Feature format

corelib/src/libs/SireIO/CMakeLists.txt

@@ -48,6 +48,7 @@ set ( SIREIO_HEADERS
       netcdffile.h
       pdb.h
       pdb2.h
+      pdbx.h
       perturbationslibrary.h
       protoms.h
       sdf.h
@@ -95,6 +96,7 @@ set ( SIREIO_SOURCES
       netcdffile.cpp
       pdb.cpp
       pdb2.cpp
+      pdbx.cpp
       perturbationslibrary.cpp
       protoms.cpp
       sdf.cpp

corelib/src/libs/SireIO/amberprm.cpp

@@ -383,6 +383,7 @@ void AmberPrm::rebuildLJParameters()
 
     const auto acoeffs = float_data.value("LENNARD_JONES_ACOEF");
     const auto bcoeffs = float_data.value("LENNARD_JONES_BCOEF");
+    const auto ccoeffs = float_data.value("LENNARD_JONES_CCOEF");
 
     const auto hbond_acoeffs = float_data.value("HBOND_ACOEF");
     const auto hbond_bcoeffs = float_data.value("HBOND_BCOEF");
@@ -401,6 +402,17 @@ void AmberPrm::rebuildLJParameters()
                                   CODELOC);
     }
 
+    if ((not ccoeffs.isEmpty()) and (ccoeffs.count() != acoeffs.count()))
+    {
+        throw SireIO::parse_error(QObject::tr("Incorrect number of LJ coefficients for the number of specified "
+                                              "atom types! Should be %1 for %2 types, but actually have "
+                                              "%3 LJ C-coefficients")
+                                      .arg((ntypes * (ntypes + 1)) / 2)
+                                      .arg(ntypes)
+                                      .arg(ccoeffs.count()),
+                                  CODELOC);
+    }
+
     if (nb_parm_index.count() != ntypes * ntypes)
     {
         throw SireIO::parse_error(QObject::tr("Incorrect number of non-bonded parameter indicies. There should "
@@ -424,11 +436,12 @@ void AmberPrm::rebuildLJParameters()
 
     const auto acoeffs_data = acoeffs.constData();
     const auto bcoeffs_data = bcoeffs.constData();
+
     const auto hbond_acoeffs_data = hbond_acoeffs.constData();
     const auto hbond_bcoeffs_data = hbond_bcoeffs.constData();
     const auto nb_parm_index_data = nb_parm_index.constData();
 
-    auto build_lj = [&](int i)
+    for (int i = 0; i < ntypes; ++i)
     {
         // amber stores the A and B coefficients as the product of all
         // possible combinations. We need to find the values from the
@@ -461,22 +474,39 @@ void AmberPrm::rebuildLJParameters()
 
             lj_data_array[i] = LJParameter(sigma * angstrom, epsilon * kcal_per_mol);
         }
-    };
+    }
 
-    if (usesParallel())
+    if (not ccoeffs.isEmpty())
     {
-        tbb::parallel_for(tbb::blocked_range<int>(0, ntypes), [&](tbb::blocked_range<int> r)
-                          {
-            for (int i = r.begin(); i < r.end(); ++i)
+        // we need to create a matrix mapping the C4 terms for pairs
+        // of LJ parameters
+        QHash<LJParameter, QHash<LJParameter, double>> lj_c4_values;
+
+        const auto ccoeffs_data = ccoeffs.constData();
+
+        // find all of the C4 co-efficients for all of the types
+        for (int i = 0; i < ntypes; ++i)
+        {
+            for (int j = 0; i < ntypes; ++j)
             {
-                build_lj(i);
-            } });
-    }
-    else
-    {
+                const int idx = nb_parm_index_data[ntypes * i + j];
+
+                const double ccoeff = ccoeffs_data[idx - 1];
+
+                if (ccoeff != 0)
+                {
+                    const auto &lj0 = lj_data_array[i];
+                    const auto &lj1 = lj_data_array[j];
+
+                    lj_c4_values[lj0][lj1] = ccoeff;
+                    lj_c4_values[lj1][lj0] = ccoeff;
+                }
+            }
+        }
+
+        // now give each LJParameter its C4 values for all other types
         for (int i = 0; i < ntypes; ++i)
         {
-            build_lj(i);
         }
     }
 

corelib/src/libs/SireIO/mol2.cpp

@@ -2380,6 +2380,9 @@ void Mol2::addToSystem(System &system, const PropertyMap &map) const
     // you should loop through each molecule in the system and work out
     // which ones are described in the file, and then add data from the file
     // to thise molecules.
+    throw SireError::unsupported(QObject::tr(
+                                     "You cannot add data from a mol2 file to an existing system!"),
+                                 CODELOC);
 }
 
 /** Internal function used to get the molecule structure for molecule 'imol'. */