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Commit 9f176bd2 authored by JonStargaryen's avatar JonStargaryen
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add alpha-oonly option to asa calc

parent 8a76a3fa
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......@@ -18,7 +18,8 @@ export const ShrakeRupleyComputationParams = {
numberOfSpherePoints: PD.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: PD.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: PD.Boolean(false, { description: 'Include non-polymer atoms as occluders.' })
nonPolymer: PD.Boolean(false, { description: 'Include non-polymer atoms as occluders.' }),
alphaOnly: PD.Boolean(false, { description: 'Compute only using alpha-carbons, if true increase probeSize accordingly (e.g., 4 A).' })
};
export type ShrakeRupleyComputationParams = typeof ShrakeRupleyComputationParams
export type ShrakeRupleyComputationProps = PD.Values<ShrakeRupleyComputationParams>
......@@ -57,12 +58,13 @@ namespace AccessibleSurfaceArea {
function initialize(structure: Structure, props: ShrakeRupleyComputationProps): ShrakeRupleyContext {
const { elementCount, atomicResidueCount } = structure;
const { probeSize, nonPolymer, numberOfSpherePoints } = props;
const { probeSize, nonPolymer, alphaOnly, numberOfSpherePoints } = props;
return {
structure,
probeSize,
nonPolymer,
alphaOnly,
spherePoints: generateSpherePoints(numberOfSpherePoints),
scalingConstant: 4.0 * Math.PI / numberOfSpherePoints,
maxLookupRadius: 2 * props.probeSize + 2 * VdWLookup[2], // 2x probe size + 2x largest VdW
......
......@@ -12,6 +12,7 @@ export interface ShrakeRupleyContext {
spherePoints: Vec3[],
probeSize: number,
nonPolymer: boolean,
alphaOnly: boolean,
scalingConstant: number,
maxLookupRadius: number,
atomRadiusType: Int8Array,
......
......@@ -50,15 +50,15 @@ export function assignRadiusForHeavyAtoms(ctx: ShrakeRupleyContext) {
continue;
}
const atomId = label_atom_id(l);
const moleculeType = getElementMoleculeType(unit, eI);
// skip water and optionally non-polymer groups
if (moleculeType === MoleculeType.Water || (!ctx.nonPolymer && !isPolymer(moleculeType))) {
if (moleculeType === MoleculeType.Water || (!ctx.nonPolymer && !isPolymer(moleculeType)) || (ctx.alphaOnly && atomId !== 'CA')) {
atomRadiusType[mj] = VdWLookup[0];
serialResidueIndex[mj] = -1;
continue;
}
const atomId = label_atom_id(l);
const compId = label_comp_id(l);
if (isNucleic(moleculeType)) {
......
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