From 43e0abc2779109cec369acd3f87ebf5fd9f0f4fb Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 27 May 2019 12:11:31 +0200
Subject: [PATCH] Delete residues/chains that don't contain atoms after molck
cleanup by default
---
modules/mol/alg/doc/molalg.rst | 6 +++++-
modules/mol/alg/pymod/export_molck.cc | 2 +-
modules/mol/alg/src/molck.cc | 10 ++++++++--
modules/mol/alg/src/molck.hh | 3 ++-
4 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 51de4cca6..cf72694bc 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -1877,7 +1877,7 @@ API
The API here is set such that the functions modify the passed structure *ent*
in-place. If this is not ok, please work on a copy of the structure.
-.. function:: Molck(ent, lib, settings)
+.. function:: Molck(ent, lib, settings, [prune=True])
Runs Molck on provided entity.
@@ -1887,6 +1887,10 @@ API
:type lib: :class:`~ost.conop.CompoundLib`
:param settings: Molck settings
:type settings: :class:`MolckSettings`
+ :param prune: Whether to remove residues/chains that don't contain atoms
+ anymore after Molck cleanup
+ :type prune: `bool`
+
.. function:: MapNonStandardResidues(ent, lib)
diff --git a/modules/mol/alg/pymod/export_molck.cc b/modules/mol/alg/pymod/export_molck.cc
index e5e27dac5..c626a6ce3 100644
--- a/modules/mol/alg/pymod/export_molck.cc
+++ b/modules/mol/alg/pymod/export_molck.cc
@@ -133,5 +133,5 @@ void export_Molck()
def("CleanUpElementColumn", &CleanUpElementColumn, (arg("ent"), arg("lib")));
- def("Molck", &Molck, (arg("ent"), arg("lib"), arg("settings")));
+ def("Molck", &Molck, (arg("ent"), arg("lib"), arg("settings"), arg("prune")=true));
}
diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index 1eaf1988a..1a140b559 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -174,7 +174,8 @@ void CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
void Molck(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
- const MolckSettings& settings = MolckSettings()){
+ const MolckSettings& settings,
+ bool prune) {
if(!lib) {
throw ost::Error("Require valid compound library!");
@@ -193,7 +194,12 @@ void Molck(ost::mol::EntityHandle& ent,
settings.colored);
if (settings.assign_elem) {
CleanUpElementColumn(ent, lib);
- }
+ }
+
+ if(prune) {
+ ost::mol::XCSEditor edi = ent.EditXCS();
+ edi.Prune();
+ }
}
}}} // ns
\ No newline at end of file
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index b25b1b81e..f021ef7ec 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -97,7 +97,8 @@ void CleanUpElementColumn(ost::mol::EntityHandle& ent,
void Molck(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
- const MolckSettings& settings);
+ const MolckSettings& settings,
+ bool prune = true);
}}} // namespace
--
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