From a1c64afac713774f61aef7d817a286eab86bd71d Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 21 Sep 2011 15:28:03 +0200
Subject: [PATCH] Testing reading only CA in the mmcif parser
---
modules/io/src/mol/mmcif_reader.cc | 2 +-
modules/io/tests/test_mmcif_reader.cc | 79 ++++++++++++++++++++++-----
2 files changed, 66 insertions(+), 15 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 37eb2caa6..756669d51 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -280,7 +280,7 @@ bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
{
// ATOM name
atom_name = columns[indices_[LABEL_ATOM_ID]];
- if (profile_.calpha_only) { // unit test profile
+ if (profile_.calpha_only) {
if (atom_name != StringRef("CA", 2)) {
return false;
}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 4362d4ce8..bff617cca 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -68,6 +68,24 @@ public:
using MMCifParser::GetInfo;
};
+void SetAtomSiteHeader(StarLoopDesc* mmcif_h)
+{
+ mmcif_h->Clear();
+ mmcif_h->SetCategory(StringRef("atom_site", 9));
+ mmcif_h->Add(StringRef("auth_asym_id", 12));
+ mmcif_h->Add(StringRef("id", 2));
+ mmcif_h->Add(StringRef("label_alt_id", 12));
+ mmcif_h->Add(StringRef("label_asym_id", 13));
+ mmcif_h->Add(StringRef("label_atom_id", 13));
+ mmcif_h->Add(StringRef("label_comp_id", 13));
+ mmcif_h->Add(StringRef("label_entity_id", 15));
+ mmcif_h->Add(StringRef("label_seq_id", 12));
+ mmcif_h->Add(StringRef("type_symbol", 11));
+ mmcif_h->Add(StringRef("Cartn_x", 7));
+ mmcif_h->Add(StringRef("Cartn_y", 7));
+ mmcif_h->Add(StringRef("Cartn_z", 7));
+}
+
BOOST_AUTO_TEST_SUITE( io );
BOOST_AUTO_TEST_CASE(mmcif_isvalidpdbident)
@@ -239,19 +257,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parse_models)
mol::EntityHandle eh = mol::CreateEntity();
StarLoopDesc tmmcif_h;
TestMMCifParserProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
- tmmcif_h.SetCategory(StringRef("atom_site", 9));
- tmmcif_h.Add(StringRef("auth_asym_id", 12));
- tmmcif_h.Add(StringRef("id", 2));
- tmmcif_h.Add(StringRef("label_alt_id", 12));
- tmmcif_h.Add(StringRef("label_asym_id", 13));
- tmmcif_h.Add(StringRef("label_atom_id", 13));
- tmmcif_h.Add(StringRef("label_comp_id", 13));
- tmmcif_h.Add(StringRef("label_entity_id", 15));
- tmmcif_h.Add(StringRef("label_seq_id", 12));
- tmmcif_h.Add(StringRef("type_symbol", 11));
- tmmcif_h.Add(StringRef("Cartn_x", 7));
- tmmcif_h.Add(StringRef("Cartn_y", 7));
- tmmcif_h.Add(StringRef("Cartn_z", 7));
+ SetAtomSiteHeader(&tmmcif_h);
tmmcif_p.OnBeginLoop(tmmcif_h);
tmmcif_h.Add(StringRef("pdbx_PDB_model_num", 18));
BOOST_CHECK_THROW(tmmcif_p.OnBeginLoop(tmmcif_h), IOException);
@@ -802,6 +808,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
std::ifstream s("testfiles/mmcif/atom_site.mmcif");
IOProfile profile;
+ StarLoopDesc tmmcif_h;
TestMMCifParserProtected tmmcif_p(s, eh, profile);
std::vector<StringRef> columns;
String chain_name;
@@ -809,7 +816,7 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
mol::ResNum resnum(0);
bool valid_res_num = false;
char alt_loc;
- //StringRef atom_name;
+ StringRef atom_name;
BOOST_MESSAGE(" testing valid line");
//tmmcif_p.ParseAtomIdent();
@@ -842,6 +849,50 @@ BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
this->TryStoreIdx(CARTN_Z, "Cartn_z", header);
*/
+ BOOST_MESSAGE(" testing profile to read calpha only");
+ {
+ profile.calpha_only = true;
+ // set up dummy header to pre-set indices
+ SetAtomSiteHeader(&tmmcif_h);
+ tmmcif_p.OnBeginLoop(tmmcif_h);
+ // create CA dummy line
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("2", 1));
+ columns.push_back(StringRef(".", 1));
+ columns.push_back(StringRef("A", 1));
+ columns.push_back(StringRef("CA", 2));
+ columns.push_back(StringRef("VAL", 3));
+ columns.push_back(StringRef("1", 1)); // label_entity_id
+ columns.push_back(StringRef("11", 2)); // label_seq_id
+ columns.push_back(StringRef("C", 1)); // type_symbol
+ columns.push_back(StringRef("25.369", 6)); // Cartn_x
+ columns.push_back(StringRef("30.691", 6)); // Cartn_y
+ columns.push_back(StringRef("11.795", 6)); // Cartn_z
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, chain_name, res_name,
+ resnum, valid_res_num, atom_name,
+ alt_loc), true);
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.pop_back();
+ columns.push_back(StringRef("CB", 2));
+ columns.push_back(StringRef("VAL", 3));
+ columns.push_back(StringRef("1", 1)); // label_entity_id
+ columns.push_back(StringRef("11", 2)); // label_seq_id
+ columns.push_back(StringRef("C", 1)); // type_symbol
+ columns.push_back(StringRef("25.369", 6)); // Cartn_x
+ columns.push_back(StringRef("30.691", 6)); // Cartn_y
+ columns.push_back(StringRef("11.795", 6)); // Cartn_z
+ BOOST_CHECK_EQUAL(tmmcif_p.ParseAtomIdent(columns, chain_name, res_name,
+ resnum, valid_res_num, atom_name,
+ alt_loc), false);
+ }
+ BOOST_MESSAGE(" done.");
+
BOOST_MESSAGE(" done.");
}
--
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