mirror of
https://github.com/PDB-REDO/libcifpp.git
synced 2026-06-04 13:54:25 +08:00
591 lines
16 KiB
C++
591 lines
16 KiB
C++
/*-
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* SPDX-License-Identifier: BSD-2-Clause
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*
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* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice, this
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* list of conditions and the following disclaimer
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#define BOOST_TEST_ALTERNATIVE_INIT_API
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#include <boost/test/included/unit_test.hpp>
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#include <stdexcept>
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#include <cif++.hpp>
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#include <Eigen/Eigenvalues>
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namespace tt = boost::test_tools;
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namespace utf = boost::unit_test;
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std::filesystem::path gTestDir = std::filesystem::current_path(); // filled in first test
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// --------------------------------------------------------------------
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cif::file operator""_cf(const char *text, size_t length)
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{
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struct membuf : public std::streambuf
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{
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membuf(char *text, size_t length)
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{
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this->setg(text, text, text + length);
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}
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} buffer(const_cast<char *>(text), length);
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std::istream is(&buffer);
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return cif::file(is);
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}
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// --------------------------------------------------------------------
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bool init_unit_test()
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{
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cif::VERBOSE = 1;
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// not a test, just initialize test dir
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if (boost::unit_test::framework::master_test_suite().argc == 2)
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gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
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// do this now, avoids the need for installing
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cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
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// initialize CCD location
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cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
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return true;
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}
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// --------------------------------------------------------------------
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// 3d tests
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BOOST_AUTO_TEST_CASE(t1)
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{
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// std::random_device rnd;
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// std::mt19937 gen(rnd());
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// std::uniform_real_distribution<float> dis(0, 1);
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// Quaternion q{ dis(gen), dis(gen), dis(gen), dis(gen) };
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// q = Normalize(q);
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// Quaternion q{ 0.1, 0.2, 0.3, 0.4 };
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cif::quaternion q{ 0.5, 0.5, 0.5, 0.5 };
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q = normalize(q);
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const auto &&[angle0, axis0] = cif::quaternion_to_angle_axis(q);
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std::vector<cif::point> p1{
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{ 16.979f, 13.301f, 44.555f },
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{ 18.150f, 13.525f, 43.680f },
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{ 18.656f, 14.966f, 43.784f },
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{ 17.890f, 15.889f, 44.078f },
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{ 17.678f, 13.270f, 42.255f },
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{ 16.248f, 13.734f, 42.347f },
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{ 15.762f, 13.216f, 43.724f }
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};
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auto p2 = p1;
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cif::center_points(p1);
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for (auto &p : p2)
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p.rotate(q);
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cif::center_points(p2);
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auto q2 = cif::align_points(p1, p2);
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const auto &&[angle, axis] = cif::quaternion_to_angle_axis(q2);
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BOOST_TEST(std::fmod(360 + angle, 360) == std::fmod(360 - angle0, 360), tt::tolerance(0.01));
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for (auto &p : p1)
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p.rotate(q2);
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auto rmsd = cif::RMSd(p1, p2);
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BOOST_TEST(rmsd < 1e-5);
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// std::cout << "rmsd: " << RMSd(p1, p2) << '\n';
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}
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BOOST_AUTO_TEST_CASE(t2)
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{
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cif::point p[] = {
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{ 1, 1, 0 },
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{ 2, 1, 0 },
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{ 1, 2, 0 }
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};
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cif::point xp = cif::cross_product(p[1] - p[0], p[2] - p[0]);
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auto q = cif::construct_from_angle_axis(45, xp); // mmcif::Normalize(Quaternion{45 * mmcif::kPI / 180, xp.mX, xp.mY, xp.mZ});
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auto &&[angle, axis] = cif::quaternion_to_angle_axis(q);
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BOOST_TEST(angle == 45, tt::tolerance(0.01));
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}
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BOOST_AUTO_TEST_CASE(t3)
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{
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cif::point p[] = {
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{ 1, 1, 0 },
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{ 2, 1, 0 },
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{ 1, 2, 0 }
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};
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cif::point xp = cif::cross_product(p[1] - p[0], p[2] - p[0]);
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auto q = cif::construct_from_angle_axis(45, xp); // mmcif::Normalize(Quaternion{45 * mmcif::kPI / 180, xp.mX, xp.mY, xp.mZ});
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auto v = p[1];
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v -= p[0];
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v.rotate(q);
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v += p[0];
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std::cout << v << '\n';
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double a = cif::angle(v, p[0], p[1]);
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BOOST_TEST(a == 45, tt::tolerance(0.01));
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}
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BOOST_AUTO_TEST_CASE(dh_q_0)
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{
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cif::point axis(1, 0, 0);
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cif::point p(1, 1, 0);
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cif::point t[3] =
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{
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{ 0, 1, 0 },
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{ 0, 0, 0 },
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{ 1, 0, 0 }
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};
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auto a = cif::dihedral_angle(t[0], t[1], t[2], p);
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BOOST_TEST(a == 0, tt::tolerance(0.01f));
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auto q = cif::construct_from_angle_axis(90, axis);
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p.rotate(q);
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BOOST_TEST(p.m_x == 1, tt::tolerance(0.01f));
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BOOST_TEST(p.m_y == 0, tt::tolerance(0.01f));
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BOOST_TEST(p.m_z == 1, tt::tolerance(0.01f));
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a = cif::dihedral_angle(t[0], t[1], t[2], p);
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BOOST_TEST(a == 90, tt::tolerance(0.01f));
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q = cif::construct_from_angle_axis(-90, axis);
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p.rotate(q);
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BOOST_TEST(p.m_x == 1, tt::tolerance(0.01f));
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BOOST_TEST(p.m_y == 1, tt::tolerance(0.01f));
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BOOST_TEST(p.m_z == 0, tt::tolerance(0.01f));
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a = cif::dihedral_angle(t[0], t[1], t[2], p);
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BOOST_TEST(a == 0, tt::tolerance(0.01f));
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}
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BOOST_AUTO_TEST_CASE(dh_q_1)
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{
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struct
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{
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float angle;
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cif::point pts[4];
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} tests[] = {
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{ -97.5f,
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{ { 68.8649979f, -7.34800005f, 54.3769989f },
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{ 68.1350021f, -8.18700027f, 53.6489983f },
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{ 68.7760239f, -9.07335377f, 52.7140236f },
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{ 68.9000015f, -10.3944235f, 53.2217026f } } },
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{ 80.3f,
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{ { 0.304512024f, 0.531184196f, 2.25860214f },
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{ 0.956512451f, 0.0321846008f, 1.07460022f },
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{ 0, 0, 0 },
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{ 0.21336633f, -1.09552193f, -0.878999829f } } },
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{ -97.5f,
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{ { 0.088973999f, 1.72535372f, 1.66297531f },
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{ -0.641021729f, 0.886353493f, 0.93497467f },
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{ 0, 0, 0 },
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{ 1.29433727f, -0.395142615f, 0.432300746f } } },
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{ -97.5f,
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{
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{ 0.088973999f, 1.72535372f, 1.66297531f },
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{ -0.641021729f, 0.886353493f, 0.93497467f },
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{ 0, 0, 0 },
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{ 1.33983064f, 0.384027064f, -0.275154471f },
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} }
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};
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for (auto &&[angle, pts] : tests)
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{
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auto q = cif::construct_for_dihedral_angle(pts[0], pts[1], pts[2], pts[3], angle, 1);
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pts[3].rotate(q, pts[2]);
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auto dh = cif::dihedral_angle(pts[0], pts[1], pts[2], pts[3]);
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BOOST_TEST(dh == angle, tt::tolerance(0.1f));
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}
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}
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// --------------------------------------------------------------------
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BOOST_AUTO_TEST_CASE(m2q_0, *utf::tolerance(0.001f))
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{
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for (size_t i = 0; i < cif::kSymopNrTableSize; ++i)
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{
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auto d = cif::kSymopNrTable[i].symop().data();
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cif::matrix3x3<float> rot;
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float Qxx = rot(0, 0) = d[0];
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float Qxy = rot(0, 1) = d[1];
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float Qxz = rot(0, 2) = d[2];
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float Qyx = rot(1, 0) = d[3];
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float Qyy = rot(1, 1) = d[4];
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float Qyz = rot(1, 2) = d[5];
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float Qzx = rot(2, 0) = d[6];
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float Qzy = rot(2, 1) = d[7];
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float Qzz = rot(2, 2) = d[8];
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Eigen::Matrix4f em;
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em << Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
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Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
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Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
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Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz;
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Eigen::EigenSolver<Eigen::Matrix4f> es(em / 3);
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auto ev = es.eigenvalues();
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size_t bestJ = 0;
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float bestEV = -1;
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for (size_t j = 0; j < 4; ++j)
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{
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if (bestEV < ev[j].real())
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{
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bestEV = ev[j].real();
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bestJ = j;
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}
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}
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if (std::abs(bestEV - 1) > 0.01)
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continue; // not a rotation matrix
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auto col = es.eigenvectors().col(bestJ);
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auto q = normalize(cif::quaternion{
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static_cast<float>(col(3).real()),
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static_cast<float>(col(0).real()),
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static_cast<float>(col(1).real()),
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static_cast<float>(col(2).real()) });
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cif::point p1{ 1, 1, 1 };
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cif::point p2 = p1;
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p2.rotate(q);
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cif::point p3 = rot * p1;
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BOOST_TEST(p2.m_x == p3.m_x);
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BOOST_TEST(p2.m_y == p3.m_y);
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BOOST_TEST(p2.m_z == p3.m_z);
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}
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}
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// BOOST_AUTO_TEST_CASE(m2q_1, *utf::tolerance(0.001f))
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// {
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// for (size_t i = 0; i < cif::kSymopNrTableSize; ++i)
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// {
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// auto d = cif::kSymopNrTable[i].symop().data();
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// cif::matrix3x3<float> rot;
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// float Qxx = rot(0, 0) = d[0];
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// float Qxy = rot(0, 1) = d[1];
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// float Qxz = rot(0, 2) = d[2];
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// float Qyx = rot(1, 0) = d[3];
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// float Qyy = rot(1, 1) = d[4];
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// float Qyz = rot(1, 2) = d[5];
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// float Qzx = rot(2, 0) = d[6];
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// float Qzy = rot(2, 1) = d[7];
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// float Qzz = rot(2, 2) = d[8];
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// cif::matrix4x4<float> m({
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// Qxx - Qyy - Qzz, Qyx + Qxy, Qzx + Qxz, Qzy - Qyz,
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// Qyx + Qxy, Qyy - Qxx - Qzz, Qzy + Qyz, Qxz - Qzx,
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// Qzx + Qxz, Qzy + Qyz, Qzz - Qxx - Qyy, Qyx - Qxy,
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// Qzy - Qyz, Qxz - Qzx, Qyx - Qxy, Qxx + Qyy + Qzz
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// });
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// auto &&[ev, em] = cif::eigen(m * (1/3.0f), false);
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// size_t bestJ = 0;
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// float bestEV = -1;
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// for (size_t j = 0; j < 4; ++j)
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// {
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// if (bestEV < ev[j])
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// {
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// bestEV = ev[j];
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// bestJ = j;
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// }
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// }
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// if (std::abs(bestEV - 1) > 0.01)
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// continue; // not a rotation matrix
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// auto q = normalize(cif::quaternion{
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// static_cast<float>(em(bestJ, 3)),
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// static_cast<float>(em(bestJ, 0)),
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// static_cast<float>(em(bestJ, 1)),
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// static_cast<float>(em(bestJ, 2)) });
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// cif::point p1{ 1, 1, 1 };
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// cif::point p2 = p1;
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// p2.rotate(q);
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// cif::point p3 = rot * p1;
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// BOOST_TEST(p2.m_x == p3.m_x);
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// BOOST_TEST(p2.m_y == p3.m_y);
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// BOOST_TEST(p2.m_z == p3.m_z);
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// }
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// }
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// --------------------------------------------------------------------
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BOOST_AUTO_TEST_CASE(symm_1)
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{
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cif::cell c(10, 10, 10);
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cif::point p{ 1, 1, 1 };
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cif::point f = fractional(p, c);
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BOOST_TEST(f.m_x == 0.1f, tt::tolerance(0.01));
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BOOST_TEST(f.m_y == 0.1f, tt::tolerance(0.01));
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BOOST_TEST(f.m_z == 0.1f, tt::tolerance(0.01));
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cif::point o = orthogonal(f, c);
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BOOST_TEST(o.m_x == 1.f, tt::tolerance(0.01));
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BOOST_TEST(o.m_y == 1.f, tt::tolerance(0.01));
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BOOST_TEST(o.m_z == 1.f, tt::tolerance(0.01));
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}
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BOOST_AUTO_TEST_CASE(symm_2)
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{
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using namespace cif::literals;
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auto symop = "1_555"_symop;
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BOOST_TEST(symop.is_identity() == true);
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}
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BOOST_AUTO_TEST_CASE(symm_3)
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{
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using namespace cif::literals;
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cif::spacegroup sg(18);
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BOOST_TEST(sg.size() == 4);
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BOOST_TEST(sg.get_name() == "P 21 21 2");
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}
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BOOST_AUTO_TEST_CASE(symm_4, *utf::tolerance(0.1f))
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{
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using namespace cif::literals;
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// based on 2b8h
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auto sg = cif::spacegroup(154); // p 32 2 1
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auto c = cif::cell(107.516, 107.516, 338.487, 90.00, 90.00, 120.00);
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cif::point a{ -8.688, 79.351, 10.439 }; // O6 NAG A 500
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cif::point b{ -35.356, 33.693, -3.236 }; // CG2 THR D 400
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cif::point sb( -6.916, 79.34, 3.236); // 4_565 copy of b
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BOOST_TEST(distance(a, sg(a, c, "1_455"_symop)) == static_cast<float>(c.get_a()));
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BOOST_TEST(distance(a, sg(a, c, "1_545"_symop)) == static_cast<float>(c.get_b()));
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BOOST_TEST(distance(a, sg(a, c, "1_554"_symop)) == static_cast<float>(c.get_c()));
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auto sb2 = sg(b, c, "4_565"_symop);
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BOOST_TEST(sb.m_x == sb2.m_x);
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BOOST_TEST(sb.m_y == sb2.m_y);
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BOOST_TEST(sb.m_z == sb2.m_z);
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BOOST_TEST(distance(a, sb2) == 7.42f);
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}
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// --------------------------------------------------------------------
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BOOST_AUTO_TEST_CASE(symm_4wvp_1, *utf::tolerance(0.1f))
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{
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using namespace cif::literals;
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cif::file f(gTestDir / "4wvp.cif.gz");
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auto &db = f.front();
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cif::mm::structure s(db);
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cif::crystal c(db);
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cif::point p{ -78.722, 98.528, 11.994 };
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auto a = s.get_residue("A", 10, "").get_atom_by_atom_id("O");
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auto sp1 = c.symmetry_copy(a.get_location(), "2_565"_symop);
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BOOST_TEST(sp1.m_x == p.m_x);
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BOOST_TEST(sp1.m_y == p.m_y);
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BOOST_TEST(sp1.m_z == p.m_z);
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const auto &[d, sp2, so] = c.closest_symmetry_copy(p, a.get_location());
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BOOST_TEST(d < 1);
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BOOST_TEST(sp2.m_x == p.m_x);
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BOOST_TEST(sp2.m_y == p.m_y);
|
|
BOOST_TEST(sp2.m_z == p.m_z);
|
|
|
|
}
|
|
|
|
BOOST_AUTO_TEST_CASE(symm_2bi3_1, *utf::tolerance(0.1f))
|
|
{
|
|
cif::file f(gTestDir / "2bi3.cif.gz");
|
|
|
|
auto &db = f.front();
|
|
cif::mm::structure s(db);
|
|
|
|
cif::crystal c(db);
|
|
|
|
auto struct_conn = db["struct_conn"];
|
|
for (const auto &[
|
|
asym1, seqid1, authseqid1, atomid1, symm1,
|
|
asym2, seqid2, authseqid2, atomid2, symm2,
|
|
dist] : struct_conn.find<
|
|
std::string,int,std::string,std::string,std::string,
|
|
std::string,int,std::string,std::string,std::string,
|
|
float>(
|
|
cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
|
|
"ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
|
|
"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry",
|
|
"pdbx_dist_value"
|
|
))
|
|
{
|
|
auto &r1 = s.get_residue(asym1, seqid1, authseqid1);
|
|
auto &r2 = s.get_residue(asym2, seqid2, authseqid2);
|
|
|
|
auto a1 = r1.get_atom_by_atom_id(atomid1);
|
|
auto a2 = r2.get_atom_by_atom_id(atomid2);
|
|
|
|
auto sa1 = c.symmetry_copy(a1.get_location(), cif::sym_op(symm1));
|
|
auto sa2 = c.symmetry_copy(a2.get_location(), cif::sym_op(symm2));
|
|
|
|
BOOST_TEST(cif::distance(sa1, sa2) == dist);
|
|
|
|
auto pa1 = a1.get_location();
|
|
|
|
const auto &[d, p, so] = c.closest_symmetry_copy(pa1, a2.get_location());
|
|
|
|
BOOST_TEST(p.m_x == sa2.m_x);
|
|
BOOST_TEST(p.m_y == sa2.m_y);
|
|
BOOST_TEST(p.m_z == sa2.m_z);
|
|
|
|
BOOST_TEST(d == dist);
|
|
BOOST_TEST(so.string() == symm2);
|
|
}
|
|
}
|
|
|
|
BOOST_AUTO_TEST_CASE(symm_2bi3_1a, *utf::tolerance(0.1f))
|
|
{
|
|
using namespace cif::literals;
|
|
|
|
cif::file f(gTestDir / "2bi3.cif.gz");
|
|
|
|
auto &db = f.front();
|
|
|
|
cif::crystal c(db);
|
|
auto struct_conn = db["struct_conn"];
|
|
auto atom_site = db["atom_site"];
|
|
|
|
for (const auto &[
|
|
asym1, seqid1, authseqid1, atomid1, symm1,
|
|
asym2, seqid2, authseqid2, atomid2, symm2,
|
|
dist] : struct_conn.find<
|
|
std::string,std::optional<int>,std::string,std::string,std::string,
|
|
std::string,std::optional<int>,std::string,std::string,std::string,
|
|
float>(
|
|
cif::key("ptnr1_symmetry") != "1_555" or cif::key("ptnr2_symmetry") != "1_555",
|
|
"ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_auth_seq_id", "ptnr1_label_atom_id", "ptnr1_symmetry",
|
|
"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_auth_seq_id", "ptnr2_label_atom_id", "ptnr2_symmetry",
|
|
"pdbx_dist_value"
|
|
))
|
|
{
|
|
cif::point p1 = atom_site.find1<float,float,float>(
|
|
"label_asym_id"_key == asym1 and "label_seq_id"_key == seqid1 and "auth_seq_id"_key == authseqid1 and "label_atom_id"_key == atomid1,
|
|
"cartn_x", "cartn_y", "cartn_z");
|
|
cif::point p2 = atom_site.find1<float,float,float>(
|
|
"label_asym_id"_key == asym2 and "label_seq_id"_key == seqid2 and "auth_seq_id"_key == authseqid2 and "label_atom_id"_key == atomid2,
|
|
"cartn_x", "cartn_y", "cartn_z");
|
|
|
|
auto sa1 = c.symmetry_copy(p1, cif::sym_op(symm1));
|
|
auto sa2 = c.symmetry_copy(p2, cif::sym_op(symm2));
|
|
|
|
BOOST_TEST(cif::distance(sa1, sa2) == dist);
|
|
|
|
const auto &[d, p, so] = c.closest_symmetry_copy(p1, p2);
|
|
|
|
BOOST_TEST(p.m_x == sa2.m_x);
|
|
BOOST_TEST(p.m_y == sa2.m_y);
|
|
BOOST_TEST(p.m_z == sa2.m_z);
|
|
|
|
BOOST_TEST(d == dist);
|
|
BOOST_TEST(so.string() == symm2);
|
|
}
|
|
}
|
|
|
|
|
|
|
|
BOOST_AUTO_TEST_CASE(symm_3bwh_1, *utf::tolerance(0.1f))
|
|
{
|
|
cif::file f(gTestDir / "3bwh.cif.gz");
|
|
|
|
auto &db = f.front();
|
|
|
|
cif::crystal c(db);
|
|
cif::mm::structure s(db);
|
|
|
|
for (auto a1 : s.atoms())
|
|
{
|
|
for (auto a2 : s.atoms())
|
|
{
|
|
if (a1 == a2)
|
|
continue;
|
|
|
|
const auto&[ d, p, so ] = c.closest_symmetry_copy(a1.get_location(), a2.get_location());
|
|
|
|
BOOST_TEST(d == distance(a1.get_location(), p));
|
|
}
|
|
}
|
|
} |