diff --git a/doc/conf/conf.py b/doc/conf/conf.py
index 9ddc034d552ed0d85a7f74aa500d22ed415ecd68..78949cd7a85e80047bb397debf755fd8385827ee 100644
--- a/doc/conf/conf.py
+++ b/doc/conf/conf.py
@@ -42,7 +42,7 @@ master_doc = 'index'
# General information about the project.
project = u'OpenStructure'
-copyright = u'2011, OpenStructure authors'
+copyright = u'2018, OpenStructure authors'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
diff --git a/modules/base/src/test_utils/compare_files.cc b/modules/base/src/test_utils/compare_files.cc
index 904b14a7fa75dde9bf4edcf3cab176966f312dc1..13dac63adcd4a2f8244303f66d187cadade08ba3 100644
--- a/modules/base/src/test_utils/compare_files.cc
+++ b/modules/base/src/test_utils/compare_files.cc
@@ -37,17 +37,18 @@ bool compare_files(const String& test, const String& gold_standard)
}
String test_line, gold_line;
while (true) {
- bool test_end=std::getline(test_stream, test_line) != 0;
- bool gold_end=std::getline(gold_stream, gold_line) != 0;
- if (!(test_end || gold_end)) {
+ bool test_read = static_cast<bool>(std::getline(test_stream, test_line));
+ bool gold_read = static_cast<bool>(std::getline(gold_stream, gold_line));
+ if (!test_read && !gold_read) {
+ // nothing to read anymore in any of the files
return true;
}
- if (!test_end) {
+ if (gold_read && !test_read) {
std::cerr << gold_standard << " contains additional line(s):"
<< std::endl << gold_line << std::endl;
return false;
}
- if (!gold_end) {
+ if (test_read && !gold_read) {
std::cerr << test << " contains additional line(s):"
<< std::endl << test_line << std::endl;
return false;
diff --git a/modules/config/base.hh b/modules/config/base.hh
index 2019437b5b47828492ec8de2422a77287d650092..b10638e7ede8f4a6f301aad7db6dd8d05b243bc0 100644
--- a/modules/config/base.hh
+++ b/modules/config/base.hh
@@ -51,28 +51,15 @@ typedef unsigned int uint;
typedef std::complex<Real> Complex;
typedef unsigned short Word;
+typedef std::string String;
+// NOTE: Before OST 1.8, we used to have round and rint functions defined here
+// -> round and rint are available for any compiler since many years now
+// -> Tested for GCC 4.1.2 - 9.0.0, clang 3.3.0 - 8.0.0, MSVC 2015 - 2017 using
+// godbolt.org. In all cases: call with float is not casted to double, but
+// kept as float which is desired behaviour for good performance.
-#ifndef round_function
-#define round_function
-#ifndef round
-inline Real round( Real d )
-{
- return floor(d+Real(0.5));
-}
-#endif
-#endif
-
-#ifndef rint_function
-#define rint_function
-#ifndef rint
-inline Real rint(Real d)
-{
- return floor(d+Real(0.5));
-}
-#endif
-#endif
-
+// NOTE: OST has not been tested in MSVC for a very long time!
#if _MSC_VER
#pragma warning(disable:4251)
#pragma warning(disable:4275)
@@ -104,7 +91,4 @@ inline double log2( double n )
#endif
-typedef std::string String;
-
-
#endif
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 585dafe3cfd87a45afcd88c6cccec4213a83a125..36e74440821905a303fd7a501268cfc422c17767 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -299,16 +299,8 @@ from source.
On some Linux distributions, there are issues with Qt4 and hence it may not be
possible to build OpenStructure with GUI support at all. This is for instance
-known to be an issue with boost versions >= 1.62.
-
-An additional problem arises for gcc versions >= 6. There an extra flag is
-required to use the C++98 standard:
-
-.. code-block:: bash
-
- cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
-
-We hope to support Qt5 and C++11 in the next OpenStructure release.
+known to be an issue with boost versions >= 1.62. We hope to support Qt5 in the
+next OpenStructure release.
**Ubuntu 16.04 with GUI**
@@ -342,12 +334,11 @@ All the dependencies can be installed from the package manager as follows:
sudo dnf install cmake eigen3-devel boost-devel libpng-devel python2-devel \
fftw-devel libtiff-devel
-Fedora 26 has gcc 7 and boost 1.63 by default. Hence, we will need to disable
-Qt4, the GUI and add the extra flag described above:
+Here, we compile a version without GUI as follows:
.. code-block:: bash
- cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DCMAKE_CXX_FLAGS='-std=c++98'
+ cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF
**macOS with Homebrew without GUI**
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index 5c1e9cbb7149115b219ceccc8e88698fa5e70e97..98b47c9cbb16ed2477cb5fb0fd001bcaee8f0c57 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -1097,7 +1097,7 @@ bool Scene::HasNode(const String& name) const
{
FindNode fn(name);
this->Apply(fn);
- return fn.node;
+ return static_cast<bool>(fn.node);
}
void Scene::Apply(const InputEvent& e, bool request_redraw)
diff --git a/modules/gfx/src/texture.hh b/modules/gfx/src/texture.hh
index aa3fec45f8f0a5d288d977dd290e40210a9c5253..cf25b9d4f83a8c86d442d4b82db0ac0346d8b433 100644
--- a/modules/gfx/src/texture.hh
+++ b/modules/gfx/src/texture.hh
@@ -51,7 +51,7 @@ public:
Texture(const Bitmap& b);
- bool IsValid() const {return d_;}
+ bool IsValid() const {return static_cast<bool>(d_);}
float* data() {return &d_[0];}
diff --git a/modules/gui/src/data_viewer/data_viewer.hh b/modules/gui/src/data_viewer/data_viewer.hh
index ca6893edc34895fde6df19e2b1344ea11affcb98..c1f18847ec36c270de0d93183342c8427dd604a1 100644
--- a/modules/gui/src/data_viewer/data_viewer.hh
+++ b/modules/gui/src/data_viewer/data_viewer.hh
@@ -25,6 +25,8 @@
#ifndef IMG_GUI_DATA_VIEWER_H
#define IMG_GUI_DATA_VIEWER_H
+#ifndef Q_MOC_RUN
+
#include <map>
#include <ost/base.hh>
@@ -42,6 +44,9 @@
#include "fft_panel.hh"
#include <ost/gui/module_config.hh>
+#endif
+
+
//fw decl
class QLabel;
diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.hh b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
index 699efd372cad4dc5b0a9f26a205b4487f5b33168..be3ac007ec7550c4242e8cbc607654c5eca12fea 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.hh
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.hh
@@ -26,10 +26,10 @@
#define DATA_VIEWER_PANEL_BASE_HH_
#include <map>
-#include <boost/shared_ptr.hpp>
-
+#ifndef Q_MOC_RUN
+#include <boost/shared_ptr.hpp>
#include <ost/base.hh>
#include <ost/img/extent.hh>
#include <ost/img/data_observer.hh>
@@ -41,6 +41,8 @@
#include <ost/img/normalizer_impl.hh>
+#endif
+
#include <QWidget>
#include <QCursor>
#include <QMenu>
diff --git a/modules/gui/src/data_viewer/fft_panel.hh b/modules/gui/src/data_viewer/fft_panel.hh
index 75a30fed87e8a1018887d10a56fd7e0465674ce0..ac0df0f56e39d148ab16735fe6e7fe3ce082244e 100644
--- a/modules/gui/src/data_viewer/fft_panel.hh
+++ b/modules/gui/src/data_viewer/fft_panel.hh
@@ -24,10 +24,14 @@
Author: Andreas Schenk
*/
+#ifndef Q_MOC_RUN
+
#include <ost/gui/module_config.hh>
#include <ost/img/data_observer.hh>
#include "data_viewer_panel_base.hh"
+#endif
+
namespace ost { namespace img { namespace gui {
class ParentDataObserver: public DataObserver
diff --git a/modules/gui/src/file_type_dialog.hh b/modules/gui/src/file_type_dialog.hh
index f1fe6ce5e5fc6e856b15c091b65d03e41309bda2..270d35131d96f77ebfee4de64420abe4f933590d 100644
--- a/modules/gui/src/file_type_dialog.hh
+++ b/modules/gui/src/file_type_dialog.hh
@@ -25,7 +25,7 @@
#include <ost/gui/module_config.hh>
-
+#ifndef Q_MOC_RUN
#include <ost/io/mol/entity_io_handler.hh>
#include <ost/io/seq/sequence_io_handler.hh>
@@ -34,6 +34,8 @@
#include <ost/io/img/map_io_handler.hh>
#endif
+#endif
+
#include <QDialog>
#include <QMetaType>
diff --git a/modules/img/base/src/base.hh b/modules/img/base/src/base.hh
index 0122a07371705cdc89808f6f3966ab67cb9e2e6a..f5d73f5f4f1aa18f897d6e4710d5108ae7380bbc 100644
--- a/modules/img/base/src/base.hh
+++ b/modules/img/base/src/base.hh
@@ -44,21 +44,11 @@
#pragma warning(disable:4231)
#endif
-
#ifdef IRIX
-inline Real round(Real x) {return rint(x);}
-inline float roundf(float x) {return (float)rint((Real)x);}
using std::cos;
using std::sin;
#endif
-#ifndef round_function
-#define round_function
-#ifndef round
-inline int round(Real x) {return floor(x+0.5);}
-#endif
-#endif
-
namespace ost { namespace img {
// String is not always predefined
diff --git a/modules/img/base/src/image_handle.cc b/modules/img/base/src/image_handle.cc
index c0059be0b852490c5e50306fffab6fca18f23208..fe84239cd624c3c3e6584151ddff9ecf1dffca3d 100644
--- a/modules/img/base/src/image_handle.cc
+++ b/modules/img/base/src/image_handle.cc
@@ -153,7 +153,7 @@ void ImageHandle::Reset(const Extent &e, DataType type,DataDomain dom)
bool ImageHandle::IsValid() const
{
- return impl_;
+ return static_cast<bool>(impl_);
}
long ImageHandle::MemSize() const
diff --git a/modules/info/src/info_handle.cc b/modules/info/src/info_handle.cc
index 9b6ecbc49a7dac0caddd7347743f9dd634cdee2c..263ae222c9ed261b0de6061631dfb94e98753bee 100644
--- a/modules/info/src/info_handle.cc
+++ b/modules/info/src/info_handle.cc
@@ -74,7 +74,7 @@ void InfoHandle::Export(const String& file) const
bool InfoHandle::IsValid() const
{
- return impl_;
+ return static_cast<bool>(impl_);
}
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 2cfac7fcef03a65e57d20a6658ad07f90b339ab6..69210a1b95e5d3e3236d3807c6827e3390fdc973 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1327,7 +1327,7 @@ BOOST_AUTO_TEST_CASE(mmcif_test_chain_mappings)
BOOST_TEST_MESSAGE(" Running mmcif_test_chain_mappings tests...");
// check compound lib
- bool compound_lib_available = SetDefaultCompoundLib();
+ bool compound_lib_available = static_cast<bool>(SetDefaultCompoundLib());
// load data
mol::EntityHandle eh = mol::CreateEntity();
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 81f3e77643c0eae354f789288741fd2d43de2b94..4636a4ce45ee911c944366545be4bc10947d82ba 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -559,8 +559,7 @@ Local Distance Test scores (lDDT, DRMSD)
"""Run lDDT from within script."""
from ost.io import LoadPDB
from ost.mol.alg import (CleanlDDTReferences,
- lDDTSettings, lDDTScorer)
- from ost.io import ReadStereoChemicalPropsFile
+ lDDTSettings, lDDTScorer)
ent_full = LoadPDB('3ia3', remote=True)
model_view = ent_full.Select('cname=A')
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 455d1e7dbd8114aeb7ef972cc50691de2e9a0e8c..18ffc17ba090c0a7b39f3e76788d6993bd1febe5 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -118,7 +118,7 @@ std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,c
std::map <String,std::pair<Real,Real> >::const_iterator find_ci= min_distance_.find(key);
if (find_ci == min_distance_.end()) {
std::stringstream serr;
- serr << "Entry for distance " << stkey << " not found in the parameter table";
+ serr << "Entry for distance " << key << " not found in the parameter table";
throw Error(serr.str());
}
return find_ci->second;
@@ -220,7 +220,7 @@ StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<
if (second_line_str_vec.size()!=4) {
std::cout << "The number of elements in one of the lines is wrong" << std::endl;
return StereoChemicalParams();
- }
+ }
StringRef item = second_line_str_vec[0];
String res = second_line_str_vec[1].str();
std::pair<bool,float> parse_value = second_line_str_vec[2].to_float();
@@ -231,13 +231,13 @@ StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<
} else {
std::cout << "One of the values in the third column is not a number" << std::endl;
return StereoChemicalParams();
- };
+ }
if (parse_stddev.first==true) {
stddev=static_cast<Real>(parse_stddev.second);
} else {
std::cout << "One of the values in the fourth column is not a number" << std::endl;
return StereoChemicalParams();
- };
+ }
std::vector<StringRef> split_item = item.split('-');
String rearranged_item;
if (split_item.size() == 2) {
@@ -264,7 +264,7 @@ StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<
} else {
std::cout << "One of the strings describing the parameter has the wrong format" << std::endl;
return StereoChemicalParams();
- }
+ }
table.SetParam(rearranged_item,res,value,stddev);
}
line_iter++;
@@ -306,7 +306,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
if (second_line_str_vec.size()!=3) {
std::cout << "The number of elements in one of the lines is wrong" << std::endl;
return ClashingDistances();
- }
+ }
String item = second_line_str_vec[0].str();
std::pair<bool,float> parse_value = second_line_str_vec[1].to_float();
@@ -317,7 +317,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
} else {
std::cout << "One of the distance values is not a number" << std::endl;
return ClashingDistances();
- };
+ }
if (parse_stddev.first==true) {
stddev=static_cast<Real>(parse_stddev.second);
} else {
@@ -329,7 +329,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
if (itemsr.size() != 3) {
std::cout << "One of the strings describing the interacting atoms has the wrong format" << std::endl;
return ClashingDistances();
- }
+ }
String ele1=eles[0].str();
String ele2=eles[1].str();
if (ele2 < ele1) {
@@ -340,7 +340,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
}
line_iter++;
}
- }
+ }
}
line_iter++;
}
diff --git a/modules/mol/base/src/bond_handle.cc b/modules/mol/base/src/bond_handle.cc
index 3be1b88bd7017c7005e2912a71d689bb398576bc..9a68a860dc5db33eea4a28fdc807407acb889ec1 100644
--- a/modules/mol/base/src/bond_handle.cc
+++ b/modules/mol/base/src/bond_handle.cc
@@ -47,7 +47,7 @@ BondHandle::operator bool() const
}
bool BondHandle::IsValid() const {
- return impl_;
+ return static_cast<bool>(impl_);
}
AtomHandle BondHandle::GetFirst() const
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index 7bc585b14662360f400d241ca77e4a48ee8b1184..f0852b73845a7ae3181109154203f40a3435d64c 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -227,7 +227,7 @@ std::ostream& operator<<(std::ostream& o, const AtomImplPtr ap)
}
bool ConnectorExists(const AtomImplPtr& a, const AtomImplPtr& b) {
- return GetConnector(a, b);
+ return static_cast<bool>(GetConnector(a, b));
}
ConnectorImplP GetConnector(const AtomImplPtr& a, const AtomImplPtr& b) {
diff --git a/modules/mol/base/src/surface_handle.hh b/modules/mol/base/src/surface_handle.hh
index 3524375d36ab919f072d3a8d19fe78d4e74d387b..a11b3a91e9768535716c30e25f5026e8fdc04c44 100644
--- a/modules/mol/base/src/surface_handle.hh
+++ b/modules/mol/base/src/surface_handle.hh
@@ -70,7 +70,7 @@ public:
// flip normals
void Invert();
- bool IsValid() const {return impl_;}
+ bool IsValid() const {return static_cast<bool>(impl_);}
bool operator==(const SurfaceHandle& ref) const { return impl_==ref.impl_; }