diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 2b0c712149e3337de117812fa12b82af58917e46..f3081a2c4fe8ad684cacf1edbf6c128fb7a04df2 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -96,7 +96,7 @@ def _ParseTmAlign(lines):
alignment = seq.CreateAlignment()
alignment.AddSequence(seq2)
alignment.AddSequence(seq1)
- return TMAlignResult(rmsd, aln_length, tm_score, tf, seq2, alignment)
+ return TMAlignResult(rmsd, tm_score, aln_length, tf, seq2, alignment)
def _RunTmAlign(tmalign, tmp_dir):
model1_filename=os.path.join(tmp_dir, 'model01.pdb')
diff --git a/modules/conop/src/amino_acids.hh b/modules/conop/src/amino_acids.hh
index aa778e3c0090f20a56752e9dbf87b2f210e8dc53..aeeb6a21de4fd6fe87a847f6bc7d73f8d0f11196 100644
--- a/modules/conop/src/amino_acids.hh
+++ b/modules/conop/src/amino_acids.hh
@@ -56,6 +56,8 @@ DLLEXPORT_OST_CONOP AminoAcid OneLetterCodeToAminoAcid(char olc);
char DLLEXPORT_OST_CONOP ResidueNameToOneLetterCode(String rn);
+char DLLEXPORT_OST_CONOP ResidueNameToOneLetterCode(String rn);
+
class AminoAcidSetIterator : public std::iterator<std::forward_iterator_tag,
AminoAcid> {
public:
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 70028c496dbe1dbc703708dbf9c6704d3d7c8203..5b6693fefbb3e4a23a999b68e9738fbf0383c7e2 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -208,4 +208,4 @@ To get the newest changes from the central git repository, enter
git pull
-in your terminal. This will fetch the newest changes.
\ No newline at end of file
+in your terminal. This will fetch the newest changes.
diff --git a/modules/gfx/src/impl/cartoon_renderer.cc b/modules/gfx/src/impl/cartoon_renderer.cc
index 354a4499ac1083c4f35f9d2a891532e5a38522d8..e8076db65da5ffc1c578238e60534806f1e6faa0 100644
--- a/modules/gfx/src/impl/cartoon_renderer.cc
+++ b/modules/gfx/src/impl/cartoon_renderer.cc
@@ -325,21 +325,21 @@ void CartoonRenderer::rebuild_spline_obj(IndexedVertexArray& va,
options_->GetStrandThickness()+factor,
options_->GetStrandProfileType(),
options_->GetStrandEcc())); // profile 2 = strand
- TraceProfile prof=profiles.back();
-// do not ever change this back to profiles.push_back(profiles.back()); it segfaults on windows
-// or you will meet two new friends of yours :)
-// looks like a compiler bug
+ TraceProfile prof=profiles.back();
+ // do not ever change this back to profiles.push_back(profiles.back()); it segfaults on windows
+ // or you will meet two new friends of yours :)
+ // looks like a compiler bug
profiles.push_back(prof); // profile 3==2, strand
profiles.push_back(get_circ_profile(detail,
- 1.7*options_->GetStrandWidth()+factor,
+ 1.7*options_->GetStrandWidth()+factor,
1.1*options_->GetStrandThickness()+factor,
- options_->GetStrandProfileType(),
- options_->GetStrandEcc())); // profile 4 = arrow start
+ options_->GetStrandProfileType(),
+ options_->GetStrandEcc())); // profile 4 = arrow start
profiles.push_back(get_circ_profile(detail,
- 0.01*options_->GetStrandWidth()+factor,
+ 0.01*options_->GetStrandWidth()+factor,
1.1*options_->GetStrandThickness()+factor,
- options_->GetStrandProfileType(),
- options_->GetStrandEcc())); // profile 5 = arrow end
+ options_->GetStrandProfileType(),
+ options_->GetStrandEcc())); // profile 5 = arrow end
}
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index 24463030764c2e6040046e9f2b99266eb96f7525..dfd9cc70200c6fe9626de4db7834d55d0a8a07ce 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -501,6 +501,7 @@ void PythonShellWidget::OnExecuteStateEntered()
set_block_type_(block_edit_start_,textCursor().block(),BLOCKTYPE_CODE);
insertPlainText(QString(QChar::ParagraphSeparator));
QString command=GetCommand();
+
QString command_trimmed=command.trimmed();
if (command_trimmed.size()>0) {
unsigned int id=PythonInterpreter::Instance().RunCommand(command);
@@ -509,7 +510,6 @@ void PythonShellWidget::OnExecuteStateEntered()
insertPlainText(QString(QChar::ParagraphSeparator));
}
block_edit_start_=textCursor().block();
-
}
diff --git a/modules/img/alg/src/stat.hh b/modules/img/alg/src/stat.hh
index 450ffc3528de44dd2eb0df9d1d9cb7fbd2dc3de7..47009785a94a72bc50d967cb8be8f99021963181 100644
--- a/modules/img/alg/src/stat.hh
+++ b/modules/img/alg/src/stat.hh
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2008-2011 by the OpenStructure authors
// Copyright (C) 2003-2010 by the IPLT authors
//
// This library is free software; you can redistribute it and/or modify it under
diff --git a/modules/io/src/mol/entity_io_mae_handler.hh b/modules/io/src/mol/entity_io_mae_handler.hh
index 5b06f96bf46a91acfc37a4beaff2b38ed90e71f5..8f09c375e7b3021073cc599ed524bda130c59900 100644
--- a/modules/io/src/mol/entity_io_mae_handler.hh
+++ b/modules/io/src/mol/entity_io_mae_handler.hh
@@ -19,7 +19,6 @@
#ifndef OST_IO_ENTITY_IO_PLUGIN_MAE_H
#define OST_IO_ENTITY_IO_PLUGIN_MAE_H
-
#include <ost/mol/entity_handle.hh>
#include <ost/mol/chain_handle.hh>
#include <ost/mol/residue_handle.hh>
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 40c0660153853bc5edbfeb8e94384194a8daf63b..f38f953f68c31dca8c6378958734589607a68ad1 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -145,8 +145,7 @@ SDFWriter::SDFWriter(const boost::filesystem::path& filename):
#else
outfile_(filename.file_string().c_str()),
#endif
- ostr_(outfile_), counter_(0), atom_indices_() {
-}
+ ostr_(outfile_), counter_(0), atom_indices_() {}
void SDFWriter::Write(const mol::EntityView& ent) {
if (!ostr_) {
diff --git a/modules/mol/alg/pymod/export_superpose_frames.cc b/modules/mol/alg/pymod/export_superpose_frames.cc
index e1d55652052388dbf7721f6d030fbe6ef0cbe79f..8f03153e54bb8823435461d7e69924444daa9a1e 100644
--- a/modules/mol/alg/pymod/export_superpose_frames.cc
+++ b/modules/mol/alg/pymod/export_superpose_frames.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2010 by the OpenStructure authors
+// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 71bcae0a9f72024250232db41f31d009c847c5e6..87e23fe8e4391c13e7046aa4a87499f52741590c 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -264,9 +264,9 @@ using an :class:`ICSEditor` is undefined and vice versa.
.. note::
- For speed reasons, the internal coordinate system is not initialized until the
- first call to :meth:`EntityHandle.EditICS`. This involves the build-up of a
- directed-graph for the bond network as well as calculating the internal
+ For speed reasons, the internal coordinate system is not initialised until
+ the first call to :meth:`EntityHandle.EditICS`. This involves the build-up of
+ a directed-graph for the bond network as well as calculating the internal
coordinate matrices.
.. class:: ICSEditor
@@ -336,5 +336,5 @@ using an :class:`ICSEditor` is undefined and vice versa.
:param angle: The angle in radians
- :raises: :exc:`RuntimeError` when one of the atoms is invalid or there is no
- bond between atom1 and atom2 or atom2 and atom3.
+ :raises: :exc:`RuntimeError` when one of the atoms is invalid or there is
+ no bond between atom1 and atom2 or atom2 and atom3.
diff --git a/modules/mol/base/pymod/export_bond.cc b/modules/mol/base/pymod/export_bond.cc
index f78455b1669dceaa2980155859559bf32a801959..5f7ab1154ad0c785cca591fd5ee47c5b01ee700c 100644
--- a/modules/mol/base/pymod/export_bond.cc
+++ b/modules/mol/base/pymod/export_bond.cc
@@ -59,8 +59,6 @@ void export_Bond()
generic_prop_def<BondHandle>(bond_handle);
class_<BondHandleList>("BondHandleList", no_init)
.def(vector_indexing_suite<BondHandleList>())
- .def(geom::VectorAdditions<BondHandleList>())
- ;
+ .def(geom::VectorAdditions<BondHandleList>());
def("BondExists", &BondExists);
}
-
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index 55d408365dc1c982c5370034af96a7f2f98de78b..e0b4c9b097097d4dbfd7dcf50ae7b6f8c8d9c184 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -186,8 +186,6 @@ void export_EntityView()
.def("GetBounds", &EntityView::GetBounds)
.add_property("bounds", &EntityView::GetBounds)
;
- to_python_converter<std::pair<EntityView, EntityView>,
- PairToTupleConverter<EntityView, EntityView> >();
def("Union", &Union);
def("Difference", &Difference);
def("Intersection", &Intersection);
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 0cb3f4df3d62de4a2b6311b8effa132c714c300f..38a0e34ff3c211e649294c2d4f72b05b8f06e429 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -327,6 +327,9 @@ void export_sequence()
class_<SeqListIter>("SeqListIter", no_init)
.def("next", &SeqListIter::next)
;
+ to_python_converter<std::pair<mol::EntityView, mol::EntityView>,
+ PairToTupleConverter<mol::EntityView, mol::EntityView> >();
+
class_<AlignmentHandle>("AlignmentHandle", init<>())
.def("GetCount", &AlignmentHandle::GetCount)
.add_property("sequence_count", &AlignmentHandle::GetCount)
@@ -397,7 +400,7 @@ void export_sequence()
.def("__getitem__", &do_slice_b)
;
implicitly_convertible<SequenceList, ConstSequenceList>();
-
+
def("CreateSequenceList", &CreateSequenceList);
def("SequenceFromChain", seq_from_chain_a);
def("SequenceFromChain", seq_from_chain_b);
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index 62539237a9a7dfe0de1105bb647f1dd5b08f2a40..acd2b13e7b44d2baa53ec57c64b8cc3d4a7b3f60 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -407,7 +407,6 @@ char SequenceHandle::operator[](size_t index) const
return this->GetString()[index];
}
-
bool Match(const ConstSequenceHandle& s1, const ConstSequenceHandle& s2)
{
return Match(s1.GetString(), s2.GetString());
@@ -427,5 +426,4 @@ bool Match(const String& s1, const String& s2)
}
return true;
}
-
}}
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index 3b3f1b1abf471f151cf79179248150960514fcc3..1c2cee610fbe20e92b9e446bf4af894d710fb433 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -273,6 +273,7 @@ public:
iterator end() const { return this->GetString().end(); }
void Append(char olc);
+
operator ConstSequenceHandle() const;
/// \brief attach entity view to sequence
///