Write Processor docs

doc/source/processors.rst

@@ -1,2 +1,18 @@
 Processor
 =========
+:class:`Processors <vermouth.processors.processor.Processor>` are relatively
+simple. They form the fundamental steps of the martinize2 pipeline. Processors
+are called via their :meth:`~vermouth.processors.processor.Processor.run_system`
+method. The default implementation of this method iterates over the molecules
+in the system, and runs the :meth:`~vermouth.processors.processor.Processor.run_molecule`
+method on them. This means that implementations of Processors must implement
+either a ``run_system`` method, or a ``run_molecule`` method. If the processor
+can be run on independent molecules the ``run_molecule`` method is preferred;
+``run_system`` should be used only for cases where the problem at hand cannot
+be separated in tasks-per-molecule.
+
+In their ``run_molecule`` method Processor implementations are free to either
+modify :class:`molecules <vermouth.molecule.Molecule>` or create new ones.
+Either way, they must return a :class:`~vermouth.molecule.Molecule`. The
+``run_system`` will be called with a :class:`~vermouth.system.System`, which
+will be modified in place.