From 5f216106822d46fedf3d55b6d08f3ea2621a3d59 Mon Sep 17 00:00:00 2001
From: supraja-968 <supraja968@gmail.com>
Date: Mon, 12 Aug 2024 14:00:39 +0200
Subject: [PATCH] 3dmol viewer updates

---
 .../(forms)/NewExperimentForm.tsx             |   7 +-
 .../(experiment)/(forms)/ThreeDMolViewer.tsx  |   2 +-
 .../(forms)/ThreeDMolViewer_backup.tsx        | 252 ++++++++++++++++++
 3 files changed, 259 insertions(+), 2 deletions(-)
 create mode 100644 frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer_backup.tsx

diff --git a/frontend/app/experiments/(experiment)/(forms)/NewExperimentForm.tsx b/frontend/app/experiments/(experiment)/(forms)/NewExperimentForm.tsx
index 312f5c54..793d4393 100644
--- a/frontend/app/experiments/(experiment)/(forms)/NewExperimentForm.tsx
+++ b/frontend/app/experiments/(experiment)/(forms)/NewExperimentForm.tsx
@@ -139,7 +139,6 @@ export default function NewExperimentForm({ task }: { task: any }) {
     <>
       <Form {...form}>
         <form onSubmit={form.handleSubmit((values) => onSubmit(values))}>
-        <ThreeDMolViewer onSubmit={handleViewerSubmit} />
           <Card className="mb-2">
             <CardContent>
               <div className="flex items-center gap-1">
@@ -159,6 +158,12 @@ export default function NewExperimentForm({ task }: { task: any }) {
               </div>
             </CardContent>
           </Card>
+          
+          <Card>
+            <CardContent>
+            <ThreeDMolViewer onSubmit={handleViewerSubmit} />
+            </CardContent>
+          </Card>
           {!!groupedInputs?.standard && (
             <>
               <Card>
diff --git a/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer.tsx b/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer.tsx
index 43f94b57..e616cb28 100644
--- a/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer.tsx
+++ b/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer.tsx
@@ -161,7 +161,7 @@ const ThreeDMolViewer: React.FC<ThreeDMolViewerProps> = ({ onSubmit }) => {
     };
     
     return (
-        <div>
+        <div className="relative">
             <div style={{ 
                 display: 'flex', 
                 justifyContent: 'center', 
diff --git a/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer_backup.tsx b/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer_backup.tsx
new file mode 100644
index 00000000..7c2de186
--- /dev/null
+++ b/frontend/app/experiments/(experiment)/(forms)/ThreeDMolViewer_backup.tsx
@@ -0,0 +1,252 @@
+import React, { useState, useEffect, useRef } from 'react';
+import axios from 'axios';
+import {FileSelect} from '@/components/shared/FileSelect';
+
+interface AtomSpec {
+    chain: string;
+    resi: number;
+}
+
+interface ThreeDMolViewerProps {
+    onSubmit: (data: { pdb: File | null; binderLength: number; hotspots: string }) => void;
+}
+
+const ThreeDMolViewer: React.FC<ThreeDMolViewerProps> = ({ onSubmit }) => {
+    const [viewer, setViewer] = useState<any>(null);
+    const [selectedResidues, setSelectedResidues] = useState<Record<string, boolean>>({});
+    const [binderLength, setBinderLength] = useState(90);
+    const fileInput = useRef<HTMLInputElement>(null);
+    const [pdbData, setPdbData] = useState<string | null>(null);
+    const [data, setData] = useState<any>(null);
+    const [fileName, setFileName] = useState('');
+
+    useEffect(() => {
+        (async () => {
+            const module = await import('3dmol/build/3Dmol.js');
+            const $3Dmol = module.default ? module.default : module;
+            const element = document.getElementById('container-01') as HTMLElement;
+            const config = { backgroundColor: 'white' };
+            const viewer = $3Dmol.createViewer(element, config);
+            setViewer(viewer);
+        })();
+    }, []);
+
+    useEffect(() => {
+        const loadPDBFile = async () => {
+            if (viewer && fileName) { // Ensure there's a filename and viewer instance
+                try {
+                    const response = await axios.get(fileName, { responseType: 'text' });
+                    viewer.addModel(response.data, "pdb");
+                    viewer.zoomTo(); // Adjust the camera to the new model
+                    viewer.render();
+                    updateStyles(); // Update visual styles if needed
+                } catch (error) {
+                    console.error("Error loading PDB file:", error);
+                }
+            }
+        };
+        loadPDBFile();
+    }, [viewer, fileName]); // Depend on fileName to refetch when it changes
+
+    useEffect(() => {
+        if (viewer) {
+            updateStyles();
+        }
+    }, [selectedResidues]);
+
+    const handleFileUpload = (fileName: string) => {
+        // Access the file object directly from the input reference
+        setFileName(fileName);
+        const file = fileInput.current?.files?.[0];
+        if (file && viewer && file.name === fileName) {
+            const reader = new FileReader();
+            reader.onload = function(e) {
+                const pdbData = e.target?.result as string;
+                setData(pdbData);
+                viewer.addModel(pdbData, "pdb");
+                viewer.zoomTo(); // Ensure the viewer adjusts to the loaded model
+                viewer.render();
+                // Enable clicking to select hotspots only after model is loaded
+                viewer.getModel().setClickable({}, true, (atom: AtomSpec) => {
+                    const residueKey = `${atom.chain}${atom.resi}`;
+                    setSelectedResidues(prev => ({
+                        ...prev,
+                        [residueKey]: !prev[residueKey]
+                    }));
+                });
+            };
+            reader.readAsText(file);
+        } else {
+            console.error("File selected does not match or viewer is not initialized");
+        }
+    };
+
+    // Ensure fileInput is accessible and used correctly
+// const handleFileSelection = (fileData: any, fileName: string) => {
+//     // Trigger native file input click
+//     setData(fileData);
+//     setFileName(fileName);  // Assuming you keep a fileName state
+//     if (viewer) {
+//         viewer.addModel(fileData, "pdb");
+//         viewer.render();
+//     }
+// };
+
+// const handleFileSelection = (selectedFileName: string) => {
+//     setFileName(selectedFileName);
+//   };
+
+// Handling file change from the native file input
+const handleFileChange = () => {
+    const file = fileInput.current?.files?.[0];
+    if (file && viewer) {
+        const reader = new FileReader();
+        reader.onload = (e) => {
+            const result = e.target?.result as string;
+            setData(result);
+            viewer.addModel(result, "pdb");
+            viewer.render();
+            updateStyles();
+        };
+        reader.readAsText(file);
+    }
+};
+
+    const updateStyles = () => {
+        if (!viewer) return;
+    
+        const allChains = new Set();
+        const chainsWithSelectedResidues = new Set();
+    
+        // First, reset styles for all residues
+        viewer.selectedAtoms({}).forEach((atom: { chain: unknown; resi: any; }) => {
+            allChains.add(atom.chain);
+            const residueKey = `${atom.chain}${atom.resi}`;
+            if (selectedResidues[residueKey]) {
+              chainsWithSelectedResidues.add(atom.chain);
+            }
+          });
+      
+          if (Object.keys(selectedResidues).length === 0) {
+            // No residues selected, set all chains to fully visible
+            viewer.setStyle({}, { cartoon: { color: 'grey', opacity: 1.0 } });
+          } else {
+            // Set default style for all chains with higher transparency
+            viewer.setStyle({}, { cartoon: { color: 'grey', opacity: 0.2 } });
+      
+            // Set style for chains with selected residues to fully visible
+            chainsWithSelectedResidues.forEach(chain => {
+              viewer.setStyle({ chain }, { cartoon: { color: 'grey', opacity: 1.0 } });
+            });
+      
+            // Set style for selected residues
+            Object.keys(selectedResidues).forEach(residueKey => {
+              const chain = residueKey[0];
+              const resi = residueKey.slice(1);
+              viewer.setStyle({ chain, resi }, { cartoon: { color: 'red', opacity: 1.0 } });
+            });
+          }
+      
+          viewer.render();
+    };
+
+    useEffect(() => {
+        if (viewer) {
+            const loadAndMakeClickable = async () => {
+                const data = await axios.get('https://files.rcsb.org/download/1UBQ.pdb').then(res => res.data);
+                viewer.addModel(data, "pdb");
+                viewer.getModel().setClickable({}, (atom: { chain: any; resi: any; }) => {
+                    const key = `${atom.chain}:${atom.resi}`;
+                    setSelectedResidues(prev => ({
+                        ...prev,
+                        [key]: !prev[key]
+                    }));
+                });
+                updateStyles();
+            };
+            loadAndMakeClickable();
+        }
+    }, [viewer]);
+    
+
+    
+  const formatSelectedResidues = () => {
+    return Object.keys(selectedResidues).map((residueKey) => {
+      const chain = residueKey[0];
+      const index = residueKey.slice(1);
+      return `${chain}${index}`;
+    }).join(', ');
+  };
+
+    const handleBinderLengthChange = (event: React.ChangeEvent<HTMLInputElement>) => {
+        setBinderLength(Number(event.target.value));
+    };
+
+    const handleSubmit = async () => {
+        const pdbFile = fileInput.current?.files?.[0] ?? null;
+        const hotspots = formatSelectedResidues();
+        onSubmit({ pdb: pdbFile, binderLength, hotspots });
+    };
+
+    const handleResidueInputChange = (event: React.ChangeEvent<HTMLInputElement>) => {
+        const input = event.target.value;
+        const newSelectedResidues: Record<string, boolean> = {};
+    
+        const residues = input.split(',').map(res => res.trim()).filter(res => res);
+    
+        residues.forEach(residue => {
+            const match = residue.match(/^([a-zA-Z]+)(\d+)$/); 
+    
+            if (match) {
+                const chain = match[1].toUpperCase(); 
+                const resi = parseInt(match[2], 10);
+                if (!isNaN(resi)) {
+                    const key = `${chain}${resi}`; 
+                    newSelectedResidues[key] = true; 
+                }
+            }
+        });
+    
+        setSelectedResidues(newSelectedResidues);
+        updateStyles();
+    };
+    
+    return (
+        <div>
+            <div style={{ 
+                display: 'flex', 
+                justifyContent: 'center', 
+                alignItems: 'center', 
+                padding: '15px', 
+                margin: 'auto', 
+                width: '953px', 
+                height: '377px', 
+                boxSizing: 'border-box' // Includes padding in the width and height
+            }}>
+                <div id="container-01" style={{ width: '100%', height: '100%' }}></div>
+            </div>
+            <FileSelect
+        onValueChange={handleFileUpload}
+        value={fileName}
+        label="Upload PDB file"
+        globPatterns={['.pdb']}
+      />
+
+            <input type="text" value={formatSelectedResidues()} onChange={handleResidueInputChange} readOnly={false} />
+            <div>
+                <label>Binder Length:</label>
+                <input
+                    type="range"
+                    min="60"
+                    max="120"
+                    value={binderLength}
+                    onChange={handleBinderLengthChange}
+                />
+                <span style={{ marginLeft: '10px' }}>{binderLength}</span>
+                <button onClick={handleSubmit}>Submit</button>
+            </div>
+        </div>
+    );
+};
+
+export default ThreeDMolViewer;
\ No newline at end of file