fix par file visualization

sulcgroup · Jun 11, 2024 · 112feb5 · 112feb5
1 parent ebaa59c
commit 112feb5
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Showing 8 changed files with 77 additions and 11 deletions.
diff --git a/dist/file_handling/aux_readers.js b/dist/file_handling/aux_readers.js
@@ -9,6 +9,9 @@ function readTraj(trajFile, system) {
 function readJson(jsonFile, system) {
     return parseFileWith(jsonFile, parseJson, [system]);
 }
+function readParFile(parFile, system) {
+    return parseFileWith(parFile, parsePar, [system]);
+}
 // Creates color overlays
 function makeLut(data, key, system) {
     let arr = data[key];
@@ -204,8 +207,8 @@ function readSelectFile(reader) {
     api.selectElementIDs(ids, true);
 }
 //reads in an anm parameter file and associates it with the last loaded system.
-function readParFile(system, reader) {
-    let lines = reader.result.split(/[\n]+/g);
+function parsePar(lines, system) {
+    lines = lines.split(/[\n]+/g);
     //remove the header
     lines = lines.slice(1);
     const size = lines.length;
@@ -216,6 +219,12 @@ function readParFile(system, reader) {
         let l = lines[i].split(/\s+/);
         //extract values
         const p = parseInt(l[0]), q = parseInt(l[1]), eqDist = parseFloat(l[2]), type = l[3], strength = parseFloat(l[4]);
+        if (!Number.isInteger(p) || !Number.isInteger(q) || !Number.isFinite(eqDist) || !Number.isFinite(strength)) {
+            notify("Cannot read par file, see console for bad line", 'error');
+            console.log("Error on par line", i);
+            console.log(l);
+            return;
+        }
         // if its a torsional ANM then there are additional parameters on some lines
         let extraParams = [];
         if (l.length > 5) {
@@ -226,7 +235,6 @@ function readParFile(system, reader) {
         if (Number.isInteger(p) && Number.isInteger(q)) {
             net.reducedEdges.addEdge(p, q, eqDist, type, strength, extraParams);
         }
-        // if (particle1 == undefined) console.log(i)
     }
     ;
     // Create and Fill Vectors

diff --git a/dist/file_handling/io.js b/dist/file_handling/io.js
@@ -282,7 +282,7 @@ class TrajectoryReader {
         centerAndPBC(system.getMonomers(), newBox);
         if (forceHandler)
             forceHandler.redraw();
-        // Signal that config has been loaded. This is used by the trajectory video loader
+        // Signal that config has been loaded. This is used by the trajectory video loader.
         document.dispatchEvent(new Event('nextConfigLoaded'));
     }
 }
diff --git a/dist/model/network.js b/dist/model/network.js
@@ -282,6 +282,16 @@ class Network {
         }
     }
     ;
+    reCalculateRotations() {
+        for (let t = 0; t < this.reducedEdges.total; t++) {
+            let i = this.reducedEdges.p1[t];
+            let j = this.reducedEdges.p2[t];
+            let newRot = this.elemcoords.rotation(i, j);
+            this.fillVec('rotations', 4, t, [newRot.w, newRot.z, newRot.y, newRot.x]);
+        }
+        this.callUpdates(["instanceRotation"]);
+    }
+    ;
     updatePositions() {
         // update all coordinates
         this.elemcoords.xI = this.particles.map(e => e.getPos().x);
@@ -292,11 +302,20 @@ class Network {
             let i = this.reducedEdges.p1[t];
             let j = this.reducedEdges.p2[t];
             let pos = this.center(i, j).toArray();
+            let dij = this.elemcoords.distance(i, j);
             this.fillVec('offsets', 3, t, [pos[0], pos[1], pos[2]]);
+            this.fillVec('scales', 3, t, [1, dij, 1]);
         }
-        this.callUpdates(["instanceOffset"]);
+        this.callUpdates(["instanceOffset", "instanceScale"]);
+    }
+    ;
+    recalculateVis() {
+        this.updatePositions();
+        this.reCalculateRotations();
     }
     ;
+    // This has never worked for single particles being rotated...
+    // Apply a rotation to all particles
     updateRotations(q) {
         for (let t = 0; t < this.reducedEdges.total; t++) {
             let currRot = this.getVec('rotations', 4, t);

diff --git a/dist/scene/PBC_switchbox.js b/dist/scene/PBC_switchbox.js
@@ -66,6 +66,11 @@ function centerAndPBC(elems, targetBox) {
     tmpSystems.forEach(s => s.callUpdates(['instanceOffset']));
     if (forceHandler)
         forceHandler.redraw();
+    if (networks.length > 0) {
+        networks.forEach(n => {
+            n.recalculateVis();
+        });
+    }
     render();
 }
 /**

diff --git a/ts/file_handling/aux_readers.ts b/ts/file_handling/aux_readers.ts
@@ -13,6 +13,10 @@ function readJson(jsonFile:File, system:System){ // this still doesn't work for
     return parseFileWith(jsonFile, parseJson, [system])
 }
 
+function readParFile(parFile:File, system:System) {
+    return parseFileWith(parFile, parsePar, [system])
+}
+
 // Creates color overlays
 function makeLut(data, key, system) {
 
@@ -222,9 +226,9 @@ function readSelectFile(reader) {
 }
 
 //reads in an anm parameter file and associates it with the last loaded system.
-function readParFile(system, reader) {
-    let lines = (reader.result as string).split(/[\n]+/g);
+function parsePar(lines, system) {
 
+    lines = lines.split(/[\n]+/g);
     //remove the header
     lines = lines.slice(1)
 
@@ -242,6 +246,13 @@ function readParFile(system, reader) {
             eqDist = parseFloat(l[2]),
             type = l[3],
             strength = parseFloat(l[4]);
+
+        if (!Number.isInteger(p) || !Number.isInteger(q) || !Number.isFinite(eqDist) || !Number.isFinite(strength)) {
+            notify("Cannot read par file, see console for bad line", 'error')
+            console.log("Error on par line", i)
+            console.log(l)
+            return
+        }
 
         // if its a torsional ANM then there are additional parameters on some lines
         let extraParams = []
@@ -253,7 +264,6 @@ function readParFile(system, reader) {
         if(Number.isInteger(p) && Number.isInteger(q)){
             net.reducedEdges.addEdge(p, q, eqDist, type, strength, extraParams);
         }
-        // if (particle1 == undefined) console.log(i)
     };
     // Create and Fill Vectors
     net.initInstances(net.reducedEdges.total);

diff --git a/ts/file_handling/io.ts b/ts/file_handling/io.ts
@@ -319,7 +319,7 @@ class TrajectoryReader {
 
             // consume a new line from the file
             l = lines[i].split(/\s+/);
-            
+
             // get the nucleotide associated with the line
             if (system.lines2ele) { currentNucleotide = system.lines2ele.get(i) } // ugly hack to get oxServe to work
             else { currentNucleotide = elements.get(i+system.globalStartId); }
@@ -333,7 +333,7 @@ class TrajectoryReader {
         centerAndPBC(system.getMonomers(), newBox);
         if (forceHandler) forceHandler.redraw();
 
-        // Signal that config has been loaded. This is used by the trajectory video loader
+        // Signal that config has been loaded. This is used by the trajectory video loader.
         document.dispatchEvent(new Event('nextConfigLoaded'));
     }
 }
diff --git a/ts/model/network.ts b/ts/model/network.ts
@@ -275,6 +275,16 @@ class Network {
         }
     }
     ;
+    reCalculateRotations() { // Re-calculate all rotations based on particle positions.
+        for(let t = 0; t < this.reducedEdges.total; t++){
+            let i = this.reducedEdges.p1[t];
+            let j = this.reducedEdges.p2[t];
+            let newRot = this.elemcoords.rotation(i, j)
+            this.fillVec('rotations', 4, t, [newRot.w, newRot.z, newRot.y, newRot.x]);
+        }
+        this.callUpdates(["instanceRotation"])
+    }
+    ;
     updatePositions(){ // Called by translation.ts
         // update all coordinates
         this.elemcoords.xI = this.particles.map(e => e.getPos().x);
@@ -285,11 +295,20 @@ class Network {
             let i = this.reducedEdges.p1[t];
             let j = this.reducedEdges.p2[t];
             let pos = this.center(i, j).toArray();
+            let dij = this.elemcoords.distance(i, j);
             this.fillVec('offsets', 3, t, [pos[0], pos[1], pos[2]]);
+            this.fillVec('scales', 3, t, [1, dij, 1]);
         }
-        this.callUpdates(["instanceOffset"])
+        this.callUpdates(["instanceOffset", "instanceScale"]);
+    }
+    ;
+    recalculateVis() {
+        this.updatePositions();
+        this.reCalculateRotations();
     }
     ;
+    // This has never worked for single particles being rotated...
+    // Apply a rotation to all particles
     updateRotations(q: THREE.Quaternion){// Called by translation.ts
         for(let t = 0; t < this.reducedEdges.total; t++){
             let currRot = this.getVec('rotations', 4, t);

diff --git a/ts/scene/PBC_switchbox.ts b/ts/scene/PBC_switchbox.ts
@@ -68,6 +68,11 @@ function centerAndPBC(elems?: BasicElement[], targetBox?: THREE.Vector3) {
     affectedSystems.forEach(s=>s.callUpdates(['instanceOffset']));
     tmpSystems.forEach(s=>s.callUpdates(['instanceOffset']));
     if(forceHandler) forceHandler.redraw();
+    if (networks.length > 0) {
+        networks.forEach(n => {
+            n.recalculateVis();
+        })
+    }
     render();
 }