From 5df55e6bf7a34837738eeb5d2f7e6e8000e311e5 Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Mon, 22 Mar 2021 17:21:47 +0100
Subject: [PATCH] SDF delimiter bugfix + multi-molecule SDF support in
mol-plugin
---
src/mol-io/reader/_spec/sdf.spec.ts | 27 ++++++++++++++++--
src/mol-io/reader/sdf/parser.ts | 27 ++++++++++++++----
src/mol-plugin-state/formats/trajectory.ts | 16 +++++++++--
src/mol-plugin-state/transforms/model.ts | 32 ++++++++++++++++++++++
4 files changed, 90 insertions(+), 12 deletions(-)
diff --git a/src/mol-io/reader/_spec/sdf.spec.ts b/src/mol-io/reader/_spec/sdf.spec.ts
index 9ab1f281c..8c65d6456 100644
--- a/src/mol-io/reader/_spec/sdf.spec.ts
+++ b/src/mol-io/reader/_spec/sdf.spec.ts
@@ -112,7 +112,22 @@ Phosphate ion
> <SYNONYMS>
Orthophosphate; Phosphate
-$$$$`;
+$$$$
+
+Comp 2
+
+5 4 0 0 0 0 999 V2000
+ 0.0000 0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+ -0.8250 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.0000 -0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+ 0.0000 0.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.8250 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
+4 1 1 0 0 0 0
+4 2 2 0 0 0 0
+4 3 1 0 0 0 0
+4 5 1 0 0 0 0
+M CHG 3 1 -1 3 -1 5 -1
+M END`;
describe('sdf reader', () => {
it('basic', async () => {
@@ -120,14 +135,20 @@ describe('sdf reader', () => {
if (parsed.isError) {
throw new Error(parsed.message);
}
- const compound = parsed.result.compounds[0];
- const { molFile, dataItems } = compound;
+ const compound1 = parsed.result.compounds[0];
+ const compound2 = parsed.result.compounds[1];
+ const { molFile, dataItems } = compound1;
const { atoms, bonds } = molFile;
+ expect(parsed.result.compounds.length).toBe(2);
+
// number of structures
expect(atoms.count).toBe(5);
expect(bonds.count).toBe(4);
+ expect(compound2.molFile.atoms.count).toBe(5);
+ expect(compound2.molFile.bonds.count).toBe(4);
+
expect(atoms.x.value(0)).toBeCloseTo(0, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(0.8250, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(0, 0.0001);
diff --git a/src/mol-io/reader/sdf/parser.ts b/src/mol-io/reader/sdf/parser.ts
index dd787ef01..fa764cde1 100644
--- a/src/mol-io/reader/sdf/parser.ts
+++ b/src/mol-io/reader/sdf/parser.ts
@@ -22,6 +22,7 @@ export interface SdfFile {
}[]
}
+const delimiter = '$$$$';
function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, data: Column<string> } {
const dataHeader = TokenBuilder.create(tokenizer.data, 32);
const data = TokenBuilder.create(tokenizer.data, 32);
@@ -29,6 +30,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
let sawHeaderToken = false;
while (tokenizer.position < tokenizer.length) {
const line = Tokenizer.readLine(tokenizer);
+ if (line.startsWith(delimiter)) break;
if (!!line) {
if (line.startsWith('> <')) {
TokenBuilder.add(dataHeader, tokenizer.tokenStart + 3, tokenizer.tokenEnd - 1);
@@ -49,9 +51,7 @@ function handleDataItems(tokenizer: Tokenizer): { dataHeader: Column<string>, da
};
}
-function handleMolFile(data: string) {
- const tokenizer = Tokenizer(data);
-
+function handleMolFile(tokenizer: Tokenizer) {
const title = Tokenizer.readLine(tokenizer).trim();
const program = Tokenizer.readLine(tokenizer).trim();
const comment = Tokenizer.readLine(tokenizer).trim();
@@ -60,6 +60,15 @@ function handleMolFile(data: string) {
const atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
+ if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
+ // try to skip to next molecule
+ while (tokenizer.position < tokenizer.length) {
+ const line = Tokenizer.readLine(tokenizer);
+ if (line.startsWith(delimiter)) break;
+ }
+ return;
+ }
+
const atoms = handleAtoms(tokenizer, atomCount);
const bonds = handleBonds(tokenizer, bondCount);
const dataItems = handleDataItems(tokenizer);
@@ -70,10 +79,16 @@ function handleMolFile(data: string) {
};
}
-const delimiter = '$$$$';
function parseInternal(data: string): Result<SdfFile> {
- const result: SdfFile = { compounds: data.split(delimiter).map(d => handleMolFile(d)) };
- return Result.success(result);
+ const tokenizer = Tokenizer(data);
+
+ const compounds: SdfFile['compounds'] = [];
+ while (tokenizer.position < tokenizer.length) {
+ const c = handleMolFile(tokenizer);
+ if (c) compounds.push(c);
+ }
+
+ return Result.success({ compounds });
}
export function parseSdf(data: string) {
diff --git a/src/mol-plugin-state/formats/trajectory.ts b/src/mol-plugin-state/formats/trajectory.ts
index 1e2d8d534..c8eca7e90 100644
--- a/src/mol-plugin-state/formats/trajectory.ts
+++ b/src/mol-plugin-state/formats/trajectory.ts
@@ -123,14 +123,23 @@ export const GroProvider: TrajectoryFormatProvider = {
};
export const MolProvider: TrajectoryFormatProvider = {
- label: 'MOL/SDF',
- description: 'MOL/SDF',
+ label: 'MOL',
+ description: 'MOL',
category: TrajectoryFormatCategory,
- stringExtensions: ['mol', 'sdf', 'sd'],
+ stringExtensions: ['mol'],
parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
visuals: defaultVisuals
};
+export const SdfProvider: TrajectoryFormatProvider = {
+ label: 'SDF',
+ description: 'SDF',
+ category: TrajectoryFormatCategory,
+ stringExtensions: ['sdf', 'sd'],
+ parse: directTrajectory(StateTransforms.Model.TrajectoryFromSDF),
+ visuals: defaultVisuals
+};
+
export const Mol2Provider: TrajectoryFormatProvider = {
label: 'MOL2',
description: 'MOL2',
@@ -148,6 +157,7 @@ export const BuiltInTrajectoryFormats = [
['gro', GroProvider] as const,
['xyz', XyzProvider] as const,
['mol', MolProvider] as const,
+ ['sdf', SdfProvider] as const,
['mol2', Mol2Provider] as const,
] as const;
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index b50cbe180..d987f7914 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -39,6 +39,7 @@ import { parseXtc } from '../../mol-io/reader/xtc/parser';
import { coordinatesFromXtc } from '../../mol-model-formats/structure/xtc';
import { parseXyz } from '../../mol-io/reader/xyz/parser';
import { trajectoryFromXyz } from '../../mol-model-formats/structure/xyz';
+import { parseSdf } from '../../mol-io/reader/sdf/parser';
export { CoordinatesFromDcd };
export { CoordinatesFromXtc };
@@ -50,6 +51,7 @@ export { TrajectoryFromPDB };
export { TrajectoryFromGRO };
export { TrajectoryFromXYZ };
export { TrajectoryFromMOL };
+export { TrajectoryFromSDF };
export { TrajectoryFromMOL2 };
export { TrajectoryFromCube };
export { TrajectoryFromCifCore };
@@ -292,6 +294,36 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
}
});
+type TrajectoryFromSDF = typeof TrajectoryFromSDF
+const TrajectoryFromSDF = PluginStateTransform.BuiltIn({
+ name: 'trajectory-from-sdf',
+ display: { name: 'Parse SDF', description: 'Parse SDF string and create trajectory.' },
+ from: [SO.Data.String],
+ to: SO.Molecule.Trajectory
+})({
+ apply({ a }) {
+ return Task.create('Parse SDF', async ctx => {
+ const parsed = await parseSdf(a.data).runInContext(ctx);
+ if (parsed.isError) throw new Error(parsed.message);
+
+ const models: Model[] = [];
+
+ for (const { molFile } of parsed.result.compounds) {
+ const traj = await trajectoryFromMol(molFile).runInContext(ctx);
+ for (let i = 0; i < traj.frameCount; i++) {
+ models.push(await Task.resolveInContext(traj.getFrameAtIndex(i), ctx));
+ }
+ }
+
+ const traj = new ArrayTrajectory(models);
+
+ const props = trajectoryProps(traj);
+ return new SO.Molecule.Trajectory(traj, props);
+ });
+ }
+});
+
+
type TrajectoryFromMOL2 = typeof TrajectoryFromMOL
const TrajectoryFromMOL2 = PluginStateTransform.BuiltIn({
name: 'trajectory-from-mol2',
--
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