From ccdd3e234fb20c209bec70254f7c9969c2bb235e Mon Sep 17 00:00:00 2001 From: Arshita Jaryal Date: Thu, 14 May 2026 19:10:01 +0530 Subject: [PATCH 1/3] Complete TypeScript migration --- app/dist/assets/index-CLOIsP4q.js | 7504 ----------------- app/dist/assets/index-DHFWRlXl.js | 7504 +++++++++++++++++ ...{index-hdzOkq2r.css => index-Y4Qzsb0-.css} | 2 +- app/dist/index.html | 4 +- app/{eslint.config.js => eslint.config.ts} | 2 +- app/index.html | 2 +- app/package-lock.json | 45 +- app/package.json | 5 +- app/src/{App.jsx => App.tsx} | 0 .../common/{Badge.jsx => Badge.tsx} | 9 +- .../common/{ErrorState.jsx => ErrorState.tsx} | 6 +- .../{GapScoreBar.jsx => GapScoreBar.tsx} | 9 +- .../{LoadingState.jsx => LoadingState.tsx} | 6 +- .../{ThemeToggle.jsx => ThemeToggle.tsx} | 7 +- ...ngSitesPanel.jsx => BindingSitesPanel.tsx} | 27 +- app/src/components/complex/ComparisonTab.jsx | 626 -- app/src/components/complex/ComparisonTab.tsx | 305 + .../{ComplexHeader.jsx => ComplexHeader.tsx} | 11 +- ...ionBrowser.jsx => ConformationBrowser.tsx} | 9 +- ...Leaderboard.jsx => DockingLeaderboard.tsx} | 17 +- .../{DockingPanel.jsx => DockingPanel.tsx} | 26 +- .../{FragmentList.jsx => FragmentList.tsx} | 7 +- .../{MetricsPanel.jsx => MetricsPanel.tsx} | 7 +- ...{MoleculePicker.jsx => MoleculePicker.tsx} | 16 +- ...{PocketTableRow.jsx => PocketTableRow.tsx} | 17 +- ...rPlaceholder.jsx => ViewerPlaceholder.tsx} | 11 +- ...orderDeltaBar.jsx => DisorderDeltaBar.tsx} | 7 +- .../{MolstarPanel.jsx => MolstarPanel.tsx} | 22 +- .../{ProteinViewer.jsx => ProteinViewer.tsx} | 41 +- .../{RevealButton.jsx => RevealButton.tsx} | 8 +- .../{ViewerFooter.jsx => ViewerFooter.tsx} | 7 +- .../{ViewerHeader.jsx => ViewerHeader.tsx} | 7 +- .../viewer/{useMolstar.js => useMolstar.ts} | 128 +- .../{TargetTable.jsx => TargetTable.tsx} | 11 +- .../layout/{Footer.jsx => Footer.tsx} | 0 .../layout/{Navbar.jsx => Navbar.tsx} | 0 .../search/{ResultCard.jsx => ResultCard.tsx} | 11 +- .../search/{SearchBar.jsx => SearchBar.tsx} | 18 +- app/src/{config.js => config.ts} | 4 +- ...{useBindingSites.js => useBindingSites.ts} | 25 +- ...emblFragments.js => useChemblFragments.ts} | 34 +- .../hooks/{useComplex.js => useComplex.ts} | 22 +- .../{useDockingJob.js => useDockingJob.ts} | 64 +- app/src/hooks/{useSearch.js => useSearch.ts} | 31 +- app/src/hooks/{useTheme.js => useTheme.ts} | 2 +- .../{useUndrugged.js => useUndrugged.ts} | 18 +- app/src/{main.jsx => main.tsx} | 4 +- app/src/pages/ComplexDetailPage.jsx | 247 - app/src/pages/ComplexDetailPage.tsx | 137 + .../{DashboardPage.jsx => DashboardPage.tsx} | 21 +- app/src/pages/{HomePage.jsx => HomePage.tsx} | 98 +- .../pages/{SearchPage.jsx => SearchPage.tsx} | 25 +- app/src/scss.d.ts | 4 + app/src/types.ts | 157 + app/src/utils/safeFetch.ts | 14 + app/tsconfig.json | 29 + app/vite-env.d.ts | 1 + app/{vite.config.js => vite.config.ts} | 0 58 files changed, 8672 insertions(+), 8709 deletions(-) delete mode 100644 app/dist/assets/index-CLOIsP4q.js create mode 100644 app/dist/assets/index-DHFWRlXl.js rename app/dist/assets/{index-hdzOkq2r.css => index-Y4Qzsb0-.css} (76%) rename app/{eslint.config.js => eslint.config.ts} (95%) rename app/src/{App.jsx => App.tsx} (100%) rename app/src/components/common/{Badge.jsx => Badge.tsx} (73%) rename app/src/components/common/{ErrorState.jsx => ErrorState.tsx} (78%) rename app/src/components/common/{GapScoreBar.jsx => GapScoreBar.tsx} (84%) rename app/src/components/common/{LoadingState.jsx => LoadingState.tsx} (73%) rename app/src/components/common/{ThemeToggle.jsx => ThemeToggle.tsx} (93%) rename app/src/components/complex/{BindingSitesPanel.jsx => BindingSitesPanel.tsx} (90%) delete mode 100644 app/src/components/complex/ComparisonTab.jsx create mode 100644 app/src/components/complex/ComparisonTab.tsx rename app/src/components/complex/{ComplexHeader.jsx => ComplexHeader.tsx} (89%) rename app/src/components/complex/{ConformationBrowser.jsx => ConformationBrowser.tsx} (90%) rename app/src/components/complex/{DockingLeaderboard.jsx => DockingLeaderboard.tsx} (96%) rename app/src/components/complex/{DockingPanel.jsx => DockingPanel.tsx} (90%) rename app/src/components/complex/{FragmentList.jsx => FragmentList.tsx} (95%) rename app/src/components/complex/{MetricsPanel.jsx => MetricsPanel.tsx} (95%) rename app/src/components/complex/{MoleculePicker.jsx => MoleculePicker.tsx} (93%) rename app/src/components/complex/{PocketTableRow.jsx => PocketTableRow.tsx} (89%) rename app/src/components/complex/{ViewerPlaceholder.jsx => ViewerPlaceholder.tsx} (87%) rename app/src/components/complex/viewer/{DisorderDeltaBar.jsx => DisorderDeltaBar.tsx} (88%) rename app/src/components/complex/viewer/{MolstarPanel.jsx => MolstarPanel.tsx} (83%) rename app/src/components/complex/viewer/{ProteinViewer.jsx => ProteinViewer.tsx} (87%) rename app/src/components/complex/viewer/{RevealButton.jsx => RevealButton.tsx} (81%) rename app/src/components/complex/viewer/{ViewerFooter.jsx => ViewerFooter.tsx} (83%) rename app/src/components/complex/viewer/{ViewerHeader.jsx => ViewerHeader.tsx} (74%) rename app/src/components/complex/viewer/{useMolstar.js => useMolstar.ts} (82%) rename app/src/components/dashboard/{TargetTable.jsx => TargetTable.tsx} (95%) rename app/src/components/layout/{Footer.jsx => Footer.tsx} (100%) rename app/src/components/layout/{Navbar.jsx => Navbar.tsx} (100%) rename app/src/components/search/{ResultCard.jsx => ResultCard.tsx} (91%) rename app/src/components/search/{SearchBar.jsx => SearchBar.tsx} (82%) rename app/src/{config.js => config.ts} (78%) rename app/src/hooks/{useBindingSites.js => useBindingSites.ts} (61%) rename app/src/hooks/{useChemblFragments.js => useChemblFragments.ts} (67%) rename app/src/hooks/{useComplex.js => useComplex.ts} (59%) rename app/src/hooks/{useDockingJob.js => useDockingJob.ts} (69%) rename app/src/hooks/{useSearch.js => useSearch.ts} (62%) rename app/src/hooks/{useTheme.js => useTheme.ts} (92%) rename app/src/hooks/{useUndrugged.js => useUndrugged.ts} (61%) rename app/src/{main.jsx => main.tsx} (62%) delete mode 100644 app/src/pages/ComplexDetailPage.jsx create mode 100644 app/src/pages/ComplexDetailPage.tsx rename app/src/pages/{DashboardPage.jsx => DashboardPage.tsx} (67%) rename app/src/pages/{HomePage.jsx => HomePage.tsx} (63%) rename app/src/pages/{SearchPage.jsx => SearchPage.tsx} (77%) create mode 100644 app/src/scss.d.ts create mode 100644 app/src/types.ts create mode 100644 app/src/utils/safeFetch.ts create mode 100644 app/tsconfig.json create mode 100644 app/vite-env.d.ts rename app/{vite.config.js => vite.config.ts} (100%) diff --git a/app/dist/assets/index-CLOIsP4q.js b/app/dist/assets/index-CLOIsP4q.js deleted file mode 100644 index 1effb64..0000000 --- a/app/dist/assets/index-CLOIsP4q.js +++ /dev/null @@ -1,7504 +0,0 @@ -var 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\`/\`\` and will default to "${Lt}"`),null):e}function Yt(e,t){let n,r,i,a,o;if(Bt(e)){let o=e.getAttribute(`action`);r=o?Ce(o,t):null,n=e.getAttribute(`method`)||It,i=Jt(e.getAttribute(`enctype`))||Lt,a=new FormData(e)}else if(zt(e)||nee(e)&&(e.type===`submit`||e.type===`image`)){let o=e.form;if(o==null)throw Error(`Cannot submit a - - - - -
- - - - val.toFixed(3)} - label={{ value: 'Disorder Delta (Δ pLDDT)', position: 'bottom', fill: '#888', fontSize: 10, fontFamily: 'monospace' }} - /> - val.toFixed(3)} - label={{ value: 'Druggability Score', angle: -90, position: 'left', fill: '#888', fontSize: 10, fontFamily: 'monospace' }} - /> - [value.toFixed(3), name]} - /> - a.avg_delta - b.avg_delta)} - line={{ stroke: '#555', strokeWidth: 1.5, strokeDasharray: '4 4' }} - > - {data.map((entry, index) => ( - = 5.0 ? '#10b981' : '#9ca3af'} /> - ))} - - - - {data.every(d => Math.abs(d.avg_delta) < 0.001) && ( -
- - Disorder Delta data not available - -
- )} -
- {!isReset && ( -

- Scroll to zoom · Drag to pan · Click reset to restore -

- )} - - ); -} - -export function ComparisonTab({ - comparison, - activePocketIdx, - handleHighlight, - monomerStructureUrl, - complexStructureUrl, - onConformationChange -}) { - if (!comparison) return ( -
- Comparison data not available. -
- ); - - const { - summary_metrics, - ddgi, - pocket_mapping, - interface_pockets, - conserved_pockets, - emergent_pockets, - graph_datasets, - property_changes, - stabilization_stats, - fragment_comparison - } = comparison; - - const hasScatterData = graph_datasets?.stabilization_scatter && graph_datasets.stabilization_scatter.length > 0; - - return ( -
- {/* 1. Summary Metrics & DDGI */} -
-
- Total Monomer Pockets - {summary_metrics.total_monomer_pockets} -
-
- Total Complex Pockets - {summary_metrics.total_dimer_pockets} -
-
- True Interface Pockets - {pocket_mapping.interface_count} -
-
0 ? 'border-success/50' : 'border-danger/50'}`}> - - DDGI Score -
- Dimerization Druggability Gain Index: Avg Dimer Score - Avg Monomer Score -
- - 0 ? 'text-success' : 'text-danger'}`}> - {ddgi > 0 ? '+' : ''}{ddgi.toFixed(3)} - -
-
- - {/* 2. Pocket Mapping & Property Changes */} -
- {/* Pocket Mapping */} -
-

Pocket Transition Map

-
-
- Conserved in both states - {pocket_mapping.conserved_count} -
-
- Disappeared upon dimerization - {pocket_mapping.monomer_only_count} -
-
- Newly emerged in dimer - {pocket_mapping.emergent_count} -
-
- -
-
Residue Stabilization Analysis
-
- Interface Residue Enrichment - {stabilization_stats.enrichment_score.toFixed(2)}x -
-
-
- - {/* Changes */} -
-

Average Property Shifts

-
- {/* Vol */} -
-
- Avg Volume - {property_changes.monomer_avg_volume.toFixed(0)} → {property_changes.dimer_avg_volume.toFixed(0)} ų -
-
- {/* Hydrophobicity */} -
-
- Avg Hydrophobicity - {property_changes.monomer_avg_hydrophobicity.toFixed(2)} → {property_changes.dimer_avg_hydrophobicity.toFixed(2)} -
-
- {/* Polarity */} -
-
- Avg Polarity - {property_changes.monomer_avg_polarity.toFixed(2)} → {property_changes.dimer_avg_polarity.toFixed(2)} -
-
- {/* Score */} -
-
- Avg Druggability - 0 ? 'text-success' : 'text-danger'}> - {summary_metrics.avg_monomer_druggability.toFixed(3)} → {summary_metrics.avg_dimer_druggability.toFixed(3)} - -
-
-
-
-
- - {/* 3. Charts */} - {hasScatterData && ( - - )} - - {/* 4. True Interface Pockets */} -
-

-
- True Interface Drug Targets -

-

- Pockets spanning multiple protein chains at the dimer interaction surface. -

- -
- - - - - - - - - - - - - - - - {interface_pockets && interface_pockets.length > 0 ? ( - interface_pockets.map((pocket, idx) => ( - - handleHighlight(residueIndices, `int-${idx}`, comparisonHighlightTarget(pocket)) - } - proteinPdbId={complexStructureUrl} - sourceType="dimer" - onConformationChange={(confs, mode) => - onConformationChange?.(confs, mode, comparisonHighlightTarget(pocket)) - } - /> - )) - ) : ( - - - - )} - -
IDScoreVolHydroPolarΔ pLDDTCenterResiduesActions
- No true interface pockets found. -
-
-
- - {/* 5b. Conserved Pockets */} -
-

-
- Conserved Pockets -

-

- Pockets retained from monomer to dimer — spatially overlapping in both structures. -

- -
- - - - - - - - - - - - - - - - {conserved_pockets && conserved_pockets.length > 0 ? ( - conserved_pockets.map((pocket, idx) => ( - - handleHighlight(residueIndices, `con-${idx}`, comparisonHighlightTarget(pocket)) - } - proteinPdbId={complexStructureUrl} - sourceType="dimer" - onConformationChange={(confs, mode) => - onConformationChange?.(confs, mode, comparisonHighlightTarget(pocket)) - } - /> - )) - ) : ( - - - - )} - -
IDScoreVolHydroPolarΔ pLDDTCenterResiduesActions
- No conserved pockets found — all monomer pockets were restructured. -
-
-
- - {/* 5. Emergent Monomer-Dimer Pockets */} -
-

-
- Emergent Dimer-only Pockets -

-

- Pockets that physically appear in the dimer but belong to a single chain (structural rearrangement). -

- -
- - - - - - - - - - - - - - - - {emergent_pockets && emergent_pockets.length > 0 ? ( - emergent_pockets.map((pocket, idx) => ( - - handleHighlight(residueIndices, `emg-${idx}`, comparisonHighlightTarget(pocket)) - } - proteinPdbId={complexStructureUrl} - sourceType="dimer" - onConformationChange={(confs, mode) => - onConformationChange?.(confs, mode, comparisonHighlightTarget(pocket)) - } - /> - )) - ) : ( - - - - )} - -
IDScoreVolHydroPolarΔ pLDDTCenterResiduesActions
- No emergent structural pockets found. -
-
-
- - {/* 6. Fragment Comparison — ChEMBL novel compounds */} - {fragment_comparison && ( - (fragment_comparison.unique_interface_fragments?.length > 0 || - fragment_comparison.unique_dimer_fragments?.length > 0) && ( -
-
-

- - - - Novel ChEMBL Fragment Suggestions -

-

- Compounds from the ChEMBL database unique to the dimerized state — not suggested for any monomer pocket. -

-
- -
- {/* Interface-specific fragments (highest value) */} -
-
-
- Interface Pocket Fragments -
- - {fragment_comparison.unique_interface_fragments?.length || 0} compounds - -
-

- Fragments targeting pockets at the protein-protein interface — highest value for PPI inhibitor design. -

- -
- - {/* Dimer-unique fragments */} -
-
-
- Dimer-only Fragments -
- - {fragment_comparison.unique_dimer_fragments?.length || 0} compounds - -
-

- Fragments unique to any dimer pocket (including emergent and conserved) not found in monomer analysis. -

- -
-
-
- ) - )} - -
- ); -} diff --git a/app/src/components/complex/ComparisonTab.tsx b/app/src/components/complex/ComparisonTab.tsx new file mode 100644 index 0000000..5c65001 --- /dev/null +++ b/app/src/components/complex/ComparisonTab.tsx @@ -0,0 +1,305 @@ +import React, { useState, useCallback, useRef, useMemo } from 'react'; +import { + BarChart, Bar, XAxis, YAxis, CartesianGrid, Tooltip, Legend, ResponsiveContainer, + ScatterChart, Scatter, ZAxis, Cell +} from 'recharts'; +import { PocketTableRow } from './PocketTableRow'; +import { FragmentList } from './FragmentList'; +import type { Pocket, ComparisonData, ScatterDataPoint, Conformation } from '../../types'; + +/** Mol* target from comparison tab */ +function comparisonHighlightTarget(pocket: Pocket): string { + return pocket.is_conserved ? 'both' : 'complex'; +} + +const CHART_MARGIN = { top: 10, right: 30, bottom: 20, left: 40 }; +const ZOOM_FACTOR = 1.3; +const MIN_ZOOM = 0.25; +const MAX_ZOOM = 8; + +interface Viewport { xMin: number; xMax: number; yMin: number; yMax: number; } + +function ScatterChartWithZoom({ data }: { data: ScatterDataPoint[] }) { + const fullExtent = useMemo(() => { + const xValues = data.map(d => d.avg_delta); + const yValues = data.map(d => d.druggability_score); + return { + xMin: Math.min(-5, Math.min(...xValues) - 1), + xMax: Math.max(5, Math.max(...xValues) + 1), + yMin: Math.min(...yValues) - 0.05, + yMax: Math.max(...yValues) + 0.05, + }; + }, [data]); + + const [viewport, setViewport] = useState(null); + const vp = viewport || fullExtent; + + const zoomLevel = useMemo(() => { + const fullW = fullExtent.xMax - fullExtent.xMin; + const curW = vp.xMax - vp.xMin; + return curW > 0 ? fullW / curW : 1; + }, [fullExtent, vp]); + + const chartRef = useRef(null); + const dragRef = useRef<{ startX: number; startY: number; vpStart: Viewport } | null>(null); + + const pixelToData = useCallback((px: number, py: number, containerRect: DOMRect) => { + const plotLeft = CHART_MARGIN.left; + const plotTop = CHART_MARGIN.top; + const plotWidth = containerRect.width - CHART_MARGIN.left - CHART_MARGIN.right; + const plotHeight = containerRect.height - CHART_MARGIN.top - CHART_MARGIN.bottom; + const fx = Math.max(0, Math.min(1, (px - plotLeft) / plotWidth)); + const fy = Math.max(0, Math.min(1, 1 - (py - plotTop) / plotHeight)); + return { + dataX: vp.xMin + fx * (vp.xMax - vp.xMin), + dataY: vp.yMin + fy * (vp.yMax - vp.yMin), + }; + }, [vp]); + + React.useEffect(() => { + const chartEl = chartRef.current; + if (!chartEl) return; + const onWheelNative = (e: WheelEvent) => { + e.preventDefault(); + const rect = chartEl.getBoundingClientRect(); + const px = e.clientX - rect.left; + const py = e.clientY - rect.top; + const { dataX, dataY } = pixelToData(px, py, rect); + const isZoomIn = e.deltaY < 0; + const factor = isZoomIn ? 1 / ZOOM_FACTOR : ZOOM_FACTOR; + const newXMin = dataX - (dataX - vp.xMin) * factor; + const newXMax = dataX + (vp.xMax - dataX) * factor; + const newYMin = dataY - (dataY - vp.yMin) * factor; + const newYMax = dataY + (vp.yMax - dataY) * factor; + const newW = newXMax - newXMin; + const fullW = fullExtent.xMax - fullExtent.xMin; + const newZoom = fullW / newW; + if (newZoom < MIN_ZOOM || newZoom > MAX_ZOOM) return; + setViewport({ xMin: newXMin, xMax: newXMax, yMin: newYMin, yMax: newYMax }); + }; + chartEl.addEventListener('wheel', onWheelNative, { passive: false }); + return () => chartEl.removeEventListener('wheel', onWheelNative); + }, [vp, fullExtent, pixelToData]); + + const handleMouseDown = useCallback((e: React.MouseEvent) => { + if (e.button !== 0) return; + e.preventDefault(); + dragRef.current = { startX: e.clientX, startY: e.clientY, vpStart: { ...vp } }; + document.body.style.cursor = 'grabbing'; + const handleMouseMove = (me: MouseEvent) => { + const dr = dragRef.current; + if (!dr) return; + const rect = chartRef.current?.getBoundingClientRect(); + if (!rect) return; + const plotWidth = rect.width - CHART_MARGIN.left - CHART_MARGIN.right; + const plotHeight = rect.height - CHART_MARGIN.top - CHART_MARGIN.bottom; + const dxData = -(( me.clientX - dr.startX) / plotWidth) * (dr.vpStart.xMax - dr.vpStart.xMin); + const dyData = ((me.clientY - dr.startY) / plotHeight) * (dr.vpStart.yMax - dr.vpStart.yMin); + setViewport({ xMin: dr.vpStart.xMin + dxData, xMax: dr.vpStart.xMax + dxData, yMin: dr.vpStart.yMin + dyData, yMax: dr.vpStart.yMax + dyData }); + }; + const handleMouseUp = () => { + dragRef.current = null; + document.body.style.cursor = ''; + window.removeEventListener('mousemove', handleMouseMove); + window.removeEventListener('mouseup', handleMouseUp); + }; + window.addEventListener('mousemove', handleMouseMove); + window.addEventListener('mouseup', handleMouseUp); + }, [vp]); + + const handleZoomIn = useCallback(() => { + const midX = (vp.xMin + vp.xMax) / 2; const midY = (vp.yMin + vp.yMax) / 2; + const factor = 1 / ZOOM_FACTOR; + setViewport({ xMin: midX - (midX - vp.xMin) * factor, xMax: midX + (vp.xMax - midX) * factor, yMin: midY - (midY - vp.yMin) * factor, yMax: midY + (vp.yMax - midY) * factor }); + }, [vp]); + + const handleZoomOut = useCallback(() => { + const midX = (vp.xMin + vp.xMax) / 2; const midY = (vp.yMin + vp.yMax) / 2; + const factor = ZOOM_FACTOR; + setViewport({ xMin: midX - (midX - vp.xMin) * factor, xMax: midX + (vp.xMax - midX) * factor, yMin: midY - (midY - vp.yMin) * factor, yMax: midY + (vp.yMax - midY) * factor }); + }, [vp]); + + const handleReset = () => setViewport(null); + const isReset = !viewport; + + return ( +
+
+

Stabilization vs Druggability (Complex Pockets)

+
+ + + +
+
+
+ + + + val.toFixed(3)} label={{ value: 'Disorder Delta (Δ pLDDT)', position: 'bottom', fill: '#888', fontSize: 10, fontFamily: 'monospace' }} /> + val.toFixed(3)} label={{ value: 'Druggability Score', angle: -90, position: 'left', fill: '#888', fontSize: 10, fontFamily: 'monospace' }} /> + [Number(value).toFixed(3), name]) as any} /> + a.avg_delta - b.avg_delta)} line={{ stroke: '#555', strokeWidth: 1.5, strokeDasharray: '4 4' }}> + {data.map((entry, index) => (= 5.0 ? '#10b981' : '#9ca3af'} />))} + + + + {data.every(d => Math.abs(d.avg_delta) < 0.001) && ( +
+ Disorder Delta data not available +
+ )} +
+ {!isReset && (

Scroll to zoom · Drag to pan · Click reset to restore

)} +
+ ); +} + +interface ComparisonTabProps { + comparison: ComparisonData | null; + activePocketIdx: string | number | null; + handleHighlight: (residueIndices: number[], pocketIdx: string | number, target?: string) => void; + monomerStructureUrl: string; + complexStructureUrl: string; + onConformationChange?: (confs: Conformation[] | null, mode: number | null, target: string) => void; +} + +export function ComparisonTab({ comparison, activePocketIdx, handleHighlight, monomerStructureUrl, complexStructureUrl, onConformationChange }: ComparisonTabProps) { + if (!comparison) return (
Comparison data not available.
); + + const { summary_metrics, ddgi, pocket_mapping, interface_pockets, conserved_pockets, emergent_pockets, graph_datasets, property_changes, stabilization_stats, fragment_comparison } = comparison; + const hasScatterData = graph_datasets?.stabilization_scatter && graph_datasets.stabilization_scatter.length > 0; + + const renderPocketTable = (pockets: Pocket[] | undefined, prefix: string) => ( + + {pockets && pockets.length > 0 ? ( + pockets.map((pocket, idx) => ( + handleHighlight(residueIndices, `${prefix}-${idx}`, comparisonHighlightTarget(pocket))} + proteinPdbId={complexStructureUrl} sourceType="dimer" + onConformationChange={(confs: any, mode: any) => onConformationChange?.(confs, mode, comparisonHighlightTarget(pocket))} /> + )) + ) : ( + No pockets found. + )} + + ); + + const tableHeader = ( + + + {['ID','Score','Vol','Hydro','Polar','Δ pLDDT','Center','Residues'].map(h => ( + {h} + ))} + Actions + + + ); + + return ( +
+ {/* 1. Summary Metrics & DDGI */} +
+
+ Total Monomer Pockets + {summary_metrics.total_monomer_pockets} +
+
+ Total Complex Pockets + {summary_metrics.total_dimer_pockets} +
+
+ True Interface Pockets + {pocket_mapping.interface_count} +
+
0 ? 'border-success/50' : 'border-danger/50'}`}> + + DDGI Score +
Dimerization Druggability Gain Index: Avg Dimer Score - Avg Monomer Score
+ + 0 ? 'text-success' : 'text-danger'}`}>{ddgi > 0 ? '+' : ''}{ddgi.toFixed(3)} +
+
+ + {/* 2. Pocket Mapping & Property Changes */} +
+
+

Pocket Transition Map

+
+
Conserved in both states{pocket_mapping.conserved_count}
+
Disappeared upon dimerization{pocket_mapping.monomer_only_count}
+
Newly emerged in dimer{pocket_mapping.emergent_count}
+
+
+
Residue Stabilization Analysis
+
Interface Residue Enrichment{stabilization_stats.enrichment_score.toFixed(2)}x
+
+
+
+

Average Property Shifts

+
+
Avg Volume{property_changes.monomer_avg_volume.toFixed(0)} → {property_changes.dimer_avg_volume.toFixed(0)} ų
+
Avg Hydrophobicity{property_changes.monomer_avg_hydrophobicity.toFixed(2)} → {property_changes.dimer_avg_hydrophobicity.toFixed(2)}
+
Avg Polarity{property_changes.monomer_avg_polarity.toFixed(2)} → {property_changes.dimer_avg_polarity.toFixed(2)}
+
Avg Druggability 0 ? 'text-success' : 'text-danger'}>{summary_metrics.avg_monomer_druggability.toFixed(3)} → {summary_metrics.avg_dimer_druggability.toFixed(3)}
+
+
+
+ + {/* 3. Charts */} + {hasScatterData && } + + {/* 4. True Interface Pockets */} +
+

True Interface Drug Targets

+

Pockets spanning multiple protein chains at the dimer interaction surface.

+
{tableHeader}{renderPocketTable(interface_pockets, 'int')}
+
+ + {/* 5b. Conserved Pockets */} +
+

Conserved Pockets

+

Pockets retained from monomer to dimer — spatially overlapping in both structures.

+
{tableHeader}{renderPocketTable(conserved_pockets, 'con')}
+
+ + {/* 5. Emergent Pockets */} +
+

Emergent Dimer-only Pockets

+

Pockets that physically appear in the dimer but belong to a single chain (structural rearrangement).

+
{tableHeader}{renderPocketTable(emergent_pockets, 'emg')}
+
+ + {/* 6. Fragment Comparison */} + {fragment_comparison && (fragment_comparison.unique_interface_fragments?.length > 0 || fragment_comparison.unique_dimer_fragments?.length > 0) && ( +
+
+

+ + Novel ChEMBL Fragment Suggestions +

+

Compounds from the ChEMBL database unique to the dimerized state — not suggested for any monomer pocket.

+
+
+
+
+
Interface Pocket Fragments
+ {fragment_comparison.unique_interface_fragments?.length || 0} compounds +
+

Fragments targeting pockets at the protein-protein interface — highest value for PPI inhibitor design.

+ +
+
+
+
Dimer-only Fragments
+ {fragment_comparison.unique_dimer_fragments?.length || 0} compounds +
+

Fragments unique to any dimer pocket (including emergent and conserved) not found in monomer analysis.

+ +
+
+
+ )} +
+ ); +} diff --git a/app/src/components/complex/ComplexHeader.jsx b/app/src/components/complex/ComplexHeader.tsx similarity index 89% rename from app/src/components/complex/ComplexHeader.jsx rename to app/src/components/complex/ComplexHeader.tsx index 0a57420..14d7257 100644 --- a/app/src/components/complex/ComplexHeader.jsx +++ b/app/src/components/complex/ComplexHeader.tsx @@ -1,7 +1,12 @@ import React from 'react'; +import type { Complex } from '../../types'; import { Badge } from '../common/Badge'; -export function ComplexHeader({ complex }) { +interface ComplexHeaderProps { + complex: Complex; +} + +export function ComplexHeader({ complex }: ComplexHeaderProps) { const { alphafold_id, protein_name, @@ -14,13 +19,13 @@ export function ComplexHeader({ complex }) { review_status } = complex; - const getDrugBadgeVariant = (count) => { + const getDrugBadgeVariant = (count: number): 'unknown' | 'undrugged' | 'drugged' => { if (count === -1) return 'unknown'; if (count === 0) return 'undrugged'; return 'drugged'; }; - const getDrugBadgeText = (count) => { + const getDrugBadgeText = (count: number): string => { if (count === -1) return 'DRUGS UNKNOWN'; if (count === 0) return 'UNDRUGGED'; return `${count} DRUGS`; diff --git a/app/src/components/complex/ConformationBrowser.jsx b/app/src/components/complex/ConformationBrowser.tsx similarity index 90% rename from app/src/components/complex/ConformationBrowser.jsx rename to app/src/components/complex/ConformationBrowser.tsx index b390339..0d675de 100644 --- a/app/src/components/complex/ConformationBrowser.jsx +++ b/app/src/components/complex/ConformationBrowser.tsx @@ -1,6 +1,13 @@ import React from 'react'; +import type { Conformation } from '../../types'; -export function ConformationBrowser({ conformations, activeMode, onSelect }) { +interface ConformationBrowserProps { + conformations: Conformation[]; + activeMode: number | null; + onSelect: (conformation: Conformation) => void; +} + +export function ConformationBrowser({ conformations, activeMode, onSelect }: ConformationBrowserProps) { if (!conformations?.length) return null; return ( diff --git a/app/src/components/complex/DockingLeaderboard.jsx b/app/src/components/complex/DockingLeaderboard.tsx similarity index 96% rename from app/src/components/complex/DockingLeaderboard.jsx rename to app/src/components/complex/DockingLeaderboard.tsx index 7a96708..c0da5ac 100644 --- a/app/src/components/complex/DockingLeaderboard.jsx +++ b/app/src/components/complex/DockingLeaderboard.tsx @@ -1,12 +1,20 @@ import React from 'react'; +import type { LeaderboardEntry, Conformation } from '../../types'; const CHEMBL_BASE_URL = 'https://www.ebi.ac.uk/chembl/compound_report_card/'; +interface DockingLeaderboardProps { + entries: LeaderboardEntry[]; + activeEntryId?: string; + onSelect?: (entry: LeaderboardEntry) => void; + onRemove?: (entryId: string) => void; +} + /** * DockingLeaderboard — Panel showing all completed docking results, sorted by binding affinity. * ChEMBL IDs are clickable links to the ChEMBL database. */ -export function DockingLeaderboard({ entries, activeEntryId, onSelect, onRemove }) { +export function DockingLeaderboard({ entries, activeEntryId, onSelect, onRemove }: DockingLeaderboardProps) { if (!entries || entries.length === 0) { return (
@@ -115,11 +123,16 @@ export function DockingLeaderboard({ entries, activeEntryId, onSelect, onRemove ); } +interface DockingResultDetailProps { + entry: LeaderboardEntry | null; + onConformationSelect?: (entry: LeaderboardEntry, mode: number) => void; +} + /** * DockingResultDetail — Shows details of a selected leaderboard entry with conformations. * Includes a ConformationBrowser so the user can switch poses from the detail panel. */ -export function DockingResultDetail({ entry, onConformationSelect }) { +export function DockingResultDetail({ entry, onConformationSelect }: DockingResultDetailProps) { const [activeMode, setActiveMode] = React.useState(1); React.useEffect(() => { diff --git a/app/src/components/complex/DockingPanel.jsx b/app/src/components/complex/DockingPanel.tsx similarity index 90% rename from app/src/components/complex/DockingPanel.jsx rename to app/src/components/complex/DockingPanel.tsx index 70e62f8..64c41fc 100644 --- a/app/src/components/complex/DockingPanel.jsx +++ b/app/src/components/complex/DockingPanel.tsx @@ -2,8 +2,28 @@ import React, { useEffect } from 'react'; import { useDockingJob } from '../../hooks/useDockingJob'; import { useChemblFragments } from '../../hooks/useChemblFragments'; import { MoleculePicker } from './MoleculePicker'; +import type { Pocket, Conformation } from '../../types'; -export function DockingPanel({ pocket, proteinPdbId, sourceType, onConformationChange, onUndock, onDockingComplete, apiBase = '/api' }) { +interface DockingPanelProps { + pocket: Pocket; + proteinPdbId: string; + sourceType?: string; + onConformationChange?: (confs: Conformation[] | null, mode: number | null) => void; + onUndock?: () => void; + onDockingComplete?: (result: { + pocketId: number; + sourceType: string; + fragmentId: string; + fragmentName: string; + smiles: string; + bindingAffinity: number; + conformations: Conformation[]; + timestamp: number; + }) => void; + apiBase?: string; +} + +export function DockingPanel({ pocket, proteinPdbId, sourceType, onConformationChange, onUndock, onDockingComplete, apiBase = '/api' }: DockingPanelProps) { const { fragments, isLoading: fragmentsLoading, @@ -36,9 +56,9 @@ export function DockingPanel({ pocket, proteinPdbId, sourceType, onConformationC onDockingComplete?.({ pocketId: pocket.pocket_id, sourceType: sourceType || 'dimer', - fragmentId: selectedFragment.chembl_id || selectedFragment.id, + fragmentId: selectedFragment.chembl_id || selectedFragment.id || '', fragmentName: selectedFragment.name || selectedFragment.chembl_id, - smiles: selectedFragment.smiles, + smiles: selectedFragment.smiles || '', bindingAffinity: conformations[0].binding_affinity, conformations, timestamp: Date.now(), diff --git a/app/src/components/complex/FragmentList.jsx b/app/src/components/complex/FragmentList.tsx similarity index 95% rename from app/src/components/complex/FragmentList.jsx rename to app/src/components/complex/FragmentList.tsx index 34ca5f8..952a0f5 100644 --- a/app/src/components/complex/FragmentList.jsx +++ b/app/src/components/complex/FragmentList.tsx @@ -1,9 +1,14 @@ import React from 'react'; +import type { Fragment } from '../../types'; + +interface FragmentListProps { + fragments?: Fragment[]; +} /** * FragmentList — displays suggested fragment molecules from the ChEMBL database for a pocket. */ -export function FragmentList({ fragments }) { +export function FragmentList({ fragments }: FragmentListProps) { if (!fragments || fragments.length === 0) { return (
diff --git a/app/src/components/complex/MetricsPanel.jsx b/app/src/components/complex/MetricsPanel.tsx similarity index 95% rename from app/src/components/complex/MetricsPanel.jsx rename to app/src/components/complex/MetricsPanel.tsx index 4c8f12b..78dd167 100644 --- a/app/src/components/complex/MetricsPanel.jsx +++ b/app/src/components/complex/MetricsPanel.tsx @@ -1,7 +1,12 @@ import React from 'react'; +import type { Complex } from '../../types'; import { toPercent } from '../common/GapScoreBar'; -export function MetricsPanel({ complex }) { +interface MetricsPanelProps { + complex: Complex; +} + +export function MetricsPanel({ complex }: MetricsPanelProps) { const { monomer_plddt_avg, dimer_plddt_avg, disorder_delta, gap_score, known_drug_names } = complex; const m_plddt = monomer_plddt_avg || 0; diff --git a/app/src/components/complex/MoleculePicker.jsx b/app/src/components/complex/MoleculePicker.tsx similarity index 93% rename from app/src/components/complex/MoleculePicker.jsx rename to app/src/components/complex/MoleculePicker.tsx index b06af9d..be7936c 100644 --- a/app/src/components/complex/MoleculePicker.jsx +++ b/app/src/components/complex/MoleculePicker.tsx @@ -1,4 +1,16 @@ import React from 'react'; +import type { Fragment } from '../../types'; + +interface MoleculePickerProps { + fragments: Fragment[]; + isLoading: boolean; + error: string | null; + selectedFragment: Fragment | null; + onSelect: (fragment: Fragment) => void; + onConfirm: () => void; + isDockingRunning: boolean; + onRetry: () => void; +} export function MoleculePicker({ fragments, @@ -9,7 +21,7 @@ export function MoleculePicker({ onConfirm, isDockingRunning, onRetry, -}) { +}: MoleculePickerProps) { return (
@@ -87,7 +99,7 @@ export function MoleculePicker({ className="font-mono text-[10px] text-text-secondary bg-bg-tertiary px-2 py-1 rounded block mb-2 truncate" > {frag.smiles?.slice(0, 60)} - {frag.smiles?.length > 60 ? '…' : ''} + {(frag.smiles?.length ?? 0) > 60 ? '…' : ''}
diff --git a/app/src/components/complex/PocketTableRow.jsx b/app/src/components/complex/PocketTableRow.tsx similarity index 89% rename from app/src/components/complex/PocketTableRow.jsx rename to app/src/components/complex/PocketTableRow.tsx index b2b117c..5907b1c 100644 --- a/app/src/components/complex/PocketTableRow.jsx +++ b/app/src/components/complex/PocketTableRow.tsx @@ -1,10 +1,23 @@ import React from 'react'; +import type { Pocket } from '../../types'; + +interface PocketTableRowProps { + pocket: Pocket; + activeTab: string; + isActive: boolean; + onHighlight: (residueIndices: number[]) => void; + proteinPdbId?: string; + sourceType?: string; + onStartDocking?: (info: { pocket: Pocket; sourceType: string; proteinPdbId: string }) => void; + isDockingActive?: boolean; + onConformationChange?: (confs: unknown, mode: unknown) => void; +} /** * PocketTableRow — displays details for a single predicted binding pocket in a table format. * "Dock Molecule" signals the parent to open the docking UI in the detail panel. */ -export function PocketTableRow({ pocket, activeTab, isActive, onHighlight, proteinPdbId, sourceType, onStartDocking, isDockingActive }) { +export function PocketTableRow({ pocket, activeTab, isActive, onHighlight, proteinPdbId, sourceType, onStartDocking, isDockingActive }: PocketTableRowProps) { const scoreColor = pocket.druggability_score >= 0.5 ? 'text-success' : pocket.druggability_score >= 0.3 @@ -90,7 +103,7 @@ export function PocketTableRow({ pocket, activeTab, isActive, onHighlight, prote disabled={!proteinPdbId} onClick={() => { if (!proteinPdbId) return; - onStartDocking?.({ pocket, sourceType, proteinPdbId }); + onStartDocking?.({ pocket, sourceType: sourceType || 'dimer', proteinPdbId }); }} className={`font-mono text-xs uppercase tracking-wider px-2 py-1 rounded border transition-colors duration-150 ${ !proteinPdbId diff --git a/app/src/components/complex/ViewerPlaceholder.jsx b/app/src/components/complex/ViewerPlaceholder.tsx similarity index 87% rename from app/src/components/complex/ViewerPlaceholder.jsx rename to app/src/components/complex/ViewerPlaceholder.tsx index c4d3851..ae793c2 100644 --- a/app/src/components/complex/ViewerPlaceholder.jsx +++ b/app/src/components/complex/ViewerPlaceholder.tsx @@ -1,7 +1,14 @@ import React from 'react'; -export function ViewerPlaceholder({ monomerUrl, complexUrl, monomerPlddt, dimerPlddt }) { - const renderPanel = (label, url, plddt, desc) => { +interface ViewerPlaceholderProps { + monomerUrl?: string; + complexUrl?: string; + monomerPlddt?: number; + dimerPlddt?: number; +} + +export function ViewerPlaceholder({ monomerUrl, complexUrl, monomerPlddt, dimerPlddt }: ViewerPlaceholderProps) { + const renderPanel = (label: string, url: string | undefined, plddt: number | undefined, desc: string) => { const filename = url ? url.split('/').pop() : 'No structure available'; return ( diff --git a/app/src/components/complex/viewer/DisorderDeltaBar.jsx b/app/src/components/complex/viewer/DisorderDeltaBar.tsx similarity index 88% rename from app/src/components/complex/viewer/DisorderDeltaBar.jsx rename to app/src/components/complex/viewer/DisorderDeltaBar.tsx index f8fe07b..8d6cf5b 100644 --- a/app/src/components/complex/viewer/DisorderDeltaBar.jsx +++ b/app/src/components/complex/viewer/DisorderDeltaBar.tsx @@ -1,6 +1,11 @@ import React from 'react'; -export function DisorderDeltaBar({ disorderDelta, visible }) { +interface DisorderDeltaBarProps { + disorderDelta?: number; + visible: boolean; +} + +export function DisorderDeltaBar({ disorderDelta, visible }: DisorderDeltaBarProps) { if (!visible) return null; const delta = disorderDelta || 0; diff --git a/app/src/components/complex/viewer/MolstarPanel.jsx b/app/src/components/complex/viewer/MolstarPanel.tsx similarity index 83% rename from app/src/components/complex/viewer/MolstarPanel.jsx rename to app/src/components/complex/viewer/MolstarPanel.tsx index de91c34..ca819a0 100644 --- a/app/src/components/complex/viewer/MolstarPanel.jsx +++ b/app/src/components/complex/viewer/MolstarPanel.tsx @@ -4,8 +4,22 @@ import { useTheme } from '../../../hooks/useTheme'; import { useMolstar } from './useMolstar'; import { ViewerHeader } from './ViewerHeader'; import { ViewerFooter } from './ViewerFooter'; +import type { Conformation, MolstarPanelHandle } from '../../../types'; -export const MolstarPanel = React.memo(forwardRef(({ structureUrl, label, plddt, description, visible = true, highlightIndices = null, representation = 'cartoon', conformations = null, activeMode = null, hideControls = false }, ref) => { +interface MolstarPanelProps { + structureUrl?: string; + label: string; + plddt?: number; + description?: string; + visible?: boolean; + highlightIndices?: number[] | null; + representation?: string; + conformations?: Conformation[] | null; + activeMode?: number | null; + hideControls?: boolean; +} + +export const MolstarPanel = React.memo(forwardRef(({ structureUrl, label, plddt, description, visible = true, highlightIndices = null, representation = 'cartoon', conformations = null, activeMode = null, hideControls = false }, ref) => { const [isFullscreen, setIsFullscreen] = useState(false); const { theme } = useTheme(); const { containerRef, isLoading, error, highlightPocket, clearPocketHighlight } = useMolstar({ @@ -41,12 +55,12 @@ export const MolstarPanel = React.memo(forwardRef(({ structureUrl, label, plddt,
{/* Mol* canvas container */}
} className="absolute inset-0" style={{ width: '100%', height: '100%', position: 'absolute' }} /> - {conformations?.length > 0 && !isLoading && !error && ( + {conformations && conformations.length > 0 && !isLoading && !error && (
@@ -102,7 +116,7 @@ export const MolstarPanel = React.memo(forwardRef(({ structureUrl, label, plddt, )}
- + ); })); diff --git a/app/src/components/complex/viewer/ProteinViewer.jsx b/app/src/components/complex/viewer/ProteinViewer.tsx similarity index 87% rename from app/src/components/complex/viewer/ProteinViewer.jsx rename to app/src/components/complex/viewer/ProteinViewer.tsx index 1d1dfdc..e608cc4 100644 --- a/app/src/components/complex/viewer/ProteinViewer.jsx +++ b/app/src/components/complex/viewer/ProteinViewer.tsx @@ -1,12 +1,35 @@ import React, { useState, useRef, useImperativeHandle, forwardRef, useMemo } from 'react'; import { MolstarPanel } from './MolstarPanel'; import { DisorderDeltaBar } from './DisorderDeltaBar'; +import type { Conformation, ProteinViewerHandle, MolstarPanelHandle } from '../../../types'; + +interface ProteinViewerProps { + monomerUrl?: string; + complexUrl?: string; + monomerPlddt?: number; + dimerPlddt?: number; + disorderDelta?: number; + monomerConformations?: Conformation[] | null; + complexConformations?: Conformation[] | null; + activeModeMonomer?: number | null; + activeModeComplex?: number | null; +} + +interface DockingState { + conformations: Conformation[] | null; + activeMode: number | null; +} + +interface ActiveHighlight { + indices: number[]; + target: string; +} /** * ProteinViewer — Displays monomer and dimer Mol* viewers side by side. * Supports synchronized conformations (docking results) for both monomer and dimer. */ -export const ProteinViewer = forwardRef( +export const ProteinViewer = forwardRef( ({ monomerUrl, complexUrl, @@ -19,29 +42,29 @@ export const ProteinViewer = forwardRef( activeModeComplex = null }, ref) => { const [isZoomed, setIsZoomed] = useState(false); - const [activeHighlight, setActiveHighlight] = useState(null); // { indices, target } + const [activeHighlight, setActiveHighlight] = useState(null); const [representation, setRepresentation] = useState('cartoon'); // Internal state for docking results triggered via imperative API - const [monomerDocking, setMonomerDocking] = useState({ conformations: null, activeMode: null }); - const [complexDocking, setComplexDocking] = useState({ conformations: null, activeMode: null }); + const [monomerDocking, setMonomerDocking] = useState({ conformations: null, activeMode: null }); + const [complexDocking, setComplexDocking] = useState({ conformations: null, activeMode: null }); const mConfs = monomerConformations ?? monomerDocking.conformations; const mMode = activeModeMonomer ?? monomerDocking.activeMode; const cConfs = complexConformations ?? complexDocking.conformations; const cMode = activeModeComplex ?? complexDocking.activeMode; - const monomerViewerRef = useRef(null); - const complexViewerRef = useRef(null); + const monomerViewerRef = useRef(null); + const complexViewerRef = useRef(null); useImperativeHandle(ref, () => ({ - highlightPocket: (residueIndices, target = 'complex') => { + highlightPocket: (residueIndices: number[], target = 'complex') => { setActiveHighlight({ indices: residueIndices, target }); }, clearPocketHighlight: () => { setActiveHighlight(null); }, - setConformations: (confs, mode, target = 'complex') => { + setConformations: (confs: Conformation[], mode: number, target = 'complex') => { if (target === 'monomer' || target === 'both') { setMonomerDocking({ conformations: confs, activeMode: mode }); } @@ -62,7 +85,7 @@ export const ProteinViewer = forwardRef( // Close zoom on Escape key React.useEffect(() => { if (!isZoomed) return; - const handleKey = (e) => { + const handleKey = (e: KeyboardEvent) => { if (e.key === 'Escape') setIsZoomed(false); }; window.addEventListener('keydown', handleKey); diff --git a/app/src/components/complex/viewer/RevealButton.jsx b/app/src/components/complex/viewer/RevealButton.tsx similarity index 81% rename from app/src/components/complex/viewer/RevealButton.jsx rename to app/src/components/complex/viewer/RevealButton.tsx index 026a841..4dd15f1 100644 --- a/app/src/components/complex/viewer/RevealButton.jsx +++ b/app/src/components/complex/viewer/RevealButton.tsx @@ -1,7 +1,13 @@ import React from 'react'; import { motion } from 'framer-motion'; -export function RevealButton({ isRevealed, onReveal, disabled }) { +interface RevealButtonProps { + isRevealed: boolean; + onReveal: () => void; + disabled?: boolean; +} + +export function RevealButton({ isRevealed, onReveal, disabled }: RevealButtonProps) { return ( diff --git a/app/src/components/complex/viewer/useMolstar.js b/app/src/components/complex/viewer/useMolstar.ts similarity index 82% rename from app/src/components/complex/viewer/useMolstar.js rename to app/src/components/complex/viewer/useMolstar.ts index 7642566..0aea695 100644 --- a/app/src/components/complex/viewer/useMolstar.js +++ b/app/src/components/complex/viewer/useMolstar.ts @@ -1,29 +1,38 @@ import { useRef, useEffect, useState, useCallback } from 'react'; -import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context'; import { DefaultPluginUISpec } from 'molstar/lib/mol-plugin-ui/spec'; import { createPluginUI } from 'molstar/lib/mol-plugin-ui'; import { PluginConfig } from 'molstar/lib/mol-plugin/config'; import { Color } from 'molstar/lib/mol-util/color'; import { createRoot } from 'react-dom/client'; -import { StructureSelection, StructureQuery, StructureProperties } from 'molstar/lib/mol-model/structure'; +import { StructureSelection } from 'molstar/lib/mol-model/structure'; import { Script } from 'molstar/lib/mol-script/script'; -import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder'; -import { Bundle } from 'molstar/lib/mol-model/structure/structure/element/bundle'; -import { Overpaint } from 'molstar/lib/mol-theme/overpaint'; import 'molstar/lib/mol-plugin-ui/skin/dark.scss'; +import type { Conformation } from '../../../types'; + +interface UseMolstarOptions { + structureUrl?: string; + label?: string; + autoLoad?: boolean; + highlightIndices?: number[] | null; + theme?: string; + representation?: string; + conformations?: Conformation[] | null; + activeMode?: number | null; + hideControls?: boolean; +} + +// Extend HTMLElement to hold React root +interface HTMLElementWithRoot extends HTMLElement { + __reactRoot?: ReturnType; +} + /** * useMolstar — React hook that encapsulates the Mol* viewer lifecycle. * * Handles initialization, structure loading from .cif URL, pLDDT coloring, * and cleanup on unmount. No Mol* code should exist outside this hook. - * - * @param {Object} options - * @param {string} options.structureUrl — URL to the .cif file - * @param {string} options.label — label for the structure - * @param {boolean} options.autoLoad — whether to load immediately (default true) - * @returns {{ containerRef, isLoading, error, resetCamera }} */ export function useMolstar({ structureUrl, @@ -35,15 +44,15 @@ export function useMolstar({ conformations = null, activeMode = null, hideControls = false, -}) { - const containerRef = useRef(null); - const pluginRef = useRef(null); +}: UseMolstarOptions) { + const containerRef = useRef(null); + const pluginRef = useRef(null); const initRef = useRef(false); const pocketActiveRef = useRef(false); // Track if a pocket highlight is active - const poseStructureRefs = useRef(new Map()); - const activeModeRef = useRef(null); + const poseStructureRefs = useRef>(new Map()); + const activeModeRef = useRef(null); const [isLoading, setIsLoading] = useState(false); - const [error, setError] = useState(null); + const [error, setError] = useState(null); // Initialize Mol* plugin useEffect(() => { @@ -89,13 +98,14 @@ export function useMolstar({ ); const plugin = await createPluginUI({ - target: containerRef.current, + target: containerRef.current as HTMLElement, spec, - render: (component, target) => { - let root = target.__reactRoot; + render: (component: any, target: any) => { + const el = target as HTMLElementWithRoot; + let root = el.__reactRoot; if (!root) { - root = createRoot(target); - target.__reactRoot = root; + root = createRoot(el); + el.__reactRoot = root; } root.render(component); }, @@ -124,10 +134,10 @@ export function useMolstar({ if (autoLoad && structureUrl) { await loadStructure(plugin, structureUrl); } - } catch (err) { + } catch (err: unknown) { console.error('[useMolstar] init failed:', err); if (!disposed) { - setError(`Viewer init failed: ${err.message}`); + setError(`Viewer init failed: ${err instanceof Error ? err.message : String(err)}`); } } }; @@ -146,6 +156,7 @@ export function useMolstar({ } initRef.current = false; }; + // eslint-disable-next-line react-hooks/exhaustive-deps }, []); // Reload structure when URL changes (after init) @@ -155,6 +166,7 @@ export function useMolstar({ if (!pluginRef.current.isInitialized) return; loadStructure(pluginRef.current, structureUrl); + // eslint-disable-next-line react-hooks/exhaustive-deps }, [structureUrl]); // Update background when theme changes @@ -177,15 +189,13 @@ export function useMolstar({ useEffect(() => { if (!pluginRef.current || !pluginRef.current.isInitialized || isLoading) return; updateRepresentationStyle(pluginRef.current, representation); + // eslint-disable-next-line react-hooks/exhaustive-deps }, [representation, isLoading]); /** * Update the representation type for all structures. - * Uses Mol*'s component manager to remove existing representations - * and add new ones with the desired type. - * Supported types: 'cartoon', 'ball-and-stick', 'gaussian-surface', 'spacefill', etc. */ - const updateRepresentationStyle = async (plugin, type) => { + const updateRepresentationStyle = async (plugin: any, type: string) => { try { const { structures } = plugin.managers.structure.hierarchy.current; if (!structures || structures.length === 0) return; @@ -216,7 +226,7 @@ export function useMolstar({ /** * Load a .cif file and apply pLDDT confidence coloring. */ - const loadStructure = async (plugin, url) => { + const loadStructure = async (plugin: any, url: string) => { setIsLoading(true); setError(null); @@ -231,14 +241,14 @@ export function useMolstar({ } // Download the CIF file - let data; + let data: any; try { data = await plugin.builders.data.download( { url, isBinary: false, label }, { state: { isGhost: true } } ); - } catch (dlErr) { - throw new Error(`Download failed for ${url}: ${dlErr.message}`); + } catch (dlErr: unknown) { + throw new Error(`Download failed for ${url}: ${dlErr instanceof Error ? dlErr.message : String(dlErr)}`); } // Detect format from URL @@ -246,7 +256,7 @@ export function useMolstar({ const format = isPdb ? 'pdb' : 'mmcif'; // Parse structure data and build trajectory - let trajectory; + let trajectory: any; try { trajectory = await plugin.builders.structure.parseTrajectory(data, format); } catch (parseErr) { @@ -269,8 +279,6 @@ export function useMolstar({ ); // Apply pLDDT confidence coloring (uncertainty theme) - // AlphaFold stores pLDDT in the B-factor column. - // Mol* 'uncertainty' theme maps B-factor → standard 4-color pLDDT scale await applyPlddtColoring(plugin); // Apply initial representation if not default (cartoon) @@ -281,9 +289,9 @@ export function useMolstar({ // Frame the camera plugin.managers.camera.reset(); - } catch (err) { + } catch (err: unknown) { console.error(`[useMolstar] Load failed for ${url}:`, err); - setError(`Failed to load: ${err.message}`); + setError(`Failed to load: ${err instanceof Error ? err.message : String(err)}`); } finally { setIsLoading(false); } @@ -306,7 +314,7 @@ export function useMolstar({ * Preload all conformations as hidden Mol* structures. * Show only the one matching initialMode. Receptor always stays visible. */ - async function preloadConformations(confs, initialMode) { + async function preloadConformations(confs: Conformation[], initialMode?: number) { const plugin = pluginRef.current; if (!plugin?.isInitialized) return; await clearAllPoses(); @@ -335,7 +343,7 @@ export function useMolstar({ const structRef = structures[structures.length - 1]; if (!structRef) continue; - const modeColors = { + const modeColors: Record> = { 1: Color(0xf97316), 2: Color(0x8b5cf6), 3: Color(0x06b6d4), @@ -373,7 +381,7 @@ export function useMolstar({ /** * Switch visible pose to `mode`. Hide previous. Does not reset camera. */ - async function showConformation(mode) { + async function showConformation(mode: number) { const plugin = pluginRef.current; if (!plugin) return; const hierarchy = plugin.managers.structure.hierarchy; @@ -396,7 +404,7 @@ export function useMolstar({ * Highlight specific residues in the 3D viewer (pocket visualization). * Uses Mol*'s native selection manager to highlight and focus the pocket. */ - const highlightPocket = useCallback(async (residueIndices) => { + const highlightPocket = useCallback(async (residueIndices: number[]) => { const plugin = pluginRef.current; if (!plugin || !residueIndices || residueIndices.length === 0) return; @@ -410,7 +418,7 @@ export function useMolstar({ // Clear previous selections plugin.managers.interactivity.lociSelects.deselectAll(); - let targetLoci = null; + let targetLoci: any = null; for (const s of structures) { if (!s.cell?.obj?.data) continue; @@ -418,9 +426,9 @@ export function useMolstar({ // Create a selection matching either label_seq_id (CIF) or auth_seq_id (PDB) const sel = Script.getStructureSelection( - Q => Q.struct.generator.atomGroups({ + (Q: any) => Q.struct.generator.atomGroups({ 'residue-test': Q.core.logic.or( - residueIndices.flatMap(idx => [ + residueIndices.flatMap((idx: number) => [ Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), idx]), Q.core.rel.eq([Q.struct.atomProperty.macromolecular.auth_seq_id(), idx]) ]) @@ -487,6 +495,7 @@ export function useMolstar({ } else { clearAllPoses().catch((e) => console.warn('[useMolstar] clearAllPoses failed:', e)); } + // eslint-disable-next-line react-hooks/exhaustive-deps }, [conformations, isLoading]); // When activeMode changes and poses are already loaded: just switch visibility @@ -495,6 +504,7 @@ export function useMolstar({ if (!plugin || activeMode == null || !poseStructureRefs.current.size) return; if (activeMode === activeModeRef.current) return; showConformation(activeMode).catch((e) => console.warn('[useMolstar] showConformation failed:', e)); + // eslint-disable-next-line react-hooks/exhaustive-deps }, [activeMode]); return { @@ -512,34 +522,23 @@ export function useMolstar({ /** * Apply pLDDT confidence coloring to all representations. - * - * AlphaFold stores pLDDT (confidence, 0-100) in the B-factor column. - * Mol*'s built-in 'uncertainty' theme uses a 'red-white-blue' scale with - * reverse=true, which maps HIGH B-factor → RED. That's correct for actual - * uncertainty, but WRONG for pLDDT where HIGH = HIGH confidence = should be BLUE. - * - * Strategy: - * 1. Apply uncertainty theme via the normal API (sets up proper B-factor reading). - * 2. Do a direct state-tree update to replace colorTheme.params.list with the - * reversed color array, so the theme factory sees blue→white→red and its - * built-in `reverse:true` flips it to red→white→blue mapping (0→red, 100→blue). */ -async function applyPlddtColoring(plugin) { +async function applyPlddtColoring(plugin: any) { const themeNames = ['uncertainty', 'plddt-confidence', 'b-factor']; const registry = plugin.representation.structure.themes.colorThemeRegistry; - let themeName = null; + let themeName: string | null = null; const availableThemes = registry._list || []; for (const name of themeNames) { - if (availableThemes.some(t => t.name === name)) { + if (availableThemes.some((t: any) => t.name === name)) { themeName = name; break; } } if (!themeName) { - console.warn('[useMolstar] No pLDDT color theme found. Available:', availableThemes.map(t => t.name)); + console.warn('[useMolstar] No pLDDT color theme found. Available:', availableThemes.map((t: any) => t.name)); return; } @@ -549,7 +548,7 @@ async function applyPlddtColoring(plugin) { // Step 1: Apply the uncertainty theme via normal API for (const s of structures) { if (!s.components) continue; - const validComponents = s.components.filter(c => c && c.representations); + const validComponents = s.components.filter((c: any) => c && c.representations); if (validComponents.length > 0) { try { await plugin.managers.structure.component.updateRepresentationsTheme( @@ -563,10 +562,6 @@ async function applyPlddtColoring(plugin) { } // Step 2: Directly patch representation state cells to flip the color list. - // The uncertainty theme default list is 'red-white-blue' with reverse=true, - // meaning domain_min(0)→blue, domain_max(100)→red. - // We swap the list to 'blue-white-red' so that with reverse=true: - // domain_min(0)→red, domain_max(100)→blue. Exactly what we want for pLDDT. try { const update = plugin.state.data.build(); let patched = false; @@ -581,9 +576,7 @@ async function applyPlddtColoring(plugin) { const ct = cell.transform.params.colorTheme; if (ct.name !== 'uncertainty') continue; - update.to(cell).update(old => { - // Reverse the color list array in-place so the theme factory's - // built-in reverse:true flips it back to the correct pLDDT mapping. + update.to(cell).update((old: any) => { if (old.colorTheme?.params?.list?.colors) { old.colorTheme.params.list.colors = [...old.colorTheme.params.list.colors].reverse(); } @@ -600,4 +593,3 @@ async function applyPlddtColoring(plugin) { console.warn('[useMolstar] Failed to patch color list for pLDDT:', e); } } - diff --git a/app/src/components/dashboard/TargetTable.jsx b/app/src/components/dashboard/TargetTable.tsx similarity index 95% rename from app/src/components/dashboard/TargetTable.jsx rename to app/src/components/dashboard/TargetTable.tsx index f02a397..0690aff 100644 --- a/app/src/components/dashboard/TargetTable.jsx +++ b/app/src/components/dashboard/TargetTable.tsx @@ -2,8 +2,15 @@ import React from 'react'; import { useNavigate } from 'react-router-dom'; import { Badge } from '../common/Badge'; import { GapScoreBar } from '../common/GapScoreBar'; +import type { Complex } from '../../types'; -export function TargetTable({ data = [], filter = 'all', onFilterChange }) { +interface TargetTableProps { + data?: Complex[]; + filter?: string; + onFilterChange: (filter: string) => void; +} + +export function TargetTable({ data = [], filter = 'all', onFilterChange }: TargetTableProps) { const navigate = useNavigate(); const filters = [ @@ -112,7 +119,7 @@ export function TargetTable({ data = [], filter = 'all', onFilterChange }) { })} {data.length === 0 && ( - + No targets found for this filter. diff --git a/app/src/components/layout/Footer.jsx b/app/src/components/layout/Footer.tsx similarity index 100% rename from app/src/components/layout/Footer.jsx rename to app/src/components/layout/Footer.tsx diff --git a/app/src/components/layout/Navbar.jsx b/app/src/components/layout/Navbar.tsx similarity index 100% rename from app/src/components/layout/Navbar.jsx rename to app/src/components/layout/Navbar.tsx diff --git a/app/src/components/search/ResultCard.jsx b/app/src/components/search/ResultCard.tsx similarity index 91% rename from app/src/components/search/ResultCard.jsx rename to app/src/components/search/ResultCard.tsx index 4c5c608..fb7688f 100644 --- a/app/src/components/search/ResultCard.jsx +++ b/app/src/components/search/ResultCard.tsx @@ -2,8 +2,13 @@ import React from 'react'; import { useNavigate } from 'react-router-dom'; import { Badge } from '../common/Badge'; import { GapScoreBar } from '../common/GapScoreBar'; +import type { Complex } from '../../types'; -export function ResultCard({ complex }) { +interface ResultCardProps { + complex: Complex; +} + +export function ResultCard({ complex }: ResultCardProps) { const navigate = useNavigate(); const { @@ -24,13 +29,13 @@ export function ResultCard({ complex }) { navigate(`/complex/${uniprot_id}`); }; - const getDrugBadgeVariant = (count) => { + const getDrugBadgeVariant = (count: number): 'unknown' | 'undrugged' | 'drugged' => { if (count === -1) return 'unknown'; if (count === 0) return 'undrugged'; return 'drugged'; }; - const getDrugBadgeText = (count) => { + const getDrugBadgeText = (count: number): string => { if (count === -1) return 'DRUGS UNKNOWN'; if (count === 0) return 'UNDRUGGED'; return `${count} DRUGS`; diff --git a/app/src/components/search/SearchBar.jsx b/app/src/components/search/SearchBar.tsx similarity index 82% rename from app/src/components/search/SearchBar.jsx rename to app/src/components/search/SearchBar.tsx index fc671a6..eb12724 100644 --- a/app/src/components/search/SearchBar.jsx +++ b/app/src/components/search/SearchBar.tsx @@ -1,20 +1,26 @@ -import React, { useState, useEffect } from 'react'; +import React from 'react'; -export function SearchBar({ onSearch, loading = false, initialValue = '' }) { - const [value, setValue] = useState(initialValue); +interface SearchBarProps { + onSearch: (query: string) => void; + loading?: boolean; + initialValue?: string; +} + +export function SearchBar({ onSearch, loading = false, initialValue = '' }: SearchBarProps) { + const [value, setValue] = React.useState(initialValue); - useEffect(() => { + React.useEffect(() => { setValue(initialValue); }, [initialValue]); - const handleSubmit = (e) => { + const handleSubmit = (e: React.FormEvent) => { e.preventDefault(); if (value.trim() && !loading) { onSearch(value); } }; - const handleKeyDown = (e) => { + const handleKeyDown = (e: React.KeyboardEvent) => { if (e.key === 'Enter') { handleSubmit(e); } diff --git a/app/src/config.js b/app/src/config.ts similarity index 78% rename from app/src/config.js rename to app/src/config.ts index afb144c..66d5507 100644 --- a/app/src/config.js +++ b/app/src/config.ts @@ -1,6 +1,8 @@ +import type { DemoProtein } from './types'; + export const API_BASE = '/api'; -export const DEMO_PROTEINS = [ +export const DEMO_PROTEINS: DemoProtein[] = [ { id: 'P04637', label: 'TP53', description: 'Tumor suppressor · Human · 5 known drugs' }, { id: 'P9WIU3', label: 'FtsZ', description: 'Cell division · M. tuberculosis · 0 known drugs' }, { id: 'Q55DI5', label: 'Q55DI5', description: 'Transcription factor · D. discoideum · Dramatic reveal' } diff --git a/app/src/hooks/useBindingSites.js b/app/src/hooks/useBindingSites.ts similarity index 61% rename from app/src/hooks/useBindingSites.js rename to app/src/hooks/useBindingSites.ts index 5dfdaf1..847da31 100644 --- a/app/src/hooks/useBindingSites.js +++ b/app/src/hooks/useBindingSites.ts @@ -1,19 +1,16 @@ import { useState, useEffect, useCallback } from 'react'; import { API_BASE } from '../config'; +import { safeJson } from '../utils/safeFetch'; +import type { BindingSitesData, Pocket } from '../types'; /** * useBindingSites — fetches predicted binding sites for a complex. * Lazy-loads: only fetches when `enabled` is true. - * - * @param {string} complexId — UniProt or AlphaFold ID - * @param {boolean} enabled — whether to trigger the fetch - * @param {boolean} showAll — whether to fetch all pockets without limit - * @returns {{ pockets, totalPockets, interfaceCount, loading, error, refetch }} */ -export function useBindingSites(complexId, enabled = false) { - const [data, setData] = useState(null); +export function useBindingSites(complexId: string | undefined, enabled = false) { + const [data, setData] = useState(null); const [loading, setLoading] = useState(false); - const [error, setError] = useState(null); + const [error, setError] = useState(null); const fetchSites = useCallback(async () => { if (!complexId) return; @@ -25,15 +22,19 @@ export function useBindingSites(complexId, enabled = false) { const response = await fetch( `${API_BASE}/complex/${encodeURIComponent(complexId)}/binding-sites` ); - const body = await response.json(); + const body = await safeJson(response); if (!response.ok) { - throw new Error(body.message || 'Failed to load binding sites'); + throw new Error(body?.message || `Failed to load binding sites (HTTP ${response.status})`); + } + + if (!body) { + throw new Error('Server returned an empty response for binding sites'); } setData(body); - } catch (err) { - setError(err.message || 'An error occurred loading binding sites.'); + } catch (err: unknown) { + setError(err instanceof Error ? err.message : 'An error occurred loading binding sites.'); } finally { setLoading(false); } diff --git a/app/src/hooks/useChemblFragments.js b/app/src/hooks/useChemblFragments.ts similarity index 67% rename from app/src/hooks/useChemblFragments.js rename to app/src/hooks/useChemblFragments.ts index 840cce5..ab0dfc8 100644 --- a/app/src/hooks/useChemblFragments.js +++ b/app/src/hooks/useChemblFragments.ts @@ -1,15 +1,25 @@ import { useState, useEffect, useCallback, useRef } from 'react'; +import { safeJson } from '../utils/safeFetch'; +import type { Fragment } from '../types'; + +interface ChemblOptions { + volume?: number; + hydrophobicity?: number; + polarity?: number; + sourceType?: string; + lazy?: boolean; +} /** * Normalizes fragment data from the API to ensure required fields. */ -function normalizeFragment(f) { - if (!f || typeof f !== 'object') return f; +function normalizeFragment(f: Record): Fragment { + if (!f || typeof f !== 'object') return f as unknown as Fragment; return { ...f, - mw: f.mw != null ? f.mw : f.mol_weight, - id: f.chembl_id || f.zinc_id, - }; + mw: f.mw != null ? (f.mw as number) : (f.mol_weight as number | undefined), + id: (f.chembl_id as string) || (f.zinc_id as string), + } as Fragment; } /** @@ -18,11 +28,11 @@ function normalizeFragment(f) { * When options.lazy is true, fragments are NOT fetched automatically on mount — * call refetch() explicitly (e.g. when the user clicks "Dock Molecule"). */ -export function useChemblFragments(pocketId, options = {}, apiBase = '/api') { - const [fragments, setFragments] = useState([]); +export function useChemblFragments(pocketId: number | string | null | undefined, options: ChemblOptions = {}, apiBase = '/api') { + const [fragments, setFragments] = useState([]); const [isLoading, setIsLoading] = useState(false); - const [error, setError] = useState(null); - const cacheRef = useRef({}); + const [error, setError] = useState(null); + const cacheRef = useRef>({}); const fetchFragments = useCallback(async () => { if (pocketId == null || pocketId === '') return; @@ -49,13 +59,13 @@ export function useChemblFragments(pocketId, options = {}, apiBase = '/api') { if (!res.ok) { throw new Error(`Failed to fetch fragments: HTTP ${res.status}`); } - const json_data = await res.json(); + const json_data = await safeJson(res); const list = (Array.isArray(json_data) ? json_data : []).map(normalizeFragment); cacheRef.current[cacheKey] = list; setFragments(list); - } catch (e) { - setError(e.message || 'Unknown fragments error'); + } catch (e: unknown) { + setError(e instanceof Error ? e.message : 'Unknown fragments error'); setFragments([]); } finally { setIsLoading(false); diff --git a/app/src/hooks/useComplex.js b/app/src/hooks/useComplex.ts similarity index 59% rename from app/src/hooks/useComplex.js rename to app/src/hooks/useComplex.ts index 6032c21..30853a2 100644 --- a/app/src/hooks/useComplex.js +++ b/app/src/hooks/useComplex.ts @@ -1,13 +1,15 @@ import { useState, useEffect } from 'react'; import { API_BASE } from '../config'; +import { safeJson } from '../utils/safeFetch'; +import type { Complex } from '../types'; // Module-level cache — persists across component mounts/unmounts -const complexCache = {}; +const complexCache: Record = {}; -export function useComplex(id) { - const [complex, setComplex] = useState(null); +export function useComplex(id: string | undefined) { + const [complex, setComplex] = useState(null); const [loading, setLoading] = useState(false); - const [error, setError] = useState(null); + const [error, setError] = useState(null); useEffect(() => { if (!id) return; @@ -27,19 +29,23 @@ export function useComplex(id) { try { const response = await fetch(`${API_BASE}/complex/${encodeURIComponent(id)}`); - const body = await response.json(); + const body = await safeJson(response); if (!response.ok) { - throw new Error(body.message || 'Failed to load complex details'); + throw new Error(body?.message || `Failed to load complex details (HTTP ${response.status})`); + } + + if (!body) { + throw new Error('Server returned an empty response'); } if (isMounted) { complexCache[id] = body; setComplex(body); } - } catch (err) { + } catch (err: unknown) { if (isMounted) { - setError(err.message || 'An error occurred.'); + setError(err instanceof Error ? err.message : 'An error occurred.'); } } finally { if (isMounted) { diff --git a/app/src/hooks/useDockingJob.js b/app/src/hooks/useDockingJob.ts similarity index 69% rename from app/src/hooks/useDockingJob.js rename to app/src/hooks/useDockingJob.ts index 9cafb9a..e54d653 100644 --- a/app/src/hooks/useDockingJob.js +++ b/app/src/hooks/useDockingJob.ts @@ -1,6 +1,18 @@ import { useState, useEffect, useCallback, useRef } from 'react'; +import { safeJson } from '../utils/safeFetch'; +import type { Conformation, Fragment } from '../types'; -function normalizeConformations(statusBody) { +type DockingStep = 'idle' | 'running' | 'results' | 'error'; + +interface StatusBody { + status: string; + conformations?: Conformation[]; + pose_pdb?: string; + binding_affinity?: number; + error?: string; +} + +function normalizeConformations(statusBody: StatusBody): Conformation[] { if (Array.isArray(statusBody.conformations) && statusBody.conformations.length > 0) { return statusBody.conformations; } @@ -22,15 +34,15 @@ function normalizeConformations(statusBody) { * Orchestrates docking submission and status polling. */ export function useDockingJob(apiBase = '/api') { - const [step, setStep] = useState('idle'); - const [selectedFragment, setSelectedFragment] = useState(null); - const [conformations, setConformations] = useState([]); - const [activeConformation, setActiveConformation] = useState(null); - const [jobError, setJobError] = useState(null); - const [jobId, setJobId] = useState(null); - - const abortRef = useRef(null); - const pollTimerRef = useRef(null); + const [step, setStep] = useState('idle'); + const [selectedFragment, setSelectedFragment] = useState(null); + const [conformations, setConformations] = useState([]); + const [activeConformation, setActiveConformation] = useState(null); + const [jobError, setJobError] = useState(null); + const [jobId, setJobId] = useState(null); + + const abortRef = useRef(null); + const pollTimerRef = useRef | null>(null); const mountedRef = useRef(true); useEffect(() => { @@ -69,16 +81,16 @@ export function useDockingJob(apiBase = '/api') { setJobId(null); }, [clearPoll]); - const selectFragment = useCallback((f) => { + const selectFragment = useCallback((f: Fragment) => { setSelectedFragment(f); }, []); - const setActiveConformationCb = useCallback((c) => { + const setActiveConformationCb = useCallback((c: Conformation) => { setActiveConformation(c); }, []); const submitDocking = useCallback( - async (pocketId, proteinPdbId, sourceType) => { + async (pocketId: number, proteinPdbId: string, sourceType?: string) => { if (!selectedFragment?.smiles || !proteinPdbId) return; clearPoll(); @@ -117,7 +129,12 @@ export function useDockingJob(apiBase = '/api') { return; } - const body = await res.json(); + const body = await safeJson(res); + if (!body) { + setJobError('Server returned an empty response after docking submission'); + setStep('error'); + return; + } const id = body.job_id; if (!id) { setJobError('Missing job_id from server'); @@ -139,7 +156,12 @@ export function useDockingJob(apiBase = '/api') { setStep('error'); return; } - const result = await st.json(); + const result = await safeJson(st); + if (!result) { + setJobError('Server returned an empty status response'); + setStep('error'); + return; + } const status = result.status; if (status === 'done') { @@ -163,18 +185,18 @@ export function useDockingJob(apiBase = '/api') { delay = Math.min(maxDelay, Math.round(delay * 1.5)); pollTimerRef.current = setTimeout(poll, delay); - } catch (e) { - if (!mountedRef.current || e.name === 'AbortError') return; - setJobError(e.message || String(e)); + } catch (e: unknown) { + if (!mountedRef.current || (e instanceof Error && e.name === 'AbortError')) return; + setJobError(e instanceof Error ? e.message : String(e)); setStep('error'); } }; pollTimerRef.current = setTimeout(poll, delay); - } catch (e) { + } catch (e: unknown) { clearTimeout(submitTimeout); - if (!mountedRef.current || e.name === 'AbortError') return; - setJobError(e.message || String(e)); + if (!mountedRef.current || (e instanceof Error && e.name === 'AbortError')) return; + setJobError(e instanceof Error ? e.message : String(e)); setStep('error'); } }, diff --git a/app/src/hooks/useSearch.js b/app/src/hooks/useSearch.ts similarity index 62% rename from app/src/hooks/useSearch.js rename to app/src/hooks/useSearch.ts index 2ac54e4..6822630 100644 --- a/app/src/hooks/useSearch.js +++ b/app/src/hooks/useSearch.ts @@ -1,17 +1,24 @@ import { useState, useCallback } from 'react'; import { API_BASE } from '../config'; +import { safeJson } from '../utils/safeFetch'; +import type { Complex } from '../types'; + +interface SearchCacheEntry { + results: Complex[]; + source: string | null; +} // Module-level cache — persists across component mounts/unmounts -const searchCache = {}; +const searchCache: Record = {}; export function useSearch() { - const [results, setResults] = useState([]); + const [results, setResults] = useState([]); const [loading, setLoading] = useState(false); - const [error, setError] = useState(null); - const [source, setSource] = useState(null); + const [error, setError] = useState(null); + const [source, setSource] = useState(null); const [query, setQuery] = useState(''); - const search = useCallback(async (q) => { + const search = useCallback(async (q: string) => { const trimmedQuery = q?.trim(); if (!trimmedQuery) return; @@ -31,10 +38,14 @@ export function useSearch() { try { const response = await fetch(`${API_BASE}/search?q=${encodeURIComponent(trimmedQuery)}`); - const body = await response.json(); - + const body = await safeJson(response); + if (!response.ok) { - throw new Error(body.message || 'Search failed'); + throw new Error(body?.message || `Search failed (HTTP ${response.status})`); + } + + if (!body) { + throw new Error('Server returned an empty response'); } const fetchedResults = body.results || []; @@ -45,8 +56,8 @@ export function useSearch() { setResults(fetchedResults); setSource(fetchedSource); - } catch (err) { - setError(err.message || 'An error occurred during search.'); + } catch (err: unknown) { + setError(err instanceof Error ? err.message : 'An error occurred during search.'); setResults([]); } finally { setLoading(false); diff --git a/app/src/hooks/useTheme.js b/app/src/hooks/useTheme.ts similarity index 92% rename from app/src/hooks/useTheme.js rename to app/src/hooks/useTheme.ts index 69c7024..725b8a9 100644 --- a/app/src/hooks/useTheme.js +++ b/app/src/hooks/useTheme.ts @@ -1,7 +1,7 @@ import { useState, useEffect } from 'react'; export function useTheme() { - const [theme, setTheme] = useState(() => { + const [theme, setTheme] = useState(() => { // Initializer const savedTheme = localStorage.getItem('ProtPocket-theme'); return savedTheme ? savedTheme : 'light'; diff --git a/app/src/hooks/useUndrugged.js b/app/src/hooks/useUndrugged.ts similarity index 61% rename from app/src/hooks/useUndrugged.js rename to app/src/hooks/useUndrugged.ts index 053b6b1..2222966 100644 --- a/app/src/hooks/useUndrugged.js +++ b/app/src/hooks/useUndrugged.ts @@ -1,10 +1,12 @@ import { useState, useEffect } from 'react'; import { API_BASE } from '../config'; +import { safeJson } from '../utils/safeFetch'; +import type { Complex } from '../types'; export function useUndrugged(filter = 'all', limit = 25) { - const [data, setData] = useState([]); + const [data, setData] = useState([]); const [loading, setLoading] = useState(false); - const [error, setError] = useState(null); + const [error, setError] = useState(null); useEffect(() => { let isMounted = true; @@ -16,21 +18,21 @@ export function useUndrugged(filter = 'all', limit = 25) { try { const url = new URL(`${API_BASE}/undrugged`, window.location.origin); url.searchParams.append('filter', filter); - url.searchParams.append('limit', limit); + url.searchParams.append('limit', String(limit)); const response = await fetch(url.pathname + url.search); - const body = await response.json(); + const body = await safeJson(response); if (!response.ok) { - throw new Error(body.message || 'Failed to load targets'); + throw new Error(body?.message || `Failed to load targets (HTTP ${response.status})`); } if (isMounted) { - setData(body.results || []); + setData(body?.results || []); } - } catch (err) { + } catch (err: unknown) { if (isMounted) { - setError(err.message || 'An error occurred.'); + setError(err instanceof Error ? err.message : 'An error occurred.'); } } finally { if (isMounted) { diff --git a/app/src/main.jsx b/app/src/main.tsx similarity index 62% rename from app/src/main.jsx rename to app/src/main.tsx index 54b39dd..964aeb4 100644 --- a/app/src/main.jsx +++ b/app/src/main.tsx @@ -1,9 +1,9 @@ import React from 'react' import ReactDOM from 'react-dom/client' -import App from './App.jsx' +import App from './App' import './index.css' -ReactDOM.createRoot(document.getElementById('root')).render( +ReactDOM.createRoot(document.getElementById('root')!).render( , diff --git a/app/src/pages/ComplexDetailPage.jsx b/app/src/pages/ComplexDetailPage.jsx deleted file mode 100644 index 69f0e62..0000000 --- a/app/src/pages/ComplexDetailPage.jsx +++ /dev/null @@ -1,247 +0,0 @@ -import React, { useState, useCallback } from 'react'; -import { useParams, useNavigate } from 'react-router-dom'; -import { useComplex } from '../hooks/useComplex'; -import { ComplexHeader } from '../components/complex/ComplexHeader'; -import { ProteinViewer } from '../components/complex/viewer/ProteinViewer'; -import { MetricsPanel } from '../components/complex/MetricsPanel'; -import { BindingSitesPanel } from '../components/complex/BindingSitesPanel'; -import { DockingPanel } from '../components/complex/DockingPanel'; -import { DockingLeaderboard, DockingResultDetail } from '../components/complex/DockingLeaderboard'; -import { LoadingState } from '../components/common/LoadingState'; -import { ErrorState } from '../components/common/ErrorState'; - -export function ComplexDetailPage() { - const { id } = useParams(); - const navigate = useNavigate(); - const { complex, loading, error } = useComplex(id); - const viewerRef = React.useRef(null); - - // Leaderboard state - const [leaderboard, setLeaderboard] = useState([]); - const [selectedEntry, setSelectedEntry] = useState(null); - - // Active docking pocket state — set when user clicks "Dock Molecule" on a pocket row - const [activeDocking, setActiveDocking] = useState(null); // { pocket, sourceType, proteinPdbId, activeTab } - - // Called when user clicks "Dock Molecule" on a pocket row - const handleStartDocking = useCallback((info) => { - // If clicking the same pocket, toggle off - if (activeDocking?.pocket?.pocket_id === info.pocket.pocket_id && activeDocking?.sourceType === info.sourceType) { - viewerRef.current?.clearConformations?.('both'); - setActiveDocking(null); - return; - } - // Clear any previous docked molecule before switching - viewerRef.current?.clearConformations?.('both'); - setActiveDocking(info); - setSelectedEntry(null); - }, [activeDocking]); - - // Called when docking completes - const handleDockingComplete = useCallback((result) => { - const entryId = `${result.sourceType}-${result.pocketId}-${result.fragmentId}-${Date.now()}`; - const newEntry = { ...result, id: entryId }; - setLeaderboard((prev) => { - if (prev.some(e => e.pocketId === result.pocketId && e.fragmentId === result.fragmentId && e.sourceType === result.sourceType)) { - return prev; - } - return [...prev, newEntry]; - }); - setSelectedEntry(newEntry); - setActiveDocking(null); - // Clear any old pose, then show the new one - viewerRef.current?.clearConformations?.('both'); - const target = result.sourceType === 'monomer' ? 'monomer' : 'complex'; - if (result.conformations?.length) { - viewerRef.current?.setConformations?.(result.conformations, 1, target); - } - }, []); - - // Called when undock/re-dock is clicked in DockingPanel - const handleUndock = useCallback(() => { - viewerRef.current?.clearConformations?.('both'); - viewerRef.current?.clearPocketHighlight?.(); - }, []); - - // Called when user selects a leaderboard entry - const handleLeaderboardSelect = useCallback((entry) => { - setSelectedEntry(entry); - setActiveDocking(null); - // Clear old pose first, then show the selected one - viewerRef.current?.clearConformations?.('both'); - const target = entry.sourceType === 'monomer' ? 'monomer' : 'complex'; - if (entry.conformations?.length) { - viewerRef.current?.setConformations?.(entry.conformations, 1, target); - } - }, []); - - // Called when user removes a leaderboard entry - const handleLeaderboardRemove = useCallback((entryId) => { - setLeaderboard((prev) => prev.filter(e => e.id !== entryId)); - setSelectedEntry((prev) => prev?.id === entryId ? null : prev); - }, []); - - // Called when user clicks a conformation in the detail panel - const handleConformationSelect = useCallback((entry, mode) => { - const target = entry.sourceType === 'monomer' ? 'monomer' : 'complex'; - if (entry.conformations?.length) { - viewerRef.current?.setConformations?.(entry.conformations, mode, target); - } - }, []); - - // Determine what to show in the right panel - const renderRightPanel = () => { - // If actively docking a pocket, show DockingPanel - if (activeDocking) { - return ( -
-
-
- - - - - Dock — Pocket #{activeDocking.pocket.pocket_id} - - - {activeDocking.sourceType} - -
- -
- { - const target = activeDocking.activeTab === 'monomer' ? 'monomer' : 'complex'; - if (confs) { - viewerRef.current?.setConformations?.(confs, mode, target); - } else { - viewerRef.current?.clearConformations?.(target); - } - }} - onUndock={handleUndock} - onDockingComplete={handleDockingComplete} - /> -
- ); - } - - // If a leaderboard entry is selected, show result detail - if (selectedEntry) { - return ; - } - - // Default placeholder - return ( -
- - - - - Select a pocket to dock - - - Click "Dock Molecule" on any pocket, or select a result from the leaderboard - -
- ); - }; - - return ( -
-
- - - - {loading && } - {error && } - - {!loading && !error && complex && ( -
- - - - - {/* Docking workspace — below Structural Metrics */} -
- {/* Left: Leaderboard */} -
-
-
- - - - - Docking Leaderboard - - {leaderboard.length > 0 && ( - - {leaderboard.length} - - )} -
-
-
- -
-
- - {/* Right: Docking UI or Result Detail */} -
- {renderRightPanel()} -
-
- - viewerRef.current?.highlightPocket?.(indices, target)} - onClearHighlight={(target) => { - viewerRef.current?.clearPocketHighlight?.(target); - viewerRef.current?.clearConformations?.(target); - }} - monomerStructureUrl={complex.monomer_structure_url?.replace(/\.cif$/i, '.pdb') || ''} - complexStructureUrl={complex.complex_structure_url?.replace(/\.cif$/i, '.pdb') || complex.uniprot_id || ''} - onConformationChange={(confs, mode, target) => viewerRef.current?.setConformations?.(confs, mode, target)} - onStartDocking={handleStartDocking} - activeDockingPocketId={activeDocking?.pocket?.pocket_id} - /> -
- )} -
-
- ); -} diff --git a/app/src/pages/ComplexDetailPage.tsx b/app/src/pages/ComplexDetailPage.tsx new file mode 100644 index 0000000..bc77e07 --- /dev/null +++ b/app/src/pages/ComplexDetailPage.tsx @@ -0,0 +1,137 @@ +import React, { useState, useCallback } from 'react'; +import { useParams, useNavigate } from 'react-router-dom'; +import { useComplex } from '../hooks/useComplex'; +import { ComplexHeader } from '../components/complex/ComplexHeader'; +import { ProteinViewer } from '../components/complex/viewer/ProteinViewer'; +import { MetricsPanel } from '../components/complex/MetricsPanel'; +import { BindingSitesPanel } from '../components/complex/BindingSitesPanel'; +import { DockingPanel } from '../components/complex/DockingPanel'; +import { DockingLeaderboard, DockingResultDetail } from '../components/complex/DockingLeaderboard'; +import { LoadingState } from '../components/common/LoadingState'; +import { ErrorState } from '../components/common/ErrorState'; +import type { Conformation, LeaderboardEntry, Pocket, ProteinViewerHandle, DockingInfo } from '../types'; + +export function ComplexDetailPage() { + const { id } = useParams<{ id: string }>(); + const navigate = useNavigate(); + const { complex, loading, error } = useComplex(id); + const viewerRef = React.useRef(null); + + const [leaderboard, setLeaderboard] = useState([]); + const [selectedEntry, setSelectedEntry] = useState(null); + const [activeDocking, setActiveDocking] = useState<(DockingInfo & { activeTab?: string }) | null>(null); + + const handleStartDocking = useCallback((info: DockingInfo) => { + if (activeDocking?.pocket?.pocket_id === info.pocket.pocket_id && activeDocking?.sourceType === info.sourceType) { + viewerRef.current?.clearConformations?.('both'); + setActiveDocking(null); + return; + } + viewerRef.current?.clearConformations?.('both'); + setActiveDocking(info); + setSelectedEntry(null); + }, [activeDocking]); + + const handleDockingComplete = useCallback((result: { pocketId: number; sourceType: string; fragmentId: string; fragmentName: string; smiles: string; bindingAffinity: number; conformations: Conformation[]; timestamp: number }) => { + const entryId = `${result.sourceType}-${result.pocketId}-${result.fragmentId}-${Date.now()}`; + const newEntry: LeaderboardEntry = { ...result, id: entryId }; + setLeaderboard((prev) => { + if (prev.some(e => e.pocketId === result.pocketId && e.fragmentId === result.fragmentId && e.sourceType === result.sourceType)) return prev; + return [...prev, newEntry]; + }); + setSelectedEntry(newEntry); + setActiveDocking(null); + viewerRef.current?.clearConformations?.('both'); + const target = result.sourceType === 'monomer' ? 'monomer' : 'complex'; + if (result.conformations?.length) { viewerRef.current?.setConformations?.(result.conformations, 1, target); } + }, []); + + const handleUndock = useCallback(() => { + viewerRef.current?.clearConformations?.('both'); + viewerRef.current?.clearPocketHighlight?.(); + }, []); + + const handleLeaderboardSelect = useCallback((entry: LeaderboardEntry) => { + setSelectedEntry(entry); + setActiveDocking(null); + viewerRef.current?.clearConformations?.('both'); + const target = entry.sourceType === 'monomer' ? 'monomer' : 'complex'; + if (entry.conformations?.length) { viewerRef.current?.setConformations?.(entry.conformations, 1, target); } + }, []); + + const handleLeaderboardRemove = useCallback((entryId: string) => { + setLeaderboard((prev) => prev.filter(e => e.id !== entryId)); + setSelectedEntry((prev) => prev?.id === entryId ? null : prev); + }, []); + + const handleConformationSelect = useCallback((entry: LeaderboardEntry, mode: number) => { + const target = entry.sourceType === 'monomer' ? 'monomer' : 'complex'; + if (entry.conformations?.length) { viewerRef.current?.setConformations?.(entry.conformations, mode, target); } + }, []); + + const renderRightPanel = () => { + if (activeDocking) { + return ( +
+
+
+ + Dock — Pocket #{activeDocking.pocket.pocket_id} + {activeDocking.sourceType} +
+ +
+ { const target = activeDocking.activeTab === 'monomer' ? 'monomer' : 'complex'; if (confs) { viewerRef.current?.setConformations?.(confs, mode!, target); } else { viewerRef.current?.clearConformations?.(target); } }} + onUndock={handleUndock} onDockingComplete={handleDockingComplete} /> +
+ ); + } + if (selectedEntry) { return ; } + return ( +
+ + Select a pocket to dock + Click "Dock Molecule" on any pocket, or select a result from the leaderboard +
+ ); + }; + + return ( +
+
+ + {loading && } + {error && } + {!loading && !error && complex && ( +
+ + + +
+
+
+
+ + Docking Leaderboard + {leaderboard.length > 0 && ({leaderboard.length})} +
+
+
+ +
+
+
{renderRightPanel()}
+
+ viewerRef.current?.highlightPocket?.(indices, target)} + onClearHighlight={(target) => { viewerRef.current?.clearPocketHighlight?.(target); viewerRef.current?.clearConformations?.(target); }} + monomerStructureUrl={complex.monomer_structure_url?.replace(/\.cif$/i, '.pdb') || ''} + complexStructureUrl={complex.complex_structure_url?.replace(/\.cif$/i, '.pdb') || complex.uniprot_id || ''} + onConformationChange={(confs, mode, target) => viewerRef.current?.setConformations?.(confs!, mode!, target)} + onStartDocking={handleStartDocking} activeDockingPocketId={activeDocking?.pocket?.pocket_id} /> +
+ )} +
+
+ ); +} diff --git a/app/src/pages/DashboardPage.jsx b/app/src/pages/DashboardPage.tsx similarity index 67% rename from app/src/pages/DashboardPage.jsx rename to app/src/pages/DashboardPage.tsx index 193bc21..c946222 100644 --- a/app/src/pages/DashboardPage.jsx +++ b/app/src/pages/DashboardPage.tsx @@ -11,28 +11,13 @@ export function DashboardPage() { return (
-
-

- Undrugged Target Leaderboard -

-

- Complexes are ranked by their structural gap score—the difference in AlphaFold confidence - between the monomeric and homodimeric states. A higher score indicates a region that only - becomes ordered upon interaction, revealing a potentially druggable cryptic pocket. -

+

Undrugged Target Leaderboard

+

Complexes are ranked by their structural gap score—the difference in AlphaFold confidence between the monomeric and homodimeric states. A higher score indicates a region that only becomes ordered upon interaction, revealing a potentially druggable cryptic pocket.

- {loading && } {error && } - - {!loading && !error && data && data.length > 0 && ( - - )} + {!loading && !error && data && data.length > 0 && ()} {!loading && !error && (!data || data.length === 0) && (
No targets found for the selected filter. diff --git a/app/src/pages/HomePage.jsx b/app/src/pages/HomePage.tsx similarity index 63% rename from app/src/pages/HomePage.jsx rename to app/src/pages/HomePage.tsx index 969e627..1c9d447 100644 --- a/app/src/pages/HomePage.jsx +++ b/app/src/pages/HomePage.tsx @@ -7,7 +7,7 @@ import { MolstarPanel } from '../components/complex/viewer/MolstarPanel'; export function HomePage() { const navigate = useNavigate(); - const handleSearch = (query) => { + const handleSearch = (query: string) => { navigate(`/search?q=${encodeURIComponent(query)}`); }; @@ -18,46 +18,22 @@ export function HomePage() { ]; const pipelineSteps = [ - { - num: '01', - title: 'Discover', - desc: 'Sifting through 1.7M AlphaFold complexes for high-confidence, undrugged WHO and human disease targets.' - }, - { - num: '02', - title: 'Reveal', - desc: 'Calculating thermodynamic Disorder Delta to find hidden structures that only stabilize upon dimerization.' - }, - { - num: '03', - title: 'Target', - desc: 'Running fpocket to autonomously identify geometric cavities situated on these stabilizing interfaces.' - }, - { - num: '04', - title: 'Dock', - desc: 'Performing high-throughput molecular docking of candidates directly inside the pocket using AutoDock Vina.' - } + { num: '01', title: 'Discover', desc: 'Sifting through 1.7M AlphaFold complexes for high-confidence, undrugged WHO and human disease targets.' }, + { num: '02', title: 'Reveal', desc: 'Calculating thermodynamic Disorder Delta to find hidden structures that only stabilize upon dimerization.' }, + { num: '03', title: 'Target', desc: 'Running fpocket to autonomously identify geometric cavities situated on these stabilizing interfaces.' }, + { num: '04', title: 'Dock', desc: 'Performing high-throughput molecular docking of candidates directly inside the pocket using AutoDock Vina.' } ]; return (
- {/* Section 1 — Hero */}
- - End-to-End Drug Lead Generation Platform - -

- From predicted complex to drug lead. Fast. -

-

- ProtPocket surfaces the highest-priority undrugged targets from the AlphaFold complex dataset. We compute structural gap scores and interface pocket viability to jumpstart novel therapeutic design. -

+ End-to-End Drug Lead Generation Platform +

From predicted complex to drug lead. Fast.

+

ProtPocket surfaces the highest-priority undrugged targets from the AlphaFold complex dataset. We compute structural gap scores and interface pocket viability to jumpstart novel therapeutic design.

-
@@ -81,17 +57,12 @@ export function HomePage() {

The Pipeline

-

- We cross-reference AlphaFold structures, ChEMBL drug data, and WHO priority lists in real-time, feeding the best candidates into our autonomous pocket analysis engine. -

+

We cross-reference AlphaFold structures, ChEMBL drug data, and WHO priority lists in real-time, feeding the best candidates into our autonomous pocket analysis engine.

-
{pipelineSteps.map((step, idx) => (
-
- {step.num} -
+
{step.num}

{step.title}

{step.desc}

@@ -100,44 +71,21 @@ export function HomePage() {
- {/* Section 4 — The Science (Interface Pockets) */} + {/* Section 4 — The Science */}
- - The Holy Grail of PPIs - -

- Targeting the Disorder Delta -

-

- Many proteins appear completely disordered as single monomers, but snap into highly stable structures when bound to their partner. We call this the Disorder Delta. -

-

- By combining thermodynamic confidence scoring (pLDDT) with geometric cavity detection (fpocket), ProtPocket flags cavities that sit exactly on these newly stabilized interfaces. These are the prime targets for Protein-Protein Interaction (PPI) inhibitors. -

+ The Holy Grail of PPIs +

Targeting the Disorder Delta

+

Many proteins appear completely disordered as single monomers, but snap into highly stable structures when bound to their partner. We call this the Disorder Delta.

+

By combining thermodynamic confidence scoring (pLDDT) with geometric cavity detection (fpocket), ProtPocket flags cavities that sit exactly on these newly stabilized interfaces. These are the prime targets for Protein-Protein Interaction (PPI) inhibitors.

- {/* Dual Mol* Viewer Setup for Q55DI5 */}
- +
- +
@@ -150,19 +98,12 @@ export function HomePage() {

Analyze Live Targets

Select a curated complex to see the pipeline in action
-
{DEMO_PROTEINS.map((protein) => ( -
navigate(`/complex/${protein.id}`)} - className="flex flex-col gap-4 p-6 bg-bg-secondary border border-border rounded-lg hover:border-accent hover:shadow-[0_4px_20px_rgba(0,0,0,0.05)] cursor-pointer transition-all duration-300" - > +
navigate(`/complex/${protein.id}`)} className="flex flex-col gap-4 p-6 bg-bg-secondary border border-border rounded-lg hover:border-accent hover:shadow-[0_4px_20px_rgba(0,0,0,0.05)] cursor-pointer transition-all duration-300">
{protein.label} -
- ↗ -
+
↗
{protein.description}
@@ -170,7 +111,6 @@ export function HomePage() {
-
); } diff --git a/app/src/pages/SearchPage.jsx b/app/src/pages/SearchPage.tsx similarity index 77% rename from app/src/pages/SearchPage.jsx rename to app/src/pages/SearchPage.tsx index e6be6fd..c5dbbb5 100644 --- a/app/src/pages/SearchPage.jsx +++ b/app/src/pages/SearchPage.tsx @@ -12,15 +12,11 @@ export function SearchPage() { const { search, results, loading, error, source, query } = useSearch(); useEffect(() => { - if (q) { - search(q); - } + if (q) { search(q); } + // eslint-disable-next-line react-hooks/exhaustive-deps }, [q]); - const handleSearch = (newQuery) => { - setSearchParams({ q: newQuery }); - }; - + const handleSearch = (newQuery: string) => { setSearchParams({ q: newQuery }); }; const hasSearched = !!query; const hasResults = results.length > 0; @@ -28,11 +24,8 @@ export function SearchPage() {
- {loading && } - {error && } - {!loading && !error && hasSearched && (
{hasResults ? ( @@ -42,19 +35,13 @@ export function SearchPage() { source: {source}
- {results.map((complex) => ( - - ))} + {results.map((complex) => ())}
) : (
- - No targets found matching "{query}" - - - Try adjusting your search terms or exploring the dashboard. - + No targets found matching "{query}" + Try adjusting your search terms or exploring the dashboard.
)}
diff --git a/app/src/scss.d.ts b/app/src/scss.d.ts new file mode 100644 index 0000000..18ded59 --- /dev/null +++ b/app/src/scss.d.ts @@ -0,0 +1,4 @@ +declare module '*.scss' { + const content: string; + export default content; +} diff --git a/app/src/types.ts b/app/src/types.ts new file mode 100644 index 0000000..9893839 --- /dev/null +++ b/app/src/types.ts @@ -0,0 +1,157 @@ +// ── Shared domain types ──────────────────────────────────────────── +// Inferred from existing code usage; kept minimal to avoid deep refactors. + +export interface DemoProtein { + id: string; + label: string; + description: string; +} + +export interface Complex { + uniprot_id: string; + alphafold_id: string; + protein_name: string; + gene_name: string; + organism: string; + disease_associations: string[]; + is_who_pathogen: boolean; + drug_count: number; + review_status: string; + monomer_plddt_avg: number; + dimer_plddt_avg: number; + disorder_delta: number; + gap_score: number; + category: string; + known_drug_names: string[]; + monomer_structure_url: string; + complex_structure_url: string; +} + +export interface Pocket { + pocket_id: number; + druggability_score: number; + volume: number; + hydrophobicity: number; + polarity: number; + avg_plddt: number; + avg_disorder_delta: number; + center: [number, number, number] | null; + residue_names: string[]; + residue_indices: number[]; + is_interface_pocket: boolean; + is_conserved: boolean; + is_emergent: boolean; +} + +export interface Conformation { + mode: number; + binding_affinity: number; + rmsd_lb: number; + rmsd_ub: number; + pose_pdb: string; +} + +export interface Fragment { + chembl_id: string; + zinc_id?: string; + id?: string; + name?: string; + smiles?: string; + mw?: number; + mol_weight?: number; + logp?: number; +} + +export interface LeaderboardEntry { + id: string; + pocketId: number; + sourceType: string; + fragmentId: string; + fragmentName: string; + smiles: string; + bindingAffinity: number; + conformations: Conformation[]; + timestamp: number; +} + +export interface BindingSitesData { + pockets: Pocket[]; + total_pockets: number; + monomer_pockets: Pocket[]; + monomer_total_pockets: number; + interface_pocket_count: number; + comparison: ComparisonData | null; +} + +export interface ComparisonData { + summary_metrics: { + total_monomer_pockets: number; + total_dimer_pockets: number; + avg_monomer_druggability: number; + avg_dimer_druggability: number; + }; + ddgi: number; + pocket_mapping: { + conserved_count: number; + monomer_only_count: number; + emergent_count: number; + interface_count: number; + }; + interface_pockets: Pocket[]; + conserved_pockets: Pocket[]; + emergent_pockets: Pocket[]; + graph_datasets: { + stabilization_scatter: ScatterDataPoint[]; + }; + property_changes: { + monomer_avg_volume: number; + dimer_avg_volume: number; + monomer_avg_hydrophobicity: number; + dimer_avg_hydrophobicity: number; + monomer_avg_polarity: number; + dimer_avg_polarity: number; + }; + stabilization_stats: { + enrichment_score: number; + }; + fragment_comparison: { + unique_interface_fragments: Fragment[]; + unique_dimer_fragments: Fragment[]; + } | null; +} + +export interface ScatterDataPoint { + avg_delta: number; + druggability_score: number; +} + +export interface DockingInfo { + pocket: Pocket; + sourceType: string; + proteinPdbId: string; + activeTab?: string; +} + +export interface DockingResult { + pocketId: number; + sourceType: string; + fragmentId: string; + fragmentName: string; + smiles: string; + bindingAffinity: number; + conformations: Conformation[]; + timestamp: number; +} + +// Mol* viewer imperative handle +export interface ProteinViewerHandle { + highlightPocket: (residueIndices: number[], target?: string) => void; + clearPocketHighlight: (target?: string) => void; + setConformations: (confs: Conformation[], mode: number, target?: string) => void; + clearConformations: (target?: string) => void; +} + +export interface MolstarPanelHandle { + highlightPocket: (residueIndices: number[]) => Promise; + clearPocketHighlight: () => Promise; +} diff --git a/app/src/utils/safeFetch.ts b/app/src/utils/safeFetch.ts new file mode 100644 index 0000000..23dcde5 --- /dev/null +++ b/app/src/utils/safeFetch.ts @@ -0,0 +1,14 @@ +/** + * Safely parse a Response body as JSON. + * Returns `null` if the body is empty or not valid JSON, + * instead of throwing "Unexpected end of JSON input". + */ +export async function safeJson(response: Response): Promise { + const text = await response.text(); + if (!text || text.trim().length === 0) return null; + try { + return JSON.parse(text) as T; + } catch { + return null; + } +} diff --git a/app/tsconfig.json b/app/tsconfig.json new file mode 100644 index 0000000..d8b1a0d --- /dev/null +++ b/app/tsconfig.json @@ -0,0 +1,29 @@ +{ + "compilerOptions": { + "target": "ES2020", + "useDefineForClassFields": true, + "lib": ["ES2020", "DOM", "DOM.Iterable"], + "module": "ESNext", + "skipLibCheck": true, + + /* Bundler mode */ + "moduleResolution": "bundler", + "allowImportingTsExtensions": true, + "isolatedModules": true, + "moduleDetection": "force", + "noEmit": true, + "jsx": "react-jsx", + + /* Linting */ + "strict": true, + "noUnusedLocals": false, + "noUnusedParameters": false, + "noFallthroughCasesInSwitch": true, + + /* Allow JS interop */ + "allowJs": true, + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true + }, + "include": ["src", "vite-env.d.ts"] +} diff --git a/app/vite-env.d.ts b/app/vite-env.d.ts new file mode 100644 index 0000000..11f02fe --- /dev/null +++ b/app/vite-env.d.ts @@ -0,0 +1 @@ +/// diff --git a/app/vite.config.js b/app/vite.config.ts similarity index 100% rename from app/vite.config.js rename to app/vite.config.ts From 96e10d1eb71a88d6434394184086881a8b3bb48b Mon Sep 17 00:00:00 2001 From: Arshita Jaryal Date: Thu, 14 May 2026 19:17:08 +0530 Subject: [PATCH 2/3] Remove dist from tracking --- .gitignore | 2 + app/dist/assets/index-DHFWRlXl.js | 7504 ---------------------------- app/dist/assets/index-Y4Qzsb0-.css | 2 - app/dist/favicon.png | Bin 87962 -> 0 bytes app/dist/index.html | 17 - 5 files changed, 2 insertions(+), 7523 deletions(-) delete mode 100644 app/dist/assets/index-DHFWRlXl.js delete mode 100644 app/dist/assets/index-Y4Qzsb0-.css delete mode 100644 app/dist/favicon.png delete mode 100644 app/dist/index.html diff --git a/.gitignore b/.gitignore index 7f9db40..96ac8a2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ .env node_modules/ /tmp/ +dist/ +app/dist/ \ No newline at end of file diff --git a/app/dist/assets/index-DHFWRlXl.js b/app/dist/assets/index-DHFWRlXl.js deleted file mode 100644 index ff4bcf0..0000000 --- a/app/dist/assets/index-DHFWRlXl.js +++ /dev/null @@ -1,7504 +0,0 @@ -var 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