From 06927aaabad8b41cc3bbfc28e2a998ae8538a9ec Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 3 May 2019 17:04:47 -0700
Subject: [PATCH] ihm parsing tweaks
---
src/mol-model-formats/structure/mmcif/parser.ts | 7 +++----
src/mol-plugin/state/transforms/helpers.ts | 2 +-
2 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 4c4067686..4c92a0b9e 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -324,14 +324,13 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
}
async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
- if (format.data.atom_site._rowCount && !format.data.atom_site.ihm_model_id.isDefined) {
- throw new Error('expected _atom_site.ihm_model_id to be defined')
- }
+ // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
+ const atom_sites_modelColumn = format.data.atom_site.ihm_model_id.isDefined ? format.data.atom_site.ihm_model_id : format.data.atom_site.pdbx_PDB_model_num
const { ihm_model_list } = format.data;
const entities = getEntities(format)
- const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
+ const atom_sites = splitTable(format.data.atom_site, atom_sites_modelColumn);
// TODO: will coarse IHM records require sorting or will we trust it?
// ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
// If the sorting is implemented, updated mol-model/structure/properties: atom.sourceIndex
diff --git a/src/mol-plugin/state/transforms/helpers.ts b/src/mol-plugin/state/transforms/helpers.ts
index 730f140e5..2a72f7a52 100644
--- a/src/mol-plugin/state/transforms/helpers.ts
+++ b/src/mol-plugin/state/transforms/helpers.ts
@@ -42,7 +42,7 @@ export function getStructureTransparency(structure: Structure, script: Script, v
* Attaches ComputedSecondaryStructure property when unavailable in sourceData
*/
export async function ensureSecondaryStructure(s: Structure) {
- if (s.model.sourceData.kind === 'mmCIF') {
+ if (s.model && s.model.sourceData.kind === 'mmCIF') {
if (!s.model.sourceData.data.struct_conf.id.isDefined && !s.model.sourceData.data.struct_sheet_range.id.isDefined) {
await ComputedSecondaryStructure.attachFromCifOrCompute(s)
}
--
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