Squashed 'modules/core/dependency/python-ihm/' changes from 0a6e31129…

…e..1d6f0599b1

1d6f0599b1 Fix typos
b190922c24 Fix typos
614bf5e84e Fix hyperlinks
1e2e35a308 Merge pull request ihmwg/python-ihm#122 from grandrea/cross_linkers_ag
1828c76e41 Match names in doc against Python code
1c53df70b9 Match crosslink names with dictionary
da722510f7 Drop testing with Python 2.7
779b38d71f formatting
d0a038af5d define dsbu, PhoX and tbu-PhoX. Missing smiles and inchi on PhoX and tbu-PhoX as they don't seem to exist yet.
1022dbf56e define photoL
363f48172d define photoL
1805462213 define photoL
a05ef17b53 Fill in entity for Residues in asyms
57c2d25f40 Remove db_name parameter from DatabaseLocation
660ccf8fb1 Make sure that input and output are not the same file

git-subtree-dir: modules/core/dependency/python-ihm
git-subtree-split: 1d6f0599b180267a13d64a0dd1ddcc2a1910d5d8

modules/core/dependency/python-ihm/.github/workflows/testpy.yml

@@ -11,8 +11,6 @@ jobs:
         os: [ubuntu-22.04]
         python-version: ['3.7', '3.8', '3.9', '3.10',  '3.11']
         include:
-        - os: ubuntu-20.04
-          python-version: '2.7'
         - os: ubuntu-20.04
           python-version: '3.6'
         - os: macos-latest

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

@@ -1,3 +1,10 @@
+HEAD
+====
+  - :class:`ihm.location.DatabaseLocation` no longer accepts a ``db_name``
+    parameter. Derived classes (such as :class:`ihm.location.PDBLocation`)
+    should be used instead; the base class should only be used for "other"
+    databases that are not described in the IHM dictionary (#116).
+
 0.38 - 2023-05-26
 =================
   - Convenience classes are added to describe datasets stored in

modules/core/dependency/python-ihm/docs/cross_linkers.rst

@@ -49,3 +49,30 @@ The :mod:`ihm.cross_linkers` Python module
    SDA (NHS-Diazirine) (succinimidyl 4,4′-azipentanoate) cross-linker that
    links primary amines with nearly any other functional group via
    long-wave UV-light activation.
+
+.. data:: photo_leucine
+
+   L-photo-leucine. Non-canonical amino acid incorporated at leucine
+   positions that links leucine to any other functional group via long-wave
+   UV-light activation.
+   See `Suchanek et al, 2005 <https://doi.org/10.1038/nmeth752>`_.
+
+.. data:: dsbu
+
+   dsbu (disuccinimidyl dibutyric urea) cross-linker that links a primary
+   amine with another primary amine (non-water-soluble).
+   Cleavable in the gas phase using collision-induced dissociation.
+   See `Müller et al, 2011 <https://doi.org/10.1021/ac101241t>`_.
+
+.. data:: phoX
+
+   PhoX cross-linker that links a primary amine with another primary amine.
+   The spacer group contains a phosphonate group, making the cross-linker
+   IMAC-enrichable. Also known by the name DSPP. See
+   `Steigenberger et al, 2019 <https://doi.org/10.1021/acscentsci.9b00416>`_.
+
+.. data:: tbuphoX
+
+   Tert-butyl PhoX cross-linker. Similar to PhoX, but containing a tert-butyl
+   group that renders the cross-linker cell permeable.
+   See `Jiang et al, 2021 <https://doi.org/10.1002/anie.202113937>`_.

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

@@ -575,7 +575,7 @@ class Software(object):
     """Software used as part of the modeling protocol.
 
        :param str name: The name of the software.
-       :param str classification: The major function of the sofware, for
+       :param str classification: The major function of the software, for
               example 'model building', 'sample preparation',
               'data collection'.
        :param str description: A longer text description of the software.
@@ -1086,6 +1086,8 @@ class Residue(object):
     def __init__(self, seq_id, entity=None, asym=None):
         self.entity = entity
         self.asym = asym
+        if entity is None and asym:
+            self.entity = asym.entity
         # todo: check id for validity (at property read time)
         self.seq_id = seq_id
 
@@ -1106,8 +1108,7 @@ def _get_ins_code(self):
                             "for asymmetric units")
 
     def _get_comp(self):
-        entity = self.entity or self.asym.entity
-        return entity.sequence[self.seq_id - 1]
+        return self.entity.sequence[self.seq_id - 1]
     comp = property(_get_comp,
                     doc="Chemical component (residue type)")
 

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

@@ -64,3 +64,26 @@
     inchi='1S/C9H11N3O4/c1-9(10-11-9)5-4-8(15)16-12-6(13)2-3-'
           '7(12)14/h2-5H2,1H3',
     inchi_key=' SYYLQNPWAPHRFV-UHFFFAOYSA-N')
+
+photo_leucine = ihm.ChemDescriptor(
+    'L-Photo-Leucine', chemical_name='L-Photo-Leucine',
+    smiles='CC1(C[C@H](N)C(O)=O)N=N1',
+    inchi='1S/C5H9N3O2/c1-5(7-8-5)'
+          '2-3(6)4(9)10/h3H,2,6H2,1H3,(H,9,10)/t3-/m0/s1',
+    inchi_key='MJRDGTVDJKACQZ-VKHMYHEASA-N')
+
+dsbu = ihm.ChemDescriptor(
+    'DSBU', chemical_name='disuccinimidyl dibutyric urea',
+    smiles='O=C(NCCCC(=O)ON1C(=O)CCC1=O)NCCCC(=O)ON2C(=O)CCC2=O',
+    inchi='S/C17H22N4O9/c22-11-5-6-12(23)20(11)29-15(26)'
+          '3-1-9-18-17(28)19-10-2-4-16(27)30-21-13(24)7-8-14(21)'
+          '25/h1-10H2,(H2,18,19,28)',
+    inchi_key='XZSQCCZQFXUQCY-UHFFFAOYSA-N')
+
+phoX = ihm.ChemDescriptor(
+    'DSPP', chemical_name='(3,5-bis(((2,5-dioxopyrrolidin-1-yl)oxy)'
+                          'carbonyl) phenyl)phosphonic acid')
+
+tbuphoX = ihm.ChemDescriptor(
+    'TBDSPP', chemical_name='tert-butyl disuccinimidyl'
+                            'phenyl phosphonate, tBu-PhoX')

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

@@ -718,7 +718,7 @@ def get_next_id(self):
         self.index += 1
         while self.ids[self.index] in self.seen_ids:
             self.index += 1
-        # Note tha we don't need to add our own IDs to seen_ids since
+        # Note that we don't need to add our own IDs to seen_ids since
         # they are already guaranteed to be unique
         return self.ids[self.index]
 

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

@@ -504,7 +504,7 @@ def _get_mask_and_type(data):
             mask[i] = 1 if val is None else 2
         else:
             seen_types.add(type(val))
-    # If a mix of types, coerce to that of the highest precendence
+    # If a mix of types, coerce to that of the highest precedence
     # (mixed int/float can be represented as float; mix int/float/str can
     # be represented as str; bool is represented as str)
     if not seen_types or bool in seen_types or str in seen_types:

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

@@ -61,18 +61,21 @@ def __hash__(self):
 
 class DatabaseLocation(Location):
     """A dataset stored in an official database (PDB, EMDB, PRIDE, etc.).
+       Generally a subclass should be used specific to the database -
+       for example, :class:`PDBLocation`, :class:`EMDBLocation`, or
+       :class:`PRIDELocation`, although this base class can be used directly
+       for "other" databases not currently supported by the IHM dictionary.
 
-       :param str db_name: The name of the database.
        :param str db_code: The accession code inside the database.
        :param str version: The version of the dataset in the database.
        :param str details: Additional details about the dataset, if known.
     """
 
     _eq_keys = Location._eq_keys + ['db_name', 'access_code', 'version']
+    db_name = 'Other'
 
-    def __init__(self, db_name, db_code, version=None, details=None):
+    def __init__(self, db_code, version=None, details=None):
         super(DatabaseLocation, self).__init__(details)
-        self.db_name = db_name
         self.access_code = db_code
         self.version = version
 
@@ -81,154 +84,98 @@ class EMDBLocation(DatabaseLocation):
     """Something stored in the EMDB database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'EMDB'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(EMDBLocation, self).__init__(self._db_name, db_code,
-                                           version, details)
+    db_name = 'EMDB'
 
 
 class PDBLocation(DatabaseLocation):
     """Something stored in the PDB database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'PDB'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(PDBLocation, self).__init__(self._db_name, db_code,
-                                          version, details)
+    db_name = 'PDB'
 
 
 class PDBDevLocation(DatabaseLocation):
     """Something stored in the PDB-Dev database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'PDB-Dev'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(PDBDevLocation, self).__init__(self._db_name, db_code,
-                                             version, details)
+    db_name = 'PDB-Dev'
 
 
 class ModelArchiveLocation(DatabaseLocation):
     """Something stored in Model Archive.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'MODEL ARCHIVE'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(ModelArchiveLocation, self).__init__(self._db_name, db_code,
-                                                   version, details)
+    db_name = 'MODEL ARCHIVE'
 
 
 class BMRBLocation(DatabaseLocation):
     """Something stored in the BMRB database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'BMRB'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(BMRBLocation, self).__init__(self._db_name, db_code,
-                                           version, details)
+    db_name = 'BMRB'
 
 
 class MassIVELocation(DatabaseLocation):
     """Something stored in the MassIVE database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'MASSIVE'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(MassIVELocation, self).__init__(self._db_name, db_code, version,
-                                              details)
+    db_name = 'MASSIVE'
 
 
 class EMPIARLocation(DatabaseLocation):
     """Something stored in the EMPIAR database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'EMPIAR'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(EMPIARLocation, self).__init__(self._db_name, db_code, version,
-                                             details)
+    db_name = 'EMPIAR'
 
 
 class SASBDBLocation(DatabaseLocation):
     """Something stored in the SASBDB database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'SASBDB'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(SASBDBLocation, self).__init__(self._db_name, db_code, version,
-                                             details)
+    db_name = 'SASBDB'
 
 
 class PRIDELocation(DatabaseLocation):
     """Something stored in the PRIDE database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'PRIDE'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(PRIDELocation, self).__init__(self._db_name, db_code, version,
-                                            details)
+    db_name = 'PRIDE'
 
 
 class JPOSTLocation(DatabaseLocation):
     """Something stored in the JPOST database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'jPOSTrepo'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(JPOSTLocation, self).__init__(self._db_name, db_code, version,
-                                            details)
+    db_name = 'jPOSTrepo'
 
 
 class BioGRIDLocation(DatabaseLocation):
     """Something stored in the BioGRID database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'BioGRID'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(BioGRIDLocation, self).__init__(self._db_name, db_code, version,
-                                              details)
+    db_name = 'BioGRID'
 
 
 class ProXLLocation(DatabaseLocation):
     """Something stored in the ProXL database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'ProXL'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(ProXLLocation, self).__init__(self._db_name, db_code, version,
-                                            details)
+    db_name = 'ProXL'
 
 
 class IProXLocation(DatabaseLocation):
     """Something stored in the iProX database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'iProX'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(IProXLocation, self).__init__(self._db_name, db_code, version,
-                                            details)
+    db_name = 'iProX'
 
 
 class AlphaFoldDBLocation(DatabaseLocation):
     """Something stored in the AlphaFoldDB database.
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
-    _db_name = 'AlphaFoldDB'
-
-    def __init__(self, db_code, version=None, details=None):
-        super(AlphaFoldDBLocation, self).__init__(
-            self._db_name, db_code, version, details)
+    db_name = 'AlphaFoldDB'
 
 
 class FileLocation(Location):

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

@@ -1421,11 +1421,11 @@ def __init__(self, *args):
         super(_DatasetDBRefHandler, self).__init__(*args)
         # Map data_type to corresponding
         # subclass of ihm.location.DatabaseLocation
+        # or ihm.location.DatabaseLocation itself
         self.type_map = dict(
-            (x[1]._db_name.lower(), x[1])
+            (x[1].db_name.lower(), x[1])
             for x in inspect.getmembers(ihm.location, inspect.isclass)
-            if issubclass(x[1], ihm.location.DatabaseLocation)
-            and x[1] is not ihm.location.DatabaseLocation)
+            if issubclass(x[1], ihm.location.DatabaseLocation))
 
     def __call__(self, dataset_list_id, db_name, id, version, details,
                  accession_code):
@@ -1434,7 +1434,7 @@ def __call__(self, dataset_list_id, db_name, id, version, details,
         dbloc = self.sysr.db_locations.get_by_id(id,
                                                  self.type_map.get(typ, None))
         # Preserve user-provided name for unknown databases
-        if dbloc.db_name is None and db_name is not None:
+        if dbloc.db_name == 'Other' and db_name is not None:
             dbloc.db_name = db_name
         ds.location = dbloc
         self.copy_if_present(

modules/core/dependency/python-ihm/src/ihm_format.c

@@ -229,7 +229,7 @@ struct ihm_mapping {
   ihm_destroy_callback value_destroy_func;
 };
 
-/* Make a new mapping from case-insensitive strings to arbitary pointers.
+/* Make a new mapping from case-insensitive strings to arbitrary pointers.
    The mapping uses a simple binary search (more memory efficient than
    a hash table and generally faster too since the number of keys is quite
    small). */

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

@@ -1230,7 +1230,7 @@ def test_dataset_dumper_duplicates_details(self):
     def test_dataset_dumper_duplicates_samedata_sameloc(self):
         """DatasetDumper doesn't duplicate same datasets in same location"""
         system = ihm.System()
-        loc1 = ihm.location.DatabaseLocation("mydb", "abc", "1.0", "")
+        loc1 = ihm.location.DatabaseLocation("abc", "1.0", "")
 
         # Identical datasets in the same location aren't duplicated
         cx1 = ihm.dataset.CXMSDataset(loc1)
@@ -1246,8 +1246,8 @@ def test_dataset_dumper_duplicates_samedata_sameloc(self):
     def test_dataset_dumper_duplicates_samedata_diffloc(self):
         """DatasetDumper is OK with same datasets in different locations"""
         system = ihm.System()
-        loc1 = ihm.location.DatabaseLocation("mydb", "abc", "1.0", "")
-        loc2 = ihm.location.DatabaseLocation("mydb", "xyz", "1.0", "")
+        loc1 = ihm.location.DatabaseLocation("abc", "1.0", "")
+        loc2 = ihm.location.DatabaseLocation("xyz", "1.0", "")
         cx1 = ihm.dataset.CXMSDataset(loc1)
         cx2 = ihm.dataset.CXMSDataset(loc2)
         dump = ihm.dumper._DatasetDumper()
@@ -1261,7 +1261,7 @@ def test_dataset_dumper_duplicates_diffdata_sameloc(self):
         """DatasetDumper is OK with different datasets in same location"""
         system = ihm.System()
         # Different datasets in same location are OK (but odd)
-        loc2 = ihm.location.DatabaseLocation("mydb", "xyz", "1.0", "")
+        loc2 = ihm.location.DatabaseLocation("xyz", "1.0", "")
         cx2 = ihm.dataset.CXMSDataset(loc2)
         em3d = ihm.dataset.EMDensityDataset(loc2)
         dump = ihm.dumper._DatasetDumper()

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

@@ -26,7 +26,7 @@ def test_probe_eq(self):
         self.assertTrue(p_ref != p_unequal)
 
     def test_probe_descriptor_init(self):
-        """ Test initalization of ProbeDescriptor """
+        """ Test initialization of ProbeDescriptor """
         p = ihm.flr.ProbeDescriptor(reactive_probe_chem_descriptor='foo',
                                     chromophore_chem_descriptor='bar',
                                     chromophore_center_atom='foo2')
@@ -399,7 +399,7 @@ def test_exp_condition_eq(self):
         self.assertTrue(e_ref != e_unequal)
 
     def test_fret_analysis_init(self):
-        """Test initalization of FRETAnalysis."""
+        """Test initialization of FRETAnalysis."""
         f = ihm.flr.FRETAnalysis(
             experiment='this_experiment',
             sample_probe_1='this_sample_probe_1',