From 8549c314dfb8e4fe7e0ee4b33b97308f114393a2 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 26 Sep 2011 16:17:16 +0200
Subject: [PATCH] Fixed unit test for struct_conf parsing
---
modules/io/doc/mmcif.rst | 1 +
modules/io/src/mol/mmcif_reader.cc | 32 +++++++++++++--------------
modules/io/src/mol/mmcif_reader.hh | 22 +++++++++---------
modules/io/tests/test_mmcif_reader.cc | 10 +++------
4 files changed, 32 insertions(+), 33 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 03305a881..b0467c62a 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -34,6 +34,7 @@ The following categories of a mmCIF file are considered by the parser:
:class:`MMCifInfoStructDetails`.
* ``struct_conf``: Stores secondary structure information (practically helices)
in the :class:`entity <ost.mol.EntityHandle>`
+* ``struct_sheet_range``
Info Classes
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 4050f9644..e1222db86 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -265,17 +265,17 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
} else if (header.GetCategory() == "struct_conf") {
category_ = STRUCT_CONF;
// mandatory items
- this->TryStoreIdx(BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
- this->TryStoreIdx(BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
- this->TryStoreIdx(BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
- this->TryStoreIdx(CONF_TYPE_ID, "conf_type_id", header);
- this->TryStoreIdx(END_LABEL_ASYM_ID, "end_label_asym_id", header);
- this->TryStoreIdx(END_LABEL_COMP_ID, "end_label_comp_id", header);
- this->TryStoreIdx(END_LABEL_SEQ_ID, "end_label_seq_id", header);
- this->TryStoreIdx(STRUCT_CONF_ID, "id", header);
+ this->TryStoreIdx(SC_BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+ this->TryStoreIdx(SC_BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+ this->TryStoreIdx(SC_BEG_LABEL_SEQ_ID, "beg_label_seq_id", header);
+ this->TryStoreIdx(SC_CONF_TYPE_ID, "conf_type_id", header);
+ this->TryStoreIdx(SC_END_LABEL_ASYM_ID, "end_label_asym_id", header);
+ this->TryStoreIdx(SC_END_LABEL_COMP_ID, "end_label_comp_id", header);
+ this->TryStoreIdx(SC_END_LABEL_SEQ_ID, "end_label_seq_id", header);
+ this->TryStoreIdx(SC_ID, "id", header);
// optional items
- indices_[BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
- indices_[END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
+ indices_[SC_BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+ indices_[SC_END_AUTH_ASYM_ID] = header.GetIndex("end_auth_asym_id");
cat_available = true;
}
category_counts_[category_]++;
@@ -1163,20 +1163,20 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
int s_res_num;
int e_res_num;
// fetch start and end
- s_res_num = this->TryGetInt(columns[indices_[BEG_LABEL_SEQ_ID]],
+ s_res_num = this->TryGetInt(columns[indices_[SC_BEG_LABEL_SEQ_ID]],
"struct_conf.beg_label_seq_id");
- e_res_num = this->TryGetInt(columns[indices_[END_LABEL_SEQ_ID]],
+ e_res_num = this->TryGetInt(columns[indices_[SC_END_LABEL_SEQ_ID]],
"struct_conf.end_label_seq_id");
if(auth_chain_id_) {
- if (indices_[BEG_AUTH_ASYM_ID] != -1) {
- chain_name = columns[indices_[BEG_AUTH_ASYM_ID]];
+ if (indices_[SC_BEG_AUTH_ASYM_ID] != -1) {
+ chain_name = columns[indices_[SC_BEG_AUTH_ASYM_ID]];
} else {
throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
"Chain name by author requested but 'struct_conf.beg_auth_asym_id' is not set.",
this->GetCurrentLinenum()));
}
} else {
- chain_name = columns[indices_[BEG_LABEL_ASYM_ID]];
+ chain_name = columns[indices_[SC_BEG_LABEL_ASYM_ID]];
}
if (restrict_chains_.size() == 0 ||
@@ -1186,7 +1186,7 @@ void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
chain_name.str()};
MMCifSecStructElement type =
- DetermineSecStructType(columns[indices_[CONF_TYPE_ID]]);
+ DetermineSecStructType(columns[indices_[SC_CONF_TYPE_ID]]);
if (type == MMCIF_HELIX) {
helix_list_.push_back(hse);
} else if (type == MMCIF_STRAND) {
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index c8a8b5181..6005831d8 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -53,6 +53,7 @@ namespace ost { namespace io {
/// \li pdbx_struct_oper_list
/// \li struct
/// \li struct_conf
+/// \li struct_sheet_range
class DLLEXPORT_OST_IO MMCifParser : public StarParser {
public:
/// \brief create a MMCifParser
@@ -428,16 +429,16 @@ private:
/// \enum items of the struct_conf category
typedef enum {
- BEG_AUTH_ASYM_ID, ///< Starting residue, points to atom_site.auth_asym_id
- BEG_LABEL_ASYM_ID, ///< Starting residue, points to atom_site.label_asym_id
- BEG_LABEL_COMP_ID, ///< Starting residue, points to atom_site.label_comp_id
- BEG_LABEL_SEQ_ID, ///< Starting residue, points to atom_site.label_seq_id
- CONF_TYPE_ID, ///< Pointer to struct_conf_type.id
- END_AUTH_ASYM_ID, ///< Ending residue, points to atom_site.auth_asym_id
- END_LABEL_ASYM_ID, ///< Ending residue, points to atom_site.label_asym_id
- END_LABEL_COMP_ID, ///< Ending residue, points to atom_site.label_comp_id
- END_LABEL_SEQ_ID, ///< Ending residue, points to atom_site.label_seq_id
- STRUCT_CONF_ID, ///< Unique identifier
+ SC_BEG_AUTH_ASYM_ID, ///< Starting residue (atom_site.auth_asym_id)
+ SC_BEG_LABEL_ASYM_ID, ///< Starting residue (atom_site.label_asym_id)
+ SC_BEG_LABEL_COMP_ID, ///< Starting residue (atom_site.label_comp_id)
+ SC_BEG_LABEL_SEQ_ID, ///< Starting residue (atom_site.label_seq_id)
+ SC_CONF_TYPE_ID, ///< Pointer to struct_conf_type.id
+ SC_END_AUTH_ASYM_ID, ///< Ending residue, points to atom_site.auth_asym_id
+ SC_END_LABEL_ASYM_ID, ///< Ending residue, points to atom_site.label_asym_id
+ SC_END_LABEL_COMP_ID, ///< Ending residue, points to atom_site.label_comp_id
+ SC_END_LABEL_SEQ_ID, ///< Ending residue, points to atom_site.label_seq_id
+ SC_ID, ///< Unique identifier
} StructConfItems;
/// \enum categories of the mmcif format
@@ -454,6 +455,7 @@ private:
PDBX_STRUCT_OPER_LIST,
STRUCT,
STRUCT_CONF,
+ STRUCT_SHEET_RANGE,
DONT_KNOW
} MMCifCategory;
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 667684c6e..621a5856d 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1136,13 +1136,9 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
// pick chains, iterate residues, check for correct sec.struct.
ch = eh.FindChain("A");
rl = ch.GetResidueList();
- for (rs = rl.begin(); rs != rl.end(); ++rs) {
- std::cout << "Foo " << (char)rs->GetSecStructure() << std::endl;
- if (rs->GetSecStructure().IsExtended()) {
- std::cout << "Bar" << std::endl;
- }
- //BOOST_CHECK_EQUAL(rs->GetSecStructure().IsHelical());
- }
+ BOOST_CHECK_EQUAL(rl[0].GetSecStructure().IsHelical(), true);
+ BOOST_CHECK_EQUAL(rl[1].GetSecStructure().IsHelical(), true);
+ BOOST_CHECK_EQUAL(rl[2].GetSecStructure().IsExtended(), true);
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" reading data fields which should not fail...");
--
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