Merge branch 'master' into develop

doc/html/_sources/modelling/pipeline.txt → doc/html/_sources/modelling/pipeline.rst.txt

@@ -176,77 +176,9 @@ Build Raw Modelling Handle
 
     :return: A deep copy of the current handle
     :rtype:  :class:`ModellingHandle`
+    
 
-
-.. function:: BuildRawModel(aln, include_ligands=False, chain_names=\
-              "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz",\
-              spdbv_style=False)
-
-  Builds a raw (pseudo) model from the alignment. Can either take a single
-  alignment handle or an alignment handle list. Every list item is treated as a
-  single chain in the final raw model.
-
-  Each alignment handle must contain exactly two sequences and the second
-  sequence is considered the template sequence, which must have a 
-  :class:`~ost.mol.EntityView` attached.
-
-  This is a basic protein core modelling algorithm that copies backbone
-  coordinates based on the sequence alignment. For matching residues, the
-  side chain coordinates are also copied. Gaps are ignored. Hydrogen an
-  deuterium atoms are not copied into the model.
-
-  The function tries to reuse as much as possible from the template. Modified
-  residues are treated as follows:
-
-    - Selenium methionine residues are converted to methionine
-
-    - Side chains which contain all atoms of the parent amino acid, e.g.
-      phosphoserine are copied as a whole with the modifications stripped off.
-
-  Residues with missing backbone atoms and D-peptides are generally skipped and
-  treated as gaps. Missing Cbeta atoms in backbone are ok and reconstructed.
-  If all residues are skipped (e.g. Calpha traces), we report an error and
-  return an empty model.
-
-  Residue numbers are set such that missing residue in gaps are honoured and
-  subsequent loop modelling can insert new residues without having to renumber.
-  **The numbering of residues starts for every chain with the value 1**.
-  
-  The returned :class:`ModellingHandle` stores the obtained raw model as well
-  as information about insertions and deletions in the gaps list.
-
-  :param aln: Single alignment handle for raw model with single chain or
-              list of alignment handles for raw model with multiple chains.
-  :type aln:  :class:`~ost.seq.AlignmentHandle` / :class:`~ost.seq.AlignmentList`
-
-  :param include_ligands: True, if we wish to include ligands in the model. This
-                          searches for ligands in all OST handles of the views
-                          attached to the alignments. Ligands are identified
-                          with the `ligand` property in the handle (set by OST
-                          based on HET records) or by the chain name '_' (as set
-                          in SMTL). All ligands are added to a new chain named
-                          '_'.
-  :type include_ligands:  :class:`bool`
-
-  :param chain_names: Chains are named by a single chanacter taken from this.
-  :type chain_names:  :class:`str`
-
-  :param spdbv_style: True, if we need a model in the old SPDBV style.
-  :type spdbv_style:  :class:`bool`
-
-  :return: Raw (pseudo) model from the alignment.
-  :rtype:  :class:`ModellingHandle`
-
-  :raises: A :exc:`RuntimeError` when: 
-           
-           - the alignments do not have two sequences
-           - the second sequence does not have an attached structure
-           - the residues of the template structure do not match with the
-             alignment sequence (note that you can set an "offset" (see
-             :meth:`~ost.seq.AlignmentHandle.SetSequenceOffset`) for the
-             template sequence (but not for the target))
-           - the target sequence has a non-zero offset (cannot be honored as
-             the resulting model will always start its residue numbering at 1)
+.. autofunction:: BuildRawModel
 
 The Default Pipeline
 --------------------------------------------------------------------------------
@@ -443,3 +375,11 @@ Modelling Steps
   :members:
 
 .. autofunction:: AddModellingIssue
+
+
+Alignment Fiddling
+--------------------------------------------------------------------------------
+
+.. autofunction:: DeleteGapCols
+
+.. autofunction:: PullTerminalDeletions