[med-svn] [Git][med-team/python-biopython][master] 2 commits: d/t/mini-ccd.cif: include definition of SO4 molecule.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Oct 31 22:21:18 GMT 2024
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 <emollier at debian.org> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20241031/adc4cced/attachment-0001.htm>
More information about the debian-med-commit
mailing list