From beb1b2655ee6629beb9b0a4fe82a379f507e329a Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Sun, 17 Jul 2022 17:58:57 +0200
Subject: [PATCH] scan all entities when looking for struct_conn etries -
solves PDB loading issue
---
.../structure/property/bonds/struct_conn.ts | 30 +++++++++++--------
1 file changed, 17 insertions(+), 13 deletions(-)
diff --git a/src/mol-model-formats/structure/property/bonds/struct_conn.ts b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
index d8b2ca61e..f5f38998e 100644
--- a/src/mol-model-formats/structure/property/bonds/struct_conn.ts
+++ b/src/mol-model-formats/structure/property/bonds/struct_conn.ts
@@ -111,24 +111,28 @@ export namespace StructConn {
symmetry: struct_conn.ptnr2_symmetry
};
+ const entityIds = Array.from(model.entities.data.id.toArray());
const _p = (row: number, ps: typeof p1) => {
if (ps.label_asym_id.valueKind(row) !== Column.ValueKind.Present) return void 0;
const asymId = ps.label_asym_id.value(row);
- const entityIndex = model.atomicHierarchy.index.findEntity(asymId);
- if (entityIndex < 0) return void 0;
- const residueIndex = model.atomicHierarchy.index.findResidue(
- model.entities.data.id.value(entityIndex),
- asymId,
- ps.auth_seq_id.value(row),
- ps.ins_code.value(row)
- );
- if (residueIndex < 0) return void 0;
const atomName = ps.label_atom_id.value(row);
// turns out "mismat" records might not have atom name value
- if (!atomName) return void 0;
- const atomIndex = model.atomicHierarchy.index.findAtomOnResidue(residueIndex, atomName, ps.label_alt_id.value(row));
- if (atomIndex < 0) return void 0;
- return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) };
+ if (!atomName) return undefined;
+
+ const altId = ps.label_alt_id.value(row);
+ for (const eId of entityIds) {
+ const residueIndex = model.atomicHierarchy.index.findResidue(
+ eId,
+ asymId,
+ ps.auth_seq_id.value(row),
+ ps.ins_code.value(row)
+ );
+ if (residueIndex < 0) continue;
+ const atomIndex = model.atomicHierarchy.index.findAtomOnResidue(residueIndex, atomName, altId);
+ if (atomIndex < 0) continue;
+ return { residueIndex, atomIndex, symmetry: ps.symmetry.value(row) };
+ }
+ return void 0;
};
const entries: StructConn.Entry[] = [];
--
GitLab