From 91fff322ac650d4a13c51e3d7b21432da1422419 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 25 Mar 2019 16:11:18 -0700
Subject: [PATCH] support for nucleotides
---
.../unit/accessible-surface-area/compute.ts | 37 ++++++++++++++-----
1 file changed, 28 insertions(+), 9 deletions(-)
diff --git a/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts b/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
index d1ddf02db..01d5f5ea3 100644
--- a/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
+++ b/src/mol-model/structure/structure/unit/accessible-surface-area/compute.ts
@@ -8,17 +8,22 @@ import Unit from '../../unit'
import { Vec3 } from 'mol-math/linear-algebra';
import { AccessibleSurfaceAreaComputationParams, AccessibleSurfaceArea, SolventAccessibility } from './data';
import { isHydrogen, getElementIdx } from '../links/common'; // TODO these functions are relevant for many tasks: move them somewhere actually common
-import { MoleculeType, ElementSymbol, MaxAsa, DefaultMaxAsa } from 'mol-model/structure/model/types';
+import { ElementSymbol, MaxAsa, DefaultMaxAsa, isPolymer, isNucleic } from 'mol-model/structure/model/types';
import { VdwRadius } from 'mol-model/structure/model/properties/atomic/measures';
import { ParamDefinition as PD } from 'mol-util/param-definition'
+// Chothia's amino acid atoms vdw radii
const trigonalCarbonVdw = 1.76;
const tetrahedralCarbonVdw = 1.87;
const trigonalNitrogenVdw = 1.65;
const tetrahedralNitrogenVdw = 1.50;
/** deviating radii from definition in types.ts */
-const oxygenVdw = 1.4;
+const oxygenVdw = 1.40;
const sulfurVdw = 1.85;
+// Chothia's nucleotide atom vdw radii
+const nucCarbonVdw = 1.80;
+const nucNitrogenVdw = 1.60;
+const nucPhosphorusVdw = 1.40;
const missingAccessibleSurfaceAreaValue = -1.0;
interface AccessibleSurfaceAreaContext {
@@ -33,7 +38,7 @@ interface AccessibleSurfaceAreaContext {
buried?: Uint8Array
}
-/**
+/**
* 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).
*/
@@ -60,8 +65,8 @@ function normalizeAccessibleSurfaceArea(ctx: AccessibleSurfaceAreaContext) {
const { accessibleSurfaceArea, relativeAccessibleSurfaceArea } = ctx;
for (let i = 0; i < residues.label_comp_id.rowCount; ++i) {
- // skip entities not part of a peptide chain
- if (derived.residue.moleculeType[i] !== MoleculeType.protein) continue;
+ // skip entities not part of a polymer chain
+ if (!isPolymer(derived.residue.moleculeType[i])) continue;
const maxAsa = (MaxAsa as any)[residues.label_comp_id.value(i)];
const rasa = accessibleSurfaceArea![i] / (maxAsa === undefined ? DefaultMaxAsa : maxAsa);
@@ -167,8 +172,8 @@ function assignRadiusForHeavyAtoms(ctx: AccessibleSurfaceAreaContext) {
continue;
}
- // skip non-peptide groups
- if (moleculeType[raI] !== MoleculeType.protein) {
+ // skip non-polymer groups
+ if (!isPolymer(moleculeType[raI])) {
ctx.atomRadius[aI] = missingAccessibleSurfaceAreaValue;
continue;
}
@@ -177,7 +182,7 @@ function assignRadiusForHeavyAtoms(ctx: AccessibleSurfaceAreaContext) {
const element = type_symbol.value(aI);
const resn = label_comp_id.value(raI)!;
- ctx.atomRadius[aI] = determineRadius(atomId, element, resn);
+ ctx.atomRadius[aI] = isNucleic(moleculeType[raI]) ? determineRadiusNucl(atomId, element, resn) : determineRadiusAmino(atomId, element, resn);
}
}
@@ -186,7 +191,7 @@ function assignRadiusForHeavyAtoms(ctx: AccessibleSurfaceAreaContext) {
* J.Mol.Biol.105,1-14. NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly
* the heavy atoms to account for Hydrogens.
*/
-function determineRadius(atomId: string, element: ElementSymbol, compId: string): number {
+function determineRadiusAmino(atomId: string, element: ElementSymbol, compId: string): number {
switch (element) {
case 'O':
return oxygenVdw;
@@ -214,6 +219,20 @@ function determineRadius(atomId: string, element: ElementSymbol, compId: string)
return VdwRadius(element);
}
+function determineRadiusNucl(atomId: string, element: ElementSymbol, compId: string): number {
+ switch (element) {
+ case 'C':
+ return nucCarbonVdw;
+ case 'N':
+ return nucNitrogenVdw;
+ case 'P':
+ return nucPhosphorusVdw;
+ case 'O':
+ return oxygenVdw;
+ }
+ return VdwRadius(element);
+}
+
function initialize(unit: Unit.Atomic, params: PD.Values<AccessibleSurfaceAreaComputationParams>): AccessibleSurfaceAreaContext {
return {
unit: unit,
--
GitLab