From e2abe0f52a6694730ee60a257167d8242f65c9a6 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 10 Sep 2019 16:48:36 -0700
Subject: [PATCH] pdb-parser, atom-site fixes
---
src/mol-model-formats/structure/pdb/atom-site.ts | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/src/mol-model-formats/structure/pdb/atom-site.ts b/src/mol-model-formats/structure/pdb/atom-site.ts
index 320d88595..c47fa9d97 100644
--- a/src/mol-model-formats/structure/pdb/atom-site.ts
+++ b/src/mol-model-formats/structure/pdb/atom-site.ts
@@ -108,9 +108,9 @@ export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer,
// 27 AChar Code for insertion of residues.
if (str.charCodeAt(s + 26) === 32) { // ' '
- TokenBuilder.add(sites.label_alt_id, 0, 0);
+ TokenBuilder.add(sites.pdbx_PDB_ins_code, 0, 0);
} else {
- TokenBuilder.add(sites.label_alt_id, s + 26, s + 27);
+ TokenBuilder.add(sites.pdbx_PDB_ins_code, s + 26, s + 27);
}
// 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
@@ -129,7 +129,7 @@ export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer,
if (length >= 66) {
TokenBuilder.addToken(sites.B_iso_or_equiv, Tokenizer.trim(data, s + 60, s + 66));
} else {
- TokenBuilder.add(sites.label_alt_id, 0, 0);
+ TokenBuilder.add(sites.B_iso_or_equiv, 0, 0);
}
// 73 - 76 LString(4) Segment identifier, left-justified.
@@ -148,6 +148,9 @@ export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer,
guessElementSymbolTokens(sites.type_symbol, str, s + 12, s + 16)
}
+ // 79 - 80 LString(2) charge Charge on the atom.
+ // TODO
+
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
--
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