take include/exclude flags into account when displaying aromatic bonds

- this allows to show aromatic rings only when explicitely given

src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts

@@ -133,7 +133,7 @@ function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme
             const o = edges[edgeIndex].props.order;
             const f = BitFlags.create(edges[edgeIndex].props.flag);
             if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
-                // show metall coordinations and hydrogen bonds with dashed cylinders
+                // show metallic coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
             } else if (o === 3) {
                 return LinkStyle.Triple;

src/mol-repr/structure/visual/bond-inter-unit-line.ts

@@ -71,7 +71,7 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
             const o = edges[edgeIndex].props.order;
             const f = BitFlags.create(edges[edgeIndex].props.flag);
             if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
-                // show metall coordinations and hydrogen bonds with dashed cylinders
+                // show metallic coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
             } else if (o === 3) {
                 return LinkStyle.Triple;

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -16,7 +16,7 @@ import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkBuilderProps,
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
-import { BondCylinderParams, BondIterator, eachIntraBond, getIntraBondLoci, makeIntraBondIgnoreTest } from './util/bond';
+import { BondCylinderParams, BondIterator, eachIntraBond, getIntraBondLoci, ignoreBondType, makeIntraBondIgnoreTest } from './util/bond';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { IntAdjacencyGraph } from '../../../mol-math/graph';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
@@ -33,7 +33,11 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
     const bonds = unit.bonds;
     const { edgeCount, a, b, edgeProps, offset } = bonds;
     const { order: _order, flags: _flags } = edgeProps;
-    const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds } = props;
+    const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds, includeTypes, excludeTypes } = props;
+
+    const include = BondType.fromNames(includeTypes);
+    const exclude = BondType.fromNames(excludeTypes);
+    const ignoreComputedAromatic = ignoreBondType(include, exclude, BondType.Flag.Computed);
 
     const vRef = Vec3(), delta = Vec3();
     const pos = unit.conformation.invariantPosition;
@@ -123,7 +127,7 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
             const o = _order[edgeIndex];
             const f = _flags[edgeIndex];
             if (isBondType(f, BondType.Flag.MetallicCoordination) || isBondType(f, BondType.Flag.HydrogenBond)) {
-                // show metall coordinations and hydrogen bonds with dashed cylinders
+                // show metallic coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
             } else if (o === 3) {
                 return LinkStyle.Triple;
@@ -133,7 +137,7 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
                 const bR = elementAromaticRingIndices.get(bI);
                 const arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
 
-                if (arCount || isBondType(f, BondType.Flag.Aromatic)) {
+                if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
                     } else {

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -14,7 +14,7 @@ import { LinkStyle, createLinkLines, LinkBuilderProps } from './util/link';
 import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';
-import { BondIterator, BondLineParams, getIntraBondLoci, eachIntraBond, makeIntraBondIgnoreTest } from './util/bond';
+import { BondIterator, BondLineParams, getIntraBondLoci, eachIntraBond, makeIntraBondIgnoreTest, ignoreBondType } from './util/bond';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { Lines } from '../../../mol-geo/geometry/lines/lines';
 import { IntAdjacencyGraph } from '../../../mol-math/graph';
@@ -36,10 +36,14 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
     const elements = unit.elements;
     const bonds = unit.bonds;
     const { edgeCount, a, b, edgeProps, offset } = bonds;
+    if (!edgeCount) return Lines.createEmpty(lines);
+
     const { order: _order, flags: _flags } = edgeProps;
-    const { sizeFactor, aromaticBonds } = props;
+    const { sizeFactor, aromaticBonds, includeTypes, excludeTypes } = props;
 
-    if (!edgeCount) return Lines.createEmpty(lines);
+    const include = BondType.fromNames(includeTypes);
+    const exclude = BondType.fromNames(excludeTypes);
+    const ignoreComputedAromatic = ignoreBondType(include, exclude, BondType.Flag.Computed);
 
     const vRef = Vec3();
     const pos = unit.conformation.invariantPosition;
@@ -84,7 +88,7 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
             const o = _order[edgeIndex];
             const f = _flags[edgeIndex];
             if (isBondType(f, BondType.Flag.MetallicCoordination) || isBondType(f, BondType.Flag.HydrogenBond)) {
-                // show metall coordinations and hydrogen bonds with dashed cylinders
+                // show metallic coordinations and hydrogen bonds with dashed cylinders
                 return LinkStyle.Dashed;
             } else if (o === 3) {
                 return LinkStyle.Triple;
@@ -94,7 +98,7 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
                 const bR = elementAromaticRingIndices.get(bI);
                 const arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
 
-                if (arCount || isBondType(f, BondType.Flag.Aromatic)) {
+                if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
                     } else {