diff --git a/modules/conop/doc/connectivity.rst b/modules/conop/doc/connectivity.rst
index 636b8a7104a967b8a17d56039cdd4a4862f6bb13..8686790cc2398668466b08abc2d30cd004ba326c 100644
--- a/modules/conop/doc/connectivity.rst
+++ b/modules/conop/doc/connectivity.rst
@@ -40,76 +40,112 @@ 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 connectivity algorithm that connects
-two atoms if they are closer than a certain threshold. The RuleBasedProcessor
-uses 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. If a :doc:`compound library <compoundlib>` is
-present, the :class:`RuleBasedProcessor` is enabled by default, otherwise the
+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
+connectivity algorithm that connects two atoms if they are closer than a certain
+threshold. The RuleBasedProcessor uses 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. If a
+:doc:`compound library <compoundlib>` is present, the
+:class:`RuleBasedProcessor` is enabled by default, otherwise the
:class:`HeuristicProcessor` is used as a fallback.
-The Processor base class
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
.. class:: Processor
- .. attribute:: connect
+ .. attribute:: check_bond_feasibility
- Whether to connect atoms by bonds. Enabled by default. This also sets the
- :attr:`~ost.mol.ResidueHandle.is_protein` property of residues when peptide
- bonds are created. Turn this off if you would like to speed up the loading
- process and do not require connectivity information to be present in your
- structures.
+ Whether an additional bond feasibility check is performed. Disabled by
+ default. If turned on, atoms are only connected by bonds if they are within
+ a reasonable distance (as defined by :func:`IsBondFeasible`).
:type: :class:`bool`
- .. attribute:: zero_occ_treatment
+ .. attribute:: assign_torsions
- Controls the behaviour of importing atoms with zero occupancy. By default, this
- is set to silent.
+ Whether backbone torsions should be added to the backbone. Enabled by
+ default. If turned on, PHI, PSI and OMEGA torsions are assigned to the
+ peptide residues. See also :func:`AssignBackboneTorsions`.
- :type: :class:`str`
+ :type: :class:`bool`
- .. attribute:: check_bond_feasibility
+ .. attribute:: connect
- 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`.
+ Whether to connect atoms by bonds. Enabled by default. Turn this off if you
+ would like to speed up the loading process and do not require connectivity
+ information to be present in your structures. Note though that
+ :attr:`peptide_bonds` may be ignored if this is turned off.
:type: :class:`bool`
- .. attribute:: assign_torsions
+ .. attribute:: peptide_bonds
- 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`.
+ Whether to connect residues by peptide bonds. Enabled by default. This also
+ sets the :attr:`~ost.mol.ResidueHandle.is_protein` property of residues when
+ peptide bonds are created. Turn this off if you would like to create your
+ own peptide bonds.
:type: :class:`bool`
+ .. attribute:: zero_occ_treatment
+
+ Controls the behaviour of importing atoms with zero occupancy. By default,
+ this is set to warn.
+
+ :type: :class:`ConopAction`
.. method:: Process(ent)
Processess the entity *ent* according to the current options.
-The RuleBasedProcessor class
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. class:: HeuristicProcessor(check_bond_feasibility=False, \
+ assign_torsions=True, connect=True, \
+ peptide_bonds=True, zero_occ_treatment=CONOP_WARN)
+
+ The :class:`HeuristicProcessor` implements the :class:`Processor` interface.
+ Refer to its documentation for methods and accessors common to all processor.
+
+ :param check_bond_feasibility: Sets :attr:`~Processor.check_bond_feasibility`
+ :param assign_torsions: Sets :attr:`~Processor.assign_torsions`
+ :param connect: Sets :attr:`~Processor.connect`
+ :param peptide_bonds: Sets :attr:`~Processor.peptide_bonds`
+ :param zero_occ_treatment: Sets :attr:`~Processor.zero_occ_treatment`
+
+
+.. class:: RuleBasedProcessor(compound_lib, fix_elements=True, \
+ strict_hydrogens=False, \
+ unknown_res_treatment=CONOP_WARN, \
+ unknown_atom_treatment=CONOP_WARN, \
+ check_bond_feasibility=False, \
+ assign_torsions=True, connect=True, \
+ peptide_bonds=True, zero_occ_treatment=CONOP_WARN)
+
+ The :class:`RuleBasedProcessor` implements the :class:`Processor` interface.
+ Refer to its documentation for methods and accessors common to all processor.
+
+ :param compound_lib: The compound library to use
+ :type compound_lib: :class:`CompoundLib`
+ :param fix_elements: Sets :attr:`fix_elements`
+ :param strict_hydrogens: Sets :attr:`strict_hydrogens`
+ :param unknown_res_treatment: Sets :attr:`unk_atom_treatment`
+ :param unknown_atom_treatment: Sets :attr:`unk_res_treatment`
+ :param check_bond_feasibility: Sets :attr:`~Processor.check_bond_feasibility`
+ :param assign_torsions: Sets :attr:`~Processor.assign_torsions`
+ :param connect: Sets :attr:`~Processor.connect`
+ :param peptide_bonds: Sets :attr:`~Processor.peptide_bonds`
+ :param zero_occ_treatment: Sets :attr:`~Processor.zero_occ_treatment`
-.. class:: RuleBasedProcessor(compound_lib)
+ .. attribute:: fix_elements
- :param compound_lib: The compound library
- :type compound_lib: :class:`CompoundLib`
-
- The :class:`RuleBasedProcessor` implements the :class:`Processor` interface.
- Refer to its documentation for methods and accessors common to all processor.
+ Whether the element of the atom should be changed to the atom defined in the
+ compound library. Enabled by default.
+
+ :type: :class:`bool`
-
.. attribute:: strict_hydrogens
Whether to use strict hydrogen naming rules outlined in the compound library.
@@ -119,22 +155,21 @@ The RuleBasedProcessor class
.. attribute:: unk_atom_treatment
- Treatment upon encountering an unknown atom. Default: 'warn'.
-
+ Treatment upon encountering an unknown atom. Warn by default.
- :type: :class:`str`
+ :type: :class:`ConopAction`
.. attribute:: unk_res_treatment
- Treatment upon encountering an unknown residue
-
- :type: :class:`str`
+ Treatment upon encountering an unknown residue. Warn by default.
- .. attribute:: fix_elements
+ :type: :class:`ConopAction`
- Whether the element of the atom should be changed to the atom defined in the
- compound library. Enabled by default.
- :type: :class:`bool`
+.. class:: ConopAction
+ Defines actions to take when certain events happen during processing. Possible
+ values:
+ ``CONOP_WARN``, ``CONOP_SILENT``, ``CONOP_REMOVE``, ``CONOP_REMOVE_ATOM``,
+ ``CONOP_REMOVE_RESIDUE``, ``CONOP_FATAL``
diff --git a/modules/conop/pymod/export_processor.cc b/modules/conop/pymod/export_processor.cc
index 1f9a74281a7587c68d43ee32c321a7a90ef597b5..37e4d8bfcdffccfd569216b4d6085231ab9c486d 100644
--- a/modules/conop/pymod/export_processor.cc
+++ b/modules/conop/pymod/export_processor.cc
@@ -80,10 +80,14 @@ void export_processor() {
.add_property("check_bond_feasibility",
&Processor::GetCheckBondFeasibility,
&Processor::SetCheckBondFeasibility)
- .add_property("connect", &Processor::GetConnect,
- &Processor::SetConnect)
.add_property("assign_torsions", &Processor::GetAssignTorsions,
- &Processor::SetAssignTorsions)
+ &Processor::SetAssignTorsions)
+ .add_property("connect", &Processor::GetConnect,
+ &Processor::SetConnect)
+ .add_property("peptide_bonds", &Processor::GetConnectAminoAcids,
+ &Processor::SetConnectAminoAcids)
+ .add_property("zero_occ_treatment", &Processor::GetZeroOccTreatment,
+ &Processor::SetZeroOccTreatment)
.def("Process", &Processor::Process,
(arg("ent"), arg("log_diags")=true))
;