add q-score for ligand validation

moorhen-coot · Nov 11, 2024 · f594095 · f594095
1 parent f6ba809
commit f594095
Show file tree

Hide file tree

Showing 5 changed files with 70 additions and 6 deletions.
diff --git a/baby-gru/package.json b/baby-gru/package.json
@@ -1,6 +1,6 @@
 {
   "name": "moorhen",
-  "version": "0.10.2",
+  "version": "0.10.3",
   "private": false,
   "main": "moorhen.js",
   "types": "./types/main.d.ts",

diff --git a/baby-gru/src/components/card/MoorhenLigandCard.tsx b/baby-gru/src/components/card/MoorhenLigandCard.tsx
@@ -5,12 +5,14 @@ import { useEffect, useRef, useState } from "react";
 import { CenterFocusStrongOutlined, HelpOutlined, RadioButtonCheckedOutlined, RadioButtonUncheckedOutlined } from "@mui/icons-material";
 import parse from 'html-react-parser'
 import { convertViewtoPx, guid } from "../../utils/utils";
-import { Popover, Table, TableBody, TableCell, TableContainer, TableHead, TableRow } from "@mui/material";
+import { LinearProgress, Popover, Table, TableBody, TableCell, TableContainer, TableHead, TableRow } from "@mui/material";
+import { libcootApi } from "../../types/libcoot";
 
 export const MoorhenLigandCard = (props: {
     ligand: moorhen.LigandInfo;
     molecule: moorhen.Molecule;
-    validationStyles?: moorhen.RepresentationStyles[]
+    validationStyles?: moorhen.RepresentationStyles[];
+    calculateQScore?: boolean;
 }) => {
 
     const validationLabels = {
@@ -24,16 +26,18 @@ export const MoorhenLigandCard = (props: {
 
     const [showState, setShowState] = useState<{ [key: string]: boolean }>({})
     const [showInfoTable, setShowInfoTable] = useState<boolean>(false)
+    const [qScore, setQScore] = useState<number | null>(null)
 
     const isDark = useSelector((state: moorhen.State) => state.sceneSettings.isDark)
     const height = useSelector((state: moorhen.State) => state.sceneSettings.height)
     const width = useSelector((state: moorhen.State) => state.sceneSettings.width)
+    const activeMap = useSelector((state: moorhen.State) => state.generalStates.activeMap)
 
     const defaultValidationStyles = [
         'contact_dots', 'chemical_features', 'ligand_environment', 'ligand_validation'
     ]
 
-    const { ligand, molecule, validationStyles } = { validationStyles: defaultValidationStyles,  ...props }
+    const { ligand, molecule, validationStyles, calculateQScore } = { validationStyles: defaultValidationStyles, calculateQScore: false,  ...props }
 
     useEffect(() => {
         const changedState = { ...showState }
@@ -46,6 +50,16 @@ export const MoorhenLigandCard = (props: {
         }
     }, [])
 
+    useEffect(() => {
+        const getQScore = async () => {
+            if (activeMap && calculateQScore) {
+                const qScoreResponse = await molecule.calculateQscore(activeMap, ligand.cid)
+                setQScore(qScoreResponse?.[0]?.value)
+            }    
+        }
+        getQScore()
+    }, [])
+
     const getToggleButton = (style: string, label: string) => {
         return <ToggleButton
                 key={`${style}-${molecule.molNo}-${ligand.cid}`}
@@ -114,7 +128,16 @@ export const MoorhenLigandCard = (props: {
                                 </Table>
                             </TableContainer>
                             </Popover>}
-                            {ligand.svg ? parse(ligand.svg) : <span>{ligand.cid}</span>}
+                            <Stack direction="vertical" gap={1}>
+                                {ligand.svg ? parse(ligand.svg) : <span>{ligand.cid}</span>}
+                                {(calculateQScore && activeMap) ?
+                                <div style={{ display: "flex", justifyContent: "center" }}>
+                                    {
+                                    qScore ? <span>Q-Score: {qScore.toFixed(2)}</span> : <LinearProgress variant="indeterminate" style={{ width: "50%" }}/>
+                                    }
+                                </div>
+                                : null}
+                            </Stack>
                     </Col>
                     <Col className='col-3' style={{margin: '0', padding:'0', justifyContent: 'right', display:'flex'}}>
                         <Stack direction='vertical' gap={1} style={{display: 'flex', justifyContent: 'center'}}>

diff --git a/baby-gru/src/components/validation-tools/MoorhenLigandValidation.tsx b/baby-gru/src/components/validation-tools/MoorhenLigandValidation.tsx
@@ -28,7 +28,7 @@ export const MoorhenLigandValidation = (props: moorhen.CollectedProps) => {
         }
 
         return ligandInfo.map((ligand, index) => {
-            return <MoorhenLigandCard key={`${ligand.cid}-${selectedModel}`} ligand={ligand} molecule={selectedMolecule}/>
+            return <MoorhenLigandCard key={`${ligand.cid}-${selectedModel}`} ligand={ligand} molecule={selectedMolecule} calculateQScore={true}/>
         })
     }
 

diff --git a/baby-gru/src/types/moorhen.d.ts b/baby-gru/src/types/moorhen.d.ts
@@ -241,6 +241,7 @@ export namespace moorhen {
         getLigandSVG(resName: string, useCache?: boolean): Promise<string>;
         isValidSelection(cid: string): Promise<boolean>;
         fetchHeaderInfo(useCache?: boolean): Promise<libcootApi.headerInfoJS>;
+        calculateQscore(activeMap: Map, cid?: string): Promise<libcootApi.ValidationInformationJS[]>;
         type: string;
         adaptativeBondsEnabled: boolean;
         cachedLigandSVGs: {[key: string]: string};

diff --git a/baby-gru/src/utils/MoorhenMolecule.ts b/baby-gru/src/utils/MoorhenMolecule.ts
@@ -2471,4 +2471,44 @@ export class MoorhenMolecule implements moorhen.Molecule {
 
         return headerInfo.data.result.result
     }
+
+    /**
+     * Calculate the Q-Score for a CID
+     * @param {string} cid - The CID selection used to calcualte the qscore
+     * @param {moorhen.Map} activeMap - The map instance used in the refinement
+     */
+    async calculateQscore(activeMap: moorhen.Map, cid?: string) {
+        if (!cid) {
+            const result = await this.commandCentre.current.cootCommand({
+                command: 'get_q_score',
+                commandArgs: [ this.molNo, activeMap.molNo ],
+                returnType: 'validation_data',
+            }, false) as moorhen.WorkerResponse<libcootApi.ValidationInformationJS[]>
+            return result.data.result.result    
+        } else {
+            //Here we copy the ligand into a separate fragment and calculate the q-score.
+            // Newer versions can do this directly with molecules_container.get_q_score_for_cid
+            const copyMoleculeResponse = await this.commandCentre.current.cootCommand({
+                returnType: "status",
+                command: "copy_fragment_using_cid",
+                commandArgs: [this.molNo, cid],
+            }, true) as moorhen.WorkerResponse<number>
+            const qScoreResponse = await this.commandCentre.current.cootCommand({
+                command: 'get_q_score',
+                commandArgs: [copyMoleculeResponse.data.result.result, activeMap.molNo],
+                returnType: "validation_data"
+            }, false) as moorhen.WorkerResponse<libcootApi.ValidationInformationJS[]>
+            await this.commandCentre.current.cootCommand({
+                returnType: 'status',
+                commandArgs: [copyMoleculeResponse.data.result.result],
+                command: "close_molecule"
+            }, false) as moorhen.WorkerResponse<number>
+            await this.commandCentre.current.cootCommand({
+                returnType: 'status',
+                commandArgs: [ ],
+                command: "end_delete_closed_molecules"
+            }, false) as moorhen.WorkerResponse<number>
+            return qScoreResponse.data.result.result
+        }
+    }
 }
-Original file line number
+Diff line change
@@ Expand Up @@
             }
             return ligandInfo.map((ligand, index) => {
-                return <MoorhenLigandCard key={`${ligand.cid}-${selectedModel}`} ligand={ligand} molecule={selectedMolecule}/>
+                return <MoorhenLigandCard key={`${ligand.cid}-${selectedModel}`} ligand={ligand} molecule={selectedMolecule} calculateQScore={true}/>
             })
         }
@@ Expand Down @@