From 52a59696cf9a1964812b6a29d127fb7fed37991f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 4 Jun 2019 12:55:58 -0700
Subject: [PATCH] fixed and updated rcsb assembly symmetry prop
---
.vscode/settings.json | 3 +-
README.md | 5 ++-
package.json | 4 +-
src/mol-model-props/rcsb/assembly-symmetry.ts | 4 +-
.../rcsb/graphql/symmetry.gql.ts | 42 ++++++++++---------
src/mol-model-props/rcsb/graphql/types.ts | 8 +++-
.../rcsb/themes/assembly-symmetry-cluster.ts | 17 +++++---
7 files changed, 49 insertions(+), 34 deletions(-)
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 8776880ee..9f20238be 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -3,6 +3,7 @@
"files.associations": {
"*.glsl.ts": "glsl",
"*.frag.ts": "glsl",
- "*.vert.ts": "glsl"
+ "*.vert.ts": "glsl",
+ "*.gql.ts": "graphql"
},
}
\ No newline at end of file
diff --git a/README.md b/README.md
index e81cadce5..dc5685f7f 100644
--- a/README.md
+++ b/README.md
@@ -120,12 +120,13 @@ If node complains about a missine acorn peer dependency, run the following comma
### Editor
-To get syntax highlighting for the shader files add the following to Visual Code's settings files
+To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extanesions are installed in the editor.
"files.associations": {
"*.glsl.ts": "glsl",
"*.frag.ts": "glsl",
- "*.vert.ts": "glsl"
+ "*.vert.ts": "glsl",
+ "*.gql.ts": "graphql"
},
## Contributing
diff --git a/package.json b/package.json
index 7f8548805..17263a4da 100644
--- a/package.json
+++ b/package.json
@@ -13,11 +13,11 @@
"scripts": {
"lint": "tslint src/**/*.ts",
"test": "npm run lint && jest",
- "build": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" lib/ && tsc",
+ "build": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html}\" lib/ && tsc",
"postinstall": "npm run build",
"watch": "concurrently --kill-others \"npm:watch-ts\" \"npm:watch-extra\" \"npm:watch-webpack\"",
"watch-ts": "tsc -watch",
- "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" lib/ --watch",
+ "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html}\" lib/ --watch",
"build-webpack": "webpack --mode production",
"watch-webpack": "webpack -w --mode development --display minimal",
"model-server": "node lib/servers/model/server.js",
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index 2507935c5..150a93ef4 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -273,9 +273,9 @@ export namespace AssemblySymmetry {
console.error(e)
return false;
}
- if (!result || !result.assemblies) return false;
+ if (!result || !result.entry || !result.entry.assemblies) return false;
- db = createDatabaseFromJson(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
+ db = createDatabaseFromJson(result.entry.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
}
model.customProperties.add(Descriptor);
diff --git a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
index 87aec81b1..91395a77b 100644
--- a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
+++ b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
@@ -1,26 +1,28 @@
export default `query AssemblySymmetry($pdbId: String!) {
- assemblies(pdbId: $pdbId) {
- pdbx_struct_assembly {
- id
- }
- rcsb_struct_symmetry {
- clusters {
- avg_rmsd
- members {
- asym_id
- pdbx_struct_oper_list_ids
- }
+ entry(pdbId: $pdbId) {
+ assemblies {
+ pdbx_struct_assembly {
+ id
}
- kind
- oligomeric_state
- rotation_axes {
- start
- end
- order
+ rcsb_struct_symmetry {
+ clusters {
+ avg_rmsd
+ members {
+ asym_id
+ pdbx_struct_oper_list_ids
+ }
+ }
+ kind
+ oligomeric_state
+ rotation_axes {
+ start
+ end
+ order
+ }
+ stoichiometry
+ symbol
+ type
}
- stoichiometry
- symbol
- type
}
}
}`
\ No newline at end of file
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index fc3e89fbf..44ffbca48 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,4 +1,4 @@
-// Generated in 2019-03-01T14:48:33-08:00
+// Generated in 2019-06-04T12:44:49-07:00
export type Maybe<T> = T | null;
/** Built-in scalar representing an instant in time */
@@ -19,6 +19,12 @@ export namespace AssemblySymmetry {
export type Query = {
__typename?: "Query";
+ entry: Maybe<Entry>;
+ };
+
+ export type Entry = {
+ __typename?: "CoreEntry";
+
assemblies: Maybe<(Maybe<Assemblies>)[]>;
};
diff --git a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
index 8af6802ea..86866a062 100644
--- a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
+++ b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.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>
*/
@@ -9,11 +9,13 @@ import { ColorTheme, LocationColor } from '../../../mol-theme/color';
import { ParamDefinition as PD } from '../../../mol-util/param-definition'
import { Table } from '../../../mol-data/db';
import { AssemblySymmetry } from '../assembly-symmetry';
-import { ColorScale, Color } from '../../../mol-util/color';
+import { Color } from '../../../mol-util/color';
import { Unit, StructureElement, StructureProperties } from '../../../mol-model/structure';
import { Location } from '../../../mol-model/location';
-import { ColorListName, ColorListOptions } from '../../../mol-util/color/scale';
+import { ScaleLegend } from '../../../mol-util/color/scale';
import { getSymmetrySelectParam } from '../util';
+import { getPalette, getPaletteParams } from '../../../mol-theme/color/util';
+import { TableLegend } from '../../../mol-util/color/tables';
const DefaultColor = Color(0xCCCCCC)
@@ -32,7 +34,7 @@ function clusterMemberKey(assemblyId: string, asymId: string, operList: string[]
}
export const AssemblySymmetryClusterColorThemeParams = {
- list: PD.Select<ColorListName>('Viridis', ColorListOptions),
+ ...getPaletteParams({ scaleList: 'RedYellowBlue' }),
symmetryId: getSymmetrySelectParam(),
}
export type AssemblySymmetryClusterColorThemeParams = typeof AssemblySymmetryClusterColorThemeParams
@@ -44,6 +46,7 @@ export function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDataContext
export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props: PD.Values<AssemblySymmetryClusterColorThemeParams>): ColorTheme<AssemblySymmetryClusterColorThemeParams> {
let color: LocationColor = () => DefaultColor
+ let legend: ScaleLegend | TableLegend | undefined
const { symmetryId } = props
@@ -68,7 +71,8 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
}
}
- const scale = ColorScale.create({ listOrName: props.list, domain: [ 0, clusters._rowCount - 1 ] })
+ const palette = getPalette(clusters._rowCount, props)
+ legend = palette.legend
color = (location: Location): Color => {
if (StructureElement.isLocation(location)) {
@@ -76,7 +80,7 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
if (assembly && assembly.id === symmetry.assembly_id) {
const asymId = getAsymId(location.unit)(location)
const cluster = clusterByMember.get(clusterMemberKey(assembly.id, asymId, assembly.operList))
- return cluster !== undefined ? scale.color(cluster) : DefaultColor
+ return cluster !== undefined ? palette.color(cluster) : DefaultColor
}
}
return DefaultColor
@@ -91,6 +95,7 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
color,
props,
description: 'Assigns chain colors according to assembly symmetry cluster membership.',
+ legend
}
}
--
GitLab