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Commit a68e0534 by Maarten L. Hekkelman
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Remove tests

parent 25a90e3b
Showing with 0 additions and 800 deletions
test/REA.cif deleted 100644 → 0
data_REA
#
_chem_comp.id REA
_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.three_letter_code REA
_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 C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 REA 1
REA C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 REA 2
REA C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 REA 3
REA C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 REA 4
REA C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 REA 5
REA C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 REA 6
REA C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 REA 7
REA C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 REA 8
REA C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 REA 9
REA C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 REA 10
REA C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 REA 11
REA C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 REA 12
REA C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 REA 13
REA C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 REA 14
REA C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 REA 15
REA C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 REA 16
REA C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 REA 17
REA C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 REA 18
REA C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 REA 19
REA C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 REA 20
REA O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 REA 21
REA O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 REA 22
REA H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 REA 23
REA H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 REA 24
REA H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 REA 25
REA H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 REA 26
REA H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 REA 27
REA H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 REA 28
REA H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 REA 29
REA H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 REA 30
REA H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 REA 31
REA H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 REA 32
REA H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 REA 33
REA H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 REA 34
REA H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 REA 35
REA H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 REA 36
REA H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 REA 37
REA H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 REA 38
REA H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 REA 39
REA H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 REA 40
REA H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 REA 41
REA H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 REA 42
REA H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 REA 43
REA H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 REA 44
REA H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 REA 45
REA H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 REA 46
REA H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 REA 47
REA H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 REA 48
REA H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 REA 49
REA HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 REA 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 C1 C2 SING N N 1
REA C1 C6 SING N N 2
REA C1 C16 SING N N 3
REA C1 C17 SING N N 4
REA C2 C3 SING N N 5
REA C2 H21 SING N N 6
REA C2 H22 SING N N 7
REA C3 C4 SING N N 8
REA C3 H31 SING N N 9
REA C3 H32 SING N N 10
REA C4 C5 SING N N 11
REA C4 H41 SING N N 12
REA C4 H42 SING N N 13
REA C5 C6 DOUB N N 14
REA C5 C18 SING N N 15
REA C6 C7 SING N N 16
REA C7 C8 DOUB N E 17
REA C7 H7 SING N N 18
REA C8 C9 SING N N 19
REA C8 H8 SING N N 20
REA C9 C10 DOUB N E 21
REA C9 C19 SING N N 22
REA C10 C11 SING N N 23
REA C10 H10 SING N N 24
REA C11 C12 DOUB N E 25
REA C11 H11 SING N N 26
REA C12 C13 SING N N 27
REA C12 H12 SING N N 28
REA C13 C14 DOUB N E 29
REA C13 C20 SING N N 30
REA C14 C15 SING N N 31
REA C14 H14 SING N N 32
REA C15 O1 DOUB N N 33
REA C15 O2 SING N N 34
REA C16 H161 SING N N 35
REA C16 H162 SING N N 36
REA C16 H163 SING N N 37
REA C17 H171 SING N N 38
REA C17 H172 SING N N 39
REA C17 H173 SING N N 40
REA C18 H181 SING N N 41
REA C18 H182 SING N N 42
REA C18 H183 SING N N 43
REA C19 H191 SING N N 44
REA C19 H192 SING N N 45
REA C19 H193 SING N N 46
REA C20 H201 SING N N 47
REA C20 H202 SING N N 48
REA C20 H203 SING N N 49
REA 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 SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
REA 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 InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
REA 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 SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
REA 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 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 "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
REA "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 "Create component" 1999-07-08 RCSB
REA "Modify descriptor" 2011-06-04 RCSB
REA "Other modification" 2016-10-18 RCSB
#
test/RXA.cif deleted 100644 → 0
data_RXA
#
_chem_comp.id RXA
_chem_comp.name "RENAMED 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.three_letter_code RXA
_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
RXA C1 C1 C 0 1 N N N 21.972 29.831 16.739 -4.684 0.932 -0.497 C1 RXA 1
RXA C2 C2 C 0 1 N N N 20.921 30.524 15.841 -5.837 0.190 -1.176 C2 RXA 2
RXA C3 C3 C 0 1 N N N 20.245 29.635 14.848 -6.441 -0.798 -0.171 C3 RXA 3
RXA C4 C4 C 0 1 N N N 19.555 28.479 15.488 -5.418 -1.903 0.100 C4 RXA 4
RXA C5 C5 C 0 1 N N N 20.389 27.812 16.587 -4.082 -1.301 0.429 C5 RXA 5
RXA C6 C6 C 0 1 N N N 21.425 28.446 17.218 -3.756 -0.048 0.161 C6 RXA 6
RXA C7 C7 C 0 1 N N N 22.242 27.851 18.297 -2.457 0.396 0.516 C7 RXA 7
RXA C8 C8 C 0 1 N N N 21.868 26.977 19.240 -1.363 -0.229 0.007 C8 RXA 8
RXA C9 C9 C 0 1 N N N 22.705 26.434 20.286 -0.076 0.257 0.298 C9 RXA 9
RXA C10 C10 C 0 1 N N N 22.159 25.536 21.131 1.022 -0.370 -0.213 C10 RXA 10
RXA C11 C11 C 0 1 N N N 22.875 24.924 22.234 2.306 0.115 0.077 C11 RXA 11
RXA C12 C12 C 0 1 N N N 22.237 24.026 22.990 3.405 -0.513 -0.435 C12 RXA 12
RXA C13 C13 C 0 1 N N N 22.856 23.377 24.125 4.689 -0.028 -0.144 C13 RXA 13
RXA C14 C14 C 0 1 N N N 22.135 22.473 24.834 5.787 -0.655 -0.656 C14 RXA 14
RXA C15 C15 C 0 1 N N N 22.563 21.710 26.016 7.077 -0.265 -0.244 C15 RXA 15
RXA C16 C16 C 0 1 N N N 22.238 30.737 17.948 -5.246 1.886 0.559 C16 RXA 16
RXA C17 C17 C 0 1 N N N 23.292 29.620 15.948 -3.911 1.737 -1.544 C17 RXA 17
RXA C18 C18 C 0 1 N N N 19.791 26.449 16.947 -3.056 -2.175 1.103 C18 RXA 18
RXA C19 C19 C 0 1 N N N 24.181 26.841 20.385 0.090 1.471 1.175 C19 RXA 19
RXA C20 C20 C 0 1 N N N 24.303 23.747 24.489 4.855 1.186 0.733 C20 RXA 20
RXA O1 O1 O 0 1 N N N 23.640 21.075 25.978 7.210 0.553 0.648 O1 RXA 21
RXA O2 O2 O 0 1 N N N 21.840 21.712 27.037 8.166 -0.798 -0.840 O2 RXA 22
RXA H21 H21 H 0 1 N N N 20.147 30.955 16.494 -6.598 0.905 -1.490 H21 RXA 23
RXA H22 H22 H 0 1 N N N 21.425 31.330 15.288 -5.462 -0.353 -2.044 H22 RXA 24
RXA H31 H31 H 0 1 N N N 19.501 30.227 14.295 -6.673 -0.278 0.759 H31 RXA 25
RXA H32 H32 H 0 1 N N N 21.001 29.250 14.148 -7.349 -1.234 -0.586 H32 RXA 26
RXA H41 H41 H 0 1 N N N 18.613 28.835 15.931 -5.756 -2.511 0.938 H41 RXA 27
RXA H42 H42 H 0 1 N N N 19.335 27.730 14.713 -5.322 -2.531 -0.786 H42 RXA 28
RXA H7 H7 H 0 1 N N N 23.276 28.162 18.329 -2.337 1.230 1.191 H7 RXA 29
RXA H8 H8 H 0 1 N N N 20.840 26.645 19.217 -1.482 -1.100 -0.622 H8 RXA 30
RXA H10 H10 H 0 1 N N N 21.127 25.256 20.977 0.903 -1.241 -0.842 H10 RXA 31
RXA H11 H11 H 0 1 N N N 23.902 25.189 22.440 2.425 0.985 0.706 H11 RXA 32
RXA H12 H12 H 0 1 N N N 21.216 23.774 22.743 3.286 -1.383 -1.063 H12 RXA 33
RXA H14 H14 H 0 1 N N N 21.127 22.292 24.490 5.667 -1.451 -1.376 H14 RXA 34
RXA H161 H161 H 0 0 N N N 22.984 30.265 18.604 -5.802 1.316 1.303 H161 RXA 35
RXA H162 H162 H 0 0 N N N 22.618 31.709 17.601 -4.426 2.415 1.044 H162 RXA 36
RXA H163 H163 H 0 0 N N N 21.302 30.887 18.506 -5.911 2.605 0.081 H163 RXA 37
RXA H171 H171 H 0 0 N N N 24.033 29.127 16.595 -4.598 2.394 -2.077 H171 RXA 38
RXA H172 H172 H 0 0 N N N 23.095 28.989 15.069 -3.146 2.335 -1.050 H172 RXA 39
RXA H173 H173 H 0 0 N N N 23.683 30.595 15.620 -3.439 1.054 -2.251 H173 RXA 40
RXA H181 H181 H 0 0 N N N 20.397 25.979 17.736 -3.448 -3.187 1.201 H181 RXA 41
RXA H182 H182 H 0 0 N N N 18.761 26.584 17.308 -2.145 -2.194 0.503 H182 RXA 42
RXA H183 H183 H 0 0 N N N 19.786 25.804 16.056 -2.831 -1.775 2.092 H183 RXA 43
RXA H191 H191 H 0 0 N N N 24.647 26.327 21.238 0.171 1.159 2.216 H191 RXA 44
RXA H192 H192 H 0 0 N N N 24.702 26.559 19.458 0.993 2.008 0.885 H192 RXA 45
RXA H193 H193 H 0 0 N N N 24.252 27.929 20.529 -0.774 2.125 1.058 H193 RXA 46
RXA H201 H201 H 0 0 N N N 24.620 23.168 25.369 5.026 0.871 1.762 H201 RXA 47
RXA H202 H202 H 0 0 N N N 24.965 23.516 23.641 5.707 1.771 0.386 H202 RXA 48
RXA H203 H203 H 0 0 N N N 24.360 24.822 24.717 3.952 1.795 0.685 H203 RXA 49
RXA HO2 HO2 H 0 1 N N N 22.244 21.180 27.713 9.006 -0.469 -0.490 HO2 RXA 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
RXA C1 C2 SING N N 1
RXA C1 C6 SING N N 2
RXA C1 C16 SING N N 3
RXA C1 C17 SING N N 4
RXA C2 C3 SING N N 5
RXA C2 H21 SING N N 6
RXA C2 H22 SING N N 7
RXA C3 C4 SING N N 8
RXA C3 H31 SING N N 9
RXA C3 H32 SING N N 10
RXA C4 C5 SING N N 11
RXA C4 H41 SING N N 12
RXA C4 H42 SING N N 13
RXA C5 C6 DOUB N N 14
RXA C5 C18 SING N N 15
RXA C6 C7 SING N N 16
RXA C7 C8 DOUB N E 17
RXA C7 H7 SING N N 18
RXA C8 C9 SING N N 19
RXA C8 H8 SING N N 20
RXA C9 C10 DOUB N E 21
RXA C9 C19 SING N N 22
RXA C10 C11 SING N N 23
RXA C10 H10 SING N N 24
RXA C11 C12 DOUB N E 25
RXA C11 H11 SING N N 26
RXA C12 C13 SING N N 27
RXA C12 H12 SING N N 28
RXA C13 C14 DOUB N E 29
RXA C13 C20 SING N N 30
RXA C14 C15 SING N N 31
RXA C14 H14 SING N N 32
RXA C15 O1 DOUB N N 33
RXA C15 O2 SING N N 34
RXA C16 H161 SING N N 35
RXA C16 H162 SING N N 36
RXA C16 H163 SING N N 37
RXA C17 H171 SING N N 38
RXA C17 H172 SING N N 39
RXA C17 H173 SING N N 40
RXA C18 H181 SING N N 41
RXA C18 H182 SING N N 42
RXA C18 H183 SING N N 43
RXA C19 H191 SING N N 44
RXA C19 H192 SING N N 45
RXA C19 H193 SING N N 46
RXA C20 H201 SING N N 47
RXA C20 H202 SING N N 48
RXA C20 H203 SING N N 49
RXA 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
RXA SMILES ACDLabs 12.01 "C1(CCCC(=C1\C=C\C(=C\C=C\C(=C\C(=O)O)C)C)C)(C)C"
RXA 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+"
RXA InChIKey InChI 1.03 SHGAZHPCJJPHSC-YCNIQYBTSA-N
RXA SMILES_CANONICAL CACTVS 3.385 "CC1=C(\C=C\C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1"
RXA SMILES CACTVS 3.385 "CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1"
RXA 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"
RXA 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
RXA "SYSTEMATIC NAME" ACDLabs 12.01 "retinoic acid"
RXA "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
RXA "Create component" 1999-07-08 RCSB
RXA "Modify descriptor" 2011-06-04 RCSB
RXA "Other modification" 2016-10-18 RCSB
#
test/UN_.cif deleted 100644 → 0
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
UN_ UN_ UN_NINE L-peptide 13 6 .
#
data_comp_UN_
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
UN_ N N NT3 1 0.227 -1.259 0.452
UN_ H H H 0 0.069 -1.019 1.421
UN_ H2 H H 0 1.104 -1.640 0.356
UN_ H3 H H 0 -0.424 -1.909 0.174
UN_ CA C CH1 0 0.103 -0.030 -0.392
UN_ HA H H 0 0.160 -0.299 -1.339
UN_ CB C CH3 0 -1.244 0.625 -0.159
UN_ HB3 H H 0 -1.857 -0.018 0.234
UN_ HB2 H H 0 -1.605 0.932 -1.008
UN_ HB1 H H 0 -1.150 1.385 0.442
UN_ C C C 0 1.270 0.922 -0.094
UN_ O O O 0 2.008 1.323 -0.994
UN_ OXT O OC -1 1.498 1.305 1.054
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
UN_ N n/a CA START
UN_ H N . .
UN_ H2 N . .
UN_ H3 N . .
UN_ CA N C .
UN_ HA CA . .
UN_ CB CA HB3 .
UN_ HB1 CB . .
UN_ HB2 CB . .
UN_ HB3 CB . .
UN_ C CA . END
UN_ O C . .
UN_ OXT C . .
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
UN_ CB CA SINGLE n 1.509 0.014
UN_ CA C SINGLE n 1.533 0.011
UN_ C O DOUBLE n 1.247 0.019
UN_ C OXT SINGLE n 1.247 0.019
UN_ CA N SINGLE n 1.482 0.010
UN_ CB HB3 SINGLE n 0.972 0.015
UN_ CB HB2 SINGLE n 0.972 0.015
UN_ CB HB1 SINGLE n 0.972 0.015
UN_ CA HA SINGLE n 0.986 0.020
UN_ N H SINGLE n 0.911 0.020
UN_ N H2 SINGLE n 0.911 0.020
UN_ N H3 SINGLE n 0.911 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
UN_ CA CB HB3 109.546 1.50
UN_ CA CB HB2 109.546 1.50
UN_ CA CB HB1 109.546 1.50
UN_ HB3 CB HB2 109.386 1.50
UN_ HB3 CB HB1 109.386 1.50
UN_ HB2 CB HB1 109.386 1.50
UN_ CB CA C 111.490 1.50
UN_ CB CA N 109.912 1.50
UN_ CB CA HA 108.878 1.50
UN_ C CA N 109.627 1.50
UN_ C CA HA 108.541 1.50
UN_ N CA HA 108.529 1.50
UN_ CA C O 117.159 1.57
UN_ CA C OXT 117.159 1.57
UN_ O C OXT 125.683 1.50
UN_ CA N H 109.643 1.50
UN_ CA N H2 109.643 1.50
UN_ CA N H3 109.643 1.50
UN_ H N H2 109.028 2.41
UN_ H N H3 109.028 2.41
UN_ H2 N H3 109.028 2.41
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
UN_ hh1 N CA CB HB3 60.000 15.000 3
UN_ sp2_sp3_1 O C CA CB 0.000 10.00 6
UN_ sp3_sp3_10 CB CA N H 180.000 10.00 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
UN_ chir_1 CA N C CB positive
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
UN_ plan-1 C 0.020
UN_ plan-1 CA 0.020
UN_ plan-1 O 0.020
UN_ plan-1 OXT 0.020
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
UN_ SMILES ACDLabs 10.04 "O=C(O)C(N)C"
UN_ SMILES_CANONICAL CACTVS 3.341 "C[C@H](N)C(O)=O"
UN_ SMILES CACTVS 3.341 "C[CH](N)C(O)=O"
UN_ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H](C(=O)O)N"
UN_ SMILES "OpenEye OEToolkits" 1.5.0 "CC(C(=O)O)N"
UN_ InChI InChI 1.03 "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1"
UN_ InChIKey InChI 1.03 QNAYBMKLOCPYGJ-REOHCLBHSA-N
UN_ ? acedrg 195 "dictionary generator"
UN_ ? acedrg_database 11 "data source"
UN_ ? rdkit 2017.03.2 "Chemoinformatics tool"
UN_ ? refmac5 5.8.0189 "optimization tool"
test/pdb2cif-test.cpp deleted 100644 → 0
#include "../include/cif++/cif.hpp"
#include "../include/cif++/pdb/PDB2Cif.hpp""
#include <iostream>
#include <fstream>
// #include "pdb2cif.h"
int main(int argc, char* argv[])
{
using namespace std::literals;
if (argc != 2)
{
std::cerr << "Usage: pdb2cif-test <input-file>" << std::endl;
exit(1);
}
std::ifstream is(argv[1]);
if (not is.is_open())
throw std::runtime_error("Could not open file "s + argv[1]);
cif::File f;
ReadPDBFile(is, f);
f.save(std::cout);
return 0;
}
test/rename-compound-test.cpp deleted 100644 → 0
#include "../include/cif++/Cif++.hpp"
#include "../include/cif++/PDB2Cif.hpp"
#include "../include/cif++/Structure.hpp"
#include <iostream>
#include <fstream>
int main(int argc, char* argv[])
{
cif::VERBOSE = 3;
try
{
std::filesystem::path testdir = std::filesystem::current_path();
if (argc == 3)
testdir = argv[2];
if (std::filesystem::exists(testdir / ".." / "data" / "ccd-subset.cif"))
cif::add_file_resource("components.cif", testdir / ".." / "data" / "ccd-subset.cif");
if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx.dic"))
cif::add_file_resource("mmcif_pdbx.dic", testdir / ".." / "rsrc" / "mmcif_pdbx.dic");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif");
mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif");
mmcif::File f(testdir / ".."/"examples"/"1cbs.cif.gz");
mmcif::Structure structure(f);
auto &res = structure.getResidue("B");
structure.changeResidue(res, "RXA", {});
structure.cleanupEmptyCategories();
f.save(std::cout);
}
catch (const std::exception& e)
{
std::cerr << e.what() << std::endl;
exit(1);
}
return 0;
}
test/sugar-test.cpp deleted 100644 → 0
/*-
* 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_ALTERNATIVE_INIT_API
#include <boost/test/included/unit_test.hpp>
#include <stdexcept>
#include <cif++.hpp>
#include <cif++/structure/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);
}
// --------------------------------------------------------------------
std::filesystem::path gTestDir = std::filesystem::current_path();
bool init_unit_test()
{
cif::VERBOSE = 1;
// not a test, just initialize test dir
if (boost::unit_test::framework::master_test_suite().argc == 2)
gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
// do this now, avoids the need for installing
cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
// initialize CCD location
cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
mmcif::CompoundFactory::instance().pushDictionary(gTestDir / "HEM.cif");
return true;
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(sugar_name_1)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
auto &db = s.datablock();
auto &entity = db["entity"];
auto &branches = s.branches();
BOOST_CHECK_EQUAL(branches.size(), 4);
for (auto &branch : branches)
{
auto entityID = branch.front().entityID();
auto name = entity.find1<std::string>("id"_key == entityID, "pdbx_description");
BOOST_CHECK_EQUAL(branch.name(), name);
}
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_1)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
// collect atoms from asym L first
auto &NAG = s.getResidue("L");
auto nagAtoms = NAG.atoms();
std::vector<std::vector<cif::Item>> ai;
auto &db = s.datablock();
auto &as = db["atom_site"];
for (auto r : as.find("label_asym_id"_key == "L"))
ai.emplace_back(r.begin(), r.end());
s.removeResidue(NAG);
auto &branch = s.createBranch(ai);
BOOST_CHECK_EQUAL(branch.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(branch.size(), 1);
BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_2)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
// Get branch for H
auto &bH = s.getBranchByAsymID("H");
BOOST_CHECK_EQUAL(bH.size(), 2);
std::vector<std::vector<cif::Item>> ai[2];
auto &db = s.datablock();
auto &as = db["atom_site"];
for (size_t i = 0; i < 2; ++i)
{
for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
ai[i].emplace_back(r.begin(), r.end());
}
s.removeBranch(bH);
auto &bN = s.createBranch(ai[0]);
s.extendBranch(bN.asymID(), ai[1], 1, "O4");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 2);
file.save(gTestDir / "test-create_sugar_2.cif");
BOOST_CHECK_NO_THROW(mmcif::Structure s2(file));
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(delete_sugar_1)
{
using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
mmcif::File file(example.string());
mmcif::Structure s(file);
// Get branch for H
auto &bG = s.getBranchByAsymID("G");
BOOST_CHECK_EQUAL(bG.size(), 4);
s.removeResidue(bG[1]);
BOOST_CHECK_EQUAL(bG.size(), 1);
auto &bN = s.getBranchByAsymID("G");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 1);
file.save(gTestDir / "test-create_sugar_3.cif");
BOOST_CHECK_NO_THROW(mmcif::Structure s2(file));
}
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