From 84e18c0102700a772d820800fe082874ea1bfa8f Mon Sep 17 00:00:00 2001
From: B13nch3n <stefan.bienert@me.com>
Date: Wed, 22 Jul 2020 13:17:10 +0200
Subject: [PATCH] SCHWED-4851: some unit tests for branched entities
---
modules/io/tests/test_mmcif_reader.cc | 69 +++++++++++++++++++++++++--
1 file changed, 64 insertions(+), 5 deletions(-)
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index b6fa90f1f..dd0f40fbb 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -62,6 +62,7 @@ public:
using MMCifReader::ParseStructConf;
using MMCifReader::ParseStructSheetRange;
using MMCifReader::ParsePdbxEntityBranch;
+ using MMCifReader::ParsePdbxEntityBranchLink;
using MMCifReader::TryStoreIdx;
using MMCifReader::SetRestrictChains;
using MMCifReader::SetReadSeqRes;
@@ -1419,13 +1420,8 @@ BOOST_AUTO_TEST_CASE(mmcif_test_revisions_new)
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 chain type recognition...");
{
@@ -1462,4 +1458,67 @@ BOOST_AUTO_TEST_CASE(mmcif_pdbx_entity_branch_tests)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_pdbx_entity_branch_link_tests)
+{
+ BOOST_TEST_MESSAGE(" Running mmcif_pdbx_entity_branch_link_tests...");
+ mol::EntityHandle eh = mol::CreateEntity();
+ StarLoopDesc tmmcif_h;
+
+ BOOST_TEST_MESSAGE(" testing link retrieval...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ // build dummy pdbx_entity_branch_link header
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_entity_branch_link", 23));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("atom_id_1", 9));
+ tmmcif_h.Add(StringRef("atom_id_2", 9));
+ tmmcif_h.Add(StringRef("comp_id_1", 9));
+ tmmcif_h.Add(StringRef("comp_id_2", 9));
+ tmmcif_h.Add(StringRef("entity_branch_list_num_1", 24));
+ tmmcif_h.Add(StringRef("entity_branch_list_num_2", 24));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("C1", 2));
+ columns.push_back(StringRef("O3", 2));
+ columns.push_back(StringRef("MAN", 3));
+ columns.push_back(StringRef("BMA", 3));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("1", 1));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParsePdbxEntityBranchLink(columns));
+ }
+ BOOST_TEST_MESSAGE(" done.");
+ BOOST_TEST_MESSAGE(" testing link with bond order...");
+ {
+ TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
+ std::vector<StringRef> columns;
+
+ // build dummy pdbx_entity_branch_link header
+ tmmcif_h.Clear();
+ tmmcif_h.SetCategory(StringRef("pdbx_entity_branch_link", 23));
+ tmmcif_h.Add(StringRef("entity_id", 9));
+ tmmcif_h.Add(StringRef("atom_id_1", 9));
+ tmmcif_h.Add(StringRef("atom_id_2", 9));
+ tmmcif_h.Add(StringRef("comp_id_1", 9));
+ tmmcif_h.Add(StringRef("comp_id_2", 9));
+ tmmcif_h.Add(StringRef("entity_branch_list_num_1", 24));
+ tmmcif_h.Add(StringRef("entity_branch_list_num_2", 24));
+ tmmcif_h.Add(StringRef("value_order", 11));
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("C1", 2));
+ columns.push_back(StringRef("O3", 2));
+ columns.push_back(StringRef("MAN", 3));
+ columns.push_back(StringRef("BMA", 3));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef("1", 1));
+ columns.push_back(StringRef("2", 1));
+ BOOST_CHECK_NO_THROW(tmmcif_p.ParsePdbxEntityBranchLink(columns));
+ }
+ BOOST_TEST_MESSAGE(" done.");
+ BOOST_TEST_MESSAGE(" done.");
+}
+
BOOST_AUTO_TEST_SUITE_END();
--
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