From 11c7024edd0c4768ae334e5115be3ce5ac3b363e Mon Sep 17 00:00:00 2001 From: Alexander Rose <alexander.rose@weirdbyte.de> Date: Tue, 2 Jun 2020 17:49:50 -0700 Subject: [PATCH] tweaks for dnatco confal pyramids MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - added Michal and Jiří as contributors - add preset to annotation group - legend for color theme - add as extension to viewer --- package.json | 4 +++- src/apps/viewer/index.ts | 2 ++ src/extensions/dnatco/confal-pyramids/behavior.ts | 2 +- src/extensions/dnatco/confal-pyramids/color.ts | 8 ++++++++ 4 files changed, 14 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 35bbea1c7..74a4cfc2f 100644 --- a/package.json +++ b/package.json @@ -80,7 +80,9 @@ "Alexander Rose <alexander.rose@weirdbyte.de>", "David Sehnal <david.sehnal@gmail.com>", "Sebastian Bittrich <sebastian.bittrich@rcsb.org>", - "Ludovic Autin <autin@scripps.edu>" + "Ludovic Autin <autin@scripps.edu>", + "Michal Malý <michal.maly@ibt.cas.cz>", + "Jiří Černý <jiri.cerny@ibt.cas.cz>" ], "license": "MIT", "devDependencies": { diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts index cc87379f4..1265ae8eb 100644 --- a/src/apps/viewer/index.ts +++ b/src/apps/viewer/index.ts @@ -24,6 +24,7 @@ import { PluginState } from '../../mol-plugin/state'; import { DownloadDensity } from '../../mol-plugin-state/actions/volume'; import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout'; import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory'; +import { DnatcoConfalPyramids } from '../../extensions/dnatco'; require('mol-plugin-ui/skin/light.scss'); @@ -32,6 +33,7 @@ export { setProductionMode, setDebugMode } from '../../mol-util/debug'; const Extensions = { 'cellpack': PluginSpec.Behavior(CellPack), + 'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids), 'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport), 'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry), 'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport) diff --git a/src/extensions/dnatco/confal-pyramids/behavior.ts b/src/extensions/dnatco/confal-pyramids/behavior.ts index 23df06b36..3c38c9f54 100644 --- a/src/extensions/dnatco/confal-pyramids/behavior.ts +++ b/src/extensions/dnatco/confal-pyramids/behavior.ts @@ -18,7 +18,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition'; export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider({ id: 'preset-structure-representation-confal-pyramids', display: { - name: 'Confal Pyramids', + name: 'Confal Pyramids', group: 'Annotation', description: 'Schematic depiction of conformer class and confal value.', }, isApplicable(a) { diff --git a/src/extensions/dnatco/confal-pyramids/color.ts b/src/extensions/dnatco/confal-pyramids/color.ts index ededefa0d..e13b52ec7 100644 --- a/src/extensions/dnatco/confal-pyramids/color.ts +++ b/src/extensions/dnatco/confal-pyramids/color.ts @@ -13,6 +13,8 @@ import { ColorTheme } from '../../../mol-theme/color'; import { ThemeDataContext } from '../../../mol-theme/theme'; import { Color } from '../../../mol-util/color'; import { ParamDefinition as PD } from '../../../mol-util/param-definition'; +import { TableLegend } from '../../../mol-util/legend'; +import { iterableToArray } from '../../../mol-data/util'; const DefaultColor = Color(0xCCCCCC); const Description = 'Assigns colors to confal pyramids'; @@ -160,6 +162,12 @@ export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values color, props, description: Description, + legend: TableLegend(iterableToArray(ColorMapping.entries()).map(([conformer, color]) => { + return [conformer, color] as [string, Color]; + }).concat([ + [ 'Error', ErrorColor ], + [ 'Unknown', DefaultColor ] + ])) }; } -- GitLab