Adding maps to PDB react-router scenes and tidying before I move to m…

…y own branch on github and use pull requests.
moorhen-coot · Jan 11, 2024 · 040320e · 040320e
1 parent 9f27e7a
commit 040320e
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Showing 2 changed files with 83 additions and 20 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 package-lock.json
 public/baby-gru/*
 dist/*
-node_modules/*
+node_modules/*
+**/.DS_Store
diff --git a/src/MoorhenRouter.tsx b/src/MoorhenRouter.tsx
@@ -1,5 +1,5 @@
 
-import { MoorhenContainer, MoorhenMolecule, addMolecule } from 'moorhen'
+import { MoorhenContainer, MoorhenMolecule, MoorhenMap, addMolecule, addMap, setActiveMap } from 'moorhen'
 import { webGL } from 'moorhen/types/mgWebGL';
 import { moorhen } from 'moorhen/types/moorhen';
 import { useEffect, useRef } from 'react';
@@ -10,35 +10,93 @@ export const MoorhenRouter: React.FC = () => {
     return <RouterProvider router={moorhenRouter} />
 };
 
-const MoorhenContainerWithPdb: React.FC = () => {
+const WrappedMoorhenContainer: React.FC = () => {
     const glRef = useRef<webGL.MGWebGL | null>(null)
     const commandCentre = useRef<moorhen.CommandCentre | null>(null)
     const dispatch = useDispatch()
     const cootInitialized = useSelector((state: moorhen.State) => state.generalStates.cootInitialized)
-    const urlPrefix = ""
+    const urlPrefix: string = ""
 
-    const { pdbId } = useParams()
+    const { pdbId, tutorialNumber } = useParams()
 
     const collectedProps = {
         glRef, commandCentre, urlPrefix
     }
 
+    const tutorialMtzColumnNames: { [key: string]: any } = {
+        1: { F: "FWT", PHI: "PHWT", Fobs: 'FP', SigFobs: 'SIGFP', FreeR: 'FREE' },
+        2: { F: "FWT", PHI: "PHWT", Fobs: 'FP', SigFobs: 'SIGFP', FreeR: 'FREE' },
+        3: { F: "FWT", PHI: "PHWT", Fobs: 'F', SigFobs: 'SIGF', FreeR: 'FREER' }
+    }
+
+    const loadTutorial = async (tutorialNumber: string) => {
+        const newMolecule = new MoorhenMolecule(commandCentre, glRef, "")
+        const newMap = new MoorhenMap(commandCentre, glRef)
+        const newDiffMap = new MoorhenMap(commandCentre, glRef)
+        await newMolecule.loadToCootFromURL(`${urlPrefix}/baby-gru/tutorials/moorhen-tutorial-structure-number-${tutorialNumber}.pdb`, `mol-${tutorialNumber}`)
+        await newMolecule.fetchIfDirtyAndDraw('CBs')
+        dispatch(addMolecule(newMolecule))
+        await newMolecule.centreOn('/*/*/*/*', false)
+        await newMap.loadToCootFromMtzURL(
+            `${urlPrefix}/baby-gru/tutorials/moorhen-tutorial-map-number-${tutorialNumber}.mtz`,
+            `map-${tutorialNumber}`,
+            { isDifference: false, useWeight: false, calcStructFact: true, ...tutorialMtzColumnNames[tutorialNumber] }
+        )
+        await newDiffMap.loadToCootFromMtzURL(
+            `${urlPrefix}/baby-gru/tutorials/moorhen-tutorial-map-number-${tutorialNumber}.mtz`,
+            `diff-map-${tutorialNumber}`,
+            { F: "DELFWT", PHI: "PHDELWT", isDifference: true, useWeight: false }
+        )
+        dispatch(addMap(newMap))
+        dispatch(addMap(newDiffMap))
+        dispatch(setActiveMap(newMap))
+    }
+
+    const loadPdb = async (pdbId: string) => {
+        const newMolecule: moorhen.Molecule = new MoorhenMolecule(commandCentre, glRef, "")
+        const pdbCode: string = pdbId.toLowerCase()
+        const coordUrl: string = `https://www.ebi.ac.uk/pdbe/entry-files/download/${pdbCode}.cif`
+        await newMolecule.loadToCootFromURL(coordUrl, pdbCode)
+        await newMolecule.addRepresentation("CRs", "/*/*")
+        await newMolecule.fetchIfDirtyAndDraw("ligands")
+        newMolecule.centreOn("/*/*")
+        glRef.current?.setZoom(4.0)
+        dispatch(addMolecule(newMolecule))
+        const newMap = new MoorhenMap(commandCentre, glRef)
+        const newDiffMap = new MoorhenMap(commandCentre, glRef)
+        try {
+            await newMap.loadToCootFromMapURL(
+                `https://www.ebi.ac.uk/pdbe/entry-files/${pdbCode}.ccp4`,
+                `${pdbCode}-2FoFc`,
+                false
+            )
+            dispatch(addMap(newMap))
+        }
+        catch (err) {
+        }
+        try {
+            await newDiffMap.loadToCootFromMapURL(
+                `https://www.ebi.ac.uk/pdbe/entry-files/${pdbCode}_diff.ccp4`,
+                `${pdbCode}-FoFc`,
+                true
+            )
+            dispatch(addMap(newDiffMap))
+        }
+        catch (err) {
+        }
+    }
+
     useEffect(() => {
-        if (pdbId && cootInitialized) {
-            const asyncFunc = async () => {
-                const newMolecule: moorhen.Molecule = new MoorhenMolecule(commandCentre, glRef, "")
-                const pdbCode: string = pdbId.toLowerCase()
-                const coordUrl: string = `https://www.ebi.ac.uk/pdbe/entry-files/download/${pdbCode}.cif`
-                await newMolecule.loadToCootFromURL(coordUrl, pdbCode)
-                await newMolecule.addRepresentation("CRs", "/*/*")
-                await newMolecule.fetchIfDirtyAndDraw("ligands")
-                newMolecule.centreOn("/*/*")
-                glRef.current?.setZoom(4.0)
-                dispatch(addMolecule(newMolecule))
+        if (cootInitialized) {
+            if (pdbId) {
+                loadPdb(pdbId)
+            }
+            else if (tutorialNumber) {
+                loadTutorial(tutorialNumber)
             }
-            asyncFunc()
         }
-    }, [pdbId, cootInitialized])
+    }, [pdbId, tutorialNumber, cootInitialized])
+
     return <MoorhenContainer {...collectedProps} />
 }
 
@@ -54,11 +112,15 @@ const moorhenRouter = createBrowserRouter(
         },
         {
             path: "/pdb/:pdbId",
-            element: <MoorhenContainerWithPdb />,
+            element: <WrappedMoorhenContainer />,
         },
         {
             path: "/:pdbId",
-            element: <MoorhenContainerWithPdb />,
+            element: <WrappedMoorhenContainer />,
+        },
+        {
+            path: "/tutorial/:tutorialNumber",
+            element: <WrappedMoorhenContainer />,
         },
     ]
 )