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1d430e8c47b5573809f4bc07272ecfdf49a2d4b1
libcifpp/test/model-test.cpp
Maarten L. Hekkelman 56aab89176 Refactored validator_factory interface
2026-01-05 08:30:30 +01:00

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/*-
* 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.
*/
#include "test-main.hpp"
#include <stdexcept>
#include <cif++.hpp>
// --------------------------------------------------------------------
cif::file operator""_cf(const char *text, std::size_t length)
{
struct membuf : public std::streambuf
{
membuf(char *text, std::size_t length)
{
this->setg(text, text, text + length);
}
} buffer(const_cast<char *>(text), length);
std::istream is(&buffer);
return cif::file(is);
}
// --------------------------------------------------------------------
TEST_CASE("create_nonpoly_1")
{
cif::VERBOSE = 1;
cif::file file;
auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
dbi->load_dictionary("mmcif_pdbx.dic");
cif::mm::structure structure(file);
std::string entity_id = structure.create_non_poly_entity("HEM");
auto atoms = R"(
data_HEM
loop_
_atom_site.id
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
1 HETATM C CHA . ? -5.248 39.769 -0.250 1.00 7.67 ?
2 HETATM C CHB . ? -3.774 36.790 3.280 1.00 7.05 ?
3 HETATM C CHC . ? -2.879 33.328 0.013 1.00 7.69 ?
4 HETATM C CHD . ? -4.342 36.262 -3.536 1.00 8.00 ?
# that's enough to test with
)"_cf;
atoms.front().load_dictionary("mmcif_pdbx.dic");
auto &hem_data = atoms["HEM"];
auto &atom_site = hem_data["atom_site"];
auto hem_atoms = atom_site.rows();
std::vector<cif::mm::atom> atom_data;
for (auto hem_atom : hem_atoms)
atom_data.emplace_back(hem_data, hem_atom);
structure.create_non_poly(entity_id, atom_data);
auto expected = R"(
data_TEST
#
_pdbx_nonpoly_scheme.asym_id A
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.entity_id 1
_pdbx_nonpoly_scheme.mon_id HEM
_pdbx_nonpoly_scheme.pdb_seq_num 1
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id HEM
_pdbx_nonpoly_scheme.auth_mon_id HEM
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
loop_
_atom_site.id
_atom_site.auth_asym_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_atom_site.group_PDB
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
1 A ? A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 1.00 7.67 ? 1 HEM CHA 1
2 A ? A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 1.00 7.05 ? 1 HEM CHB 1
3 A ? A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 1.00 7.69 ? 1 HEM CHC 1
4 A ? A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 1.00 8.00 ? 1 HEM CHD 1
#
_chem_comp.id HEM
_chem_comp.type NON-POLYMER
_chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE'
_chem_comp.formula 'C34 H32 Fe N4 O4'
_chem_comp.formula_weight 616.487000
#
_pdbx_entity_nonpoly.entity_id 1
_pdbx_entity_nonpoly.name 'PROTOPORPHYRIN IX CONTAINING FE'
_pdbx_entity_nonpoly.comp_id HEM
#
_entity.id 1
_entity.type non-polymer
_entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE'
_entity.formula_weight 616.487000
#
_struct_asym.id A
_struct_asym.entity_id 1
_struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.details ?
#
_atom_type.symbol C
)"_cf;
expected.front().load_dictionary("mmcif_pdbx.dic");
if (not(expected.front() == structure.get_datablock()))
{
std::cerr << expected.front() << '\n'
<< '\n'
<< structure.get_datablock() << '\n';
REQUIRE(false);
}
}
// --------------------------------------------------------------------
TEST_CASE("create_nonpoly_2")
{
cif::VERBOSE = 1;
cif::file file;
auto &&[dbi, ignore] = file.emplace("TEST"); // create a datablock
dbi->load_dictionary("mmcif_pdbx.dic");
cif::mm::structure structure(file);
cif::file lig(gTestDir / "HEM.cif");
auto &chem_comp_atom = lig["HEM"]["chem_comp_atom"];
std::vector<cif::row_initializer> atoms;
for (const auto &[type_symbol, label_atom_id, Cartn_x, Cartn_y, Cartn_z] :
chem_comp_atom.rows<std::string, std::string, float, float, float>(
"type_symbol", "atom_id", "model_Cartn_x", "model_Cartn_y", "model_Cartn_z"))
{
atoms.emplace_back(cif::row_initializer{
{ "type_symbol", type_symbol },
{ "label_atom_id", label_atom_id },
{ "auth_atom_id", label_atom_id },
{ "Cartn_x", Cartn_x },
{ "Cartn_y", Cartn_y },
{ "Cartn_z", Cartn_z } });
if (atoms.size() == 4)
break;
}
std::string entity_id = structure.create_non_poly_entity("HEM");
structure.create_non_poly(entity_id, atoms);
auto expected = R"(
data_TEST
#
_pdbx_nonpoly_scheme.asym_id A
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.entity_id 1
_pdbx_nonpoly_scheme.mon_id HEM
_pdbx_nonpoly_scheme.pdb_seq_num 1
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id HEM
_pdbx_nonpoly_scheme.auth_mon_id HEM
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
loop_
_atom_site.id
_atom_site.auth_asym_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_atom_site.group_PDB
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
1 A ? A CHA HEM 1 . C HETATM ? 2.748 -19.531 39.896 1.00 ? 1 HEM CHA 1
2 A ? A CHB HEM 1 . C HETATM ? 3.258 -17.744 35.477 1.00 ? 1 HEM CHB 1
3 A ? A CHC HEM 1 . C HETATM ? 1.703 -21.9 33.637 1.00 ? 1 HEM CHC 1
4 A ? A CHD HEM 1 . C HETATM ? 1.149 -23.677 38.059 1.00 ? 1 HEM CHD 1
#
_chem_comp.id HEM
_chem_comp.type NON-POLYMER
_chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE'
_chem_comp.formula 'C34 H32 Fe N4 O4'
_chem_comp.formula_weight 616.487000
#
_pdbx_entity_nonpoly.entity_id 1
_pdbx_entity_nonpoly.name 'PROTOPORPHYRIN IX CONTAINING FE'
_pdbx_entity_nonpoly.comp_id HEM
#
_entity.id 1
_entity.type non-polymer
_entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE'
_entity.formula_weight 616.487000
#
_struct_asym.id A
_struct_asym.entity_id 1
_struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.details ?
#
_atom_type.symbol C
)"_cf;
expected.front().load_dictionary("mmcif_pdbx.dic");
REQUIRE(expected.front() == structure.get_datablock());
if (not(expected.front() == structure.get_datablock()))
{
// REQUIRE(false);
std::cout << expected.front() << '\n'
<< '\n'
<< structure.get_datablock() << '\n';
expected.save("/tmp/a");
file.save("/tmp/b");
}
}
// --------------------------------------------------------------------
TEST_CASE("test_atom_id")
{
auto data = R"(
data_TEST
#
_pdbx_nonpoly_scheme.asym_id A
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.entity_id 1
_pdbx_nonpoly_scheme.mon_id HEM
_pdbx_nonpoly_scheme.pdb_seq_num 1
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id HEM
_pdbx_nonpoly_scheme.auth_mon_id HEM
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
loop_
_atom_site.id
_atom_site.auth_asym_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_atom_site.group_PDB
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
1 A ? A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 1.00 7.67 ? 1 HEM CHA 1
3 A ? A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 1.00 7.05 ? 1 HEM CHB 1
2 A ? A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 1.00 7.69 ? 1 HEM CHC 1
4 A ? A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 1.00 8.00 ? 1 HEM CHD 1
#
_chem_comp.id HEM
_chem_comp.type NON-POLYMER
_chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE'
_chem_comp.formula 'C34 H32 Fe N4 O4'
_chem_comp.formula_weight 616.487000
#
_pdbx_entity_nonpoly.entity_id 1
_pdbx_entity_nonpoly.name 'PROTOPORPHYRIN IX CONTAINING FE'
_pdbx_entity_nonpoly.comp_id HEM
#
_entity.id 1
_entity.type non-polymer
_entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE'
_entity.formula_weight 616.487000
#
_struct_asym.id A
_struct_asym.entity_id 1
_struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.details ?
#
)"_cf;
data.front().load_dictionary("mmcif_pdbx.dic");
cif::mm::structure s(data);
REQUIRE(s.get_atom_by_id("1").get_label_atom_id() == "CHA");
REQUIRE(s.get_atom_by_id("2").get_label_atom_id() == "CHC");
REQUIRE(s.get_atom_by_id("3").get_label_atom_id() == "CHB");
REQUIRE(s.get_atom_by_id("4").get_label_atom_id() == "CHD");
}
// --------------------------------------------------------------------
TEST_CASE("atom_numbers_1")
{
const std::filesystem::path test1(gTestDir / ".." / "examples" / "1cbs.cif.gz");
cif::file file(test1.string());
cif::mm::structure structure(file);
auto &db = file.front();
auto &atoms = structure.atoms();
auto ai = atoms.begin();
for (const auto &[id, label_asym_id, label_seq_id, label_atom_id, auth_seq_id, label_comp_id] :
db["atom_site"].rows<std::string, std::string, int, std::string, std::string, std::string>("id", "label_asym_id", "label_seq_id", "label_atom_id", "auth_seq_id", "label_comp_id"))
{
auto atom = structure.get_atom_by_id(id);
REQUIRE(atom.get_label_asym_id() == label_asym_id);
REQUIRE(atom.get_label_seq_id() == label_seq_id);
REQUIRE(atom.get_label_atom_id() == label_atom_id);
REQUIRE(atom.get_auth_seq_id() == auth_seq_id);
REQUIRE(atom.get_label_comp_id() == label_comp_id);
REQUIRE(ai != atoms.end());
REQUIRE(ai->id() == id);
++ai;
}
REQUIRE(ai == atoms.end());
}
// --------------------------------------------------------------------
TEST_CASE("test_load_2")
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
cif::file file(example.string());
auto &db = file.front();
cif::mm::structure s(file);
REQUIRE(s.polymers().size() == 1UL);
auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
for (auto &poly : s.polymers())
{
REQUIRE(poly.size() == pdbx_poly_seq_scheme.find("asym_id"_key == poly.get_asym_id()).size());
}
}
TEST_CASE("remove_residue_1")
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
cif::file file(example.string());
cif::mm::structure s(file);
s.remove_residue(s.get_residue("B"));
REQUIRE_NOTHROW(s.validate_atoms());
}
// --------------------------------------------------------------------
// Tests for structure_open_options
TEST_CASE("options_1")
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / ".." / "examples" / "1cbs.cif.gz");
cif::file file(example.string());
auto &cf = cif::compound_factory::instance();
SECTION("skip_water")
{
cif::mm::structure s(file, 1, { .skip_water = true });
REQUIRE_NOTHROW(s.validate_atoms());
for (auto a : s.atoms())
CHECK_FALSE(a.is_water());
}
SECTION("skip_hetatom")
{
cif::mm::structure s(file, 1, { .skip_hetatom = true });
REQUIRE_NOTHROW(s.validate_atoms());
for (auto a : s.atoms())
CHECK((a.is_water() or cf.is_peptide(a.get_label_comp_id()) or cf.is_base(a.get_label_comp_id())));
}
SECTION("selected_asyms")
{
cif::mm::structure s(file, 1, { .asyms = { "A" } });
REQUIRE_NOTHROW(s.validate_atoms());
for (auto a : s.atoms())
CHECK(a.get_label_asym_id() == "A");
}
SECTION("min-b-factor")
{
cif::mm::structure s(file, 1, { .min_b_factor = 20.f });
REQUIRE_NOTHROW(s.validate_atoms());
for (auto a : s.atoms())
CHECK(a.get_property_float("B_iso_or_equiv") >= 20.f);
}
SECTION("max-b-factor")
{
cif::mm::structure s(file, 1, { .max_b_factor = 20.f });
REQUIRE_NOTHROW(s.validate_atoms());
for (auto a : s.atoms())
CHECK(a.get_property_float("B_iso_or_equiv") <= 20.f);
}
}
TEST_CASE("options_2")
{
auto data = R"(
data_TEST
#
_pdbx_nonpoly_scheme.asym_id A
_pdbx_nonpoly_scheme.ndb_seq_num 1
_pdbx_nonpoly_scheme.entity_id 1
_pdbx_nonpoly_scheme.mon_id HEM
_pdbx_nonpoly_scheme.pdb_seq_num 1
_pdbx_nonpoly_scheme.auth_seq_num 1
_pdbx_nonpoly_scheme.pdb_mon_id HEM
_pdbx_nonpoly_scheme.auth_mon_id HEM
_pdbx_nonpoly_scheme.pdb_strand_id A
_pdbx_nonpoly_scheme.pdb_ins_code .
#
loop_
_atom_site.id
_atom_site.auth_asym_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.type_symbol
_atom_site.group_PDB
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
1 A A A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.75 7.67 ? 1 HEM CHA 1
3 A A A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 0.75 7.05 ? 1 HEM CHB 1
2 A A A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 0.75 7.69 ? 1 HEM CHC 1
4 A A A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.75 8.00 ? 1 HEM CHD 1
5 A B A CHA HEM 1 . C HETATM ? -5.248 39.769 -0.250 0.25 7.67 ? 1 HEM CHA 1
6 A B A CHB HEM 1 . C HETATM ? -3.774 36.790 3.280 0.25 7.05 ? 1 HEM CHB 1
7 A B A CHC HEM 1 . C HETATM ? -2.879 33.328 0.013 0.25 7.69 ? 1 HEM CHC 1
8 A B A CHD HEM 1 . C HETATM ? -4.342 36.262 -3.536 0.25 8.00 ? 1 HEM CHD 1
#
_chem_comp.id HEM
_chem_comp.type NON-POLYMER
_chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE'
_chem_comp.formula 'C34 H32 Fe N4 O4'
_chem_comp.formula_weight 616.487000
#
_pdbx_entity_nonpoly.entity_id 1
_pdbx_entity_nonpoly.name 'PROTOPORPHYRIN IX CONTAINING FE'
_pdbx_entity_nonpoly.comp_id HEM
#
_entity.id 1
_entity.type non-polymer
_entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE'
_entity.formula_weight 616.487000
#
_struct_asym.id A
_struct_asym.entity_id 1
_struct_asym.pdbx_blank_PDB_chainid_flag N
_struct_asym.pdbx_modified N
_struct_asym.details ?
#
)"_cf;
data.front().load_dictionary("mmcif_pdbx.dic");
SECTION("max")
{
cif::mm::structure s(data, 1, {
.occupancy_mode = cif::mm::occupancy_policy::MAX
});
REQUIRE(s.atoms().size() == 4);
CHECK(s.atoms().front().get_label_alt_id() == "A");
}
SECTION("min")
{
cif::mm::structure s(data, 1, {
.occupancy_mode = cif::mm::occupancy_policy::MIN
});
REQUIRE(s.atoms().size() == 4);
CHECK(s.atoms().front().get_label_alt_id() == "B");
}
SECTION("unoccupied")
{
cif::mm::structure s(data, 1, {
.occupancy_mode = cif::mm::occupancy_policy::UNOCCUPIED
});
CHECK(s.atoms().empty());
}
}
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