Squashed 'modules/core/dependency/python-ihm/' changes from f49b8e991…

…7..a8122418ca

a8122418ca Prepare for 0.41 release
fb63400f75 Add more info on steps
1584b66a82 Remove unused variable
fd16469460 Use seq_id internally for branched entities
65405a13dd Account for new atom_site.auth_comp_id in examples
c98b9c755f Add atom_site.auth_comp_id
c22c2988ac Add _pdbx_branch_scheme.pdb_mon_id
3ed7b65da3 Skip pdbx_entity_nonpoly table for branched entity
5d69a98b33 Sort output to make a little more readable

git-subtree-dir: modules/core/dependency/python-ihm
git-subtree-split: a8122418ca30d3341d2dcbbd98b465a2fbe1a829

modules/core/dependency/python-ihm/ChangeLog.rst

@@ -1,3 +1,10 @@
+0.41 - 2023-10-02
+=================
+  - More complete support for oligosaccharides, in particular correct
+    numbering for atoms in `atom_site`, and the addition of some
+    data items to the output which are required for full
+    dictionary compliance.
+
 0.40 - 2023-09-25
 =================
   - Basic support for oligosaccharides is now provided. New classes are

modules/core/dependency/python-ihm/MANIFEST.in

@@ -4,4 +4,4 @@ include examples/*
 include util/make-mmcif.py
 include src/ihm_format.h
 include src/ihm_format.i
-include src/ihm_format_wrap_0.40.c
+include src/ihm_format_wrap_0.41.c

modules/core/dependency/python-ihm/ihm/__init__.py

@@ -20,7 +20,7 @@
 import json
 from . import util
 
-__version__ = '0.40'
+__version__ = '0.41'
 
 
 class __UnknownValue(object):
@@ -1341,7 +1341,7 @@ def __call__(self, seq_id_begin, seq_id_end):
         return EntityRange(self, seq_id_begin, seq_id_end)
 
     def __get_seq_id_range(self):
-        if self.is_polymeric():
+        if self.is_polymeric() or self.is_branched():
             return (1, len(self.sequence))
         else:
             # Nonpolymers don't have the concept of seq_id

modules/core/dependency/python-ihm/ihm/dictionary.py

@@ -143,7 +143,8 @@ def _check_linked_items(self):
                 # the chem_comp_* categories don't need to be fully populated
                 if cat in self.dictionary.categories \
                    and not cat.startswith('chem_comp_'):
-                    missing = self._seen_ids[child] - self._seen_ids[parent]
+                    missing = sorted(self._seen_ids[child]
+                                     - self._seen_ids[parent])
                     self.errors.append(
                         "The following IDs referenced by %s "
                         "were not defined in the parent category (%s): %s"

modules/core/dependency/python-ihm/ihm/dumper.py

@@ -597,7 +597,7 @@ def dump(self, system, writer):
         with writer.loop("_pdbx_entity_nonpoly",
                          ["entity_id", "name", "comp_id"]) as lp:
             for entity in system.entities:
-                if entity.is_polymeric():
+                if entity.is_polymeric() or entity.is_branched():
                     continue
                 lp.write(entity_id=entity._id, name=entity.description,
                          comp_id=entity.sequence[0].id)
@@ -734,7 +734,7 @@ def dump(self, system, writer):
         with writer.loop("_pdbx_branch_scheme",
                          ["asym_id", "entity_id", "mon_id", "num",
                           "pdb_seq_num", "auth_seq_num",
-                          "auth_mon_id", "pdb_asym_id"]) as lp:
+                          "auth_mon_id", "pdb_mon_id", "pdb_asym_id"]) as lp:
             for asym in system.asym_units:
                 entity = asym.entity
                 if not entity.is_branched():
@@ -747,8 +747,8 @@ def dump(self, system, writer):
                              num=num + 1,
                              pdb_seq_num=auth_seq_num,
                              auth_seq_num=auth_seq_num,
-                             mon_id=comp.id,
-                             auth_mon_id=comp.id)
+                             mon_id=comp.id, auth_mon_id=comp.id,
+                             pdb_mon_id=comp.id)
 
 
 class _BranchDescriptorDumper(Dumper):
@@ -1460,6 +1460,9 @@ def __call__(self, obj):
         else:
             type_check = self._type_check_atom
             seq_id_range = (obj.seq_id, obj.seq_id)
+            # Allow seq_id to be either 1 or None for ligands
+            if obj.seq_id == 1 and asym.entity.type == 'non-polymer':
+                seq_id_range = (None, None)
             self._check_duplicate_atom(obj)
         self._check_assembly(obj, asym, seq_id_range)
         self._check_representation(obj, asym, type_check, seq_id_range)
@@ -1591,7 +1594,7 @@ def dump_atoms(self, system, writer, add_ihm=True):
               "label_alt_id", "label_comp_id", "label_seq_id", "auth_seq_id",
               "pdbx_PDB_ins_code", "label_asym_id", "Cartn_x", "Cartn_y",
               "Cartn_z", "occupancy", "label_entity_id", "auth_asym_id",
-              "B_iso_or_equiv", "pdbx_PDB_model_num"]
+              "auth_comp_id", "B_iso_or_equiv", "pdbx_PDB_model_num"]
         if add_ihm:
             it.append("ihm_model_id")
         with writer.loop("_atom_site", it) as lp:
@@ -1600,8 +1603,10 @@ def dump_atoms(self, system, writer, add_ihm=True):
                 for atom in model.get_atoms():
                     rngcheck(atom)
                     seq_id = 1 if atom.seq_id is None else atom.seq_id
+                    label_seq_id = atom.seq_id
+                    if not atom.asym_unit.entity.is_polymeric():
+                        label_seq_id = None
                     comp = atom.asym_unit.sequence[seq_id - 1]
-                    water = isinstance(atom.asym_unit, ihm.WaterAsymUnit)
                     seen_types[atom.type_symbol] = None
                     auth_seq_id, ins = \
                         atom.asym_unit._get_auth_seq_id_ins_code(seq_id)
@@ -1612,8 +1617,8 @@ def dump_atoms(self, system, writer, add_ihm=True):
                              label_comp_id=comp.id,
                              label_asym_id=atom.asym_unit._id,
                              label_entity_id=atom.asym_unit.entity._id,
-                             label_seq_id=None if water else atom.seq_id,
-                             auth_seq_id=auth_seq_id,
+                             label_seq_id=label_seq_id,
+                             auth_seq_id=auth_seq_id, auth_comp_id=comp.id,
                              pdbx_PDB_ins_code=ins or ihm.unknown,
                              auth_asym_id=atom.asym_unit.strand_id,
                              Cartn_x=atom.x, Cartn_y=atom.y, Cartn_z=atom.z,

modules/core/dependency/python-ihm/ihm/model.py

@@ -44,7 +44,9 @@ class Atom(object):
        :type asym_unit: :class:`ihm.AsymUnit`
        :param int seq_id: The sequence ID of the residue represented by this
               atom. This should generally be a number starting at 1 for any
-              polymer chain or water, or None for a ligand.
+              polymer chain, water, or oligosaccharide. For ligands, a seq_id
+              is not needed (as a given asym can only contain a single ligand),
+              so either 1 or None can be used.
        :param str atom_id: The name of the atom in the residue
        :param str type_symbol: Element name
        :param float x: x coordinate of the atom

modules/core/dependency/python-ihm/ihm/reader.py

@@ -1994,8 +1994,9 @@ def __init__(self, *args):
         self._missing_sequence = collections.defaultdict(dict)
         self._seq_id_map = {}
 
-    def _get_water_seq_id(self, auth_seq_id, pdbx_pdb_ins_code, asym):
-        """Get an internal seq_id for a water, given author-provided info"""
+    def _get_seq_id_from_auth(self, auth_seq_id, pdbx_pdb_ins_code, asym):
+        """Get an internal seq_id for something not a polymer (nonpolymer,
+           water, branched), given author-provided info"""
         if asym._id not in self._seq_id_map:
             m = {}
             # Make reverse mapping from author-provided info to seq_id
@@ -2028,23 +2029,24 @@ def __call__(self, pdbx_pdb_model_num, label_asym_id, b_iso_or_equiv,
         else:
             asym = self.sysr.asym_units.get_by_id(label_asym_id)
         auth_seq_id = self.get_int_or_string(auth_seq_id)
-        water = isinstance(asym, ihm.WaterAsymUnit)
-        if water:
+        if seq_id is None:
             # Fill in our internal seq_id if possible
-            seq_id = self._get_water_seq_id(auth_seq_id, pdbx_pdb_ins_code,
-                                            asym)
+            our_seq_id = self._get_seq_id_from_auth(
+                auth_seq_id, pdbx_pdb_ins_code, asym)
+        else:
+            our_seq_id = seq_id
         biso = self.get_float(b_iso_or_equiv)
         occupancy = self.get_float(occupancy)
         group = 'ATOM' if group_pdb is None else group_pdb
         a = ihm.model.Atom(
-            asym_unit=asym, seq_id=seq_id, atom_id=label_atom_id,
+            asym_unit=asym, seq_id=our_seq_id, atom_id=label_atom_id,
             type_symbol=type_symbol, x=float(cartn_x), y=float(cartn_y),
             z=float(cartn_z), het=group != 'ATOM', biso=biso,
             occupancy=occupancy)
         model.add_atom(a)
 
         # Note any residues that have different seq_id and auth_seq_id
-        if (auth_seq_id is not None and not water and
+        if (auth_seq_id is not None and seq_id is not None and
                 (seq_id != auth_seq_id
                  or pdbx_pdb_ins_code not in (None, ihm.unknown))):
             if asym.auth_seq_id_map == 0:

modules/core/dependency/python-ihm/make-release.sh

@@ -3,13 +3,13 @@
 # First, do
 # - Update AuditConformDumper to match latest IHM dictionary if necessary
 # - Run util/validate-outputs.py to make sure all example outputs validate
+#   (cd util; PYTHONPATH=.. python3 ./validate-outputs.py)
 # - Update ChangeLog.rst and util/python-ihm.spec with the release number
 # - Update release number in ihm/__init__.py, MANIFEST.in, and setup.py
 # - Commit, tag, and push
 # - Make release on GitHub
 # - Upload the release tarball from
 #   https://github.com/ihmwg/python-ihm/releases to Zenodo as a new release
-# - Build SRPM and upload to COPR
 # - Make sure there are no extraneous .py files (setup.py will include them
 #   in the pypi package)
 
@@ -23,4 +23,4 @@ python3 setup.py sdist
 rm -f "src/ihm_format_wrap_${VERSION}.c"
 
 echo "Now use 'twine upload dist/ihm-${VERSION}.tar.gz' to publish the release on PyPi."
-echo "Then, update the conda-forge and Homebrew packages to match."
+echo "Then, update the conda-forge, COPR, and Homebrew packages to match."

modules/core/dependency/python-ihm/setup.py

@@ -7,7 +7,7 @@
 import sys
 import os
 
-VERSION = "0.40"
+VERSION = "0.41"
 
 copy_args = sys.argv[1:]
 

modules/core/dependency/python-ihm/test/test_dumper.py

@@ -805,7 +805,9 @@ def test_entity_nonpoly_dumper(self):
         # Non-polymeric entity
         e2 = ihm.Entity([ihm.NonPolymerChemComp('HEM')], description='heme')
         e3 = ihm.Entity([ihm.WaterChemComp()])
-        system.entities.extend((e1, e2, e3))
+        # Branched entity
+        e4 = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        system.entities.extend((e1, e2, e3, e4))
 
         ed = ihm.dumper._EntityDumper()
         ed.finalize(system)  # Assign entity IDs
@@ -2101,10 +2103,13 @@ def test_range_checker_repr_seq_id(self):
                                   x=1.0, y=2.0, z=3.0, radius=4.0)
         self.assertRaises(ValueError, rngcheck, sphere)
 
-        # Atom in a nonpolymer must have no seq_id
+        # Atom in a nonpolymer must have no seq_id (or seq_id==1)
         atom = ihm.model.Atom(asym_unit=asym_nonpol, seq_id=None, atom_id='C',
                               type_symbol='C', x=1.0, y=2.0, z=3.0)
         rngcheck(atom)
+        atom = ihm.model.Atom(asym_unit=asym_nonpol, seq_id=1, atom_id='C',
+                              type_symbol='C', x=1.0, y=2.0, z=3.0)
+        rngcheck(atom)
         atom = ihm.model.Atom(asym_unit=asym2, seq_id=None, atom_id='C',
                               type_symbol='C', x=1.0, y=2.0, z=3.0)
         self.assertRaises(ValueError, rngcheck, atom)
@@ -2328,12 +2333,13 @@ def test_model_dumper_atoms(self):
 _atom_site.occupancy
 _atom_site.label_entity_id
 _atom_site.auth_asym_id
+_atom_site.auth_comp_id
 _atom_site.B_iso_or_equiv
 _atom_site.pdbx_PDB_model_num
 _atom_site.ihm_model_id
-ATOM 1 C C . ALA 1 1 ? X 1.000 2.000 3.000 . 9 X . 1 1
-HETATM 2 C CA . ALA 1 1 ? X 10.000 20.000 30.000 . 9 X . 1 1
-ATOM 3 N N . CYS 2 2 ? X 4.000 5.000 6.000 0.200 9 X 42.000 1 1
+ATOM 1 C C . ALA 1 1 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1
+HETATM 2 C CA . ALA 1 1 ? X 10.000 20.000 30.000 . 9 X ALA . 1 1
+ATOM 3 N N . CYS 2 2 ? X 4.000 5.000 6.000 0.200 9 X CYS 42.000 1 1
 #
 #
 loop_
@@ -2352,19 +2358,19 @@ def test_model_dumper_atoms(self):
         asym.auth_seq_id_map = -1
         out = _get_dumper_output(dumper, system)
         self.assertEqual(
-            out.split('\n')[43:46:2],
-            ["ATOM 1 C C . ALA 1 0 ? X 1.000 2.000 3.000 . 9 X . 1 1",
+            out.split('\n')[44:47:2],
+            ["ATOM 1 C C . ALA 1 0 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1",
              "ATOM 3 N N . CYS 2 1 ? X 4.000 5.000 6.000 "
-             "0.200 9 X 42.000 1 1"])
+             "0.200 9 X CYS 42.000 1 1"])
 
         # With auth_seq_id map
         asym.auth_seq_id_map = {1: 42, 2: 99}
         out = _get_dumper_output(dumper, system)
         self.assertEqual(
-            out.split('\n')[43:46:2],
-            ["ATOM 1 C C . ALA 1 42 ? X 1.000 2.000 3.000 . 9 X . 1 1",
+            out.split('\n')[44:47:2],
+            ["ATOM 1 C C . ALA 1 42 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1",
              "ATOM 3 N N . CYS 2 99 ? X 4.000 5.000 6.000 "
-             "0.200 9 X 42.000 1 1"])
+             "0.200 9 X CYS 42.000 1 1"])
 
     def test_model_dumper_water_atoms(self):
         """Test ModelDumper with water atoms"""
@@ -2394,10 +2400,10 @@ def test_model_dumper_water_atoms(self):
 
         out = _get_dumper_output(dumper, system)
         self.assertEqual(
-            out.split('\n')[43:46],
-            ['HETATM 1 O O . HOH . 42 ? X 1.000 2.000 3.000 . 9 X . 1 1',
-             'HETATM 2 O O . HOH . 99 ? X 4.000 5.000 6.000 . 9 X . 1 1',
-             'HETATM 3 O O . HOH . 3 ? X 7.000 8.000 9.000 . 9 X . 1 1'])
+            out.split('\n')[44:47],
+            ['HETATM 1 O O . HOH . 42 ? X 1.000 2.000 3.000 . 9 X HOH . 1 1',
+             'HETATM 2 O O . HOH . 99 ? X 4.000 5.000 6.000 . 9 X HOH . 1 1',
+             'HETATM 3 O O . HOH . 3 ? X 7.000 8.000 9.000 . 9 X HOH . 1 1'])
 
     def test_ensemble_dumper(self):
         """Test EnsembleDumper"""
@@ -4515,9 +4521,10 @@ def test_branch_scheme_dumper(self):
 _pdbx_branch_scheme.pdb_seq_num
 _pdbx_branch_scheme.auth_seq_num
 _pdbx_branch_scheme.auth_mon_id
+_pdbx_branch_scheme.pdb_mon_id
 _pdbx_branch_scheme.pdb_asym_id
-A 1 NAG 1 1 1 NAG A
-B 2 FUC 1 6 6 FUC B
+A 1 NAG 1 1 1 NAG NAG A
+B 2 FUC 1 6 6 FUC FUC B
 #
 """)
 

modules/core/dependency/python-ihm/test/test_examples.py

@@ -41,7 +41,7 @@ def test_simple_docking_example(self):
             # can read it
             with open(os.path.join(tmpdir, 'output.cif')) as fh:
                 contents = fh.readlines()
-            self.assertEqual(len(contents), 317)
+            self.assertEqual(len(contents), 318)
             with open(os.path.join(tmpdir, 'output.cif')) as fh:
                 s, = ihm.reader.read(fh)
 
@@ -70,7 +70,7 @@ def test_ligands_water_example(self):
         # can read it
         with open(out) as fh:
             contents = fh.readlines()
-        self.assertEqual(len(contents), 253)
+        self.assertEqual(len(contents), 254)
         with open(out) as fh:
             s, = ihm.reader.read(fh)
         # Make sure that resulting Python objects are picklable

modules/core/dependency/python-ihm/test/test_main.py

@@ -223,9 +223,10 @@ def test_entity(self):
         self.assertNotEqual(e1, e3)
         self.assertEqual(e1.seq_id_range, (1, 4))
         self.assertEqual(e3.seq_id_range, (1, 5))
-        # seq_id does not exist for nonpolymers or branched entities
+        # seq_id does not exist for nonpolymers
         self.assertEqual(heme.seq_id_range, (None, None))
-        self.assertEqual(sugar.seq_id_range, (None, None))
+        # We do have an internal seq_id_range for branched entities
+        self.assertEqual(sugar.seq_id_range, (1, 1))
 
     def test_entity_weight(self):
         """Test Entity.formula_weight"""
@@ -466,9 +467,10 @@ def test_asym_range(self):
         asugar = ihm.AsymUnit(sugar)
         a._id = 42
         self.assertEqual(a.seq_id_range, (1, 6))
-        # seq_id is not defined for nonpolymers or branched entities
+        # seq_id is not defined for nonpolymers
         self.assertEqual(aheme.seq_id_range, (None, None))
-        self.assertEqual(asugar.seq_id_range, (None, None))
+        # We use seq_id internally for branched entities
+        self.assertEqual(asugar.seq_id_range, (1, 1))
         r = a(3, 4)
         self.assertEqual(r.seq_id_range, (3, 4))
         self.assertEqual(r._id, 42)

modules/core/dependency/python-ihm/util/python-ihm.spec

@@ -1,7 +1,7 @@
 Name:          python3-ihm
 License:       MIT
 Group:         Applications/Engineering
-Version:       0.40
+Version:       0.41
 Release:       1%{?dist}
 Summary:       Package for handling IHM mmCIF and BinaryCIF files
 Packager:      Ben Webb <[email protected]>
@@ -36,6 +36,9 @@ sed -i -e "s/install_requires=\['msgpack'\]/#/" setup.py
 %defattr(-,root,root)
 
 %changelog
+* Mon Oct 02 2023 Ben Webb <[email protected]>   0.41-1
+- Update to latest upstream.
+
 * Mon Sep 25 2023 Ben Webb <[email protected]>   0.40-1
 - Update to latest upstream.