Squashed 'modules/core/dependency/python-ihm/' changes from c75b4bdd9…

…5..29985eda1e

29985eda1e Update copyright year
78b985e34c Fix use of Sphinx data::
0c3d63071b Improve cross linker docs
e2decbe80d Fix documentation of cross-linkers
b57bc554d4 Add a module with commonly-used cross-linkers
5d46a680dc Test ChemDescriptors referenced by restraints
2883917c4a Use chemical descriptors in cross link restraints
3552247632 Fix typo
826dc56f30 Add basic support for chemical descriptors
1768608ab5 Fix typo
0bb0e3a048 ihm_feature_pseudo_site -> ihm_pseudo_site_feature
6cec1809b4 Add support for pseudo sites
756ebed7d6 Use trusty for Python 2.6 builds
8b8b554ba7 Check to see if Travis works with Python 3.7 now
4c9485782e Prepare for 0.4 release

git-subtree-dir: modules/core/dependency/python-ihm
git-subtree-split: 29985eda1e1e73a27a8d75c7ed43926eed6008d2

modules/core/dependency/python-ihm/.travis.yml

@@ -1,9 +1,14 @@
 sudo: false
 language: python
+dist: xenial
 python:
-  - 2.6
   - 2.7
   - 3.6
+  - 3.7
+matrix:
+  include:
+    - dist: trusty
+      python: 2.6
 addons:
   apt:
     packages:

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

@@ -1,11 +1,31 @@
 HEAD
 ====
-
+ - :class:`ihm.restraint.CrossLinkRestraint` now takes an
+   :class:`ihm.ChemDescriptor` object rather than the name of the cross-linker
+   used. This allows the use of novel cross-linkers (beyond those currently
+   listed in a fixed enumeration in the IHM dictionary).
+   :class:`ihm.ChemDescriptor` allows for the chemical structure of the
+   cross-linker to be uniquely specified, as a SMILES or INCHI string.
+   The :mod:`ihm.cross_linkers` module provides chemical descriptors for
+   some commonly-used cross-linkers.
+ - Pseudo sites are now supported. :class:`ihm.restraint.PseudoSiteFeature`
+   allows points or spheres with arbitrary coordinates to be designated as
+   features, which can then be used in
+   :class:`ihm.restraint.DerivedDistanceRestraint`.
+
+0.4 - 2018-12-17
+================
  - Certain restraints can now be grouped using the
    :class:`ihm.restraint.RestraintGroup` class. Due to limitations of the
    underlying dictionary, this only works for some restraint types (currently
    only :class:`ihm.restraint.DerivedDistanceRestraint`) and all restraints
    in the group must be of the same type.
+ - Bugfix: the the model's representation (see :mod:`ihm.representation`)
+   need not be a strict subset of the model's :class:`ihm.Assembly`. However,
+   any :class:`ihm.model.Atom` or :class:`ihm.model.Sphere` objects must be
+   covered by both the representation and the model's :class:`ihm.Assembly`.
+ - Bugfix: the reader no longer fails to read files that contain
+   _entity.formula_weight.
 
 0.3 - 2018-11-21
 ================

modules/core/dependency/python-ihm/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 IHM Working Group
+Copyright (c) 2018-2019 IHM Working Group
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

modules/core/dependency/python-ihm/docs/conf.py

@@ -47,7 +47,7 @@
 
 # General information about the project.
 project = u'Python-IHM'
-copyright = u'2018, Benjamin Webb'
+copyright = u'2018-2019, Benjamin Webb'
 author = u'Benjamin Webb'
 
 # The version info for the project you're documenting, acts as replacement for

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

@@ -0,0 +1,16 @@
+.. highlight:: rest
+
+.. _cross_linkers_module:
+
+The :mod:`ihm.cross_linkers` Python module
+==========================================
+
+.. automodule:: ihm.cross_linkers
+
+.. data:: dss
+
+   DSS cross-linker that links a primary amine with another primary amine.
+
+.. data:: edc
+
+   EDC cross-linker that links a carboxyl group with a primary amine.

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

@@ -34,6 +34,7 @@ API Reference:
    representation
    geometry
    restraint
+   cross_linkers
    protocol
    analysis
    model

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

@@ -77,3 +77,6 @@ The :mod:`ihm` Python module
 
 .. autoclass:: Assembly
    :members:
+
+.. autoclass:: ChemDescriptor
+   :members:

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

@@ -73,6 +73,9 @@ The :mod:`ihm.restraint` Python module
 .. autoclass:: NonPolyFeature
    :members:
 
+.. autoclass:: PseudoSiteFeature
+   :members:
+
 .. autoclass:: GeometricRestraint
    :members:
 

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

@@ -20,7 +20,7 @@
     import urllib2
 import json
 
-__version__ = '0.3'
+__version__ = '0.4'
 
 #: A value that isn't known. Note that this is distinct from a value that
 #: is deliberately omitted, which is represented by Python None.
@@ -64,6 +64,12 @@ def __init__(self, title=None, id='model'):
         #: All asymmetric units used in the system. See :class:`AsymUnit`.
         self.asym_units = []
 
+        #: All orphaned chemical descriptors in the system.
+        #: See :class:`ChemDescriptor`. This can be used to track descriptors
+        #: that are not otherwise used - normally one is assigned to a
+        #: :class:`ihm.restraint.CrossLinkRestraint`.
+        self.orphan_chem_descriptors = []
+
         #: All orphaned assemblies in the system. See :class:`Assembly`.
         #: This can be used to keep track of all assemblies that are not
         #: otherwise used - normally one is assigned to a
@@ -194,6 +200,14 @@ def _all_restraints_in_groups():
                     yield r
         return itertools.chain(self.restraints, _all_restraints_in_groups())
 
+    def _all_chem_descriptors(self):
+        """Iterate over all ChemDescriptors in the system.
+           Duplicates may be present."""
+        return itertools.chain(self.orphan_chem_descriptors,
+                      (restraint.linker for restraint in self.restraints
+                                        if hasattr(restraint, 'linker')
+                                        and restraint.linker))
+
     def _all_model_groups(self, only_in_states=True):
         """Iterate over all ModelGroups in the system.
            If only_in_states is True, only return ModelGroups referenced
@@ -537,7 +551,7 @@ class ChemComp(object):
        :param str code_canonical: Canonical version of `code` (which need not
               be unique).
        :param str name: A longer human-readable name for the component.
-       :param str formula: The chemical formula. This is a spaced-separated
+       :param str formula: The chemical formula. This is a space-separated
               list of the element symbols in the component, each followed
               by an optional count (if omitted, 1 is assumed). The formula
               is terminated with the formal charge (if not zero). The element
@@ -1037,3 +1051,35 @@ class Assembly(list):
     def __init__(self, elements=(), name=None, description=None):
         super(Assembly, self).__init__(elements)
         self.name, self.description = name, description
+
+
+class ChemDescriptor(object):
+    """Description of a non-polymeric chemical component used in the experiment.
+       For example, this might be a fluorescent probe or cross-linking agent.
+       This class describes the chemical structure of the component, for
+       example with a SMILES or INCHI descriptor, so that it is uniquely
+       defined. A descriptor is typically assigned to a
+       :class:`ihm.restraint.CrossLinkRestraint`.
+
+       See :mod:`ihm.cross_linkers` for chemical descriptors of some
+       commonly-used cross-linking agents.
+
+       :param str auth_name: Author-provided name
+       :param str chem_comp_id: If this chemical is listed in the Chemical
+              Component Dictionary, its three-letter identifier
+       :param str chemical_name: The systematic (IUPAC) chemical name
+       :param str common_name: Common name for the component
+       :param str smiles: SMILES string
+       :param str smiles_canonical: Canonical SMILES string
+       :param str inchi: IUPAC INCHI descriptor
+       :param str inchi_key: Hashed INCHI key
+
+       See also :attr:`System.orphan_chem_descriptors`.
+    """
+    def __init__(self, auth_name, chem_comp_id=None, chemical_name=None,
+                 common_name=None, smiles=None, smiles_canonical=None,
+                 inchi=None, inchi_key=None):
+        self.auth_name, self.chem_comp_id = auth_name, chem_comp_id
+        self.chemical_name, self.common_name = chemical_name, common_name
+        self.smiles, self.smiles_canonical = smiles, smiles_canonical
+        self.inchi, self.inchi_key = inchi, inchi_key

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

@@ -0,0 +1,20 @@
+"""Chemical descriptors of commonly-used cross-linkers.
+
+   Each of these is an instance of the :class:`ihm.ChemDescriptor` class,
+   and so can be used anywhere these objects are required, generally for
+   :class:`ihm.restraint.CrossLinkRestraint`.
+"""
+
+import ihm
+
+dss = ihm.ChemDescriptor('DSS', chemical_name='disuccinimidyl suberate',
+              smiles='C1CC(=O)N(C1=O)OC(=O)CCCCCCC(=O)ON2C(=O)CCC2=O',
+              inchi='1S/C16H20N2O8/c19-11-7-8-12(20)17(11)25-15(23)5-'
+                    '3-1-2-4-6-16(24)26-18-13(21)9-10-14(18)22/h1-10H2',
+              inchi_key='ZWIBGKZDAWNIFC-UHFFFAOYSA-N')
+
+edc = ihm.ChemDescriptor('EDC',
+              chemical_name='1-ethyl-3-(3-dimethylaminopropyl)carbodiimide',
+              smiles='CCN=C=NCCCN(C)C',
+              inchi='1S/C8H17N3/c1-4-9-8-10-6-5-7-11(2)3/h4-7H2,1-3H3',
+              inchi_key='LMDZBCPBFSXMTL-UHFFFAOYSA-N')

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

@@ -148,6 +148,30 @@ def dump(self, system, writer):
                                 formula_weight=comp.formula_weight)
 
 
+class _ChemDescriptorDumper(_Dumper):
+    def finalize(self, system):
+        seen_desc = {}
+        # Assign IDs to all descriptors
+        self._descriptor_by_id = []
+        for d in system._all_chem_descriptors():
+            util._remove_id(d)
+        for d in system._all_chem_descriptors():
+            util._assign_id(d, seen_desc, self._descriptor_by_id)
+
+    def dump(self, system, writer):
+        with writer.loop("_ihm_chemical_descriptor",
+                ["id", "auth_name", "chem_comp_id", "chemical_name",
+                 "common_name", "smiles", "smiles_canonical", "inchi",
+                 "inchi_key"]) as l:
+            for d in self._descriptor_by_id:
+                l.write(id=d._id, auth_name=d.auth_name,
+                        chem_comp_id=d.chem_comp_id,
+                        chemical_name=d.chemical_name,
+                        common_name=d.common_name, smiles=d.smiles,
+                        smiles_canonical=d.smiles_canonical, inchi=d.inchi,
+                        inchi_key=d.inchi_key)
+
+
 class _EntityDumper(_Dumper):
     def finalize(self, system):
         # Assign IDs and check for duplicates
@@ -1346,6 +1370,7 @@ def dump(self, system, writer):
         self.dump_poly_residue(writer)
         self.dump_poly_atom(writer)
         self.dump_non_poly(writer)
+        self.dump_pseudo_site(writer)
 
     def dump_list(self, writer):
         with writer.loop("_ihm_feature_list",
@@ -1417,6 +1442,16 @@ def dump_non_poly(self, writer):
                                 atom_id=None)
                         ordinal += 1
 
+    def dump_pseudo_site(self, writer):
+        with writer.loop("_ihm_pseudo_site_feature",
+                         ["feature_id", "Cartn_x", "Cartn_y",
+                          "Cartn_z", "radius", "description"]) as l:
+            for f in self._features_by_id:
+                if not isinstance(f, restraint.PseudoSiteFeature):
+                    continue
+                l.write(feature_id=f._id, Cartn_x=f.x, Cartn_y=f.y,
+                        Cartn_z=f.z, radius=f.radius, description=f.description)
+
 
 class _CrossLinkDumper(_Dumper):
     def _all_restraints(self, system):
@@ -1438,7 +1473,7 @@ def finalize_experimental(self, system):
                     # Assign identical cross-links the same ID and group ID
                     sig = (xl.residue1.entity, xl.residue1.seq_id,
                            xl.residue2.entity, xl.residue2.seq_id,
-                           r.linker_type)
+                           r.linker)
                     if sig in seen_cross_links:
                         xl._id, xl._group_id = seen_cross_links[sig]
                     else:
@@ -1461,7 +1496,7 @@ def finalize_modeling(self, system):
                 ex_xl = xl.experimental_cross_link
                 sig = (xl.asym1._id, ex_xl.residue1.seq_id, xl.atom1,
                        xl.asym2._id, ex_xl.residue2.seq_id, xl.atom2,
-                       r.linker_type)
+                       r.linker)
                 if sig in seen_cross_links:
                     xl._id = seen_cross_links[sig]
                 else:
@@ -1481,7 +1516,8 @@ def dump_list(self, system, writer):
                           "entity_id_1", "seq_id_1", "comp_id_1",
                           "entity_description_2",
                           "entity_id_2", "seq_id_2", "comp_id_2",
-                          "linker_type", "dataset_list_id"]) as l:
+                          "linker_descriptor_id", "linker_type",
+                          "dataset_list_id"]) as l:
             for r, xl in self._ex_xls_by_id:
                 entity1 = xl.residue1.entity
                 entity2 = xl.residue2.entity
@@ -1496,7 +1532,8 @@ def dump_list(self, system, writer):
                         entity_id_2=entity2._id,
                         seq_id_2=xl.residue2.seq_id,
                         comp_id_2=seq2[xl.residue2.seq_id-1].id,
-                        linker_type=r.linker_type,
+                        linker_descriptor_id=r.linker._id,
+                        linker_type=r.linker.auth_name,
                         dataset_list_id=r.dataset._id)
 
     def dump_restraint(self, system, writer):
@@ -1794,7 +1831,7 @@ def write(fh, systems, format='mmCIF'):
                _AuditConformDumper(), _SoftwareDumper(),
                _CitationDumper(),
                _AuditAuthorDumper(),
-               _ChemCompDumper(),
+               _ChemCompDumper(), _ChemDescriptorDumper(),
                _EntityDumper(),
                _EntityPolyDumper(),
                _EntityNonPolyDumper(),