molstar 3.31.2 → 3.31.4

package/lib/mol-plugin-ui/skin/blue.scss

@@ -1,2 +1,2 @@
-@import 'colors/blue';
+@import 'colors/blue';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

package/lib/mol-plugin-ui/skin/dark.scss

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/light.scss

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.js

@@ -182,7 +182,8 @@ export function InterUnitBondCylinderImpostorVisual(materialId) {
         getLoci: getInterBondLoci,
         eachLocation: eachInterBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            state.createGeometry = (newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
+            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -203,7 +203,8 @@ export function IntraUnitBondCylinderImpostorVisual(materialId) {
         getLoci: getIntraBondLoci,
         eachLocation: eachIntraBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
-            state.createGeometry = (newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
+            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

package/lib/mol-repr/structure/visual/util/link.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Zhenyu Zhang <jump2cn@gmail.com>
  */
 import { Vec3 } from '../../../../mol-math/linear-algebra';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';

package/lib/mol-repr/structure/visual/util/link.js

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Zhenyu Zhang <jump2cn@gmail.com>
  */
 import { Vec3 } from '../../../../mol-math/linear-algebra';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
@@ -21,7 +22,7 @@ export var LinkCylinderParams = {
     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 }),
-    dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
+    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),
     stubCap: PD.Boolean(true),
@@ -32,7 +33,7 @@ export var LinkLineParams = {
     linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
     linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
     aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
-    dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
+    dashCount: PD.Numeric(4, { min: 0, max: 10, step: 2 }),
 };
 export var DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
 var tmpV12 = Vec3();
@@ -117,7 +118,12 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
         else if (linkStyle === 1 /* LinkStyle.Dashed */) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * dashScale;
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
-            addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
+            if (segmentCount > 1) {
+                addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
+            }
+            else {
+                addCylinder(builderState, va, vb, 0.5, cylinderProps);
+            }
         }
         else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
             var order = (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */) ? 2 :
@@ -237,9 +243,15 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         }
         else if (linkStyle === 1 /* LinkStyle.Dashed */) {
-            v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
-            v3sub(vb, vb, tmpV12);
-            builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
+            if (segmentCount > 1) {
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
+                v3sub(vb, vb, tmpV12);
+                builder.addFixedCountDashes(va, vb, 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);
+            }
         }
         else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
             var order = (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */) ? 2 :
@@ -341,9 +353,15 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
         }
         else if (linkStyle === 1 /* LinkStyle.Dashed */) {
-            v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
-            v3sub(vb, vb, tmpV12);
-            builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
+            if (segmentCount > 1) {
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
+                v3sub(vb, vb, tmpV12);
+                builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
+            }
+            else {
+                v3scale(vm, v3add(vm, va, vb), 0.5);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+            }
         }
         else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
             var order = linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ ? 2 :

package/lib/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;

package/lib/mol-util/data-source.js

@@ -343,7 +343,8 @@ var _fs = undefined;
 function getFS() {
     if (_fs)
         return _fs;
-    _fs = require('fs');
+    var req = require; // To fool webpack
+    _fs = req('fs');
     return _fs;
 }
 /** Alternative implementation of ajaxGetInternal (because xhr2 does not support file:// protocol) */