diff --git a/src/apps/structure-info/index.ts b/src/apps/structure-info/index.ts
index c98178e02529df6c4982212619c75a59b999089c..5233f459b883ed17617f53fff9391cb95ba1a944 100644
--- a/src/apps/structure-info/index.ts
+++ b/src/apps/structure-info/index.ts
@@ -10,7 +10,7 @@ require('util.promisify').shim();
// import { Table } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
-import { Model, Structure, ElementSet, Unit } from 'mol-model/structure'
+import { Model, Structure, ElementSet, Unit, ElementGroup } from 'mol-model/structure'
import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
@@ -22,7 +22,8 @@ async function parseCif(data: string|Uint8Array) {
}
async function getPdb(pdb: string) {
- const data = await fetch(`https://files.rcsb.org/download/${pdb}.cif`)
+ //const data = await fetch(`https://files.rcsb.org/download/${pdb}.cif`)
+ const data = await fetch(`http://www.ebi.ac.uk/pdbe/static/entry/${pdb}_updated.cif`);
const parsed = await parseCif(await data.text())
return CIF.schema.mmCIF(parsed.result.blocks[0])
}
@@ -39,7 +40,6 @@ export function atomLabel(model: Model, aI: number) {
function printBonds(structure: Structure) {
-
const { units, elements } = structure;
const unitIds = ElementSet.unitIndices(elements);
@@ -50,11 +50,18 @@ function printBonds(structure: Structure) {
const { count, offset, neighbor } = Unit.getGroupBonds(unit, group);
const { model } = unit;
- for (let j = 0; j < count; ++j) {
+ if (!count) continue;
+
+ for (let j = 0; j < offset.length - 1; ++j) {
const start = offset[j];
const end = offset[j + 1];
- for (let bI = start; bI < end; bI++) {
- console.log(`${atomLabel(model, j)} -- ${atomLabel(model, neighbor[bI])}`)
+
+ if (end <= start) continue;
+
+ const aI = ElementGroup.getAt(group, j);
+ for (let _bI = start; _bI < end; _bI++) {
+ const bI = ElementGroup.getAt(group, neighbor[_bI])
+ console.log(`${atomLabel(model, aI)} -- ${atomLabel(model, bI)}`);
}
}
}
diff --git a/src/mol-math/geometry/lookup3d/grid.ts b/src/mol-math/geometry/lookup3d/grid.ts
index 69d65672ea3a03c5a188ebdcaf91e6c70833de10..7abb47781969df8deb176c5e1f9918f3cf2b532d 100644
--- a/src/mol-math/geometry/lookup3d/grid.ts
+++ b/src/mol-math/geometry/lookup3d/grid.ts
@@ -256,7 +256,7 @@ function query(ctx: QueryContext): boolean {
if (distSq <= rSq) {
if (maxRadius > 0 && Math.sqrt(distSq) - radius![idx] > inputRadius) continue;
if (isCheck) return true;
- Result.add(result, idx, distSq);
+ Result.add(result, bucketArray[i], distSq);
}
}
}
diff --git a/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
index 7e58040f13444d26e3078682619944767c9061df..fb078c889fb924c543659b995eb6b6eea3e28eba 100644
--- a/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
+++ b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
@@ -112,7 +112,7 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
const { x, y, z } = unit.model.conformation;
const atomCount = ElementGroup.size(atoms);
- const { residueKey } = unit.model.hierarchy;
+ const { residueIndex } = unit;
const { type_symbol, label_atom_id, label_alt_id } = unit.model.hierarchy.atoms;
const { label_comp_id } = unit.model.hierarchy.residues;
const query3d = Unit.getLookup3d(unit, atoms);
@@ -130,12 +130,10 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
for (let _aI = 0; _aI < atomCount; _aI++) {
const aI = ElementGroup.getAt(atoms, _aI);
- const raI = residueKey.value(aI);
- // const rowA = dataIndex[aI]; // TODO
- const rowA = aI;
+ const raI = residueIndex[aI];
if (!params.forceCompute && raI !== lastResidue) {
- const resn = label_comp_id.value(rowA)!;
+ const resn = label_comp_id.value(raI)!;
if (!!component && component.entries.has(resn)) {
componentMap = component.entries.get(resn)!.map;
} else {
@@ -144,37 +142,35 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
}
lastResidue = raI;
- const componentPairs = componentMap ? componentMap.get(label_atom_id.value(rowA)) : void 0;
+ const componentPairs = componentMap ? componentMap.get(label_atom_id.value(aI)) : void 0;
- const aeI = idx(type_symbol.value(rowA)!);
+ const aeI = idx(type_symbol.value(aI)!);
const { indices, count, squaredDistances } = query3d.find(x[aI], y[aI], z[aI], MAX_RADIUS);
const isHa = isHydrogen(aeI);
const thresholdA = threshold(aeI);
- const altA = label_alt_id.value(rowA);
+ const altA = label_alt_id.value(aI);
const metalA = MetalsSet.has(aeI);
const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
for (let ni = 0; ni < count; ni++) {
- const bI = indices[ni];
+ const _bI = indices[ni];
+ const bI = ElementGroup.getAt(atoms, _bI);
if (bI <= aI) continue;
- // const rowB = dataIndex[bI]; // TODO
- const rowB = bI;
-
- const altB = label_alt_id.value(rowB);
+ const altB = label_alt_id.value(bI);
if (altA && altB && altA !== altB) continue;
- const beI = idx(type_symbol.value(rowB)!);
+ const beI = idx(type_symbol.value(bI)!);
const isMetal = metalA || MetalsSet.has(beI);
- const rbI = residueKey.value(bI);
+ const rbI = residueIndex[bI];
// handle "component dictionary" bonds.
if (raI === rbI && componentPairs) {
- const e = componentPairs.get(label_atom_id.value(rowB)!);
+ const e = componentPairs.get(label_atom_id.value(bI)!);
if (e) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
order[order.length] = e.order;
let flag = e.flags;
if (isMetal) {
@@ -198,8 +194,8 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
for (const se of structConnEntries) {
for (const p of se.partners) {
if (p.atomIndex === bI) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
flags[flags.length] = se.flags;
order[order.length] = se.order;
added = true;
@@ -213,8 +209,8 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
if (isHa || isHb) {
if (dist < params.maxHbondLength) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
order[order.length] = 1;
flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
}
@@ -228,8 +224,8 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
if (dist <= pairingThreshold) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
order[order.length] = 1;
flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
}
@@ -237,6 +233,7 @@ function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondCompu
}
const bonds = computePerAtomBonds(atomA, atomB, order, flags, atomCount);
+
return {
offset: bonds.offsets,
neighbor: bonds.neighbor,
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 0084b15e6b1bdce018db1016e16f7ccc539294a7..2109cc10b299b6932a99f05acf410f86abdb45f9 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -103,7 +103,7 @@ namespace Unit {
group.__bonds__ = computeUnitBonds(unit, group);
return group.__bonds__;
}
-
+
throw 'not implemented';
}
}