diff --git a/modules/conop/doc/connectivity.rst b/modules/conop/doc/connectivity.rst index e379494601a31f27a15673f6b7992e140102c287..e18baf87427bab4bb68c5cddf520a80a70dd0424 100644 --- a/modules/conop/doc/connectivity.rst +++ b/modules/conop/doc/connectivity.rst @@ -40,14 +40,19 @@ Processors The exact behaviour for a processor is implementation-specific. So far, two classes implement the processor interface: A heuristic and a rule-based processor. The processors mainly differ in the source of their connectivity -information. The `HeuristicProcessor` uses a hard-coded heuristic connectivity +information. + +The `HeuristicProcessor` uses a hard-coded heuristic connectivity table for the 20 standard amino acids as well as nucleotides. For other compounds such as ligands the `HeuristicProcessor` runs a distance-based -connectivity algorithm that connects two atoms if they are closer than a certain -threshold. The `RuleBasedProcessor` uses the -:doc:`compound library <compoundlib>`, a connectivity library containing all -molecular components present in the PDB files on PDB.org. The library can easily -be extended with custom connectivity information, if required. +connectivity algorithm that connects two atoms if they belong to the same or +two consecutive residues, and are within a +:func:`reasonable distance <ost.conop.IsBondFeasible>` of each other. + +The `RuleBasedProcessor` uses the :doc:`compound library <compoundlib>`, +a connectivity library containing all molecular components present in the +PDB files on PDB.org. The library can easily be extended with custom +connectivity information, if required. .. class:: Processor diff --git a/modules/conop/doc/functions.rst b/modules/conop/doc/functions.rst index 7b3618a9f3bc15ba5d5dcdc4318bc1d0f5096012..456ab200f733bfb565d0f167d46c86abbd76307d 100644 --- a/modules/conop/doc/functions.rst +++ b/modules/conop/doc/functions.rst @@ -33,9 +33,12 @@ Conop Functions .. 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. + :return: True, if *atom_a* and *atom_b* are within a reasonable distance for + a bond to be present, namely if the distance between the two atoms + is between 0.0625 and 0.375 times the square of the sum of the + :attr:`van der Waals radii <ost.mol.AtomHandle.radius>` of the two + atom. + :rtype: :class:`bool` :param atom_a: Atom to be checked. :type atom_a: :class:`~ost.mol.AtomHandle`