From b77994d01f64cd3831c364472c45a5973fd326bb Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 10 Jan 2020 15:30:29 -0800
Subject: [PATCH] improved bond handling
- filter (include/exclude) type in repr
- cleaned-up bond types and names
---
.../structure/mmcif/bonds/struct_conn.ts | 4 +-
src/mol-model/structure/model/types.ts | 42 ++++++++++++++++---
.../util/structure-selection-helper.ts | 2 +-
.../visual/bond-inter-unit-cylinder.ts | 26 ++++++++----
.../visual/bond-intra-unit-cylinder.ts | 24 +++++++----
src/mol-repr/structure/visual/util/bond.ts | 10 ++++-
src/mol-script/runtime/query/table.ts | 11 +----
7 files changed, 82 insertions(+), 37 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
index 9850bc6a6..b29c31dce 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
@@ -235,9 +235,9 @@ export namespace StructConn {
case 'covale':
flags = BondType.Flag.Covalent;
break;
- case 'disulf': flags = BondType.Flag.Covalent | BondType.Flag.Sulfide; break;
+ case 'disulf': flags = BondType.Flag.Covalent | BondType.Flag.Disulfide; break;
case 'hydrog':
- flags = BondType.Flag.Hydrogen;
+ flags = BondType.Flag.HydrogenBond;
break;
case 'metalc': flags = BondType.Flag.MetallicCoordination; break;
}
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 88f5513e7..d59187274 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -592,11 +592,10 @@ export namespace BondType {
None = 0x0,
Covalent = 0x1,
MetallicCoordination = 0x2,
- Hydrogen = 0x4,
- Ionic = 0x8,
- Sulfide = 0x10,
- Aromatic = 0x20,
- Computed = 0x40
+ HydrogenBond = 0x4,
+ Disulfide = 0x8,
+ Aromatic = 0x10,
+ Computed = 0x20
// currently at most 16 flags are supported!!
}
@@ -607,6 +606,39 @@ export namespace BondType {
export function isCovalent(flags: BondType.Flag) {
return (flags & BondType.Flag.Covalent) !== 0;
}
+
+ export const Names = {
+ 'covalent': Flag.Covalent,
+ 'metal-coordination': Flag.MetallicCoordination,
+ 'hydrogen-bond': Flag.HydrogenBond,
+ 'disulfide': Flag.HydrogenBond,
+ 'aromatic': Flag.HydrogenBond,
+ 'computed': Flag.HydrogenBond,
+ }
+ export type Names = keyof typeof Names
+
+ export function isName(name: string): name is Names {
+ return name in Names
+ }
+
+ export function fromName(name: Names): Flag {
+ switch (name) {
+ case 'covalent': return Flag.Covalent;
+ case 'metal-coordination': return Flag.MetallicCoordination;
+ case 'hydrogen-bond': return Flag.HydrogenBond;
+ case 'disulfide': return Flag.Disulfide;
+ case 'aromatic': return Flag.Aromatic;
+ case 'computed': return Flag.Computed;
+ }
+ }
+
+ export function fromNames(names: Names[]): Flag {
+ let f = Flag.None
+ for (let i = 0, il = names.length; i < il; ++i) {
+ f |= fromName(names[i])
+ }
+ return f
+ }
}
/**
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
index 64929a2e2..a24f03399 100644
--- a/src/mol-plugin/util/structure-selection-helper.ts
+++ b/src/mol-plugin/util/structure-selection-helper.ts
@@ -264,7 +264,7 @@ const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.
MS.struct.generator.bondedAtomicPairs({
0: MS.core.flags.hasAny([
MS.struct.bondProperty.flags(),
- MS.core.type.bitflags([BondType.Flag.Sulfide])
+ MS.core.type.bitflags([BondType.Flag.Disulfide])
])
})
])
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
index 013ff64aa..e2813e6d5 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -10,14 +10,15 @@ import { Structure, StructureElement, Bond, Unit } from '../../../mol-model/stru
import { Theme } from '../../../mol-theme/theme';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { Vec3 } from '../../../mol-math/linear-algebra';
-import { BitFlags } from '../../../mol-util';
-import { createBondCylinderMesh, BondCylinderParams, BondIterator } from './util/bond';
+import { BitFlags, arrayEqual } from '../../../mol-util';
+import { createBondCylinderMesh, BondCylinderParams, BondIterator, ignoreBondType } from './util/bond';
import { ComplexMeshParams, ComplexVisual, ComplexMeshVisual } from '../complex-visual';
import { VisualUpdateState } from '../../util';
import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
import { Interval, OrderedSet } from '../../../mol-data/int';
import { isHydrogen } from './util/common';
+import { BondType } from '../../../mol-model/structure/model/types';
const tmpRefPosBondIt = new Bond.ElementBondIterator()
function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, index: StructureElement.UnitIndex) {
@@ -36,7 +37,16 @@ const tmpLoc = StructureElement.Location.create()
function createInterUnitBondCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitBondParams>, mesh?: Mesh) {
const bonds = structure.interUnitBonds
const { edgeCount, edges } = bonds
- const { sizeFactor, sizeAspectRatio, ignoreHydrogens } = props
+ const { sizeFactor, sizeAspectRatio, ignoreHydrogens, includeTypes, excludeTypes } = props
+
+ const include = BondType.fromNames(includeTypes)
+ const exclude = BondType.fromNames(excludeTypes)
+
+ const ignoreHydrogen = ignoreHydrogens ? (edgeIndex: number) => {
+ const b = edges[edgeIndex]
+ const uA = b.unitA, uB = b.unitB
+ return isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])
+ } : () => false
if (!edgeCount) return Mesh.createEmpty(mesh)
@@ -75,11 +85,7 @@ function createInterUnitBondCylinderMesh(ctx: VisualContext, structure: Structur
const sizeB = theme.size.size(tmpLoc)
return Math.min(sizeA, sizeB) * sizeFactor * sizeAspectRatio
},
- ignore: ignoreHydrogens ? (edgeIndex: number) => {
- const b = edges[edgeIndex]
- const uA = b.unitA, uB = b.unitB
- return isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])
- } : () => false
+ ignore: (edgeIndex: number) => ignoreHydrogen(edgeIndex) || ignoreBondType(include, exclude, edges[edgeIndex].props.flag)
}
return createBondCylinderMesh(ctx, builderProps, props, mesh)
@@ -109,7 +115,9 @@ export function InterUnitBondVisual(materialId: number): ComplexVisual<InterUnit
newProps.bondScale !== currentProps.bondScale ||
newProps.bondSpacing !== currentProps.bondSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.bondCap !== currentProps.bondCap
+ newProps.bondCap !== currentProps.bondCap ||
+ !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
+ !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes)
)
}
}, materialId)
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index a07c04b85..d3844f4b9 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -11,14 +11,15 @@ import { Unit, Structure, StructureElement, Bond } from '../../../mol-model/stru
import { Theme } from '../../../mol-theme/theme';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { Vec3 } from '../../../mol-math/linear-algebra';
-import { BitFlags } from '../../../mol-util';
-import { createBondCylinderMesh, BondCylinderParams, BondIterator } from './util/bond';
+import { BitFlags, arrayEqual } from '../../../mol-util';
+import { createBondCylinderMesh, BondCylinderParams, BondIterator, ignoreBondType } from './util/bond';
import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
import { Interval, OrderedSet } from '../../../mol-data/int';
import { isHydrogen } from './util/common';
+import { BondType } from '../../../mol-model/structure/model/types';
function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitBondParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -29,7 +30,14 @@ function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structu
const bonds = unit.bonds
const { edgeCount, a, b, edgeProps, offset } = bonds
const { order: _order, flags: _flags } = edgeProps
- const { sizeFactor, sizeAspectRatio, ignoreHydrogens } = props
+ const { sizeFactor, sizeAspectRatio, ignoreHydrogens, includeTypes, excludeTypes } = props
+
+ const include = BondType.fromNames(includeTypes)
+ const exclude = BondType.fromNames(excludeTypes)
+
+ const ignoreHydrogen = ignoreHydrogens ? (edgeIndex: number) => {
+ return isHydrogen(unit, elements[a[edgeIndex]]) || isHydrogen(unit, elements[b[edgeIndex]])
+ } : () => false
if (!edgeCount) return Mesh.createEmpty(mesh)
@@ -68,9 +76,7 @@ function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structu
const sizeB = theme.size.size(location)
return Math.min(sizeA, sizeB) * sizeFactor * sizeAspectRatio
},
- ignore: ignoreHydrogens ? (edgeIndex: number) => {
- return isHydrogen(unit, elements[a[edgeIndex]]) || isHydrogen(unit, elements[b[edgeIndex]])
- } : () => false
+ ignore: (edgeIndex: number) => ignoreHydrogen(edgeIndex) || ignoreBondType(include, exclude, _flags[edgeIndex])
}
return createBondCylinderMesh(ctx, builderProps, props, mesh)
@@ -100,7 +106,9 @@ export function IntraUnitBondVisual(materialId: number): UnitsVisual<IntraUnitBo
newProps.bondScale !== currentProps.bondScale ||
newProps.bondSpacing !== currentProps.bondSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.bondCap !== currentProps.bondCap
+ newProps.bondCap !== currentProps.bondCap ||
+ !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
+ !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes)
)
}
}, materialId)
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index 5088ba970..fdc46e8c8 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -21,10 +21,16 @@ export const BondCylinderParams = {
bondSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
bondCap: PD.Boolean(false),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }),
+ includeTypes: PD.MultiSelect(Object.keys(BondType.Names) as BondType.Names[], PD.objectToOptions(BondType.Names)),
+ excludeTypes: PD.MultiSelect([] as BondType.Names[], PD.objectToOptions(BondType.Names)),
}
export const DefaultBondCylinderProps = PD.getDefaultValues(BondCylinderParams)
export type BondCylinderProps = typeof DefaultBondCylinderProps
+export function ignoreBondType(include: BondType.Flag, exclude: BondType.Flag, f: BondType.Flag) {
+ return !BondType.is(include, f) || BondType.is(exclude, f)
+}
+
const tmpShiftV12 = Vec3.zero()
const tmpShiftV13 = Vec3.zero()
@@ -99,7 +105,7 @@ export function createBondCylinderMesh(ctx: VisualContext, bondBuilder: BondCyli
const f = flags(edgeIndex)
builderState.currentGroup = edgeIndex
- if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.Hydrogen)) {
+ if (BondType.is(f, BondType.Flag.MetallicCoordination) || BondType.is(f, BondType.Flag.HydrogenBond)) {
// show metall coordinations and hydrogen bonds with dashed cylinders
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius / 3
cylinderProps.topCap = cylinderProps.bottomCap = true
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index afa124280..4eaa59ebc 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -353,16 +353,7 @@ function atomProp(p: (e: StructureElement.Location) => any): (ctx: QueryContext,
}
function bondFlag(current: BondType, f: string): BondType {
- switch (f.toLowerCase()) {
- case 'covalent': return current | BondType.Flag.Covalent;
- case 'metallic': return current | BondType.Flag.MetallicCoordination;
- case 'ionic': return current | BondType.Flag.Ionic;
- case 'hydrogen': return current | BondType.Flag.Hydrogen;
- case 'sulfide': return current | BondType.Flag.Sulfide;
- case 'aromatic': return current | BondType.Flag.Aromatic;
- case 'computed': return current | BondType.Flag.Computed;
- default: return current;
- }
+ return current | (BondType.isName(f) ? BondType.fromName(f) : BondType.Flag.None)
}
function secondaryStructureFlag(current: SecondaryStructureType, f: string): SecondaryStructureType {
--
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