Allow for single aromatic dash count

src/mol-geo/geometry/cylinders/cylinders-builder.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { ChunkedArray } from '../../../mol-data/util';
@@ -43,16 +44,23 @@ export namespace CylindersBuilder {
 
         const addFixedCountDashes = (start: Vec3, end: Vec3, segmentCount: number, radiusScale: number, topCap: boolean, bottomCap: boolean, group: number) => {
             const d = Vec3.distance(start, end);
+            const isOdd = segmentCount % 2 !== 0;
+            segmentCount++;
             const s = Math.floor(segmentCount / 2);
             const step = 1 / segmentCount;
+            const offset = step / 2;
 
             Vec3.sub(tmpDir, end, start);
             for (let j = 0; j < s; ++j) {
-                const f = step * (j * 2 + 1);
+                const f = step * (j * 2 + 1) + offset;
                 Vec3.setMagnitude(tmpDir, tmpDir, d * f);
                 Vec3.add(tmpVecA, start, tmpDir);
-                Vec3.setMagnitude(tmpDir, tmpDir, d * step * ((j + 1) * 2));
-                Vec3.add(tmpVecB, start, tmpDir);
+                if (isOdd && j === s - 1) {
+                    Vec3.copy(tmpVecB, end);
+                } else {
+                    Vec3.setMagnitude(tmpDir, tmpDir, d * (step * ((j + 1) * 2) + offset));
+                    Vec3.add(tmpVecB, start, tmpDir);
+                }
                 add(tmpVecA[0], tmpVecA[1], tmpVecA[2], tmpVecB[0], tmpVecB[1], tmpVecB[2], radiusScale, topCap, bottomCap, group);
             }
         };

src/mol-repr/structure/visual/util/link.ts

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Zhenyu Zhang <jump2cn@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { Vec3 } from '../../../../mol-math/linear-algebra';
@@ -25,7 +26,7 @@ export const LinkCylinderParams = {
     linkCap: PD.Boolean(false),
     aromaticScale: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
     aromaticSpacing: PD.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
-    aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
+    aromaticDashCount: PD.Numeric(2, { min: 1, max: 6, step: 1 }),
     dashCount: PD.Numeric(4, { min: 0, max: 10, step: 2 }),
     dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
     dashCap: PD.Boolean(true),
@@ -286,10 +287,6 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
 
     // automatically adjust length for evenly spaced dashed cylinders
     const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
-    const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
-
-    const aromaticSegmentCount = aromaticDashCount + 1;
-    const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
 
     for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex)) continue;
@@ -308,13 +305,11 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
             v3scale(vm, v3add(vm, va, vb), 0.5);
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         } else if (linkStyle === LinkStyle.Dashed) {
+            v3scale(vm, v3add(vm, va, vb), 0.5);
             if (segmentCount > 1) {
-                v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
-                v3sub(vb, vb, tmpV12);
-                builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
+                builder.addFixedCountDashes(va, vm, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
             } else {
-                v3scale(vm, v3add(vm, va, vb), 0.5);
-                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], dashScale, dashCap, dashCap, edgeIndex);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], dashScale, dashCap, dashCap, colorModeFlag, edgeIndex);
             }
         } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
             const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
@@ -330,22 +325,19 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
 
                 const aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
 
-                v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
-                v3sub(vb, vb, tmpV12);
-
-                v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+                v3setMagnitude(tmpV12, v3sub(tmpV12, vm, va), linkRadius * 0.5);
                 v3add(va, va, tmpV12);
 
                 v3setMagnitude(vShift, vShift, aromaticOffset);
                 v3sub(va, va, vShift);
-                v3sub(vb, vb, vShift);
-                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
+                v3sub(vm, vm, vShift);
+                builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, edgeIndex);
 
                 if (linkStyle === LinkStyle.MirroredAromatic) {
                     v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
-                    v3add(vb, vb, vShift);
-                    builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
+                    v3add(vm, vm, vShift);
+                    builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, edgeIndex);
                 }
             } else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
                 const multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
@@ -353,7 +345,7 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
 
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
 
-                v3setMagnitude(tmpV12, v3sub(tmpV12, va, vb), linkRadius / 1.5);
+                v3setMagnitude(tmpV12, v3sub(tmpV12, va, vm), linkRadius / 1.5);
                 v3sub(va, va, tmpV12);
 
                 if (order === 3) builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
@@ -366,11 +358,11 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
                 builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
             }
         } else if (linkStyle === LinkStyle.Disk) {
-            v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
+            v3scale(tmpV12, v3sub(tmpV12, vm, va), 0.475);
             v3add(va, va, tmpV12);
-            v3sub(vb, vb, tmpV12);
+            v3sub(vm, vm, tmpV12);
 
-            builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], 1, linkCap, linkStub, edgeIndex);
+            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         }
     }
 
@@ -505,4 +497,4 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
     } else {
         return { lines: l };
     }
-}
+}