From 1cc4a05020d2c34ac54141b0e8966f858b913553 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 20 Feb 2019 11:15:36 +0100
Subject: [PATCH] mol-plugin: return deposited structure if assemly is not
found
---
src/apps/basic-wrapper/index.html | 1 +
src/mol-plugin/state/transforms/model.ts | 23 +++++++++++++++++++----
2 files changed, 20 insertions(+), 4 deletions(-)
diff --git a/src/apps/basic-wrapper/index.html b/src/apps/basic-wrapper/index.html
index 38c2bf792..348530291 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/apps/basic-wrapper/index.html
@@ -50,6 +50,7 @@
// var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
// var format = 'pdb';
+ // var assemblyId = 'deposited';
BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
BasicMolStarWrapper.setBackground(0xffffff);
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index dcc0b6b9a..bc45a15ad 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -22,6 +22,7 @@ import { volumeFromDsn6 } from 'mol-model-formats/volume/dsn6';
import { trajectoryFromMmCIF } from 'mol-model-formats/structure/mmcif';
import { parsePDB } from 'mol-io/reader/pdb/parser';
import { trajectoryFromPDB } from 'mol-model-formats/structure/pdb';
+import { Assembly } from 'mol-model/structure/model/properties/symmetry';
export { TrajectoryFromMmCif }
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
@@ -141,12 +142,26 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
return Task.create('Build Assembly', async ctx => {
const model = a.data;
let id = params.id;
- let asm = ModelSymmetry.findAssembly(model, id || '');
- if (!!id && id !== 'deposited' && !asm) throw new Error(`Assembly '${id}' not found`);
+ let asm: Assembly | undefined = void 0;
+
+ // if no id is specified, use the 1st assembly.
+ if (!id && model.symmetry.assemblies.length !== 0) {
+ id = model.symmetry.assemblies[0].id;
+ }
+
+ if (model.symmetry.assemblies.length === 0) {
+ if (id !== 'deposited') {
+ plugin.log.warn(`Model '${a.label}' has no assembly, returning deposited structure.`);
+ }
+ } else {
+ asm = ModelSymmetry.findAssembly(model, id || '');
+ if (!asm) {
+ plugin.log.warn(`Model '${a.label}' has no assembly called '${id}', returning deposited structure.`);
+ }
+ }
const base = Structure.ofModel(model);
- if ((id && !asm) || model.symmetry.assemblies.length === 0) {
- if (!!id && id !== 'deposited') plugin.log.warn(`Model '${a.label}' has no assembly, returning deposited structure.`);
+ if (!asm) {
const label = { label: a.data.label, description: structureDesc(base) };
return new SO.Molecule.Structure(base, label);
}
--
GitLab