From 678c01560da443eca2191a8b626450d1e074d525 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 27 Oct 2022 09:50:45 +0200
Subject: [PATCH] ensure proper processing of Entity when calling Molck
---
modules/mol/alg/doc/molalg.rst | 19 +++++++++++++++----
modules/mol/alg/pymod/export_molck.cc | 5 +++--
modules/mol/alg/src/molck.cc | 27 ++++++++++++++++++++-------
modules/mol/alg/src/molck.hh | 5 +++--
4 files changed, 41 insertions(+), 15 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 89b170b95..3f44eae5d 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -1356,7 +1356,8 @@ API
.. function:: Molck(ent, lib, settings, [prune=True])
- Runs Molck on provided entity.
+ Runs Molck on provided entity. Reprocesses *ent* with
+ :class:`ost.conop.HeuristicProcessor` and given *lib* once done.
:param ent: Structure to check
:type ent: :class:`~ost.mol.EntityHandle`
@@ -1369,8 +1370,7 @@ API
:type prune: :class:`bool`
-
-.. function:: MapNonStandardResidues(ent, lib)
+.. function:: MapNonStandardResidues(ent, lib, reprocess=True)
Maps modified residues back to the parent amino acid, for example MSE -> MET.
@@ -1378,10 +1378,16 @@ API
:type ent: :class:`~ost.mol.EntityHandle`
:param lib: Compound library
:type lib: :class:`~ost.conop.CompoundLib`
+ :param reprocess: The function generates a deep copy of *ent*. Highly
+ recommended to enable *reprocess* that runs
+ :class:`ost.conop.HeuristicProcessor` with given *lib*.
+ If set to False, you'll have no connectivity etc. after
+ calling this function.
.. function:: RemoveAtoms(ent, lib, rm_unk_atoms=False, rm_non_std=False, \
rm_hyd_atoms=True, rm_oxt_atoms=False, \
- rm_zero_occ_atoms=False, colored=False)
+ rm_zero_occ_atoms=False, colored=False,
+ reprocess=True)
Removes atoms and residues according to some criteria.
@@ -1395,6 +1401,11 @@ API
:param rm_oxt_atoms: See :attr:`MolckSettings.rm_oxt_atoms`
:param rm_zero_occ_atoms: See :attr:`MolckSettings.rm_zero_occ_atoms`
:param colored: See :attr:`MolckSettings.colored`
+ :param reprocess: Removing atoms may impact certain annotations on the
+ structure (chem class etc.) which are set by
+ :class:`ost.conop.Processor`. If set to True,
+ a :class:`ost.conop.HeuristicProcessor` with given
+ *lib* reprocesses *ent*.
.. function:: CleanUpElementColumn(ent, lib)
diff --git a/modules/mol/alg/pymod/export_molck.cc b/modules/mol/alg/pymod/export_molck.cc
index 9671434ba..aa50a674f 100644
--- a/modules/mol/alg/pymod/export_molck.cc
+++ b/modules/mol/alg/pymod/export_molck.cc
@@ -121,7 +121,7 @@ void export_Molck()
def("MapNonStandardResidues", &MapNonStandardResidues, (arg("ent"),
arg("lib"),
- arg("log_diags")=false));
+ arg("reprocess")=true));
def("RemoveAtoms", &RemoveAtoms, (arg("ent"),
arg("lib"),
@@ -130,7 +130,8 @@ void export_Molck()
arg("rm_hyd_atoms")=true,
arg("rm_oxt_atoms")=false,
arg("rm_zero_occ_atoms")=false,
- arg("colored")=false));
+ arg("colored")=false,
+ arg("reprocess")=true));
def("CleanUpElementColumn", &CleanUpElementColumn, (arg("ent"), arg("lib")));
diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index 1a140b559..d9dd3ce63 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -12,7 +12,7 @@ using namespace ost::mol;
namespace ost{ namespace mol{ namespace alg{
-void MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib, bool log_diags) {
+void MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib, bool reprocess) {
// TODO: Maybe it is possible to make it in-place operation
if(!lib) {
@@ -52,9 +52,11 @@ void MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib, bool log_diag
}
}
ent = new_ent;
- // Since we didn't do it in-place: reprocess the new entity
- RuleBasedProcessor pr(lib);
- pr.Process(ent, log_diags);
+
+ if(reprocess) {
+ RuleBasedProcessor pr(lib);
+ pr.Process(ent, false);
+ }
}
void RemoveAtoms(EntityHandle& ent,
@@ -64,7 +66,8 @@ void RemoveAtoms(EntityHandle& ent,
bool rm_hyd_atoms,
bool rm_oxt_atoms,
bool rm_zero_occ_atoms,
- bool colored /*=true*/){
+ bool colored, /*=true*/
+ bool reprocess){
if(!lib) {
throw ost::Error("Require valid compound library!");
@@ -140,6 +143,11 @@ void RemoveAtoms(EntityHandle& ent,
}
LOG_INFO(ss.str());
}
+
+ if(reprocess) {
+ RuleBasedProcessor pr(lib);
+ pr.Process(ent, false);
+ }
}
void CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
@@ -191,7 +199,8 @@ void Molck(ost::mol::EntityHandle& ent,
settings.rm_hyd_atoms,
settings.rm_oxt_atoms,
settings.rm_zero_occ_atoms,
- settings.colored);
+ settings.colored,
+ false);
if (settings.assign_elem) {
CleanUpElementColumn(ent, lib);
}
@@ -199,7 +208,11 @@ void Molck(ost::mol::EntityHandle& ent,
if(prune) {
ost::mol::XCSEditor edi = ent.EditXCS();
edi.Prune();
- }
+ }
+
+ // reprocess
+ RuleBasedProcessor pr(lib);
+ pr.Process(ent, false);
}
}}} // ns
\ No newline at end of file
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index 0dae68b93..145171b8e 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -81,7 +81,7 @@ struct MolckSettings{
void MapNonStandardResidues(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
- bool log_diags = true);
+ bool reprocess=true);
void RemoveAtoms(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
@@ -90,7 +90,8 @@ void RemoveAtoms(ost::mol::EntityHandle& ent,
bool rm_hyd_atoms,
bool rm_oxt_atoms,
bool rm_zero_occ_atoms,
- bool colored=true);
+ bool colored=true,
+ bool reprocess=true);
void CleanUpElementColumn(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib);
--
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