diff --git a/src/mol-repr/structure/registry.ts b/src/mol-repr/structure/registry.ts
index d6d28f25330e7a4a0fd59e02bddc5a10aaa8f022..5cadc109a7933a576c8e291c75c97d052765a476 100644
--- a/src/mol-repr/structure/registry.ts
+++ b/src/mol-repr/structure/registry.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>
*/
@@ -15,6 +15,7 @@ import { SpacefillRepresentationProvider } from './representation/spacefill';
import { DistanceRestraintRepresentationProvider } from './representation/distance-restraint';
import { PointRepresentationProvider } from './representation/point';
import { StructureRepresentationState } from './representation';
+import { PuttyRepresentationProvider } from './representation/putty';
export class StructureRepresentationRegistry extends RepresentationRegistry<Structure, StructureRepresentationState> {
constructor() {
@@ -34,6 +35,7 @@ export const BuiltInStructureRepresentations = {
'molecular-surface': MolecularSurfaceRepresentationProvider,
'molecular-volume': MolecularVolumeRepresentationProvider,
'point': PointRepresentationProvider,
+ 'putty': PuttyRepresentationProvider,
'spacefill': SpacefillRepresentationProvider,
}
export type BuiltInStructureRepresentationsName = keyof typeof BuiltInStructureRepresentations
diff --git a/src/mol-repr/structure/representation/cartoon.ts b/src/mol-repr/structure/representation/cartoon.ts
index d524d00d6c46b62e7253725c4d59e8aa8417c686..fa1a4f32aa77c5a530a663aead2f7c41da25066c 100644
--- a/src/mol-repr/structure/representation/cartoon.ts
+++ b/src/mol-repr/structure/representation/cartoon.ts
@@ -54,7 +54,7 @@ export function CartoonRepresentation(ctx: RepresentationContext, getParams: Rep
export const CartoonRepresentationProvider: StructureRepresentationProvider<CartoonParams> = {
label: 'Cartoon',
- description: 'Displays a ribbon smoothly following the trace atoms of polymers.',
+ description: 'Displays ribbons, planks, tubes smoothly following the trace atoms of polymers.',
factory: CartoonRepresentation,
getParams: getCartoonParams,
defaultValues: PD.getDefaultValues(CartoonParams),
diff --git a/src/mol-repr/structure/representation/putty.ts b/src/mol-repr/structure/representation/putty.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b2d7f9c98cd8afbfea14fdd2145df50a84b1ae90
--- /dev/null
+++ b/src/mol-repr/structure/representation/putty.ts
@@ -0,0 +1,56 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PolymerTubeVisual, PolymerTubeParams } from '../visual/polymer-tube-mesh';
+import { PolymerGapVisual, PolymerGapParams } from '../visual/polymer-gap-cylinder';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { UnitsRepresentation } from '../units-representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
+import { Representation, RepresentationParamsGetter, RepresentationContext } from 'mol-repr/representation';
+import { Structure, Unit } from 'mol-model/structure';
+import { ThemeRegistryContext } from 'mol-theme/theme';
+
+const PuttyVisuals = {
+ 'polymer-tube': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerTubeParams>) => UnitsRepresentation('Polymer tube mesh', ctx, getParams, PolymerTubeVisual),
+ 'polymer-gap': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerGapParams>) => UnitsRepresentation('Polymer gap cylinder', ctx, getParams, PolymerGapVisual),
+}
+type PuttyVisualName = keyof typeof PuttyVisuals
+const PuttyVisualOptions = Object.keys(PuttyVisuals).map(name => [name, name] as [PuttyVisualName, string])
+
+export const PuttyParams = {
+ ...PolymerTubeParams,
+ ...PolymerGapParams,
+ sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
+ visuals: PD.MultiSelect<PuttyVisualName>(['polymer-tube', 'polymer-gap'], PuttyVisualOptions),
+}
+export type PuttyParams = typeof PuttyParams
+export function getPuttyParams(ctx: ThemeRegistryContext, structure: Structure) {
+ const params = PD.clone(PuttyParams)
+ let hasNucleotides = false
+ let hasGaps = false
+ structure.units.forEach(u => {
+ if (!hasNucleotides && Unit.isAtomic(u) && u.nucleotideElements.length) hasNucleotides = true
+ if (!hasGaps && u.gapElements.length) hasGaps = true
+ })
+ params.visuals.defaultValue = ['polymer-tube']
+ if (hasGaps) params.visuals.defaultValue.push('polymer-gap')
+ return params
+}
+
+export type PuttyRepresentation = StructureRepresentation<PuttyParams>
+export function PuttyRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PuttyParams>): PuttyRepresentation {
+ return Representation.createMulti('Putty', ctx, getParams, StructureRepresentationStateBuilder, PuttyVisuals as unknown as Representation.Def<Structure, PuttyParams>)
+}
+
+export const PuttyRepresentationProvider: StructureRepresentationProvider<PuttyParams> = {
+ label: 'Putty',
+ description: 'Displays a tube smoothly following the trace atoms of polymers.',
+ factory: PuttyRepresentation,
+ getParams: getPuttyParams,
+ defaultValues: PD.getDefaultValues(PuttyParams),
+ defaultColorTheme: 'polymer-id',
+ defaultSizeTheme: 'uncertainty'
+}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/polymer-tube-mesh.ts b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
new file mode 100644
index 0000000000000000000000000000000000000000..94accbff631fddd68ac6de7a8b8640d53f64a7d2
--- /dev/null
+++ b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
@@ -0,0 +1,88 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, Structure } from 'mol-model/structure';
+import { UnitsVisual } from '../representation';
+import { VisualUpdateState } from '../../util';
+import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, interpolateSizes } from './util/polymer';
+import { isNucleic } from 'mol-model/structure/model/types';
+import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
+import { addTube } from 'mol-geo/geometry/mesh/builder/tube';
+import { VisualContext } from 'mol-repr/visual';
+import { Theme } from 'mol-theme/theme';
+
+export const PolymerTubeMeshParams = {
+ sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
+ linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }),
+ radialSegments: PD.Numeric(16, { min: 3, max: 56, step: 1 }),
+}
+export const DefaultPolymerTubeMeshProps = PD.getDefaultValues(PolymerTubeMeshParams)
+export type PolymerTubeMeshProps = typeof DefaultPolymerTubeMeshProps
+
+// TODO handle polymer ends properly
+
+function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerTubeMeshProps, mesh?: Mesh) {
+ const polymerElementCount = unit.polymerElements.length
+
+ if (!polymerElementCount) return Mesh.createEmpty(mesh)
+ const { sizeFactor, linearSegments, radialSegments } = props
+
+ const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2
+ const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh)
+
+ const state = createCurveSegmentState(linearSegments)
+ const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state
+
+ let i = 0
+ const polymerTraceIt = PolymerTraceIterator(unit)
+ while (polymerTraceIt.hasNext) {
+ const v = polymerTraceIt.move()
+ builderState.currentGroup = i
+
+ const isNucleicType = isNucleic(v.moleculeType)
+ const tension = isNucleicType ? 0.5 : 0.9
+ const shift = isNucleicType ? 0.3 : 0.5
+
+ interpolateCurveSegment(state, v, tension, shift)
+
+ let s0 = theme.size.size(v.centerPrev) * sizeFactor
+ let s1 = theme.size.size(v.center) * sizeFactor
+ let s2 = theme.size.size(v.centerNext) * sizeFactor
+
+ interpolateSizes(state, s0, s1, s2, s0, s1, s2, shift)
+ addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, v.first, v.last)
+
+ ++i
+ }
+
+ return MeshBuilder.getMesh(builderState)
+}
+
+export const PolymerTubeParams = {
+ ...UnitsMeshParams,
+ ...PolymerTubeMeshParams
+}
+export type PolymerTubeParams = typeof PolymerTubeParams
+
+export function PolymerTubeVisual(): UnitsVisual<PolymerTubeParams> {
+ return UnitsMeshVisual<PolymerTubeParams>({
+ defaultProps: PD.getDefaultValues(PolymerTubeParams),
+ createGeometry: createPolymerTubeMesh,
+ createLocationIterator: PolymerLocationIterator.fromGroup,
+ getLoci: getPolymerElementLoci,
+ eachLocation: eachPolymerElement,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTubeParams>, currentProps: PD.Values<PolymerTubeParams>) => {
+ state.createGeometry = (
+ newProps.sizeFactor !== currentProps.sizeFactor ||
+ newProps.linearSegments !== currentProps.linearSegments ||
+ newProps.radialSegments !== currentProps.radialSegments
+ )
+ }
+ })
+}
\ No newline at end of file
diff --git a/src/mol-theme/color/uncertainty.ts b/src/mol-theme/color/uncertainty.ts
index 857951921bcf5efb4e6e241e2805d4e9c38ff2bb..874f441a3c59a9b30f3996fe58ffbcfcbc1a61dd 100644
--- a/src/mol-theme/color/uncertainty.ts
+++ b/src/mol-theme/color/uncertainty.ts
@@ -36,6 +36,7 @@ export function getUncertainty(unit: Unit, element: ElementIndex): number {
export function UncertaintyColorTheme(ctx: ThemeDataContext, props: PD.Values<UncertaintyColorThemeParams>): ColorTheme<UncertaintyColorThemeParams> {
const scale = ColorScale.create({
+ reverse: true,
domain: props.domain,
listOrName: props.list,
})