Merge pull request #214 from michellab/devel

Merging devel into master for the 2018.2.0 release [ci skip]
michellab · Jul 12, 2018 · 0d3c66a · 0d3c66a
2 parents 2cb9cd9 + 4970350
commit 0d3c66a
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diff --git a/CHANGELOG b/CHANGELOG
@@ -3,6 +3,15 @@ SIRE changelog
 
 devel branch:
 
+    [2018.2.0] July 2018 - Improvements to the Gromacs topology reader/writer,
+               addition of code to improve matching of atoms in proteins,
+               fixing compile issues on modern Ubuntu, bugfixes for crashes
+               in the AmberPrm reader, added in text-based searching for
+               atoms, residues etc. from Systems, MoleculeGroups, Molecules,
+               etc. based on boost::spirit, updated boost to latest version, 
+               bugfixes for quantomm infinite rotation bug for ions,
+               general bugfixes.
+
     [2018.1.1] May 2018 - Small bug fixes to allow single-atom solutes
                and also to fix small issues with some parsers for BioSimSpace
 

diff --git a/compile_sire.sh b/compile_sire.sh
@@ -33,7 +33,7 @@ esac
 
 # Set the version of miniconda to use. Choose "latest" for the latest
 # miniconda, or set a specific version here
-MINICONDA_VERSION="4.2.12"
+MINICONDA_VERSION="4.5.4"
 #MINICONDA_VERSION="latest"
 
 if [ -z "$INSTALL_SIRE_DIR" ]; then

diff --git a/corelib/CMakeLists.txt b/corelib/CMakeLists.txt
@@ -7,8 +7,8 @@
 ################################
 
 set (S_VERSION_MAJOR "2018")
-set (S_VERSION_MINOR "1")
-set (S_VERSION_PATCH "1")             
+set (S_VERSION_MINOR "2")
+set (S_VERSION_PATCH "0")             
 
 set (SIRE_VERSION "${S_VERSION_MAJOR}.${S_VERSION_MINOR}.${S_VERSION_PATCH}")
 
@@ -161,6 +161,7 @@ message( STATUS "Sire will be compiled and installed to directory ${CMAKE_INSTAL
 
 # Absolutely can't run cmake in the source directory!
 if ( CMAKE_BINARY_DIR STREQUAL CMAKE_SOURCE_DIR )
+  message( STATUS "${CMAKE_BINARY_DIR} | ${CMAKE_SOURCE_DIR}" )
   message( FATAL_ERROR "You must run CMake in a different directory to the source!" ) 
 endif()
 

diff --git a/corelib/src/bundled/boost_headers.tar.gz b/corelib/src/bundled/boost_headers.tar.gz
diff --git a/corelib/src/libs/SireCAS/expression.h b/corelib/src/libs/SireCAS/expression.h
@@ -128,9 +128,9 @@ friend QDataStream& ::operator>>(QDataStream&, Expression&);
     Expression squared() const;
     Expression cubed() const;
 
-    Expression pow(const Rational &n) const;
     Expression pow(double n) const;
     Expression pow(const Complex &n) const;
+    Expression pow(const Rational &n) const;
     Expression pow(const Expression &n) const;
 
     Expression root(int n) const;
@@ -204,10 +204,10 @@ Expression operator/(double val, const Expression &ex);
 Expression operator/(const Expression &ex, const Complex &val);
 Expression operator/(const Complex &val, const Expression &ex);
 Expression pow(const Expression &ex0, int n);
-Expression pow(const Expression &ex0, const SireMaths::Rational &n);
 Expression pow(const Expression &ex0, double n);
 Expression pow(const Expression &ex0, const Expression &n);
 Expression pow(const Expression &ex0, const Complex &n);
+Expression pow(const Expression &ex0, const Rational &n);
 Expression root(const Expression &ex0, int n);
 Expression sqrt(const Expression &ex0);
 Expression cbrt(const Expression &ex0);
@@ -387,13 +387,6 @@ inline Expression pow(const Expression &ex0, int n)
     return ex0.pow(n);
 }
 
-/** Raise an expression to a rational power */
-inline Expression pow(const Expression &ex0,
-                      const SireMaths::Rational &n)
-{
-    return ex0.pow(n);
-}
-
 /** Raise an expression to a real power */
 inline Expression pow(const Expression &ex0, double n)
 {
@@ -413,6 +406,12 @@ inline Expression pow(const Expression &ex0, const Complex &n)
     return ex0.pow(n);
 }
 
+/** Raise an expression to a rational power */
+inline Expression pow(const Expression &ex0, const Rational &n)
+{
+    return ex0.pow(n);
+}
+
 /** Take the nth root of an expression */
 inline Expression root(const Expression &ex0, int n)
 {

diff --git a/corelib/src/libs/SireError/getbacktrace.cpp b/corelib/src/libs/SireError/getbacktrace.cpp
@@ -28,6 +28,9 @@
 
 #include "getbacktrace.h"
 
+#define BOOST_STACKTRACE_GNU_SOURCE_NOT_REQUIRED 1
+#include <boost/stacktrace.hpp>
+
 #include <QObject>
 #include <QString>
 #include <QRegExp>

diff --git a/corelib/src/libs/SireIO/amberprm.cpp b/corelib/src/libs/SireIO/amberprm.cpp
@@ -1081,7 +1081,9 @@ QVector<QString> getAtomTreeChains(const AmberParams &params)
 }
 
 /** Internal function used to get the amber atom types of each atom */
-QVector<QString> getAmberTypes(const AmberParams &params)
+QVector<QString> getAmberTypes(const AmberParams &params,
+                               QHash<QString,int> &unique_names,
+                               QMutex &name_mutex)
 {
     const auto info = params.info();
 
@@ -1091,7 +1093,48 @@ QVector<QString> getAmberTypes(const AmberParams &params)
 
     for (int i=0; i<info.nAtoms(); ++i)
     {
-        ambtyps[i] = t[ info.cgAtomIdx(AtomIdx(i)) ];
+        auto atomtype = t[ info.cgAtomIdx(AtomIdx(i)) ];
+
+        if (atomtype.length() > 4)
+        {
+            //we need to shorten the atom type name to 4 characters. Do this by
+            //creating a unique name...
+            QMutexLocker lkr(&name_mutex);
+
+            int index = 0;
+
+            if (unique_names.contains(atomtype))
+            {
+                index = unique_names[atomtype];
+            }
+            else
+            {
+                //find the highest index used so far
+                int highest = 0;
+
+                for (auto it = unique_names.constBegin(); it != unique_names.constEnd(); ++it)
+                {
+                    if (it.value() > highest)
+                        highest = it.value();
+                }
+
+                highest += 1;
+                unique_names.insert(atomtype, highest);
+
+                index = highest;
+            }
+
+            if (index < 1000)
+                atomtype = QString("X%1").arg(index);
+            else if (index < 10000)
+                atomtype = QString("%1").arg(index);
+            else
+                throw SireError::incompatible_error( QObject::tr(
+                    "Cannot write an Amber file as the number of atom types with string "
+                    "lengths greater than 4 is greater than 9999"), CODELOC );
+        }
+
+        ambtyps[i] = atomtype;
     }
 
     return ambtyps;
@@ -2131,22 +2174,25 @@ QStringList toLines(const QVector<AmberParams> &params,
     {
         QVector< QVector<QString> > amber_types(params.count());
 
+        QHash<QString,int> unique_types;
+        QMutex unique_mutex;
+
         if (use_parallel)
         {
             tbb::parallel_for( tbb::blocked_range<int>(0,params.count()),
                                [&](const tbb::blocked_range<int> r)
             {
                 for (int i=r.begin(); i<r.end(); ++i)
                 {
-                    amber_types[i] = getAmberTypes(params[i]);
+                    amber_types[i] = getAmberTypes(params[i], unique_types, unique_mutex);
                 }
             });
         }
         else
         {
             for (int i=0; i<params.count(); ++i)
             {
-                amber_types[i] = getAmberTypes(params[i]);
+                amber_types[i] = getAmberTypes(params[i], unique_types, unique_mutex);
             }
         }
 
@@ -3133,7 +3179,7 @@ AmberPrm::AmberPrm(const System &system, const PropertyMap &map)
     {
         throw SireIO::parse_error( QObject::tr(
             "Errors converting the system to a Amber Parm format...\n%1")
-                .arg(lines.join("\n")), CODELOC );
+                .arg(errors.join("\n")), CODELOC );
     }
 
     //we don't need params any more, so free the memory
@@ -3614,7 +3660,7 @@ MolStructureEditor AmberPrm::getMolStructure(int start_idx, int natoms,
 
         if (res_idx+1 == res_pointers.count())
         {
-            res_end_atom = res_start_atom + natoms - 1;
+            res_end_atom = res_pointers[res_start_idx] + natoms - 1;
         }
         else
         {

diff --git a/corelib/src/libs/SireIO/charmmpsf.cpp b/corelib/src/libs/SireIO/charmmpsf.cpp
@@ -860,7 +860,7 @@ CharmmPSF::CharmmPSF(const SireSystem::System &system, const PropertyMap &map) :
     try
     {
         // Extract the existing parameters from the system.
-        QString params = system.property(map["charmm-params"]).asA<StringProperty>().value();
+        QString params = system.property(map["charmm_params"]).asA<StringProperty>().value();
 
         // Convert into a list.
         charmm_params = params.split("\n");
@@ -3019,9 +3019,9 @@ void CharmmPSF::parseMolecule(
     QString segment = QString("M%1").arg(imol+1);
 
     // Extract the existing molecule name.
-    if (sire_mol.hasProperty(map["mol-name"]))
+    if (sire_mol.hasProperty(map["mol_name"]))
     {
-        segment = sire_mol.property(map["mol-name"]).toString().simplified().toUpper();
+        segment = sire_mol.property(map["mol_name"]).toString().simplified().toUpper();
     }
 
     if (usesParallel())
@@ -3570,8 +3570,8 @@ System CharmmPSF::startSystem(const QVector<QString> &param_lines, const Propert
     else           param_format = "X-PLOR";
 
     // Add the CHARMM parameters as a property.
-    system.setProperty(map["charmm-params"].source(), StringProperty(params_string));
-    system.setProperty(map["param-format"].source(), StringProperty(param_format));
+    system.setProperty(map["charmm_params"].source(), StringProperty(params_string));
+    system.setProperty(map["param_format"].source(), StringProperty(param_format));
 
     // Add the periodic box property.
     if (has_box_params)
@@ -3819,7 +3819,7 @@ MolEditor CharmmPSF::getMolecule(int imol, const PropertyMap &map) const
     auto mol = this->getMolStructure(imol, map["cutting"]).commit().edit();
 
     // Set the molecule name.
-    mol.setProperty(map["mol-name"], StringProperty(atoms[molecules[imol][0]].getSegment()));
+    mol.setProperty(map["mol_name"], StringProperty(atoms[molecules[imol][0]].getSegment()));
 
     // Get the info object that can map between AtomNum to AtomIdx etc.
     const auto molinfo = mol.info();

diff --git a/corelib/src/libs/SireIO/gro87.cpp b/corelib/src/libs/SireIO/gro87.cpp
@@ -1600,10 +1600,10 @@ int Gro87::findAtom(const MoleculeInfoData &molinfo, int atmidx, int hint,
             return partial_matches.last();
         }
         else
-            throw SireMol::missing_atom( QObject::tr(
-                "Cannot find the atom %1(%2) : %3(%4) in the set of atoms loaded "
-                "from this .gro file.")
-                    .arg(atmname).arg(atmnum).arg(resname).arg(resnum), CODELOC );
+        {
+            //we can't find the atom, so just go with the hint
+            return hint;
+        }
     }
 
     return match;