From de9e3301e7cc8dd6b2c7bfde03858ee5c634cbe2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 6 Jun 2024 09:55:20 +0200
Subject: [PATCH] fix: SCHWED-6331 make struct_ref_seq_dif.pdbx_seq_db_seq_num
optional
---
modules/io/src/mol/mmcif_reader.cc | 18 +++++++++++++-----
1 file changed, 13 insertions(+), 5 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index e95263b57..9ab20c5e2 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -319,9 +319,11 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
cat_available = true;
} else if (header.GetCategory()=="struct_ref_seq_dif") {
category_ = STRUCT_REF_SEQ_DIF;
+ // mandatory
this->TryStoreIdx(SRSD_ALIGN_ID, "align_id", header);
- this->TryStoreIdx(SRSD_SEQ_RNUM, "seq_num", header);
- this->TryStoreIdx(SRSD_DB_RNUM, "pdbx_seq_db_seq_num", header);
+ // optional
+ indices_[SRSD_SEQ_RNUM]=header.GetIndex("seq_num");
+ indices_[SRSD_DB_RNUM]=header.GetIndex("pdbx_seq_db_seq_num");
indices_[SRSD_DETAILS]=header.GetIndex("details");
cat_available = true;
} else if (header.GetCategory()=="database_PDB_rev") {
@@ -1693,17 +1695,23 @@ void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
{
String aln_id=columns[indices_[SRSD_ALIGN_ID]].str();
String db_rnum;
- if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) {
+ if (indices_[SRSD_DB_RNUM] != -1) {
db_rnum=columns[indices_[SRSD_DB_RNUM]].str();
+ } else {
+ LOG_INFO("Ignoring struct_ref_seq_dif with missing data item "
+ "pdbx_seq_db_seq_num");
+ return;
}
- std::pair<bool,int> seq_rnum(true, -1);
- if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) {
+ std::pair<bool,int> seq_rnum;
+ if (indices_[SRSD_SEQ_RNUM] != -1) {
seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]],
"_struct_ref_seq_dif.seq_num",
profile_.fault_tolerant);
}
if (!seq_rnum.first) {
+ LOG_INFO("Ignoring struct_ref_seq_dif with missing data item "
+ "seq_num");
return;
}
String details;
--
GitLab