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libcifpp
Commit 5c366ad9 by Maarten L. Hekkelman
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- remove three_letter_code for CCP4 dictionaries 

- fix test for equality of compound ID's, they are case insensitive you know
parent 836aed6e
Showing with 203 additions and 7 deletions
src/compound.cpp
......@@ -313,7 +313,7 @@ class compound_factory_impl : public std::enable_shared_from_this<compound_facto
{
for (auto cmp : impl->m_compounds)
{
if (cmp->id() == id)
if (iequals(cmp->id(), id))
{
result = cmp;
break;
......@@ -582,12 +582,12 @@ CCP4_compound_factory_impl::CCP4_compound_factory_impl(const fs::path &clibd_mon
auto &chemComps = m_file["comp_list"]["chem_comp"];
for (const auto &[group, threeLetterCode] : chemComps.rows<std::string, std::string>("group", "three_letter_code"))
for (const auto &[group, comp_id] : chemComps.rows<std::string, std::string>("group", "id"))
{
if (std::regex_match(group, peptideRx))
m_known_peptides.insert(threeLetterCode);
m_known_peptides.insert(comp_id);
else if (cif::iequals(group, "DNA") or cif::iequals(group, "RNA"))
m_known_bases.insert(threeLetterCode);
m_known_bases.insert(comp_id);
}
}
......@@ -597,7 +597,7 @@ compound *CCP4_compound_factory_impl::create(const std::string &id)
auto &cat = m_file["comp_list"]["chem_comp"];
auto rs = cat.find(cif::key("three_letter_code") == id);
auto rs = cat.find(cif::key("id") == id);
if (rs.size() == 1)
{
......
test/REA_v2.cif 0 → 100644
data_REA_v2
#
_chem_comp.id REA_v2
_chem_comp.name "RETINOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H28 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2016-10-18
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces 3KV
_chem_comp.formula_weight 300.435
_chem_comp.one_letter_code ?
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CBS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
REA_v2 C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 REA_v2 1
REA_v2 C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 REA_v2 2
REA_v2 C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 REA_v2 3
REA_v2 C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 REA_v2 4
REA_v2 C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 REA_v2 5
REA_v2 C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 REA_v2 6
REA_v2 C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 REA_v2 7
REA_v2 C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 REA_v2 8
REA_v2 C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 REA_v2 9
REA_v2 C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 REA_v2 10
REA_v2 C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 REA_v2 11
REA_v2 C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 REA_v2 12
REA_v2 C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 REA_v2 13
REA_v2 C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 REA_v2 14
REA_v2 C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 REA_v2 15
REA_v2 C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 REA_v2 16
REA_v2 C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 REA_v2 17
REA_v2 C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 REA_v2 18
REA_v2 C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 REA_v2 19
REA_v2 C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 REA_v2 20
REA_v2 O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 REA_v2 21
REA_v2 O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 REA_v2 22
REA_v2 H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 REA_v2 23
REA_v2 H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 REA_v2 24
REA_v2 H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 REA_v2 25
REA_v2 H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 REA_v2 26
REA_v2 H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 REA_v2 27
REA_v2 H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 REA_v2 28
REA_v2 H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 REA_v2 29
REA_v2 H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 REA_v2 30
REA_v2 H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 REA_v2 31
REA_v2 H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 REA_v2 32
REA_v2 H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 REA_v2 33
REA_v2 H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 REA_v2 34
REA_v2 H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 REA_v2 35
REA_v2 H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 REA_v2 36
REA_v2 H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 REA_v2 37
REA_v2 H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 REA_v2 38
REA_v2 H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 REA_v2 39
REA_v2 H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 REA_v2 40
REA_v2 H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 REA_v2 41
REA_v2 H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 REA_v2 42
REA_v2 H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 REA_v2 43
REA_v2 H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 REA_v2 44
REA_v2 H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 REA_v2 45
REA_v2 H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 REA_v2 46
REA_v2 H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 REA_v2 47
REA_v2 H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 REA_v2 48
REA_v2 H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 REA_v2 49
REA_v2 HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 REA_v2 50
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
REA_v2 C1 C2 SING N N 1
REA_v2 C1 C6 SING N N 2
REA_v2 C1 C16 SING N N 3
REA_v2 C1 C17 SING N N 4
REA_v2 C2 C3 SING N N 5
REA_v2 C2 H21 SING N N 6
REA_v2 C2 H22 SING N N 7
REA_v2 C3 C4 SING N N 8
REA_v2 C3 H31 SING N N 9
REA_v2 C3 H32 SING N N 10
REA_v2 C4 C5 SING N N 11
REA_v2 C4 H41 SING N N 12
REA_v2 C4 H42 SING N N 13
REA_v2 C5 C6 DOUB N N 14
REA_v2 C5 C18 SING N N 15
REA_v2 C6 C7 SING N N 16
REA_v2 C7 C8 DOUB N E 17
REA_v2 C7 H7 SING N N 18
REA_v2 C8 C9 SING N N 19
REA_v2 C8 H8 SING N N 20
REA_v2 C9 C10 DOUB N E 21
REA_v2 C9 C19 SING N N 22
REA_v2 C10 C11 SING N N 23
REA_v2 C10 H10 SING N N 24
REA_v2 C11 C12 DOUB N E 25
REA_v2 C11 H11 SING N N 26
REA_v2 C12 C13 SING N N 27
REA_v2 C12 H12 SING N N 28
REA_v2 C13 C14 DOUB N E 29
REA_v2 C13 C20 SING N N 30
REA_v2 C14 C15 SING N N 31
REA_v2 C14 H14 SING N N 32
REA_v2 C15 O1 DOUB N N 33
REA_v2 C15 O2 SING N N 34
REA_v2 C16 H161 SING N N 35
REA_v2 C16 H162 SING N N 36
REA_v2 C16 H163 SING N N 37
REA_v2 C17 H171 SING N N 38
REA_v2 C17 H172 SING N N 39
REA_v2 C17 H173 SING N N 40
REA_v2 C18 H181 SING N N 41
REA_v2 C18 H182 SING N N 42
REA_v2 C18 H183 SING N N 43
REA_v2 C19 H191 SING N N 44
REA_v2 C19 H192 SING N N 45
REA_v2 C19 H193 SING N N 46
REA_v2 C20 H201 SING N N 47
REA_v2 C20 H202 SING N N 48
REA_v2 C20 H203 SING N N 49
REA_v2 O2 HO2 SING N N 50
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
REA_v2 SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
REA_v2 InChI InChI 1.03 "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+"
REA_v2 InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
REA_v2 SMILES_CANONICAL CACTVS 3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"
REA_v2 SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
REA_v2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C(=O)O)/C)/C"
REA_v2 SMILES "OpenEye OEToolkits" 1.7.6 "CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
REA_v2 "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
REA_v2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
REA_v2 "CREA_v2te component" 1999-07-08 RCSB
REA_v2 "Modify descriptor" 2011-06-04 RCSB
REA_v2 "Other modification" 2016-10-18 RCSB
#
test/unit-v2-test.cpp
......@@ -3150,4 +3150,14 @@ _test.value
v = test.find1<std::optional<float>>("id"_key == 4, "value");
BOOST_CHECK(v.has_value() == false);
}
\ No newline at end of file
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(compound_test_1)
{
cif::compound_factory::instance().push_dictionary(gTestDir / "REA_v2.cif");
auto compound = cif::compound_factory::instance().create("REA_v2");
BOOST_ASSERT(compound != nullptr);
BOOST_CHECK(compound->id() == "REA_v2");
}
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