Document useful conop functions.

modules/conop/doc/connectivity.rst

@@ -78,6 +78,7 @@ The Processor base class
     Whether an additional bond feasibility check is performed. Disabled by default.
     Turn this on, if you would like to connect atoms by bonds only if they are 
     within a reasonable distance.
+    See also :func:`IsBondFeasible`.
 
     :type: :class:`bool`
 
@@ -85,6 +86,7 @@ The Processor base class
 
     Whether backbone torsions should be added to the backbone. Disabled by default.
     Set to true, to assign PHI, PSI and OMEGA torsions to the peptide residues.
+    See also :func:`AssignBackboneTorsions`.
 
     :type: :class:`bool`
 

modules/conop/doc/functions.rst

 Conop Functions
 =======================================================================
 
+.. currentmodule:: ost.conop
 
 .. function:: AssignBackboneTorsions(prev, res, next)
               AssignBackboneTorsions(chain)
               AssignBackboneTorsions(residues)
    
-   Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms 
-   are required to be connected for the torsions to be added. In addition, 
-   only residues for which :meth:`mol.ResidueHandle.IsPeptideLinking` returns 
-   true are considered.
-
-   The first signature assigns the torsions to *res*, assuming prev is 
-   the amino acid before, and *next* is the amino acid next to *res*.  
-   Both *next* and *prev* may be invalid residues.
-
-   The second and third signature assign the torsions to all peptidic 
-   residues of the chain/the residue list. The residues in the chain, 
-   the residue list are thought to run from N to C terminus.
-
-   :param prev: The amino acid before *res*
-   :type prev: :class:`~mol.ResidueHandle`
-   :type next: :class:`~mol.ResidueHandle`
-   :param next: The amino acid after *res*
-   :type res: :class:`~mol.ResidueHandle`
-   :type res: The central amino acid. Must be a valid handle
-
-.. function:: GetUnknownAtomsOfResidue(residue, compound, strict_hydrogens=False) 
+  Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms 
+  are required to be connected for the torsions to be added. In addition, 
+  only residues for which :meth:`~ost.mol.ResidueHandle.IsPeptideLinking`
+  returns True are considered.
+
+  The first signature assigns the torsions to *res*, assuming prev is 
+  the amino acid before, and *next* is the amino acid next to *res*.  
+  Both *next* and *prev* may be invalid residues.
+
+  The second and third signature assign the torsions to all peptidic 
+  residues of the chain/the residue list. The residues in the chain, 
+  the residue list are thought to run from N to C terminus.
+
+  :param prev: The amino acid before *res*
+  :type prev:  :class:`~ost.mol.ResidueHandle`
+  :param res: The central amino acid. Must be a valid handle.
+  :type res:  :class:`~ost.mol.ResidueHandle`
+  :param next: The amino acid after *res*
+  :type next:  :class:`~ost.mol.ResidueHandle`
+  :param chain: Chain to process.
+  :type chain:  :class:`~ost.mol.ChainHandle`
+  :param residues: List of residues to process.
+  :type residues:  :class:`~ost.mol.ResidueHandleList`
+
+.. function:: IsBondFeasible(atom_a, atom_b)
+
+  :return: True, if *atom_a* and *atom_b* are within a reasonable distance for a
+           bond to be present. Depends on :attr:`~ost.mol.AtomHandle.radius` of
+           atoms and heuristic formulas.
+  :rtype:  :class:`bool`
+  :param atom_a: Atom to be checked.
+  :type atom_a:  :class:`~ost.mol.AtomHandle`
+  :param atom_b: Atom to be checked.
+  :type atom_b:  :class:`~ost.mol.AtomHandle`
+
+.. function:: GetUnknownAtomsOfResidue(residue, compound, strict_hydrogens=False)
 
   Returns the list of atoms present in *residue* that are not part of the 
-  atom specifications in compound.
-
-  :param strict_hydrogens: When set to true, hydrogen atoms are checked as well.
+  atom specifications in *compound*.
+
+  :param residue: The residue to analyze.
+  :type residue:  :class:`~ost.mol.ResidueHandle`
+  :param compound: Chemical compound to compare with.
+  :type compound:  :class:`Compound`
+  :param strict_hydrogens: When set to True, hydrogen atoms are checked as well.
+  :type strict_hydrogens:  :class:`bool`
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