Merge pull request #282 from OpenBioSim/release_2024.4.0

Release 2024.4.0
OpenBioSim · Feb 5, 2025 · 14bcc19 · 14bcc19
2 parents 2f671a7 + cb9f92d
commit 14bcc19
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Showing 70 changed files with 4,189 additions and 2,253 deletions.
diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp
@@ -1032,8 +1032,12 @@ bool LambdaSchedule::hasForceSpecificEquation(const QString &stage,
 
     if (force == "*")
         return false;
-    else
-        return this->stage_equations[idx].contains(_get_lever_name(force, lever));
+
+    // If there is a default equation for this force, always return true
+    if (this->stage_equations[idx].contains(_get_lever_name(force, "*")))
+        return true;
+
+    return this->stage_equations[idx].contains(_get_lever_name(force, lever));
 }
 
 SireCAS::Expression LambdaSchedule::_getEquation(int stage,

diff --git a/corelib/src/libs/SireIO/sdf.cpp b/corelib/src/libs/SireIO/sdf.cpp
@@ -959,6 +959,13 @@ SDFMolecule parseMolecule(const Molecule &molecule, QStringList &errors, const P
                 sdfmol.addProperty("CHG", i + 1, QString::number(charge));
                 charge = 0;
             }
+            else if (charge > 0)
+            {
+                if (charge < 4)
+                {
+                    charge = 4 - charge;
+                }
+            }
             else if (charge < 0)
             {
                 switch (charge)

diff --git a/corelib/src/libs/SireMM/CMakeLists.txt b/corelib/src/libs/SireMM/CMakeLists.txt
@@ -16,7 +16,7 @@ include_directories(${TBB_INCLUDE_DIR})
 # Define the headers in SireMM
 set ( SIREMM_HEADERS
       amberparams.h
-      anglerestraint.h
+      anglerestraints.h
       angle.h
       atomfunctions.h
       atomljs.h
@@ -43,7 +43,7 @@ set ( SIREMM_HEADERS
       cljworkspace.h
       coulombpotential.h
       dihedral.h
-      dihedralrestraint.h
+      dihedralrestraints.h
       distancerestraint.h
       errors.h
       excludedpairs.h
@@ -110,7 +110,7 @@ set ( SIREMM_SOURCES
 
       amberparams.cpp
       angle.cpp
-      anglerestraint.cpp
+      anglerestraints.cpp
       atomfunctions.cpp
       atomljs.cpp
       bond.cpp
@@ -135,7 +135,7 @@ set ( SIREMM_SOURCES
       cljworkspace.cpp
       coulombpotential.cpp
       dihedral.cpp
-      dihedralrestraint.cpp
+      dihedralrestraints.cpp
       distancerestraint.cpp
       errors.cpp
       excludedpairs.cpp