Merge pull request #366 from molstar/repr-defaults-tweaks

cleaner default representation style

CHANGELOG.md

@@ -8,6 +8,9 @@ Note that since we don't clearly distinguish between a public and private interf
 
 - Fix ``xrayShaded`` & ``ignoreLight`` params not working at the same time
 - Add ``ignoreLight`` to component params
+- Tweaks for cleaner default representation style
+    - Cartoon: use ``nucleotide-ring`` instead of ``nucleotide-block``
+    - Focus: use ``xrayShaded`` instead of opacity; adjust target size; don't show non-covalent interactions twice
 - Fix representation preset side effects (changing post-processing parameters, see #363)
 - Add Quick Styles panel (default, illustrative, stylized)
 - Fix exported structure missing secondary-structure categories (#364)

src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts

@@ -27,11 +27,19 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
         expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
         targetParams: PD.Group(reprParams, {
             label: 'Target',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.22, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', excludeTypes: ['hydrogen-bond', 'metal-coordination'] },
+            })
         }),
         surroundingsParams: PD.Group(reprParams, {
             label: 'Surroundings',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.16, excludeTypes: ['hydrogen-bond', 'metal-coordination'] }
+            })
         }),
         nciParams: PD.Group(reprParams, {
             label: 'Non-covalent Int.',

src/mol-repr/structure/representation/cartoon.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -35,7 +35,7 @@ export const CartoonParams = {
     ...NucleotideRingParams,
     ...PolymerDirectionParams,
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
-    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], PD.objectToOptions(CartoonVisuals)),
+    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], PD.objectToOptions(CartoonVisuals)),
     bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
 };
 
@@ -49,7 +49,7 @@ export function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure
         if (!hasGaps && u.gapElements.length) hasGaps = true;
     });
     params.visuals.defaultValue = ['polymer-trace'];
-    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-block');
+    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-ring');
     if (hasGaps) params.visuals.defaultValue.push('polymer-gap');
     return params;
 }