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dssp
Commit e92eb4a7 by Maarten L. Hekkelman
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rename unit-test

parent 0e8aeec8
Showing with 97 additions and 131 deletions
CMakeLists.txt
...@@ -159,29 +159,27 @@ endif() ...@@ -159,29 +159,27 @@ endif()
# test # test
add_executable(unit-test ${PROJECT_SOURCE_DIR}/test/unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp) add_executable(dssp-unit-test ${PROJECT_SOURCE_DIR}/test/dssp-unit-test.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp)
if(USE_RSRC) if(USE_RSRC)
mrc_target_resources(unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic) mrc_target_resources(dssp-unit-test ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
endif() endif()
target_include_directories(unit-test PRIVATE target_include_directories(dssp-unit-test PRIVATE
${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_SOURCE_DIR}/src
${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}/include
) )
target_link_libraries(unit-test dssp_library cifpp::cifpp Boost::date_time) target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp Boost::date_time)
if(MSVC) if(MSVC)
# Specify unwind semantics so that MSVC knowns how to handle exceptions # Specify unwind semantics so that MSVC knowns how to handle exceptions
target_compile_options(unit-test PRIVATE /EHsc) target_compile_options(dssp-unit-test PRIVATE /EHsc)
endif() endif()
enable_testing() enable_testing()
add_test(NAME unit-test add_test(NAME dssp-unit-test COMMAND $<TARGET_FILE:dssp-unit-test> -- ${PROJECT_SOURCE_DIR}/test)
COMMAND $<TARGET_FILE:unit-test>
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/test)
option(DSSP_BUILD_INSTALLER "Build an installer" OFF) option(DSSP_BUILD_INSTALLER "Build an installer" OFF)
if(DSSP_BUILD_INSTALLER) if(DSSP_BUILD_INSTALLER)
......
test/dssp-test.cpp deleted 100644 → 0
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2022 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#define BOOST_TEST_ALTERNATIVE_INIT_API
#include <boost/test/included/unit_test.hpp>
#include <charconv>
#include <stdexcept>
#include <cif++/cif.hpp>
#include <cif++/dssp/DSSP.hpp>
namespace tt = boost::test_tools;
std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
// --------------------------------------------------------------------
cif::file operator""_cf(const char *text, size_t length)
{
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(text), length);
std::istream is(&buffer);
return cif::file(is);
}
// --------------------------------------------------------------------
bool init_unit_test()
{
cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
return true;
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(dssp_1)
{
cif::file f(gTestDir / "1cbs.cif");
BOOST_ASSERT(f.is_valid());
std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
dssp::DSSP dssp(f.front(), 1, 3, true);
for (auto residue : dssp)
{
std::string line;
getline(t, line);
std::cout << line << std::endl;
auto f = cif::split(line, "\t");
BOOST_CHECK_EQUAL(f.size(), 3);
if (f.size() != 3)
continue;
int seqID;
std::from_chars(f[0].begin(), f[0].end(), seqID);
std::string asymID{ f[1] };
std::string secstr{ f[2] };
if (secstr == "_")
secstr = " ";
BOOST_CHECK_EQUAL(residue.asym_id(), asymID);
BOOST_CHECK_EQUAL(residue.seq_id(), seqID);
BOOST_CHECK_EQUAL((char)residue.type(), secstr.front());
}
}
\ No newline at end of file
test/unit-test.cpp → test/dssp-unit-test.cpp
...@@ -24,17 +24,58 @@ ...@@ -24,17 +24,58 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/ */
#define BOOST_TEST_MODULE DSSP_Test
#include <boost/test/included/unit_test.hpp>
#include <boost/algorithm/string.hpp>
#include <stdexcept> #include <stdexcept>
#include "DSSP.hpp" #define BOOST_TEST_ALTERNATIVE_INIT_API
#include <boost/algorithm/string.hpp>
#include <boost/test/included/unit_test.hpp>
#include "DSSP.hpp"
#include "dssp_wrapper.hpp" #include "dssp_wrapper.hpp"
namespace ba = boost::algorithm; namespace ba = boost::algorithm;
namespace fs = std::filesystem;
// --------------------------------------------------------------------
cif::file operator""_cf(const char *text, size_t length)
{
struct membuf : public std::streambuf
{
membuf(char *text, size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(text), length);
std::istream is(&buffer);
return cif::file(is);
}
// --------------------------------------------------------------------
fs::path gTestDir = fs::current_path();
bool init_unit_test()
{
cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2)
{
gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
cif::add_data_directory(gTestDir / ".." / "rsrc");
}
// // do this now, avoids the need for installing
// cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// // initialize CCD location
// cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
return true;
}
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -42,7 +83,7 @@ BOOST_AUTO_TEST_CASE(ut_dssp) ...@@ -42,7 +83,7 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
{ {
using namespace std::literals; using namespace std::literals;
cif::file f("1cbs.cif.gz"); cif::file f(gTestDir / "1cbs.cif.gz");
BOOST_ASSERT(f.is_valid()); BOOST_ASSERT(f.is_valid());
dssp::DSSP dssp(f.front(), 1, 3, true); dssp::DSSP dssp(f.front(), 1, 3, true);
...@@ -51,18 +92,18 @@ BOOST_AUTO_TEST_CASE(ut_dssp) ...@@ -51,18 +92,18 @@ BOOST_AUTO_TEST_CASE(ut_dssp)
writeDSSP(dssp, test); writeDSSP(dssp, test);
std::ifstream reference("1cbs.dssp"); std::ifstream reference(gTestDir / "1cbs.dssp");
BOOST_CHECK(reference.is_open()); BOOST_CHECK(reference.is_open());
std::string line_t, line_r; std::string line_t, line_r;
BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r)); BOOST_CHECK(std::getline(test, line_t) and std::getline(reference, line_r));
const char* kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ===="; const char *kHeaderLineStart = "==== Secondary Structure Definition by the program DSSP, NKI version 4.0 ====";
BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0); BOOST_CHECK(line_t.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0); BOOST_CHECK(line_r.compare(0, std::strlen(kHeaderLineStart), kHeaderLineStart) == 0);
for (int line_nr = 2; ; ++line_nr) for (int line_nr = 2;; ++line_nr)
{ {
bool done_t = not std::getline(test, line_t); bool done_t = not std::getline(test, line_t);
bool done_r = not std::getline(reference, line_r); bool done_r = not std::getline(reference, line_r);
...@@ -88,7 +129,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2) ...@@ -88,7 +129,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
using namespace std::literals; using namespace std::literals;
using namespace cif::literals; using namespace cif::literals;
cif::file f("1cbs.cif.gz"); cif::file f(gTestDir / "1cbs.cif.gz");
BOOST_ASSERT(f.is_valid()); BOOST_ASSERT(f.is_valid());
dssp::DSSP dssp(f.front(), 1, 3, true); dssp::DSSP dssp(f.front(), 1, 3, true);
...@@ -97,7 +138,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2) ...@@ -97,7 +138,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
annotateDSSP(f.front(), dssp, true, test); annotateDSSP(f.front(), dssp, true, test);
cif::file rf("1cbs-dssp.cif"); cif::file rf(gTestDir / "1cbs-dssp.cif");
// structure.datablock()["software"].erase("name"_key == "dssp"); // structure.datablock()["software"].erase("name"_key == "dssp");
// rs.datablock()["software"].erase("name"_key == "dssp"); // rs.datablock()["software"].erase("name"_key == "dssp");
...@@ -107,3 +148,41 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2) ...@@ -107,3 +148,41 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
// BOOST_CHECK(f.front() == rf.front()); // BOOST_CHECK(f.front() == rf.front());
} }
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(dssp_1)
{
cif::file f(gTestDir / "1cbs.cif");
BOOST_ASSERT(f.is_valid());
std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
dssp::DSSP dssp(f.front(), 1, 3, true);
for (auto residue : dssp)
{
std::string line;
getline(t, line);
std::cout << line << std::endl;
auto f = cif::split(line, "\t");
BOOST_CHECK_EQUAL(f.size(), 3);
if (f.size() != 3)
continue;
int seqID;
std::from_chars(f[0].begin(), f[0].end(), seqID);
std::string asymID{ f[1] };
std::string secstr{ f[2] };
if (secstr == "_")
secstr = " ";
BOOST_CHECK_EQUAL(residue.asym_id(), asymID);
BOOST_CHECK_EQUAL(residue.seq_id(), seqID);
BOOST_CHECK_EQUAL((char)residue.type(), secstr.front());
}
}
\ No newline at end of file
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