diff --git a/modules/conop/doc/connectivity.rst b/modules/conop/doc/connectivity.rst index 0dfd005908a8ee624c98bb4ea070da9b9f40b5b9..0299ef5b8cee0b258b735fb92208085537ebd758 100644 --- a/modules/conop/doc/connectivity.rst +++ b/modules/conop/doc/connectivity.rst @@ -7,16 +7,14 @@ Connectivity Motivation -------------------------------------------------------------------------------- - The connectivity of atoms is notoriously difficult to come by for biological macromolecules. PDB files, the de facto standard exchange format for structural information allows bonds to be specified in CONECT records. However, they are not -mandatory. Many programs, especially the ones not requiring on connectivity of +mandatory. Many programs, especially the ones not depending on connectivity of atoms, do not write CONECT records. As a result, programs and structural biology frameworks can't rely on connectivity information to be present. The connectivity information needs to be derived in the program itself. - Loader heuristics are great if you are the one that implemented them but are problematic if you are just the user of a software that has them. As time goes on, these heuristics become buried in thousands of lines of code and they are @@ -41,12 +39,13 @@ 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 processor mainly differ in the source of their 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 +processor. The processors mainly differ in the source of their 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 a connectivity library containing all +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.