molstar
Version:
A comprehensive macromolecular library.
114 lines (113 loc) • 5.43 kB
JavaScript
;
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.StructureQualityReportColorThemeProvider = exports.StructureQualityReportColorThemeParams = void 0;
exports.StructureQualityReportColorTheme = StructureQualityReportColorTheme;
const prop_1 = require("./prop");
const structure_1 = require("../../../mol-model/structure");
const color_1 = require("../../../mol-util/color");
const legend_1 = require("../../../mol-util/legend");
const param_definition_1 = require("../../../mol-util/param-definition");
const categories_1 = require("../../../mol-theme/color/categories");
const ValidationColors = [
color_1.Color.fromRgb(170, 170, 170), // not applicable
color_1.Color.fromRgb(0, 255, 0), // 0 issues
color_1.Color.fromRgb(255, 255, 0), // 1
color_1.Color.fromRgb(255, 128, 0), // 2
color_1.Color.fromRgb(255, 0, 0), // 3 or more
];
const ValidationColorTable = [
['No Issues', ValidationColors[1]],
['One Issue', ValidationColors[2]],
['Two Issues', ValidationColors[3]],
['Three Or More Issues', ValidationColors[4]],
['Not Applicable', ValidationColors[9]]
];
exports.StructureQualityReportColorThemeParams = {
type: param_definition_1.ParamDefinition.MappedStatic('issue-count', {
'issue-count': param_definition_1.ParamDefinition.Group({}),
'specific-issue': param_definition_1.ParamDefinition.Group({
kind: param_definition_1.ParamDefinition.Text()
})
})
};
function StructureQualityReportColorTheme(ctx, props) {
let color;
if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(prop_1.StructureQualityReportProvider.descriptor)) {
const getIssues = prop_1.StructureQualityReport.getIssues;
const l = structure_1.StructureElement.Location.create(ctx.structure);
if (props.type.name === 'issue-count') {
color = (location) => {
if (structure_1.StructureElement.Location.is(location)) {
return ValidationColors[Math.min(3, getIssues(location).length) + 1];
}
else if (structure_1.Bond.isLocation(location)) {
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
return ValidationColors[Math.min(3, getIssues(l).length) + 1];
}
return ValidationColors[0];
};
}
else {
const issue = props.type.params.kind;
color = (location) => {
if (structure_1.StructureElement.Location.is(location) && getIssues(location).indexOf(issue) >= 0) {
return ValidationColors[4];
}
else if (structure_1.Bond.isLocation(location)) {
l.unit = location.aUnit;
l.element = location.aUnit.elements[location.aIndex];
return ValidationColors[Math.min(3, getIssues(l).length) + 1];
}
return ValidationColors[0];
};
}
}
else {
color = () => ValidationColors[0];
}
return {
factory: StructureQualityReportColorTheme,
granularity: 'group',
preferSmoothing: true,
color: color,
props: props,
description: 'Assigns residue colors according to the number of quality issues or a specific quality issue. Data from wwPDB Validation Report, obtained via PDBe.',
legend: (0, legend_1.TableLegend)(ValidationColorTable)
};
}
exports.StructureQualityReportColorThemeProvider = {
name: 'pdbe-structure-quality-report',
label: 'Structure Quality Report',
category: categories_1.ColorThemeCategory.Validation,
factory: StructureQualityReportColorTheme,
getParams: ctx => {
const issueTypes = prop_1.StructureQualityReport.getIssueTypes(ctx.structure);
if (issueTypes.length === 0) {
return {
type: param_definition_1.ParamDefinition.MappedStatic('issue-count', {
'issue-count': param_definition_1.ParamDefinition.Group({})
})
};
}
return {
type: param_definition_1.ParamDefinition.MappedStatic('issue-count', {
'issue-count': param_definition_1.ParamDefinition.Group({}),
'specific-issue': param_definition_1.ParamDefinition.Group({
kind: param_definition_1.ParamDefinition.Select(issueTypes[0], param_definition_1.ParamDefinition.arrayToOptions(issueTypes))
}, { isFlat: true })
})
};
},
defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.StructureQualityReportColorThemeParams),
isApplicable: (ctx) => { var _a; return prop_1.StructureQualityReport.isApplicable((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0]); },
ensureCustomProperties: {
attach: (ctx, data) => data.structure ? prop_1.StructureQualityReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
detach: (data) => data.structure && prop_1.StructureQualityReportProvider.ref(data.structure.models[0], false)
}
};