From f754026cc5e3826f4d38debad517dea7e0e935ec Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 22 Jun 2019 12:26:28 -0700
Subject: [PATCH] better entity placeholder
---
.../structure/mmcif/parser.ts | 22 ++++++++++++-------
1 file changed, 14 insertions(+), 8 deletions(-)
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index f797e919c..4ac7d77b7 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -283,14 +283,16 @@ function getEntities(format: mmCIF_Format): Entities {
if (!format.data.entity.id.isDefined) {
const entityIds = new Set<string>()
- const entityList: Partial<Table.Row<mmCIF_Schema['entity']>>[] = []
+
+ const ids: mmCIF_Schema['entity']['id']['T'][] = []
+ const types: mmCIF_Schema['entity']['type']['T'][] = []
const { label_entity_id, label_comp_id } = format.data.atom_site;
for (let i = 0 as ElementIndex, il = format.data.atom_site._rowCount; i < il; i++) {
const entityId = label_entity_id.value(i);
if (!entityIds.has(entityId)) {
- entityList.push({ id: entityId, type: getEntityType(label_comp_id.value(i)) })
- entityIds.add(entityId)
+ ids.push(entityId)
+ types.push(getEntityType(label_comp_id.value(i)))
}
}
@@ -298,8 +300,8 @@ function getEntities(format: mmCIF_Format): Entities {
for (let i = 0 as ElementIndex, il = format.data.ihm_sphere_obj_site._rowCount; i < il; i++) {
const entityId = sphere_entity_id.value(i);
if (!entityIds.has(entityId)) {
- entityList.push({ id: entityId, type: 'polymer' })
- entityIds.add(entityId)
+ ids.push(entityId)
+ types.push('polymer')
}
}
@@ -307,12 +309,16 @@ function getEntities(format: mmCIF_Format): Entities {
for (let i = 0 as ElementIndex, il = format.data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
const entityId = gaussian_entity_id.value(i);
if (!entityIds.has(entityId)) {
- entityList.push({ id: entityId, type: 'polymer' })
- entityIds.add(entityId)
+ ids.push(entityId)
+ types.push('polymer')
}
}
- entityData = Table.ofRows(mmCIF_Schema.entity, entityList)
+ entityData = Table.ofColumns(mmCIF_Schema.entity, {
+ ...format.data.entity,
+ id: Column.ofArray({ array: ids, schema: mmCIF_Schema.entity.id }),
+ type: Column.ofArray({ array: types, schema: mmCIF_Schema.entity.type }),
+ })
} else {
entityData = format.data.entity;
}
--
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