Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: cb94010c by Étienne Mollier at 2024-10-31T23:10:57+01:00 d/t/mini-ccd.cif: include definition of SO4 molecule. The definition originates from PDB's components.cif as of 2024-10-30. This resolves the noisy warning when running test_PDB_DSSP. - - - - - abbdc7ed by Étienne Mollier at 2024-10-31T23:20:49+01:00 d/changelog: initialise new entry. - - - - - 2 changed files: - debian/changelog - debian/tests/mini-ccd.cif Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +python-biopython (1.84+dfsg-5) UNRELEASED; urgency=medium + + * d/t/mini-ccd.cif: include definition of SO4 molecule. + The definition originates from PDB's components.cif as of 2024-10-30. + This resolves the noisy warning when running test_PDB_DSSP. + + -- Étienne Mollier <[email protected]> Thu, 31 Oct 2024 23:13:11 +0100 + python-biopython (1.84+dfsg-4) unstable; urgency=medium * skip-scipy-in-codonalign.patch: comment about #1086108. ===================================== debian/tests/mini-ccd.cif ===================================== @@ -2993,3 +2993,100 @@ REA "Create component" 1999-07-08 RCSB REA "Modify descriptor" 2011-06-04 RCSB REA "Other modification" 2016-10-18 RCSB # +data_SO4 +# + +_chem_comp.id SO4 +_chem_comp.name "SULFATE ION" +_chem_comp.type NON-POLYMER +_chem_comp.pdbx_type HETAI +_chem_comp.formula "O4 S" +_chem_comp.mon_nstd_parent_comp_id ? +_chem_comp.pdbx_synonyms ? +_chem_comp.pdbx_formal_charge -2 +_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 SUL +_chem_comp.formula_weight 96.063 +_chem_comp.one_letter_code ? +_chem_comp.three_letter_code SO4 +_chem_comp.pdbx_model_coordinates_details ? +_chem_comp.pdbx_model_coordinates_missing_flag N +_chem_comp.pdbx_ideal_coordinates_details ? +_chem_comp.pdbx_ideal_coordinates_missing_flag N +_chem_comp.pdbx_model_coordinates_db_code 1BXO +_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 +SO4 S S S 0 1 N N N 16.485 34.924 5.575 0.000 0.000 0.000 S SO4 1 +SO4 O1 O1 O 0 1 N N N 17.741 34.891 4.826 0.000 -1.201 -0.850 O1 SO4 2 +SO4 O2 O2 O 0 1 N N N 16.787 35.826 6.733 0.000 1.201 -0.850 O2 SO4 3 +SO4 O3 O3 O -1 1 N N N 15.440 35.551 4.401 -1.201 0.000 0.850 O3 SO4 4 +SO4 O4 O4 O -1 1 N N N 16.141 33.720 5.930 1.201 0.000 0.850 O4 SO4 5 +# # +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 +SO4 S O1 DOUB N N 1 +SO4 S O2 DOUB N N 2 +SO4 S O3 SING N N 3 +SO4 S O4 SING N N 4 +# # +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 +SO4 SMILES ACDLabs 10.04 "[O-]S([O-])(=O)=O" +SO4 SMILES_CANONICAL CACTVS 3.341 "[O-][S]([O-])(=O)=O" +SO4 SMILES CACTVS 3.341 "[O-][S]([O-])(=O)=O" +SO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]" +SO4 SMILES "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]" +SO4 InChI InChI 1.03 "InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2" +SO4 InChIKey InChI 1.03 QAOWNCQODCNURD-UHFFFAOYSA-L +# # +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 +SO4 "SYSTEMATIC NAME" ACDLabs 10.04 sulfate +SO4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 sulfate +# # +loop_ +_pdbx_chem_comp_audit.comp_id +_pdbx_chem_comp_audit.action_type +_pdbx_chem_comp_audit.date +_pdbx_chem_comp_audit.processing_site +SO4 "Create component" 1999-07-08 RCSB +SO4 "Modify descriptor" 2011-06-04 RCSB +## View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/583d849d0b90cbd6fb88afe7767489c3c860ff11...abbdc7edef831e561a4bf2813bb3abae753ae95a -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/583d849d0b90cbd6fb88afe7767489c3c860ff11...abbdc7edef831e561a4bf2813bb3abae753ae95a You're receiving this email because of your account on salsa.debian.org.
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