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libcifpp
Commit 345c4778 by Maarten L. Hekkelman
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start structure-test unit test 

added compare functions for Datablock and Category
parent 0ccb2f88
Showing with 226 additions and 51 deletions
CMakeLists.txt
...@@ -385,6 +385,7 @@ if(CIFPP_BUILD_TESTS) ...@@ -385,6 +385,7 @@ if(CIFPP_BUILD_TESTS)
list(APPEND CIFPP_tests list(APPEND CIFPP_tests
# pdb2cif # pdb2cif
rename-compound rename-compound
structure
unit) unit)
foreach(CIFPP_TEST IN LISTS CIFPP_tests) foreach(CIFPP_TEST IN LISTS CIFPP_tests)
......
include/cif++/Structure.hpp
...@@ -199,15 +199,15 @@ class Residue ...@@ -199,15 +199,15 @@ class Residue
// constructor for waters // constructor for waters
Residue(const Structure &structure, const std::string &compoundID, Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID, const std::string &authSeqID); const std::string &asymID, const std::string &authSeqID);
// constructor for a residue without a sequence number // constructor for a residue without a sequence number
Residue(const Structure &structure, const std::string &compoundID, Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID); const std::string &asymID);
// constructor for a residue with a sequence number // constructor for a residue with a sequence number
Residue(const Structure &structure, const std::string &compoundID, Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID, int seqID, const std::string &authSeqID); const std::string &asymID, int seqID, const std::string &authSeqID);
Residue(const Residue &rhs) = delete; Residue(const Residue &rhs) = delete;
Residue &operator=(const Residue &rhs) = delete; Residue &operator=(const Residue &rhs) = delete;
...@@ -297,7 +297,7 @@ class Monomer : public Residue ...@@ -297,7 +297,7 @@ class Monomer : public Residue
Monomer &operator=(Monomer &&rhs); Monomer &operator=(Monomer &&rhs);
Monomer(const Polymer &polymer, size_t index, int seqID, const std::string &authSeqID, Monomer(const Polymer &polymer, size_t index, int seqID, const std::string &authSeqID,
const std::string &compoundID); const std::string &compoundID);
bool is_first_in_chain() const; bool is_first_in_chain() const;
bool is_last_in_chain() const; bool is_last_in_chain() const;
...@@ -397,6 +397,8 @@ class File : public std::enable_shared_from_this<File> ...@@ -397,6 +397,8 @@ class File : public std::enable_shared_from_this<File>
File(const File &) = delete; File(const File &) = delete;
File &operator=(const File &) = delete; File &operator=(const File &) = delete;
cif::Datablock& createDatablock(const std::string &name);
void load(const std::string &path); void load(const std::string &path);
void save(const std::string &path); void save(const std::string &path);
...@@ -450,7 +452,7 @@ class Structure ...@@ -450,7 +452,7 @@ class Structure
// Atom getAtomByLocation(Point pt, float maxDistance) const; // Atom getAtomByLocation(Point pt, float maxDistance) const;
Atom getAtomByLabel(const std::string &atomID, const std::string &asymID, Atom getAtomByLabel(const std::string &atomID, const std::string &asymID,
const std::string &compID, int seqID, const std::string &altID = ""); const std::string &compID, int seqID, const std::string &altID = "");
/// \brief Get a residue, if \a seqID is zero, the non-polymers are searched /// \brief Get a residue, if \a seqID is zero, the non-polymers are searched
const Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID = 0) const; const Residue &getResidue(const std::string &asymID, const std::string &compID, int seqID = 0) const;
...@@ -458,7 +460,7 @@ class Structure ...@@ -458,7 +460,7 @@ class Structure
// map between auth and label locations // map between auth and label locations
std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID, std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,
const std::string &seqID, const std::string &compID, const std::string &insCode = ""); const std::string &seqID, const std::string &compID, const std::string &insCode = "");
std::tuple<std::string, std::string, std::string, std::string> MapLabelToAuth( std::tuple<std::string, std::string, std::string, std::string> MapLabelToAuth(
const std::string &asymID, int seqID, const std::string &compID); const std::string &asymID, int seqID, const std::string &compID);
...@@ -480,7 +482,20 @@ class Structure ...@@ -480,7 +482,20 @@ class Structure
void swapAtoms(Atom &a1, Atom &a2); // swap the labels for these atoms void swapAtoms(Atom &a1, Atom &a2); // swap the labels for these atoms
void moveAtom(Atom &a, Point p); // move atom to a new location void moveAtom(Atom &a, Point p); // move atom to a new location
void changeResidue(const Residue &res, const std::string &newCompound, void changeResidue(const Residue &res, const std::string &newCompound,
const std::vector<std::tuple<std::string, std::string>> &remappedAtoms); const std::vector<std::tuple<std::string, std::string>> &remappedAtoms);
/// \brief Create a new non-polymer entity, returns new ID
/// \param data The data to use to fill the entity
/// \param mon_id The mon_id for the new nonpoly
/// \param name The name of the nonpoly
/// \return The ID of the created entity
std::string createEntityNonPoly(std::vector<cif::Item> data, const std::string &mon_id);
/// \brief Create a new NonPolymer struct_asym with atoms constructed from \a atom_data, returns asym_id
/// \param entity_id The entity ID of the new nonpoly
/// \param atoms The array of atom data fields
/// \return The newly create asym ID
std::string createNonpoly(const std::string &entity_id, const std::vector<cif::Item> &atoms);
/// To sort the atoms in order of model > asym-id > res-id > atom-id /// To sort the atoms in order of model > asym-id > res-id > atom-id
/// Will asssign new atom_id's to all atoms. Be carefull /// Will asssign new atom_id's to all atoms. Be carefull
......
test/structure-test.cpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2021 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_MODULE Structure_Test
#include <boost/test/included/unit_test.hpp>
#include <stdexcept>
#include "cif++/Cif++.hpp"
#include "cif++/Structure.hpp"
// --------------------------------------------------------------------
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);
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_nonpoly_1)
{
cif::VERBOSE = 1;
// do this now, avoids the need for installing
cif::addFileResource("mmcif_pdbx_v50.dic", "../rsrc/mmcif_pdbx_v50.dic");
auto expected = R"(
data_TEST
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
1 non-polymer syn 'PROTOPORPHYRIN IX CONTAINING FE' 616.487
)"_cf;
expected.loadDictionary("mmcif_pdbx_v50.dic");
mmcif::File file;
file.file().loadDictionary("mmcif_pdbx_v50.dic");
file.createDatablock("TEST"); // create a datablock
mmcif::Structure structure(file);
structure.createEntityNonPoly({
{ "src_method", "syn" },
{ "pdbx_description", "PROTOPORPHYRIN IX CONTAINING FE" },
{ "formula_weight", 616.487 }
}, "HEM" );
BOOST_TEST(expected.firstDatablock() == structure.getFile().data());
std::cout << expected.firstDatablock() << std::endl
<< std::endl
<< structure.getFile().data() << std::endl;
// // using namespace mmcif;
// auto f = R"(data_TEST
// #
// loop_
// _test.id
// _test.name
// 1 aap
// 2 noot
// 3 mies
// )"_cf;
// auto& db = f.firstDatablock();
// BOOST_CHECK(db.getName() == "TEST");
// auto& test = db["test"];
// BOOST_CHECK(test.size() == 3);
// // wrong! the next lines will crash. And that's OK, don't do that
// // for (auto r: test)
// // test.erase(r);
// // BOOST_CHECK(test.empty());
// // test.purge();
// auto n = test.erase(cif::Key("id") == 1, [](const cif::Row& r) {
// BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
// BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap");
// });
// BOOST_CHECK_EQUAL(n, 1);
}
test/unit-test.cpp
...@@ -1664,4 +1664,4 @@ BOOST_AUTO_TEST_CASE(bondmap_2) ...@@ -1664,4 +1664,4 @@ BOOST_AUTO_TEST_CASE(bondmap_2)
mmcif::CompoundFactory::instance().pushDictionary("./UN_.cif"); mmcif::CompoundFactory::instance().pushDictionary("./UN_.cif");
BOOST_CHECK(mmcif::BondMap::atomIDsForCompound("UN_").empty() == false); BOOST_CHECK(mmcif::BondMap::atomIDsForCompound("UN_").empty() == false);
} }
\ No newline at end of file
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