From 532f5b41d3cc03f805cefb507b9d206510f2ba8c Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Mon, 22 Jul 2024 18:02:39 +0200
Subject: [PATCH] fix: allow duplicate _struct_ref_seq.align_id in
fault_tolerant mode
---
modules/io/src/mol/mmcif_info.cc | 13 +++++++++++--
modules/io/src/mol/mmcif_info.hh | 3 ++-
modules/io/src/mol/mmcif_reader.cc | 2 +-
3 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 77ae60402..da2922234 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -196,11 +196,20 @@ void MMCifInfoBioUnit::Merge(MMCifInfoBioUnit& from)
MMCifInfoStructRefSeqPtr
MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
int seq_begin, int seq_end, int db_begin,
- int db_end)
+ int db_end, bool fault_tolerant)
{
std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
if (i!=seqs_.end()) {
- throw IOException("duplicate align_id for struct_ref '"+id_+"'");
+ std::stringstream msg;
+ msg << "Duplicate align_id for struct_ref '" << id_ << "'";
+ if (fault_tolerant) {
+ msg << ". Record will be overwritten.";
+ LOG_WARNING(msg.str());
+ }
+ else {
+ throw IOException(msg.str());
+ }
+
}
MMCifInfoStructRefSeqPtr p(new MMCifInfoStructRefSeq(aid, chain_name,
seq_begin, seq_end,
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 73d3c25d2..73946c139 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -858,7 +858,8 @@ public:
const String& GetDBAccess() const { return db_access_; }
MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id,
const String& chain_name, int seq_begin,
- int seq_end, int db_begin, int db_end);
+ int seq_end, int db_begin, int db_end,
+ bool fault_tolerant);
MMCifInfoStructRefSeqPtr GetAlignedSeq(const String& align_id) const;
MMCifInfoStructRefSeqs GetAlignedSeqs() const
{
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 5ebb954dc..64d632755 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -1686,7 +1686,7 @@ void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns)
e=struct_refs_.end(); i!=e; ++i) {
if ((*i)->GetID()==sr_id) {
(*i)->AddAlignedSeq(aln_id, chain_name, entbeg.second, entend.second,
- dbbeg.second, dbend.second);
+ dbbeg.second, dbend.second, profile_.fault_tolerant);
found=true;
break;
}
--
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