From aa4c41a50c65ab0c4bf201dbb877e03fb1f04522 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 22 Dec 2023 09:03:39 +0100
Subject: [PATCH] Fail cleanly for gaps in unknown polymer chain types
This avoids silently creating invalid files if we have gaps in
oligosaccharide chains, for instance.
---
modules/io/src/mol/mmcif_writer.cc | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index e14ff97d3..230e4e359 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -1344,7 +1344,7 @@ namespace {
}
}
- if(entity_infos[entity_idx].poly_type == "polydeoxyribonucleotide") {
+ else if(entity_infos[entity_idx].poly_type == "polydeoxyribonucleotide") {
entity_infos[entity_idx].mon_ids[mon_id_idx] = "DN";
entity_infos[entity_idx].seq_olcs[mon_id_idx] = "(DN)";
entity_infos[entity_idx].seq_can_olcs[mon_id_idx] = "N";
@@ -1355,7 +1355,7 @@ namespace {
}
}
- if(entity_infos[entity_idx].poly_type == "polyribonucleotide" ||
+ else if(entity_infos[entity_idx].poly_type == "polyribonucleotide" ||
entity_infos[entity_idx].poly_type == "polydeoxyribonucleotide/polyribonucleotide hybrid") {
entity_infos[entity_idx].mon_ids[mon_id_idx] = "N";
entity_infos[entity_idx].seq_olcs[mon_id_idx] = "N";
@@ -1366,6 +1366,13 @@ namespace {
comp_infos["N"] = info;
}
}
+
+ else {
+ std::stringstream ss;
+ ss << "Gaps are not supported for polymer chains of type ";
+ ss << entity_infos[entity_idx].poly_type;
+ throw ost::io::IOException(ss.str());
+ }
}
}
}
--
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