
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||||
assertEquals(fixture, PocketDescriptorRegistry.get(fixtureName))
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||||
assertTrue(PocketDescriptorRegistry.knownNames().contains(fixtureName))
|
||||
} finally {
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||||
PocketDescriptorRegistry.unregister(fixtureName)
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||||
}
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||||
assertFalse(PocketDescriptorRegistry.knownNames().contains(fixtureName))
|
||||
assertThrows(PrankException) {
|
||||
PocketDescriptorRegistry.get(fixtureName)
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
void registryListsKnownNames() {
|
||||
Set<String> known = PocketDescriptorRegistry.knownNames()
|
||||
@@ -375,4 +402,46 @@ class PocketDescriptorsTest {
|
||||
assertEquals(rg * rg, sum, 1e-9d)
|
||||
}
|
||||
|
||||
/**
|
||||
* Boundary between the short-circuit ({@code n < 2}) and the full path.
|
||||
* Two distinct points span exactly one axis, so λ₁ > 0 and the other two
|
||||
* eigenvalues are 0. Per-dim variance of {0, 2} = mean((-1)² + 1²) = 1.
|
||||
*/
|
||||
@Test
|
||||
void principalMomentsAtExactlyTwoDistinctPointsHitsFullPath() {
|
||||
List<Atom> pts = [new Point(0d, 0d, 0d), new Point(2d, 0d, 0d)]
|
||||
PocketGrid grid = gridOfPoints(pts)
|
||||
TestPocket p = new TestPocket(); p.rank = 1
|
||||
double[] lambdas = new PrincipalMomentsDescriptor().compute(ctx(grid, p))
|
||||
assertEquals(1.0d, lambdas[0], 1e-9d)
|
||||
assertEquals(0.0d, lambdas[1], 1e-9d)
|
||||
assertEquals(0.0d, lambdas[2], 1e-9d)
|
||||
}
|
||||
|
||||
/**
|
||||
* Two coincident points: cardinality=2 takes the full path, but every
|
||||
* delta-from-centroid is 0, so the gyration tensor is zero and all
|
||||
* eigenvalues come out zero. Verifies the full path handles the
|
||||
* degenerate non-short-circuit case without producing NaN / negative
|
||||
* eigenvalues from numerical noise.
|
||||
*/
|
||||
@Test
|
||||
void principalMomentsOfTwoCoincidentPointsIsAllZeros() {
|
||||
// LongIntHashMap can't hold two entries with the same packed key — for
|
||||
// a true "two atoms at the same coord" fixture we need two distinct
|
||||
// lattice slots whose Atom positions happen to coincide. Build by hand.
|
||||
Atom a = new Point(0d, 0d, 0d)
|
||||
Atom b = new Point(0d, 0d, 0d)
|
||||
LongIntHashMap idx = new LongIntHashMap()
|
||||
idx.put(PocketGrid.pack(0, 0, 0), 0)
|
||||
idx.put(PocketGrid.pack(1, 0, 0), 1) // arbitrary distinct lattice slot
|
||||
BitSet bs = new BitSet(); bs.set(0, 2)
|
||||
Map<Integer, BitSet> assigned = [(1): bs] as LinkedHashMap
|
||||
PocketGrid grid = new PocketGrid(new Atoms([a, b]), 1.0d, 0d, 0d, 0d, idx, assigned)
|
||||
TestPocket p = new TestPocket(); p.rank = 1
|
||||
|
||||
double[] lambdas = new PrincipalMomentsDescriptor().compute(ctx(grid, p))
|
||||
assertArrayEquals([0.0d, 0.0d, 0.0d] as double[], lambdas, 1e-9d)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -110,9 +110,11 @@ class MorphologicalCloserTest {
|
||||
}
|
||||
|
||||
@Test
|
||||
void respectsMaxIters() {
|
||||
void maxItersZeroIsNoOp() {
|
||||
// With max_iters=0 the closer should return the raw shell unchanged
|
||||
// (no iteration runs).
|
||||
// (no iteration runs). Also pins the silent-non-convergence-warning fix
|
||||
// in 0e044f6b — the warning must NOT fire when maxIters=0 (a valid
|
||||
// "disable fill" configuration).
|
||||
PocketGrid grid = buildCubeGrid(2, 2, 2)
|
||||
int centerIdx = grid.latticeIndex.get(PocketGrid.pack(1, 1, 1))
|
||||
BitSet raw = new BitSet()
|
||||
@@ -124,4 +126,20 @@ class MorphologicalCloserTest {
|
||||
assertFalse(result.get(centerIdx), "no fill when max_iters=0")
|
||||
}
|
||||
|
||||
@Test
|
||||
void maxItersOneRunsExactlyOneIteration() {
|
||||
// One iteration of fill should be enough to close a single-cell U concavity:
|
||||
// the surrounded center cell has many filled neighbors and gets promoted on
|
||||
// iter 0. Pins behavior between the no-op (0) and converged cases.
|
||||
PocketGrid grid = buildCubeGrid(2, 2, 2)
|
||||
int centerIdx = grid.latticeIndex.get(PocketGrid.pack(1, 1, 1))
|
||||
BitSet raw = new BitSet()
|
||||
for (int i = 0; i < grid.pointCount; i++) {
|
||||
if (i != centerIdx) raw.set(i)
|
||||
}
|
||||
|
||||
BitSet result = CLOSER.fill(raw, grid, 3, 1)
|
||||
assertTrue(result.get(centerIdx), "the surrounded center should fill in one iter")
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -136,7 +136,7 @@ class PocketGridBuilderTest {
|
||||
TestPocket p = new TestPocket()
|
||||
p.rank = 1
|
||||
p.sasPoints = sasAt(0d, 0d, 0d)
|
||||
assertThrows(IllegalArgumentException) {
|
||||
assertThrows(cz.siret.prank.program.PrankException) {
|
||||
PocketGridBuilder.build(protein, [p] as List<Pocket>, bad)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -3,12 +3,15 @@ package cz.siret.prank.program.routines.predict.output.grid.descriptors
|
||||
import cz.siret.prank.domain.Protein
|
||||
import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.geom.Point
|
||||
import cz.siret.prank.program.params.Params
|
||||
import groovy.transform.CompileStatic
|
||||
import org.biojava.nbio.structure.Atom
|
||||
import org.biojava.nbio.structure.AtomImpl
|
||||
import org.biojava.nbio.structure.Element
|
||||
import org.biojava.nbio.structure.Group
|
||||
import org.biojava.nbio.structure.AminoAcidImpl
|
||||
import org.junit.jupiter.api.AfterEach
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*
|
||||
@@ -28,6 +31,22 @@ class VolsiteGridPointDescriptorTest {
|
||||
private static final int AROMATIC = 0, CATION = 1, ANION = 2,
|
||||
HYDROPHOBIC = 3, ACCEPTOR = 4, DONOR = 5
|
||||
|
||||
/** Radius the boundary tests build their atom distances around. */
|
||||
private static final double RADIUS = 4.0d
|
||||
|
||||
private double savedRadius
|
||||
|
||||
@BeforeEach
|
||||
void setRadius() {
|
||||
savedRadius = Params.inst.pocket_grid_volsite_radius
|
||||
Params.inst.pocket_grid_volsite_radius = RADIUS
|
||||
}
|
||||
|
||||
@AfterEach
|
||||
void restoreRadius() {
|
||||
Params.inst.pocket_grid_volsite_radius = savedRadius
|
||||
}
|
||||
|
||||
private static Atom atomAt(String element, String resName, String atomName,
|
||||
double x, double y, double z) {
|
||||
AtomImpl a = new AtomImpl()
|
||||
@@ -94,4 +113,23 @@ class VolsiteGridPointDescriptorTest {
|
||||
for (int i = 0; i < 6; i++) assertEquals(0d, out[i], 0d)
|
||||
}
|
||||
|
||||
@Test
|
||||
void singleAtomWithTwoPharmacophoreFlagsLightsBothColumns() {
|
||||
// ND1 in HIS sets BOTH donor and acceptor (VolSitePharmacophore.java).
|
||||
// The 6-flag aggregator's "two flags from one atom" path is non-trivial;
|
||||
// a regression that overwrites one with the other would slip through if
|
||||
// every other test only exercises one-flag atoms.
|
||||
Atom nd1His = atomAt("N", "HIS", "ND1", 1d, 0d, 0d)
|
||||
double[] out = new VolsiteGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, new Atoms([nd1His])))
|
||||
|
||||
assertEquals(1d, out[DONOR])
|
||||
assertEquals(1d, out[ACCEPTOR])
|
||||
// The other four must remain off.
|
||||
assertEquals(0d, out[AROMATIC])
|
||||
assertEquals(0d, out[CATION])
|
||||
assertEquals(0d, out[ANION])
|
||||
assertEquals(0d, out[HYDROPHOBIC])
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@@ -10,6 +10,7 @@ import org.biojava.nbio.structure.AtomImpl
|
||||
import org.biojava.nbio.structure.Element
|
||||
import org.biojava.nbio.structure.Group
|
||||
import org.biojava.nbio.structure.AminoAcidImpl
|
||||
import org.junit.jupiter.api.AfterEach
|
||||
import org.junit.jupiter.api.BeforeEach
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
@@ -34,14 +35,28 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
private static final int AROMATIC = 0, CATION = 1, ANION = 2,
|
||||
HYDROPHOBIC = 3, ACCEPTOR = 4, DONOR = 5
|
||||
|
||||
private double savedSigma
|
||||
|
||||
@BeforeEach
|
||||
void setSigma() {
|
||||
savedSigma = Params.inst.pocket_grid_volsite_sigma
|
||||
Params.inst.pocket_grid_volsite_sigma = SIGMA
|
||||
}
|
||||
|
||||
private static Atom atomAt(String atomName, String resName, double x, double y, double z) {
|
||||
@AfterEach
|
||||
void restoreSigma() {
|
||||
// Restore the global Params singleton so test classes that run after this
|
||||
// one (and that read pocket_grid_volsite_sigma without pinning it) aren't
|
||||
// affected by our pin.
|
||||
Params.inst.pocket_grid_volsite_sigma = savedSigma
|
||||
}
|
||||
|
||||
// Signature matches VolsiteGridPointDescriptorTest.atomAt (element, resName, atomName, x, y, z)
|
||||
// — both tests build atoms the same way so calls don't get swapped between files.
|
||||
private static Atom atomAt(String element, String resName, String atomName,
|
||||
double x, double y, double z) {
|
||||
AtomImpl a = new AtomImpl()
|
||||
a.element = Element.C
|
||||
a.element = Element.valueOfIgnoreCase(element)
|
||||
a.name = atomName
|
||||
a.x = x; a.y = y; a.z = z
|
||||
Group g = new AminoAcidImpl()
|
||||
@@ -59,7 +74,7 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
@Test
|
||||
void weightAtZeroDistanceIsOne() {
|
||||
// exp(0) = 1.0 exactly. Atom name "C" is hydrophobic.
|
||||
Atom c = atomAt("C", "ALA", 0d, 0d, 0d)
|
||||
Atom c = atomAt("C", "ALA", "C", 0d, 0d, 0d)
|
||||
double[] out = new VolsiteSmoothGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, new Atoms([c])))
|
||||
assertEquals(1.0d, out[HYDROPHOBIC], DELTA)
|
||||
@@ -69,7 +84,7 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
void weightAtSigmaMatchesGaussianFormula() {
|
||||
// At distance r = σ, weight = exp(-r²/(2σ²)) = exp(-1/2) ≈ 0.6065.
|
||||
double sigma = SIGMA
|
||||
Atom c = atomAt("C", "ALA", sigma, 0d, 0d)
|
||||
Atom c = atomAt("C", "ALA", "C", sigma, 0d, 0d)
|
||||
double[] out = new VolsiteSmoothGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, new Atoms([c])))
|
||||
assertEquals(Math.exp(-0.5d), out[HYDROPHOBIC], DELTA)
|
||||
@@ -80,8 +95,8 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
// Two hydrophobic atoms at distance σ each → sum = 2 × exp(-0.5).
|
||||
double sigma = SIGMA
|
||||
Atoms protein = new Atoms([
|
||||
atomAt("C", "ALA", sigma, 0d, 0d),
|
||||
atomAt("C", "ALA", 0d, sigma, 0d),
|
||||
atomAt("C", "ALA", "C", sigma, 0d, 0d),
|
||||
atomAt("C", "ALA", "C", 0d, sigma, 0d),
|
||||
])
|
||||
double[] out = new VolsiteSmoothGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, protein))
|
||||
@@ -94,7 +109,7 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
// exactly 4σ IS included and contributes exp(-(4σ)²/(2σ²)) = exp(-8) ≈ 3.354e-4.
|
||||
// Pins the boundary semantic (cutoff is inclusive, not strict).
|
||||
double sigma = SIGMA
|
||||
Atom c = atomAt("C", "ALA", 4d * sigma, 0d, 0d)
|
||||
Atom c = atomAt("C", "ALA", "C", 4d * sigma, 0d, 0d)
|
||||
double[] out = new VolsiteSmoothGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, new Atoms([c])))
|
||||
assertEquals(Math.exp(-8d), out[HYDROPHOBIC], DELTA)
|
||||
@@ -105,7 +120,7 @@ class VolsiteSmoothGridPointDescriptorTest {
|
||||
// 4σ is the hard cutoff (cutoutSphere is the gate). At 5σ the atom isn't even
|
||||
// in the kdtree result. Zero contribution.
|
||||
double sigma = SIGMA
|
||||
Atom c = atomAt("C", "ALA", 5d * sigma, 0d, 0d)
|
||||
Atom c = atomAt("C", "ALA", "C", 5d * sigma, 0d, 0d)
|
||||
double[] out = new VolsiteSmoothGridPointDescriptor().compute(
|
||||
ctxAt(0d, 0d, 0d, new Atoms([c])))
|
||||
assertEquals(0d, out[HYDROPHOBIC], DELTA)
|
||||
|
||||
@@ -21,24 +21,8 @@ class PocketGridChimeraXRendererTest {
|
||||
@TempDir
|
||||
Path tempDir
|
||||
|
||||
private static BitSet bits(int... values) {
|
||||
BitSet b = new BitSet()
|
||||
for (int v : values) b.set(v)
|
||||
return b
|
||||
}
|
||||
|
||||
private static PocketGrid tinyGrid() {
|
||||
Atom a = new Point(0d, 0d, 0d)
|
||||
Atom b = new Point(1d, 0d, 0d)
|
||||
Atom c = new Point(2d, 0d, 0d)
|
||||
LongIntHashMap idx = new LongIntHashMap()
|
||||
idx.put(PocketGrid.pack(0, 0, 0), 0)
|
||||
idx.put(PocketGrid.pack(1, 0, 0), 1)
|
||||
idx.put(PocketGrid.pack(2, 0, 0), 2)
|
||||
Map<Integer, BitSet> assigned = new LinkedHashMap<>()
|
||||
assigned.put(1, bits(0, 1))
|
||||
assigned.put(2, bits(1, 2))
|
||||
return new PocketGrid(new Atoms([a, b, c]), 1.0d, 0d, 0d, 0d, idx, assigned)
|
||||
return RendererTestFixtures.tinyGrid()
|
||||
}
|
||||
|
||||
@Test
|
||||
|
||||
@@ -26,24 +26,8 @@ class PocketGridPymolRendererTest {
|
||||
@TempDir
|
||||
Path tempDir
|
||||
|
||||
private static BitSet bits(int... values) {
|
||||
BitSet b = new BitSet()
|
||||
for (int v : values) b.set(v)
|
||||
return b
|
||||
}
|
||||
|
||||
private static PocketGrid tinyGrid() {
|
||||
Atom a = new Point(0d, 0d, 0d)
|
||||
Atom b = new Point(1d, 0d, 0d)
|
||||
Atom c = new Point(2d, 0d, 0d)
|
||||
LongIntHashMap idx = new LongIntHashMap()
|
||||
idx.put(PocketGrid.pack(0, 0, 0), 0)
|
||||
idx.put(PocketGrid.pack(1, 0, 0), 1)
|
||||
idx.put(PocketGrid.pack(2, 0, 0), 2)
|
||||
Map<Integer, BitSet> assigned = new LinkedHashMap<>()
|
||||
assigned.put(1, bits(0, 1))
|
||||
assigned.put(2, bits(1, 2))
|
||||
return new PocketGrid(new Atoms([a, b, c]), 1.0d, 0d, 0d, 0d, idx, assigned)
|
||||
return RendererTestFixtures.tinyGrid()
|
||||
}
|
||||
|
||||
@Test
|
||||
@@ -162,7 +146,7 @@ class PocketGridPymolRendererTest {
|
||||
new Atoms([new Point(0d, 0d, 0d) as Atom]),
|
||||
3.0d, 0d, 0d, 0d,
|
||||
makeIdx(0),
|
||||
[(1 as Integer): bits(0)] as LinkedHashMap<Integer, BitSet>)
|
||||
[(1 as Integer): RendererTestFixtures.bits(0)] as LinkedHashMap<Integer, BitSet>)
|
||||
PocketGridPymolRenderer.render(coarse, 2.5d, GAUSSIAN_ISO, tempDir.toString(), "coarse")
|
||||
String pml = new File("${tempDir}/visualizations/coarse_pocket_grid.pml").text
|
||||
assertTrue(pml.contains("alter pocket_vol_*, vdw=2.500"),
|
||||
|
||||
@@ -0,0 +1,46 @@
|
||||
package cz.siret.prank.program.visualization.renderers
|
||||
|
||||
import com.carrotsearch.hppc.LongIntHashMap
|
||||
import cz.siret.prank.geom.Atoms
|
||||
import cz.siret.prank.geom.Point
|
||||
import cz.siret.prank.program.routines.predict.output.grid.PocketGrid
|
||||
import groovy.transform.CompileStatic
|
||||
import org.biojava.nbio.structure.Atom
|
||||
|
||||
/**
|
||||
* Shared test fixtures for the pocket-grid renderer tests. Both
|
||||
* {@code PocketGridChimeraXRendererTest} and {@code PocketGridPymolRendererTest}
|
||||
* exercised an identical 3-atom / 2-pocket-overlap grid; extracted here so
|
||||
* a fixture change touches one site.
|
||||
*/
|
||||
@CompileStatic
|
||||
final class RendererTestFixtures {
|
||||
|
||||
private RendererTestFixtures() {}
|
||||
|
||||
static BitSet bits(int... values) {
|
||||
BitSet b = new BitSet()
|
||||
for (int v : values) b.set(v)
|
||||
return b
|
||||
}
|
||||
|
||||
/**
|
||||
* 3 grid points (a=0,0,0 — b=1,0,0 — c=2,0,0), spacing 1.0,
|
||||
* pocket 1 = {a, b}, pocket 2 = {b, c}. Used by the renderer tests to
|
||||
* verify per-pocket coloring, multi-membership behavior, etc.
|
||||
*/
|
||||
static PocketGrid tinyGrid() {
|
||||
Atom a = new Point(0d, 0d, 0d)
|
||||
Atom b = new Point(1d, 0d, 0d)
|
||||
Atom c = new Point(2d, 0d, 0d)
|
||||
LongIntHashMap idx = new LongIntHashMap()
|
||||
idx.put(PocketGrid.pack(0, 0, 0), 0)
|
||||
idx.put(PocketGrid.pack(1, 0, 0), 1)
|
||||
idx.put(PocketGrid.pack(2, 0, 0), 2)
|
||||
Map<Integer, BitSet> assigned = new LinkedHashMap<>()
|
||||
assigned.put(1, bits(0, 1))
|
||||
assigned.put(2, bits(1, 2))
|
||||
return new PocketGrid(new Atoms([a, b, c]), 1.0d, 0d, 0d, 0d, idx, assigned)
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user