Fix broken links

ihm/__init__.py

@@ -93,7 +93,7 @@ def __init__(self, title=None, id='model', model_details=None):
         #: List of all authors of this system, as a list of strings (last name
         #: followed by initials, e.g. "Smith, A.J."). When writing out a file,
         #: if this list is empty, the set of all citation authors (see
-        #: :attr:`Citation.authors`) is used instead.
+        #: :class:`Citation`) is used instead.
         self.authors = []
 
         #: List of all grants that supported this work. See :class:`Grant`.
@@ -681,7 +681,7 @@ class Software(object):
        passed to :class:`ihm.startmodel.StartingModel`,
        :class:`ihm.protocol.Step`,
        :class:`ihm.analysis.Step`, or
-       :class:`ihm.restraint.PredictedContactResstraint` objects.
+       :class:`ihm.restraint.PredictedContactRestraint` objects.
     """
     def __init__(self, name, classification, description, location,
                  type='program', version=None, citation=None):

ihm/analysis.py

@@ -8,9 +8,10 @@
 class Step(object):
     """A single step in an :class:`Analysis`.
 
-       Normally one of the base classes is used; see :class:`FilterStep`,
-       :class:`ClusterStep`, :class:`RescoreStep`, :class:`ValidationStep`,
-       :class:`OtherStep`, and :class:`EmptyStep`.
+       Normally one of the more specific derived classes is used;
+       see :class:`FilterStep`, :class:`ClusterStep`, :class:`RescoreStep`,
+       :class:`ValidationStep`, and :class:`EmptyStep`, although this base
+       class can be used for a generic 'other' step.
 
        :param str feature: feature energy/score;RMSD;dRMSD;other
        :param int num_models_begin: The number of models at the beginning

ihm/flr.py

@@ -203,7 +203,7 @@ class EntityAssembly(object):
     """The assembly of the entities that are in the system.
 
        :param entity: The entity to add.
-       :type entity: :class:`Entity`
+       :type entity: :class:`ihm.Entity`
        :param num_copies: The number of copies for the entity in the assembly.
     """
 
@@ -382,7 +382,7 @@ class FRETAnalysis(object):
        :type lifetime_fit_model: :class:`LifetimeFitModel`
        :param ref_measurement_group: The group of reference measurements
              in case of lifetime-based analyses.
-       :type ref_measurement_group: :class:`LifetimeRefMeasurementGroup`
+       :type ref_measurement_group: :class:`RefMeasurementGroup`
        :param str method_name: The method used for the analysis.
        :param float chi_square_reduced: The chi-square reduced as a quality
               measure for the fit.

ihm/format.py

@@ -189,7 +189,7 @@ def loop(self, category, keys):
     def write_comment(self, comment):
         """Write a simple comment to the CIF file.
            The comment will be wrapped if necessary for readability.
-           See :meth:`set_line_wrap`."""
+           See :meth:`_set_line_wrap`."""
         if self._line_wrap:
             for line in textwrap.wrap(comment, 78):
                 self.fh.write('# ' + line + '\n')

ihm/location.py

@@ -19,8 +19,8 @@ class Location(object):
            experimental dataset may be found;
          - an :class:`~ihm.model.Ensemble` to point to coordinates for an
            entire ensemble, for example as a DCD file;
-         - a :class:`LocalizationDensity` to point to an external localization
-           density, for example in MRC format;
+         - a :class:`ihm.model.LocalizationDensity` to point to an external
+           localization density, for example in MRC format;
          - :data:`ihm.System.locations` to point to other files relating
            to the modeling in general, such as a modeling control script
            (:class:`WorkflowFileLocation`) or a command script for a

ihm/model.py

@@ -138,7 +138,7 @@ def add_atom(self, atom):
 
            Note that for branched entities, the `seq_id` of the new atom
            is provisional. It should be mapped to the correct ID once the
-           input file is completely read, using :attr:`AsymUnit.num_map`.
+           input file is completely read, using :attr:`ihm.AsymUnit.num_map`.
            This is done automatically by ihm.reader when using the default
            implementation.
         """

ihm/multi_state_scheme.py

@@ -17,11 +17,10 @@ class MultiStateScheme(object):
        :param str details: Details on the scheme.
        :param connectivities: A list of connectivities that belong to
         the scheme.
-       :type connectivities: List of
-        :class:`ìhm.multi_state_scheme.Connectivity`
+       :type connectivities: List of :class:`Connectivity`
        :param relaxation_times: A list of relaxation times not assigned
         to specific connectivities, but to the scheme
-       :type relaxation_times: List of :class:`ihm.RelaxationTime`
+       :type relaxation_times: List of :class:`RelaxationTime`
     """
     def __init__(self, name, details=None, connectivities=None,
                  relaxation_times=None):

ihm/reader.py

@@ -163,7 +163,7 @@ def _make_new_object(self, newcls=None):
 
 class RangeIDMapper(object):
     """Utility class to handle mapping from mmCIF IDs to
-       :class:`ihm.AsymUnitRange` or :class:`EntityRange` objects."""
+       :class:`ihm.AsymUnitRange` or :class:`ihm.EntityRange` objects."""
 
     def __init__(self):
         self._id_map = {}
@@ -451,7 +451,7 @@ def __init__(self, model_class, starting_model_class):
         self.assemblies = IDMapper(self.system.orphan_assemblies, ihm.Assembly)
 
         #: Mapping from ID to :class:`ihm.AsymUnitRange`
-        #: or :class:`EntityRange` objects
+        #: or :class:`ihm.EntityRange` objects
         self.ranges = RangeIDMapper()
 
         #: Mapping from ID to :class:`ihm.location.Repository` objects
@@ -634,7 +634,7 @@ def __init__(self, model_class, starting_model_class):
             ihm.multi_state_scheme.KineticRate)
 
         #: Mapping from ID to
-        #: :class:`ihm.multi_state_schene.RelaxationTime` objects
+        #: :class:`ihm.multi_state_scheme.RelaxationTime` objects
         self.relaxation_times = IDMapper(
             None,
             ihm.multi_state_scheme.RelaxationTime,
@@ -801,7 +801,7 @@ def __init__(self, model_class, starting_model_class):
             self.flr_data, ihm.flr.FPSMPPModeling, *(None,) * 3)
 
         #: Mapping from ID to
-        #: :class:`ihm.flr.KineticRateFRETAnalysisConnection` objects
+        #: :class:`ihm.flr.KineticRateFretAnalysisConnection` objects
         self.flr_kinetic_rate_fret_analysis_connection = _FLRIDMapper(
             '_collection_flr_kinetic_rate_fret_analysis_connection',
             'kinetic_rate_fret_analysis_connections',
@@ -810,7 +810,7 @@ def __init__(self, model_class, starting_model_class):
             *(None,) * 3)
 
         #: Mapping from ID to
-        #: :class:`ihm.flr.KineticRateFRETAnalysisConnection` objects
+        #: :class:`ihm.flr.RelaxationTimeFretAnalysisConnection` objects
         self.flr_relaxation_time_fret_analysis_connection = _FLRIDMapper(
             '_collection_flr_relaxation_time_fret_analysis_connection',
             'relaxation_time_fret_analysis_connections',

ihm/restraint.py

@@ -587,14 +587,14 @@ def _all_entities_or_asyms(self):
 class ResidueFeature(Feature):
     """Selection of one or more residues from the system.
 
-       Residues can be selected from both :class:`AsymUnit` and
-       :class:`Entity` (the latter implies that it selects residues
+       Residues can be selected from both :class:`ihm.AsymUnit` and
+       :class:`ihm.Entity` (the latter implies that it selects residues
        in all instances of that entity). Individual residues can
-       also be selected by passing :class:`Residue` objects.
+       also be selected by passing :class:`ihm.Residue` objects.
 
-       :param sequence ranges: A list of :class:`AsymUnitRange`,
-              :class:`AsymUnit`, :class:`EntityRange`, :class:`Residue`,
-              and/or :class:`Entity` objects.
+       :param sequence ranges: A list of :class:`ihm.AsymUnitRange`,
+              :class:`ihm.AsymUnit`, :class:`ihm.EntityRange`,
+              :class:`ihm.Residue`, and/or :class:`ihm.Entity` objects.
        :param str details: Additional text describing this feature.
     """
 
@@ -628,8 +628,8 @@ def _get_entity(x):
 class AtomFeature(Feature):
     """Selection of one or more atoms from the system.
        Atoms can be selected from polymers or non-polymers (but not both).
-       Atoms can also be selected from both :class:`AsymUnit` and
-       :class:`Entity` (the latter implies that it selects atoms
+       Atoms can also be selected from both :class:`ihm.AsymUnit` and
+       :class:`ihm.Entity` (the latter implies that it selects atoms
        in all instances of that entity).
        For selecting an entire polymer or residue(s),
        see :class:`ResidueFeature`. For selecting an entire non-polymer,
@@ -659,12 +659,12 @@ class NonPolyFeature(Feature):
     """Selection of one or more non-polymers from the system.
        To select individual atoms from a non-polymer, see :class:`AtomFeature`.
 
-       Features can include both :class:`AsymUnit` and
-       :class:`Entity` (the latter implies that it selects non-polymers
+       Features can include both :class:`ihm.AsymUnit` and
+       :class:`ihm.Entity` (the latter implies that it selects non-polymers
        in all instances of that entity).
 
-       :param sequence objs: A list of :class:`AsymUnit` and/or
-              :class:`Entity` objects.
+       :param sequence objs: A list of :class:`ihm.AsymUnit` and/or
+              :class:`ihm.Entity` objects.
        :param str details: Additional text describing this feature.
     """
 

ihm/source.py

@@ -29,7 +29,7 @@ def __init__(self, ncbi_taxonomy_id=None, scientific_name=None,
 
 class Manipulated(Source):
     """An entity isolated from a genetically manipulated source.
-       See :class:`Entity`.
+       See :class:`ihm.Entity`.
 
        :param gene: Details about the gene source.
        :type gene: :class:`Details`
@@ -43,12 +43,12 @@ def __init__(self, gene=None, host=None):
 
 
 class Natural(Source, Details):
-    """An entity isolated from a natural source. See :class:`Entity`.
+    """An entity isolated from a natural source. See :class:`ihm.Entity`.
        See :class:`Details` for a description of the parameters."""
     src_method = 'nat'
 
 
 class Synthetic(Source, Details):
-    """An entity obtained synthetically. See :class:`Entity`.
+    """An entity obtained synthetically. See :class:`ihm.Entity`.
        See :class:`Details` for a description of the parameters."""
     src_method = 'syn'