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libcifpp
Commit 906f6ac1 by Maarten L. Hekkelman
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Fix all tests to work with embedded data, no CCD

parent 8d96e513
Showing with 261 additions and 3 deletions
test/HEM.cif 0 → 100644
data_HEM
#
_chem_comp.id HEM
_chem_comp.name "PROTOPORPHYRIN IX CONTAINING FE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C34 H32 Fe N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms HEME
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag Y
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces MHM
_chem_comp.formula_weight 616.487
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HEM
_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 3IA3
_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
HEM CHA CHA C 0 1 N N N 2.748 -19.531 39.896 -2.161 -0.125 0.490 CHA HEM 1
HEM CHB CHB C 0 1 N N N 3.258 -17.744 35.477 1.458 -3.419 0.306 CHB HEM 2
HEM CHC CHC C 0 1 N N N 1.703 -21.900 33.637 4.701 0.169 -0.069 CHC HEM 3
HEM CHD CHD C 0 1 N N N 1.149 -23.677 38.059 1.075 3.460 0.018 CHD HEM 4
HEM C1A C1A C 0 1 Y N N 3.031 -18.673 38.872 -1.436 -1.305 0.380 C1A HEM 5
HEM C2A C2A C 0 1 Y N N 3.578 -17.325 39.013 -2.015 -2.587 0.320 C2A HEM 6
HEM C3A C3A C 0 1 Y N N 3.705 -16.820 37.785 -1.009 -3.500 0.270 C3A HEM 7
HEM C4A C4A C 0 1 Y N N 3.256 -17.863 36.862 0.216 -2.803 0.298 C4A HEM 8
HEM CMA CMA C 0 1 N N N 4.227 -15.469 37.393 -1.175 -4.996 0.197 CMA HEM 9
HEM CAA CAA C 0 1 N N N 3.945 -16.670 40.296 -3.490 -2.893 0.314 CAA HEM 10
HEM CBA CBA C 0 1 N N N 5.391 -17.138 40.581 -3.998 -2.926 -1.129 CBA HEM 11
HEM CGA CGA C 0 1 N N N 6.095 -16.663 41.825 -5.473 -3.232 -1.136 CGA HEM 12
HEM O1A O1A O 0 1 N N N 7.098 -15.928 41.683 -6.059 -3.405 -0.094 O1A HEM 13
HEM O2A O2A O 0 1 N N N 5.657 -17.040 42.940 -6.137 -3.311 -2.300 O2A HEM 14
HEM C1B C1B C 0 1 N N N 2.888 -18.698 34.579 2.664 -2.707 0.308 C1B HEM 15
HEM C2B C2B C 0 1 N N N 2.933 -18.535 33.146 3.937 -3.328 0.418 C2B HEM 16
HEM C3B C3B C 0 1 N N N 2.499 -19.716 32.632 4.874 -2.341 0.314 C3B HEM 17
HEM C4B C4B C 0 1 N N N 2.187 -20.580 33.743 4.117 -1.079 0.139 C4B HEM 18
HEM CMB CMB C 0 1 N N N 3.391 -17.290 32.422 4.203 -4.798 0.613 CMB HEM 19
HEM CAB CAB C 0 1 N N N 2.345 -20.140 31.217 6.339 -2.497 0.365 CAB HEM 20
HEM CBB CBB C 0 1 N N N 1.755 -19.492 30.233 6.935 -3.419 -0.385 CBB HEM 21
HEM C1C C1C C 0 1 Y N N 1.395 -22.786 34.659 3.964 1.345 -0.174 C1C HEM 22
HEM C2C C2C C 0 1 Y N N 0.854 -24.130 34.500 4.531 2.601 -0.445 C2C HEM 23
HEM C3C C3C C 0 1 Y N N 0.689 -24.626 35.757 3.510 3.536 -0.437 C3C HEM 24
HEM C4C C4C C 0 1 Y N N 1.139 -23.583 36.674 2.304 2.846 -0.139 C4C HEM 25
HEM CMC CMC C 0 1 N N N 0.550 -24.782 33.175 5.991 2.880 -0.697 CMC HEM 26
HEM CAC CAC C 0 1 N N N 0.164 -25.943 36.196 3.649 4.981 -0.692 CAC HEM 27
HEM CBC CBC C 0 1 N N N 0.498 -27.158 35.750 4.201 5.407 -1.823 CBC HEM 28
HEM C1D C1D C 0 1 N N N 1.550 -22.718 38.980 -0.102 2.753 0.298 C1D HEM 29
HEM C2D C2D C 0 1 N N N 1.513 -22.879 40.415 -1.382 3.388 0.641 C2D HEM 30
HEM C3D C3D C 0 1 N N N 1.951 -21.691 40.929 -2.283 2.389 0.774 C3D HEM 31
HEM C4D C4D C 0 1 N N N 2.277 -20.826 39.811 -1.561 1.137 0.511 C4D HEM 32
HEM CMD CMD C 0 1 N N N 1.055 -24.094 41.156 -1.639 4.863 0.811 CMD HEM 33
HEM CAD CAD C 0 1 N N N 2.048 -21.326 42.352 -3.741 2.532 1.123 CAD HEM 34
HEM CBD CBD C 0 1 N N N 0.741 -20.498 42.530 -4.573 2.563 -0.160 CBD HEM 35
HEM CGD CGD C 0 1 N N N 0.578 -19.987 43.892 -6.032 2.706 0.189 CGD HEM 36
HEM O1D O1D O 0 1 N N N 1.387 -19.103 44.303 -6.372 2.776 1.347 O1D HEM 37
HEM O2D O2D O 0 1 N N N -0.401 -20.468 44.537 -6.954 2.755 -0.785 O2D HEM 38
HEM NA NA N 0 1 Y N N 2.863 -18.969 37.554 -0.068 -1.456 0.321 NA HEM 39
HEM NB NB N 0 1 N N N 2.439 -19.944 34.911 2.820 -1.386 0.207 NB HEM 40
HEM NC NC N 0 1 Y N N 1.537 -22.509 35.976 2.604 1.506 -0.033 NC HEM 41
HEM ND ND N 0 1 N N N 2.008 -21.465 38.663 -0.276 1.431 0.298 ND HEM 42
HEM FE FE FE 0 0 N N N 2.196 -20.749 36.814 1.010 0.157 -0.060 FE HEM 43
HEM HHB HHB H 0 1 N N N 3.587 -16.798 35.072 1.498 -4.508 0.309 HHB HEM 44
HEM HHC HHC H 0 1 N N N 1.553 -22.268 32.633 5.786 0.229 -0.153 HHC HEM 45
HEM HHD HHD H 0 1 N N N 0.802 -24.613 38.472 1.018 4.543 -0.083 HHD HEM 46
HEM HMA HMA H 0 1 N N N 5.316 -15.524 37.249 -1.220 -5.306 -0.847 HMA HEM 47
HEM HMAA HMAA H 0 0 N N N 3.749 -15.149 36.455 -0.328 -5.480 0.683 HMAA HEM 48
HEM HMAB HMAB H 0 0 N N N 3.998 -14.743 38.187 -2.097 -5.285 0.702 HMAB HEM 49
HEM HAA HAA H 0 1 N N N 3.905 -15.575 40.197 -3.662 -3.862 0.782 HAA HEM 50
HEM HAAA HAAA H 0 0 N N N 3.268 -16.991 41.102 -4.024 -2.121 0.869 HAAA HEM 51
HEM HBA HBA H 0 1 N N N 5.368 -18.237 40.627 -3.825 -1.956 -1.597 HBA HEM 52
HEM HBAA HBAA H 0 0 N N N 6.004 -16.819 39.725 -3.464 -3.697 -1.684 HBAA HEM 53
HEM HMB HMB H 0 1 N N N 3.319 -17.449 31.336 3.256 -5.336 0.660 HMB HEM 54
HEM HMBA HMBA H 0 0 N N N 2.753 -16.442 32.711 4.794 -5.175 -0.222 HMBA HEM 55
HEM HMBB HMBB H 0 0 N N N 4.435 -17.072 32.692 4.752 -4.948 1.543 HMBB HEM 56
HEM HAB HAB H 0 1 N N N 2.770 -21.100 30.963 6.927 -1.863 1.011 HAB HEM 57
HEM HBB HBB H 0 1 N N N 1.719 -19.927 29.245 7.994 -3.600 -0.277 HBB HEM 58
HEM HBBA HBBA H 0 0 N N N 1.308 -18.526 30.414 6.360 -3.987 -1.102 HBBA HEM 59
HEM HMC HMC H 0 1 N N N 0.153 -25.793 33.346 6.554 1.949 -0.639 HMC HEM 60
HEM HMCA HMCA H 0 0 N N N -0.196 -24.182 32.634 6.110 3.316 -1.689 HMCA HEM 61
HEM HMCB HMCB H 0 0 N N N 1.472 -24.846 32.578 6.362 3.578 0.053 HMCB HEM 62
HEM HAC HAC H 0 1 N N N -0.583 -25.916 36.975 3.303 5.694 0.042 HAC HEM 63
HEM HBC HBC H 0 1 N N N 0.027 -28.035 36.169 4.614 4.696 -2.523 HBC HEM 64
HEM HBCA HBCA H 0 0 N N N 1.239 -27.263 34.971 4.235 6.464 -2.043 HBCA HEM 65
HEM HMD HMD H 0 1 N N N 1.142 -23.919 42.238 -0.715 5.415 0.639 HMD HEM 66
HEM HMDA HMDA H 0 0 N N N 0.006 -24.304 40.902 -2.394 5.185 0.094 HMDA HEM 67
HEM HMDB HMDB H 0 0 N N N 1.680 -24.954 40.872 -1.994 5.055 1.824 HMDB HEM 68
HEM HAD HAD H 0 1 N N N 2.055 -22.216 42.999 -4.052 1.687 1.738 HAD HEM 69
HEM HADA HADA H 0 0 N N N 2.943 -20.719 42.554 -3.893 3.459 1.677 HADA HEM 70
HEM HBD HBD H 0 1 N N N 0.767 -19.646 41.835 -4.262 3.408 -0.775 HBD HEM 71
HEM HBDA HBDA H 0 0 N N N -0.119 -21.141 42.290 -4.421 1.636 -0.714 HBDA HEM 72
HEM H2A H2A H 0 1 N N N 6.201 -16.682 43.632 -7.082 -3.510 -2.254 H2A HEM 73
HEM H2D H2D H 0 1 N N N -0.445 -20.063 45.395 -7.877 2.847 -0.512 H2D HEM 74
HEM HHA HHA H 0 1 N N N 2.913 -19.150 40.893 -3.246 -0.188 0.567 HHA HEM 75
# #
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
HEM CHA C1A SING N N 1
HEM CHA C4D DOUB N N 2
HEM CHA HHA SING N N 3
HEM CHB C4A SING N N 4
HEM CHB C1B DOUB N N 5
HEM CHB HHB SING N N 6
HEM CHC C4B SING N N 7
HEM CHC C1C DOUB N N 8
HEM CHC HHC SING N N 9
HEM CHD C4C DOUB N N 10
HEM CHD C1D SING N N 11
HEM CHD HHD SING N N 12
HEM C1A C2A DOUB Y N 13
HEM C1A NA SING Y N 14
HEM C2A C3A SING Y N 15
HEM C2A CAA SING N N 16
HEM C3A C4A DOUB Y N 17
HEM C3A CMA SING N N 18
HEM C4A NA SING Y N 19
HEM CMA HMA SING N N 20
HEM CMA HMAA SING N N 21
HEM CMA HMAB SING N N 22
HEM CAA CBA SING N N 23
HEM CAA HAA SING N N 24
HEM CAA HAAA SING N N 25
HEM CBA CGA SING N N 26
HEM CBA HBA SING N N 27
HEM CBA HBAA SING N N 28
HEM CGA O1A DOUB N N 29
HEM CGA O2A SING N N 30
HEM C1B C2B SING N N 31
HEM C1B NB SING N N 32
HEM C2B C3B DOUB N N 33
HEM C2B CMB SING N N 34
HEM C3B C4B SING N N 35
HEM C3B CAB SING N N 36
HEM C4B NB DOUB N N 37
HEM CMB HMB SING N N 38
HEM CMB HMBA SING N N 39
HEM CMB HMBB SING N N 40
HEM CAB CBB DOUB N N 41
HEM CAB HAB SING N N 42
HEM CBB HBB SING N N 43
HEM CBB HBBA SING N N 44
HEM C1C C2C SING Y N 45
HEM C1C NC SING Y N 46
HEM C2C C3C DOUB Y N 47
HEM C2C CMC SING N N 48
HEM C3C C4C SING Y N 49
HEM C3C CAC SING N N 50
HEM C4C NC SING Y N 51
HEM CMC HMC SING N N 52
HEM CMC HMCA SING N N 53
HEM CMC HMCB SING N N 54
HEM CAC CBC DOUB N N 55
HEM CAC HAC SING N N 56
HEM CBC HBC SING N N 57
HEM CBC HBCA SING N N 58
HEM C1D C2D SING N N 59
HEM C1D ND DOUB N N 60
HEM C2D C3D DOUB N N 61
HEM C2D CMD SING N N 62
HEM C3D C4D SING N N 63
HEM C3D CAD SING N N 64
HEM C4D ND SING N N 65
HEM CMD HMD SING N N 66
HEM CMD HMDA SING N N 67
HEM CMD HMDB SING N N 68
HEM CAD CBD SING N N 69
HEM CAD HAD SING N N 70
HEM CAD HADA SING N N 71
HEM CBD CGD SING N N 72
HEM CBD HBD SING N N 73
HEM CBD HBDA SING N N 74
HEM CGD O1D DOUB N N 75
HEM CGD O2D SING N N 76
HEM O2A H2A SING N N 77
HEM O2D H2D SING N N 78
HEM FE NA SING N N 79
HEM FE NB SING N N 80
HEM FE NC SING N N 81
HEM FE ND SING N N 82
# #
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
HEM SMILES ACDLabs 12.01 "C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O"
HEM InChI InChI 1.03 "InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;"
HEM InChIKey InChI 1.03 KABFMIBPWCXCRK-RGGAHWMASA-L
HEM SMILES_CANONICAL CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
HEM SMILES CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
HEM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
HEM SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
# #
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
HEM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid"
HEM "SYSTEMATIC NAME" ACDLabs 12.01 "[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]iron"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HEM "Create component" 1999-07-08 RCSB
HEM "Other modification" 2016-01-20 RCSB
HEM "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HEM
_pdbx_chem_comp_synonyms.name HEME
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##
test/structure-test.cpp
...@@ -60,8 +60,10 @@ BOOST_AUTO_TEST_CASE(init) ...@@ -60,8 +60,10 @@ BOOST_AUTO_TEST_CASE(init)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1]; gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// initialize CCD location // initialize CCD location
if (std::filesystem::exists(gTestDir / ".."/"data"/"components.cif")) if (std::filesystem::exists(gTestDir / ".." / "data" / "ccd-subset.cif"))
cif::addFileResource("components.cif", gTestDir / ".."/"data"/"components.cif"); cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
test/unit-test.cpp
...@@ -56,9 +56,12 @@ cif::File operator""_cf(const char* text, size_t length) ...@@ -56,9 +56,12 @@ cif::File operator""_cf(const char* text, size_t length)
BOOST_AUTO_TEST_CASE(init) BOOST_AUTO_TEST_CASE(init)
{ {
// not a test, just initialize test dir // not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2) if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1]; gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// initialize CCD location
if (std::filesystem::exists(gTestDir / ".." / "data" / "ccd-subset.cif"))
cif::addFileResource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
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