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libcifpp
Commit 5b4c131e by Maarten L. Hekkelman
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More verbose

parent bbe71af9
Showing with 142 additions and 3 deletions
data/ccd-subset.cif
......@@ -2579,4 +2579,137 @@ NAG "Other modification" 2019-12-19 RCSB
NAG "Other modification" 2020-07-03 RCSB
NAG "Modify name" 2020-07-17 RCSB
NAG "Modify synonyms" 2020-07-17 RCSB
##
\ No newline at end of file
##
data_HIS
#
_chem_comp.id HIS
_chem_comp.name HISTIDINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H10 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 156.162
_chem_comp.one_letter_code H
_chem_comp.three_letter_code HIS
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
HIS N N N 0 1 N N N 33.472 42.685 -4.610 -0.040 -1.210 0.053 N HIS 1
HIS CA CA C 0 1 N N S 33.414 41.686 -5.673 1.172 -1.709 0.652 CA HIS 2
HIS C C C 0 1 N N N 33.773 42.279 -7.040 1.083 -3.207 0.905 C HIS 3
HIS O O O 0 1 N N N 33.497 43.444 -7.337 0.040 -3.770 1.222 O HIS 4
HIS CB CB C 0 1 N N N 32.005 41.080 -5.734 1.484 -0.975 1.962 CB HIS 5
HIS CG CG C 0 1 Y N N 31.888 39.902 -6.651 2.940 -1.060 2.353 CG HIS 6
HIS ND1 ND1 N 1 1 Y N N 32.539 38.710 -6.414 3.380 -2.075 3.129 ND1 HIS 7
HIS CD2 CD2 C 0 1 Y N N 31.199 39.734 -7.804 3.960 -0.251 2.046 CD2 HIS 8
HIS CE1 CE1 C 0 1 Y N N 32.251 37.857 -7.382 4.693 -1.908 3.317 CE1 HIS 9
HIS NE2 NE2 N 0 1 Y N N 31.439 38.453 -8.237 5.058 -0.801 2.662 NE2 HIS 10
HIS OXT OXT O 0 1 N Y N 34.382 41.455 -7.879 2.247 -3.882 0.744 OXT HIS 11
HIS H H H 0 1 N N N 33.485 42.227 -3.721 -0.102 -1.155 -0.950 H HIS 12
HIS H2 HN2 H 0 1 N Y N 34.301 43.234 -4.714 -0.715 -0.741 0.634 H2 HIS 13
HIS HA HA H 0 1 N N N 34.155 40.908 -5.439 1.965 -1.558 -0.089 HA HIS 14
HIS HB2 1HB H 0 1 N N N 31.733 40.750 -4.721 1.215 0.087 1.879 HB2 HIS 15
HIS HB3 2HB H 0 1 N N N 31.337 41.860 -6.127 0.859 -1.368 2.775 HB3 HIS 16
HIS HD1 HD1 H 0 1 N N N 33.135 38.521 -5.633 2.828 -2.838 3.511 HD1 HIS 17
HIS HD2 HD2 H 0 1 N N N 30.577 40.470 -8.292 4.108 0.647 1.479 HD2 HIS 18
HIS HE1 HE1 H 0 1 N N N 32.618 36.844 -7.461 5.340 -2.550 3.892 HE1 HIS 19
HIS HE2 HE2 H 0 1 N N N 31.061 38.039 -9.065 6.002 -0.428 2.627 HE2 HIS 20
HIS HXT HXT H 0 1 N Y N 34.553 41.905 -8.698 2.188 -4.848 0.901 HXT HIS 21
#
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
HIS N CA SING N N 1
HIS N H SING N N 2
HIS N H2 SING N N 3
HIS CA C SING N N 4
HIS CA CB SING N N 5
HIS CA HA SING N N 6
HIS C O DOUB N N 7
HIS C OXT SING N N 8
HIS CB CG SING N N 9
HIS CB HB2 SING N N 10
HIS CB HB3 SING N N 11
HIS CG ND1 SING Y N 12
HIS CG CD2 DOUB Y N 13
HIS ND1 CE1 DOUB Y N 14
HIS ND1 HD1 SING N N 15
HIS CD2 NE2 SING Y N 16
HIS CD2 HD2 SING N N 17
HIS CE1 NE2 SING Y N 18
HIS CE1 HE1 SING N N 19
HIS NE2 HE2 SING N N 20
HIS OXT HXT SING N N 21
#
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
HIS SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1cnc[nH+]1"
HIS SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1c[nH]c[nH+]1)C(O)=O"
HIS SMILES CACTVS 3.341 "N[CH](Cc1c[nH]c[nH+]1)C(O)=O"
HIS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N"
HIS SMILES "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)CC(C(=O)O)N"
HIS InChI InChI 1.03 "InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/p+1/t5-/m0/s1"
HIS InChIKey InChI 1.03 HNDVDQJCIGZPNO-YFKPBYRVSA-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
HIS "SYSTEMATIC NAME" ACDLabs 10.04 "3-(1H-imidazol-3-ium-4-yl)-L-alanine"
HIS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-(1H-imidazol-3-ium-4-yl)propanoic 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
HIS "Create component" 1999-07-08 EBI
HIS "Modify descriptor" 2011-06-04 RCSB
#
src/compound.cpp
......@@ -421,7 +421,11 @@ compound_factory_impl::compound_factory_impl(const fs::path &file, std::shared_p
cifFile.load_dictionary("mmcif_pdbx.dic");
if (not cifFile.is_valid())
{
std::cerr << "The components file " << file << " is not valid" << std::endl;
if (cif::VERBOSE < 1)
std::cerr "(use --verbose to see why)" << std::endl;
}
}
catch (const std::exception &e)
{
......@@ -467,7 +471,10 @@ compound *CCD_compound_factory_impl::create(const std::string &id)
{
ccd = cif::load_resource("components.cif");
if (not ccd)
throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
{
std::cerr << "Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data." << std::endl;
return nullptr;
}
}
else
ccd.reset(new std::ifstream(mCompoundsFile));
......
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