From 9d1d7bbf722c87926f82e960e3d5bca7af40b24f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Tue, 14 Apr 2020 16:35:41 -0700
Subject: [PATCH] moved pdbe code to extensions folder
---
src/apps/viewer/index.ts | 2 ++
src/examples/basic-wrapper/index.ts | 2 +-
src/extensions/pdbe/index.ts | 9 ++++++
.../pdbe/preferred-assembly.ts | 0
.../pdbe/struct-ref-domain.ts | 2 +-
.../structure-quality-report/behavior.ts} | 14 ++++----
.../pdbe/structure-quality-report/color.ts} | 4 +--
.../pdbe/structure-quality-report/prop.ts} | 32 +++++++++----------
.../behavior/dynamic/custom-props.ts | 4 +--
src/mol-plugin/index.ts | 2 --
src/perf-tests/mol-script.ts | 2 +-
.../model/properties/providers/pdbe.ts | 6 ++--
12 files changed, 43 insertions(+), 36 deletions(-)
create mode 100644 src/extensions/pdbe/index.ts
rename src/{mol-model-props => extensions}/pdbe/preferred-assembly.ts (100%)
rename src/{mol-model-props => extensions}/pdbe/struct-ref-domain.ts (98%)
rename src/{mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts => extensions/pdbe/structure-quality-report/behavior.ts} (84%)
rename src/{mol-model-props/pdbe/themes/structure-quality-report.ts => extensions/pdbe/structure-quality-report/color.ts} (97%)
rename src/{mol-model-props/pdbe/structure-quality-report.ts => extensions/pdbe/structure-quality-report/prop.ts} (91%)
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index 69a78551c..f27157cd1 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -16,6 +16,7 @@ import { DownloadStructure } from '../../mol-plugin-state/actions/structure';
import { PluginConfig } from '../../mol-plugin/config';
import { CellPack } from '../../extensions/cellpack';
import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
require('mol-plugin-ui/skin/light.scss');
function getParam(name: string, regex: string): string {
@@ -31,6 +32,7 @@ function init() {
behaviors: [
...DefaultPluginSpec.behaviors,
PluginSpec.Behavior(CellPack),
+ PluginSpec.Behavior(PDBeStructureQualityReport),
PluginSpec.Behavior(RCSBAssemblySymmetry),
PluginSpec.Behavior(RCSBValidationReport),
],
diff --git a/src/examples/basic-wrapper/index.ts b/src/examples/basic-wrapper/index.ts
index 9abaae674..4e776090a 100644
--- a/src/examples/basic-wrapper/index.ts
+++ b/src/examples/basic-wrapper/index.ts
@@ -10,7 +10,6 @@ import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
import { PluginCommands } from '../../mol-plugin/commands';
import { PluginContext } from '../../mol-plugin/context';
import { Script } from '../../mol-script/script';
@@ -19,6 +18,7 @@ import { StripedResidues } from './coloring';
import { CustomToastMessage } from './controls';
import './index.html';
import { buildStaticSuperposition, dynamicSuperpositionTest, StaticSuperpositionTestData } from './superposition';
+import { PDBeStructureQualityReport } from '../../extensions/pdbe';
require('mol-plugin-ui/skin/light.scss');
type LoadParams = { url: string, format?: BuiltInTrajectoryFormat, isBinary?: boolean, assemblyId?: string }
diff --git a/src/extensions/pdbe/index.ts b/src/extensions/pdbe/index.ts
new file mode 100644
index 000000000..4cef04277
--- /dev/null
+++ b/src/extensions/pdbe/index.ts
@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export { PDBeStructureQualityReport } from './structure-quality-report/behavior';
+export { PDBePreferredAssembly } from './preferred-assembly';
+export { PDBeStructRefDomain } from './struct-ref-domain';
\ No newline at end of file
diff --git a/src/mol-model-props/pdbe/preferred-assembly.ts b/src/extensions/pdbe/preferred-assembly.ts
similarity index 100%
rename from src/mol-model-props/pdbe/preferred-assembly.ts
rename to src/extensions/pdbe/preferred-assembly.ts
diff --git a/src/mol-model-props/pdbe/struct-ref-domain.ts b/src/extensions/pdbe/struct-ref-domain.ts
similarity index 98%
rename from src/mol-model-props/pdbe/struct-ref-domain.ts
rename to src/extensions/pdbe/struct-ref-domain.ts
index d82e24d84..4b025f552 100644
--- a/src/mol-model-props/pdbe/struct-ref-domain.ts
+++ b/src/extensions/pdbe/struct-ref-domain.ts
@@ -8,7 +8,7 @@ import { Column, Table } from '../../mol-data/db';
import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
-import { PropertyWrapper } from '../common/wrapper';
+import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export namespace PDBeStructRefDomain {
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts b/src/extensions/pdbe/structure-quality-report/behavior.ts
similarity index 84%
rename from src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
rename to src/extensions/pdbe/structure-quality-report/behavior.ts
index d20ceccbc..b12f8f09a 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
+++ b/src/extensions/pdbe/structure-quality-report/behavior.ts
@@ -4,13 +4,13 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet } from '../../../../../mol-data/int';
-import { StructureQualityReport, StructureQualityReportProvider } from '../../../../../mol-model-props/pdbe/structure-quality-report';
-import { StructureQualityReportColorThemeProvider } from '../../../../../mol-model-props/pdbe/themes/structure-quality-report';
-import { Loci } from '../../../../../mol-model/loci';
-import { StructureElement } from '../../../../../mol-model/structure';
-import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
-import { PluginBehavior } from '../../../behavior';
+import { OrderedSet } from '../../../mol-data/int';
+import { StructureQualityReport, StructureQualityReportProvider } from './prop';
+import { StructureQualityReportColorThemeProvider } from './color';
+import { Loci } from '../../../mol-model/loci';
+import { StructureElement } from '../../../mol-model/structure';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'pdbe-structure-quality-report-prop',
diff --git a/src/mol-model-props/pdbe/themes/structure-quality-report.ts b/src/extensions/pdbe/structure-quality-report/color.ts
similarity index 97%
rename from src/mol-model-props/pdbe/themes/structure-quality-report.ts
rename to src/extensions/pdbe/structure-quality-report/color.ts
index c021d6810..83a5a3544 100644
--- a/src/mol-model-props/pdbe/themes/structure-quality-report.ts
+++ b/src/extensions/pdbe/structure-quality-report/color.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { StructureQualityReport, StructureQualityReportProvider } from '../../../mol-model-props/pdbe/structure-quality-report';
+import { StructureQualityReport, StructureQualityReportProvider } from './prop';
import { Location } from '../../../mol-model/location';
import { StructureElement } from '../../../mol-model/structure';
import { ColorTheme, LocationColor } from '../../../mol-theme/color';
@@ -12,7 +12,7 @@ import { ThemeDataContext } from '../../../mol-theme/theme';
import { Color } from '../../../mol-util/color';
import { TableLegend } from '../../../mol-util/legend';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomProperty } from '../../common/custom-property';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
const ValidationColors = [
Color.fromRgb(170, 170, 170), // not applicable
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/extensions/pdbe/structure-quality-report/prop.ts
similarity index 91%
rename from src/mol-model-props/pdbe/structure-quality-report.ts
rename to src/extensions/pdbe/structure-quality-report/prop.ts
index f779bf157..8121efa07 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/extensions/pdbe/structure-quality-report/prop.ts
@@ -5,22 +5,22 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Column, Table } from '../../mol-data/db';
-import { toTable } from '../../mol-io/reader/cif/schema';
-import { mmCIF_residueId_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
-import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../mol-model/structure';
-import { residueIdFields } from '../../mol-model/structure/export/categories/atom_site';
-import { StructureElement, CifExportContext, Structure } from '../../mol-model/structure/structure';
-import { CustomPropSymbol } from '../../mol-script/language/symbol';
-import Type from '../../mol-script/language/type';
-import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
-import { PropertyWrapper } from '../common/wrapper';
-import { CustomModelProperty } from '../common/custom-model-property';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { CustomProperty } from '../common/custom-property';
-import { arraySetAdd } from '../../mol-util/array';
-import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { Column, Table } from '../../../mol-data/db';
+import { toTable } from '../../../mol-io/reader/cif/schema';
+import { mmCIF_residueId_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { CifWriter } from '../../../mol-io/writer/cif';
+import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
+import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
+import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
+import { CustomPropSymbol } from '../../../mol-script/language/symbol';
+import Type from '../../../mol-script/language/type';
+import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { arraySetAdd } from '../../../mol-util/array';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
export { StructureQualityReport };
diff --git a/src/mol-plugin/behavior/dynamic/custom-props.ts b/src/mol-plugin/behavior/dynamic/custom-props.ts
index 8248530a2..9b4e00b7e 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props.ts
@@ -10,6 +10,4 @@ export { Interactions } from './custom-props/computed/interactions';
export { SecondaryStructure } from './custom-props/computed/secondary-structure';
export { ValenceModel } from './custom-props/computed/valence-model';
-export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint';
-
-export { PDBeStructureQualityReport } from './custom-props/pdbe/structure-quality-report';
\ No newline at end of file
+export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint';
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 81d13c721..45c5bbd11 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -74,8 +74,6 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
-
- PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport),
],
customParamEditors: [
[CreateVolumeStreamingBehavior, VolumeStreamingCustomControls]
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index a840b606c..eb40e8848 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -8,7 +8,7 @@ import { parseMolScript } from '../mol-script/language/parser';
import * as util from 'util';
import { transpileMolScript } from '../mol-script/script/mol-script/symbols';
import { formatMolScript } from '../mol-script/language/expression-formatter';
-import { StructureQualityReport, StructureQualityReportProvider } from '../mol-model-props/pdbe/structure-quality-report';
+import { StructureQualityReport, StructureQualityReportProvider } from '../extensions/pdbe/structure-quality-report/prop';
import fetch from 'node-fetch';
// import Examples from 'mol-script/script/mol-script/examples'
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index 87a20fce8..09f818bf3 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -7,11 +7,11 @@
import * as fs from 'fs';
import * as path from 'path';
import { Model } from '../../../../mol-model/structure';
-import { StructureQualityReportProvider, StructureQualityReport } from '../../../../mol-model-props/pdbe/structure-quality-report';
+import { StructureQualityReportProvider, StructureQualityReport } from '../../../../extensions/pdbe/structure-quality-report/prop';
import { fetchRetry } from '../../utils/fetch-retry';
import { UUID } from '../../../../mol-util';
-import { PDBePreferredAssembly } from '../../../../mol-model-props/pdbe/preferred-assembly';
-import { PDBeStructRefDomain } from '../../../../mol-model-props/pdbe/struct-ref-domain';
+import { PDBePreferredAssembly } from '../../../../extensions/pdbe/preferred-assembly';
+import { PDBeStructRefDomain } from '../../../../extensions/pdbe/struct-ref-domain';
import { AttachModelProperty } from '../../property-provider';
import { ConsoleLogger } from '../../../../mol-util/console-logger';
import { getParam } from '../../../common/util';
--
GitLab