molstar
Version:
A comprehensive macromolecular library.
107 lines (106 loc) • 6.04 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.AccessibleSurfaceArea = exports.ShrakeRupleyComputationParams = void 0;
const mol_task_1 = require("../../../mol-task");
// import { BitFlags } from '../../../mol-util';
const param_definition_1 = require("../../../mol-util/param-definition");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const structure_1 = require("../../../mol-model/structure");
const radii_1 = require("./shrake-rupley/radii");
const common_1 = require("./shrake-rupley/common");
const area_1 = require("./shrake-rupley/area");
const int_1 = require("../../../mol-data/int");
exports.ShrakeRupleyComputationParams = {
numberOfSpherePoints: param_definition_1.ParamDefinition.Numeric(92, { min: 12, max: 360, step: 1 }, { description: 'Number of sphere points to sample per atom: 92 (original paper), 960 (BioJava), 3000 (EPPIC) - see Shrake A, Rupley JA: Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol 1973.' }),
probeSize: param_definition_1.ParamDefinition.Numeric(1.4, { min: 0.1, max: 4, step: 0.01 }, { description: 'Corresponds to the size of a water molecule: 1.4 (original paper), 1.5 (occassionally used)' }),
// buriedRasaThreshold: PD.Numeric(0.16, { min: 0.0, max: 1.0 }, { description: 'below this cutoff of relative accessible surface area a residue will be considered buried - see: Rost B, Sander C: Conservation and prediction of solvent accessibility in protein families. Proteins 1994.' }),
nonPolymer: param_definition_1.ParamDefinition.Boolean(false, { description: 'Include non-polymer atoms as occluders.' }),
traceOnly: param_definition_1.ParamDefinition.Boolean(false, { description: 'Compute only using alpha-carbons, if true increase probeSize accordingly (e.g., 4 A). Considers only canonical amino acids.' })
};
var AccessibleSurfaceArea;
(function (AccessibleSurfaceArea) {
/**
* Adapts the BioJava implementation by Jose Duarte. That implementation is based on the publication by Shrake, A., and
* J. A. Rupley. "Environment and Exposure to Solvent of Protein Atoms. Lysozyme and Insulin." JMB (1973).
*/
function compute(structure, props = {}) {
const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.ShrakeRupleyComputationParams), ...props };
return mol_task_1.Task.create('Compute Accessible Surface Area', async (runtime) => {
return await calculate(runtime, structure, p);
});
}
AccessibleSurfaceArea.compute = compute;
async function calculate(runtime, structure, props) {
const ctx = initialize(structure, props);
(0, radii_1.assignRadiusForHeavyAtoms)(ctx);
await (0, area_1.computeArea)(runtime, ctx);
const { area, serialResidueIndex } = ctx;
return { area, serialResidueIndex };
}
function initialize(structure, props) {
const { elementCount, atomicResidueCount } = structure;
const { probeSize, nonPolymer, traceOnly, numberOfSpherePoints } = props;
return {
structure,
probeSize,
nonPolymer,
traceOnly,
spherePoints: generateSpherePoints(numberOfSpherePoints),
scalingConstant: 4.0 * Math.PI / numberOfSpherePoints,
maxLookupRadius: 2 * props.probeSize + 2 * common_1.VdWLookup[2], // 2x probe size + 2x largest VdW
atomRadiusType: new Int8Array(elementCount),
serialResidueIndex: new Int32Array(elementCount),
area: new Float32Array(atomicResidueCount)
};
}
/** Creates a collection of points on a sphere by the Golden Section Spiral algorithm. */
function generateSpherePoints(numberOfSpherePoints) {
const points = [];
const inc = Math.PI * (3.0 - Math.sqrt(5.0));
const offset = 2.0 / numberOfSpherePoints;
for (let k = 0; k < numberOfSpherePoints; ++k) {
const y = k * offset - 1.0 + (offset / 2.0);
const r = Math.sqrt(1.0 - y * y);
const phi = k * inc;
points[points.length] = linear_algebra_1.Vec3.create(Math.cos(phi) * r, y, Math.sin(phi) * r);
}
return points;
}
AccessibleSurfaceArea.Flag = {
NA: 0 /* Flags.NA */,
Buried: 1 /* Flags.Buried */,
Accessible: 2 /* Flags.Accessible */
};
/** Get relative area for a given component id */
function normalize(compId, asa) {
const maxAsa = common_1.MaxAsa[compId] || common_1.DefaultMaxAsa;
return asa / maxAsa;
}
AccessibleSurfaceArea.normalize = normalize;
function getValue(location, accessibleSurfaceArea) {
const { area, serialResidueIndex } = accessibleSurfaceArea;
const rSI = serialResidueIndex[int_1.SortedArray.indexOf(int_1.SortedArray.ofSortedArray(location.structure.root.serialMapping.elementIndices), location.element)];
if (rSI === -1)
return -1;
return area[rSI];
}
AccessibleSurfaceArea.getValue = getValue;
function getNormalizedValue(location, accessibleSurfaceArea) {
const value = getValue(location, accessibleSurfaceArea);
return value === -1 ? -1 : normalize(structure_1.StructureProperties.atom.label_comp_id(location), value);
}
AccessibleSurfaceArea.getNormalizedValue = getNormalizedValue;
function getFlag(location, accessibleSurfaceArea) {
const value = getNormalizedValue(location, accessibleSurfaceArea);
return value === -1 ? 0 /* Flags.NA */ :
value < 0.16 ? 1 /* Flags.Buried */ :
2 /* Flags.Accessible */;
}
AccessibleSurfaceArea.getFlag = getFlag;
})(AccessibleSurfaceArea || (exports.AccessibleSurfaceArea = AccessibleSurfaceArea = {}));