add alpha-oonly option to asa calc

src/mol-model-props/computed/accessible-surface-area/shrake-rupley.ts

@@ -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

src/mol-model-props/computed/accessible-surface-area/shrake-rupley/common.ts

@@ -12,6 +12,7 @@ export interface ShrakeRupleyContext {
     spherePoints: Vec3[],
     probeSize: number,
     nonPolymer: boolean,
+    alphaOnly: boolean,
     scalingConstant: number,
     maxLookupRadius: number,
     atomRadiusType: Int8Array,

src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts

@@ -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)) {