From 6e7ef0683e50e8d423a82ca4630f7ff424feb25b Mon Sep 17 00:00:00 2001
From: B13nch3n <stefan.bienert@me.com>
Date: Fri, 10 Jul 2020 10:10:11 +0200
Subject: [PATCH] SCHWED-4696: Unit testing pdbx_entity_branch parsing
---
modules/io/tests/test_mmcif_reader.cc | 66 ++++++++++++++++++++++++++-
1 file changed, 64 insertions(+), 2 deletions(-)
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 21efd569f..65673c858 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -61,6 +61,7 @@ public:
using MMCifReader::ParseStruct;
using MMCifReader::ParseStructConf;
using MMCifReader::ParseStructSheetRange;
+ using MMCifReader::ParsePdbxEntityBranch;
using MMCifReader::TryStoreIdx;
using MMCifReader::SetRestrictChains;
using MMCifReader::SetReadSeqRes;
@@ -467,9 +468,8 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
columns.push_back(StringRef("other", 5));
BOOST_CHECK_NO_THROW(tmmcif_p.ParseEntityPoly(columns));
columns.pop_back();
- columns.pop_back();
columns.push_back(StringRef("badbadprion", 11));
- BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), IOException);
+ BOOST_CHECK_THROW(tmmcif_p.ParseEntityPoly(columns), ost::Error);
columns.pop_back();
}
BOOST_TEST_MESSAGE(" done.");
@@ -1424,4 +1424,66 @@ BOOST_AUTO_TEST_CASE(mmcif_test_revisions_new)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_pdbx_entity_branch_tests)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_pdbx_entity_branch_tests...");
+ IOProfile profile;
+ StarLoopDesc tmmcif_h;
+
+ mol::EntityHandle eh = mol::CreateEntity();
+ MMCifReader mmcif_p("testfiles/mmcif/atom_site.mmcif", eh, profile);
+
+ mmcif_p.Parse();
+
+ BOOST_TEST_MESSAGE(" testing missing corresponding entity entry...");
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::vector<StringRef> columns;
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+
+ tmmcif_h.SetCategory(StringRef("pdbx_entity_branch", 18));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("oligosaccharide", 15));
+
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxEntityBranch(columns), IOException);
+ }
+ BOOST_TEST_MESSAGE(" done.");
+ BOOST_TEST_MESSAGE(" testing chain type recognition...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ // create corresponding entity entry
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("entity", 6));
+ tmmcif_h.Add(StringRef("id", 2));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("branched", 8));
+ tmmcif_p.ParseEntity(columns);
+ columns.pop_back();
+ columns.pop_back();
+
+ // build dummy pdbx_entity_branch header
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_entity_branch", 18));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("type", 4));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("oligosaccharide", 15));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParsePdbxEntityBranch(columns));
+ columns.pop_back();
+
+ columns.push_back(StringRef("ordinarysugar", 13));
+ BOOST_CHECK_THROW(tmmcif_p.ParsePdbxEntityBranch(columns), ost::Error);
+ }
+ BOOST_TEST_MESSAGE(" done.");
+ BOOST_TEST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_SUITE_END();
--
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