From 684b9002265471b2994f86a56f2548c42cf290e7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 26 Jul 2024 08:58:40 +0200
Subject: [PATCH] mmcif writer: sanity checks - no duplicate atoms and strictly
increasing resnums
The latter is only relevant if mmcif_conform is True and triggered a segfault
before.
---
modules/io/src/mol/mmcif_writer.cc | 42 ++++++++++++++++++++++++++++--
1 file changed, 40 insertions(+), 2 deletions(-)
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 6ea364aa8..3e086fa8a 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -811,6 +811,19 @@ namespace {
String comp_id = res.GetName();
auto at_list = res.GetAtomList();
+
+ // sanity check that we have no duplicates
+ std::set<String> anames;
+ for(auto a: at_list) {
+ if(anames.find(a.GetName()) != anames.end()) {
+ std::stringstream ss;
+ ss << "Duplicate atom \"" << a.GetName() << "\" in residue ";
+ ss << a.GetResidue() << std::endl;
+ throw ost::io::IOException(ss.str());
+ }
+ anames.insert(a.GetName());
+ }
+
String auth_asym_id = res.GetChain().GetName();
if(res.HasProp("pdb_auth_chain_name")) {
auth_asym_id = res.GetStringProp("pdb_auth_chain_name");
@@ -1328,9 +1341,35 @@ namespace {
auto chain_list = ent.GetChainList();
for(auto chain: chain_list) {
String cname = chain.GetName();
+
+ auto res_list = chain.GetResidueList();
+ // sanity check that residue numbers are strictly increasing and have no
+ // insertion codes which is a requirement for mmCIF conform chains
+ // (not only for polymers)
+ for(size_t i = 0; i < res_list.size(); ++i) {
+ if(res_list[i].GetNumber().GetInsCode() != '\0') {
+ std::stringstream ss;
+ ss << "Residue number insertion codes must be empty if ";
+ ss << "mmcif_conform is enabled. Got \"";
+ ss << res_list[i].GetNumber().GetInsCode() << "\" in residue ";
+ ss << res_list[i];
+ throw ost::io::IOException(ss.str());
+ }
+ if(i>0) {
+ if(res_list[i-1].GetNumber().GetNum() >=
+ res_list[i].GetNumber().GetNum()) {
+ std::stringstream ss;
+ ss << "Residue numbers must be strictly increasing in consecutive ";
+ ss << "residues if mmcif_conform is enabled. ";
+ ss << "Got " << res_list[i-1] << " followed by " << res_list[i];
+ ss << ".";
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+
if(preassigned_polymer_chains.find(cname) !=
preassigned_polymer_chains.end()) {
- auto res_list = chain.GetResidueList();
int entity_id = preassigned_polymer_chains[cname];
AddAsymResnum(cname, res_list, entity_info[entity_id], true);
Feed_atom_site(atom_site, cname, entity_id+1, entity_info[entity_id], res_list);
@@ -1338,7 +1377,6 @@ namespace {
entity_info[entity_id], res_list);
} else {
// do automated matching
- auto res_list = chain.GetResidueList();
int entity_id = SetupEntity(cname,
chain.GetType(),
res_list,
--
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