doc: SEQRES no longer needed.

Following fixes in cd701347, setting seqres=True is no longer required
for these things to work.

actions/ost-compare-ligand-structures

@@ -250,8 +250,7 @@ def _LoadStructure(structure_path, format="auto", fault_tolerant=False):
 
     # Load the structure
     if format in ["mmcif", "cif"]:
-        entity, seqres = io.LoadMMCIF(structure_path, seqres=True,
-                                      fault_tolerant=fault_tolerant)
+        entity = io.LoadMMCIF(structure_path, fault_tolerant=fault_tolerant)
         if len(entity.residues) == 0:
             raise Exception(f"No residues found in file: {structure_path}")
     elif format == "pdb":

modules/io/doc/mmcif.rst

@@ -64,9 +64,8 @@ Notes:
   It is added as string property named "pdb_auth_chain_name" to the
   :class:`~ost.mol.ChainHandle`. The mapping is also stored in
   :class:`MMCifInfo` as :meth:`~MMCifInfo.GetMMCifPDBChainTr` and
-  :meth:`~MMCifInfo.GetPDBMMCifChainTr` if SEQRES records are read in
-  :func:`~ost.io.LoadMMCIF` and a non-empty SEQRES record exists for that chain
-  (this should exclude ligands and water).
+  :meth:`~MMCifInfo.GetPDBMMCifChainTr` if a non-empty SEQRES record exists for
+  that chain (this should exclude ligands and water).
 * Molecular entities in mmCIF are identified by an ``entity.id``, which is
   extracted from ``atom_site.label_entity_id`` for the first atom of the chain.
   It is added as string property named "entity_id" to the
@@ -99,12 +98,6 @@ Information from mmCIF files that goes beyond structural data, is kept in a
 special container, the :class:`MMCifInfo` class. Here is a detailed description
 of the annotation available.
 
-.. note::
-
-  Some fields of the ``MMCifInfo`` container are only populated if SEQRES
-  records are read in :func:`~ost.io.LoadMMCIF` and a compound library is
-  available (see :func:`~ost.conop.GetDefaultLib`)
-
 .. class:: MMCifInfo
 
   This is the container for all bits of non-molecular data pulled from a mmCIF
@@ -278,9 +271,7 @@ of the annotation available.
   .. method:: GetMMCifPDBChainTr(cif_chain_id)
 
     Get the translation of a certain mmCIF chain name to the traditional PDB
-    chain name. Only works if SEQRES records are read in
-    :func:`~ost.io.LoadMMCIF` and a compound library is available (see
-    :func:`~ost.conop.GetDefaultLib`).
+    chain name.
 
     :param cif_chain_id: atom_site.label_asym_id
     :type cif_chain_id: :class:`str`
@@ -298,8 +289,6 @@ of the annotation available.
   .. method:: GetPDBMMCifChainTr(pdb_chain_id)
 
     Get the translation of a certain PDB chain name to the mmCIF chain name.
-    Only works if SEQRES records are read in :func:`~ost.io.LoadMMCIF` and a
-    compound library is available (see :func:`~ost.conop.GetDefaultLib`).
 
     :param pdb_chain_id: atom_site.auth_asym_id
     :type pdb_chain_id: :class:`str`

modules/mol/alg/pymod/ligand_scoring.py

@@ -111,7 +111,7 @@ class LigandScorer:
         # Ligand model as SDF file
         model_ligand = io.LoadEntity("path_to_ligand.sdf", format="sdf")
         # Target loaded from mmCIF, containing the ligand
-        target, _ = io.LoadMMCIF("path_to_target.cif", seqres=True)
+        target = io.LoadMMCIF("path_to_target.cif")
 
         # Cleanup a copy of the structures
         cleaned_model = model.Copy()

modules/mol/alg/tests/test_ligand_scoring.py

@@ -22,7 +22,7 @@ def _GetTestfilePath(filename):
 @lru_cache(maxsize=None)
 def _LoadMMCIF(filename):
     path = _GetTestfilePath(filename)
-    ent, seqres = io.LoadMMCIF(path, seqres=True)
+    ent = io.LoadMMCIF(path)
     return ent
 
 

modules/mol/base/doc/entity.rst

@@ -741,11 +741,6 @@ The Handle Classes
   
   .. attribute:: is_ligand
 
-    .. warning::
-      This property is meaningless on mmCIF files loaded with
-      :func:`ost.io.LoadMMCIF` with `seqres=False` (the default), or if no
-      default compound library is set.
-
     Whether the residue is a ligand. When loading PDB structures, this property
     is set based on the HET records. This also means, that this property will
     most likely not be set properly for all except PDB files coming from