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Verified Commit 28db461a authored by Xavier Robin's avatar Xavier Robin
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doc: point to the compound library explicitly. Typos.

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modules/conop/doc/connectivity.rst
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...@@ -7,16 +7,14 @@ Connectivity ...@@ -7,16 +7,14 @@ Connectivity
Motivation Motivation
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The connectivity of atoms is notoriously difficult to come by for biological The connectivity of atoms is notoriously difficult to come by for biological
macromolecules. PDB files, the de facto standard exchange format for structural macromolecules. PDB files, the de facto standard exchange format for structural
information allows bonds to be specified in CONECT records. However, they are not 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 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 frameworks can't rely on connectivity information to be present. The connectivity
information needs to be derived in the program itself. information needs to be derived in the program itself.
Loader heuristics are great if you are the one that implemented them but are 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 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 on, these heuristics become buried in thousands of lines of code and they are
...@@ -41,12 +39,13 @@ Processors ...@@ -41,12 +39,13 @@ Processors
The exact behaviour for a processor is implementation-specific. So far, two The exact behaviour for a processor is implementation-specific. So far, two
classes implement the processor interface: A heuristic and a rule-based classes implement the processor interface: A heuristic and a rule-based
processor. The processor mainly differ in the source of their connectivity 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 table for the 20 standard amino acids as well as nucleotides. For other
compounds such as ligands the HeuristicProcessor runs a distance-based compounds such as ligands the `HeuristicProcessor` runs a distance-based
connectivity algorithm that connects two atoms if they are closer than a certain 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 molecular components present in the PDB files on PDB.org. The library can easily
be extended with custom connectivity information, if required. be extended with custom connectivity information, if required.
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