Initial support for constraints

.github/workflows/build_cmake.yml

@@ -8,10 +8,10 @@ on: [push, pull_request]
 
 env:
   BUILD_TYPE: Release
-  QT_VERSION: 5.12.8
+  QT_VERSION: 5.12.9
   MACOSX_DEPLOYMENT_TARGET: 10.12
   CCACHE_VERSION: 3.7.7
-  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON 
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON
 
 jobs:
   build:
@@ -22,8 +22,15 @@ jobs:
       matrix:
         config:
         - {
-            name: "Ubuntu Latest GCC", artifact: "Linux.tar.gz",
-            os: ubuntu-latest,
+            name: "Ubuntu 20.04 GCC", artifact: "Ubuntu2004.tar.gz",
+            os: ubuntu-20.04,
+            cc: "gcc", cxx: "g++",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON ",
+            cpack: "",
+          }
+        - {
+            name: "Ubuntu 18.04 GCC", artifact: "Ubuntu1804.tar.gz",
+            os: ubuntu-18.04,
             cc: "gcc", cxx: "g++",
             cmake_flags: "-G Ninja -DENABLE_TESTING=ON ",
             cpack: "",
@@ -47,7 +54,9 @@ jobs:
 
     - name: Install Dependencies (Linux)
       if: runner.os == 'Linux'
-      run: sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev qt5-default
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev qt5-default
     - name: Install Dependencies (macOS)
       if: runner.os == 'macOS'
       run: |

README.md

@@ -23,8 +23,8 @@ features and goals of the Avogadro project:
 ![Kitware, Inc.][KitwareLogo]
 
 Avogadro 2 is being developed as part of the [Open Chemistry][OpenChemistry]
-project by an open communit, and has been developed at [Kitware][Kitware] as an
-open source community project. The Avogadro 1.x series currently has more
+project by an open community, and has been developed at [Kitware][Kitware] as
+an open source community project. The Avogadro 1.x series currently has more
 features, and can be found [here][Avogadro1]. We will be porting more features
 to the Avogadro 2 code base, and making regular releases to get feedback from
 the community. We are actively working to make Avogadro 2 mainline in 2018.

avogadro/core/array.h

@@ -155,12 +155,12 @@ class Array
   T* data()
   {
     detachWithCopy();
-    return &d->data[0];
+    return d->data.data();
   }
 
-  const T* data() const { return &d->data[0]; }
+  const T* data() const { return d->data.data(); }
 
-  const T* constData() const { return &d->data[0]; }
+  const T* constData() const { return d->data.data(); }
 
   size_t size() const { return d->data.size(); }
 

avogadro/core/molecule.cpp

@@ -694,6 +694,35 @@ double Molecule::mass() const
   return m;
 }
 
+Vector3 Molecule::centerOfGeometry() const
+{
+  Vector3 center(0.0, 0.0, 0.0);
+  for (Index i = 0; i < atomCount(); ++i)
+    center += atom(i).position3d();
+  return center / atomCount();
+}
+
+Vector3 Molecule::centerOfMass() const
+{
+  Vector3 center(0.0, 0.0, 0.0);
+  for (Index i = 0; i < atomCount(); ++i) {
+    AtomType curr_atom = atom(i);
+    center += (curr_atom.position3d() * Elements::mass(curr_atom.atomicNumber()));
+  }
+  center /= mass();
+  center /= atomCount();
+  return center;
+}
+
+double Molecule::radius() const
+{
+  double radius = 0.0;
+  if (atomCount() > 0) {
+    radius = (centerOfGeometry() - atom(0).position3d()).norm();
+  }
+  return radius;
+}
+
 Array<double> Molecule::vibrationFrequencies() const
 {
   return m_vibrationFrequencies;

avogadro/core/molecule.h

@@ -526,6 +526,24 @@ class AVOGADROCORE_EXPORT Molecule
    */
   double mass() const;
 
+  /**
+   * @return The center of geometry of the molecule obtained by summing the
+   * coordinates of the atoms.
+   */
+  Vector3 centerOfGeometry() const;
+
+  /**
+   * @return The center of mass of the molecule obtained by summing the
+   * coordinates of the atoms weighted by mass.
+   */
+  Vector3 centerOfMass() const;
+
+  /**
+   * @return The minimum radius of a sphere centered on centerOfGeometry
+   * containing all the centers of the atoms.
+   */
+  double radius() const;
+
   /**
    * Set the basis set for the molecule, note that the molecule takes ownership
    * of the object.

avogadro/io/CMakeLists.txt

@@ -14,7 +14,7 @@ if(USE_HDF5)
     set(HDF5_LIBRARIES "hdf5")
   endif()
   include_directories(SYSTEM "${HDF5_INCLUDE_DIRS}")
-  add_definitions(-DAVO_USE_HDF5)
+  add_definitions(-DAVO_USE_HDF5 -DH5_USE_110_API)
 endif()
 
 # Add as "system headers" to avoid warnings generated by them with

avogadro/qtgui/molecule.cpp

@@ -21,14 +21,14 @@ namespace Avogadro {
 namespace QtGui {
 
 Molecule::Molecule(QObject* parent_)
-  : QObject(parent_), m_undoMolecule(new RWMolecule(*this, this))
+  : QObject(parent_), m_undoMolecule(new RWMolecule(*this, this)), constraints()
 {
   m_undoMolecule->setInteractive(true);
 }
 
 Molecule::Molecule(const Molecule& other)
   : QObject(), Core::Molecule(other),
-    m_undoMolecule(new RWMolecule(*this, this))
+    m_undoMolecule(new RWMolecule(*this, this)), constraints()
 {
   m_undoMolecule->setInteractive(true);
   // Now assign the unique ids
@@ -40,7 +40,7 @@ Molecule::Molecule(const Molecule& other)
 }
 
 Molecule::Molecule(const Core::Molecule& other)
-  : QObject(), Core::Molecule(other)
+  : QObject(), Core::Molecule(other), constraints()
 {
   // Now assign the unique ids
   for (Index i = 0; i < atomCount(); i++)

avogadro/qtgui/molecule.h

@@ -28,6 +28,11 @@
 #include <QtCore/QObject>
 
 namespace Avogadro {
+
+namespace QtPlugins {
+    class ConstraintsModel;
+}
+
 namespace QtGui {
 
 class Mesh;
@@ -45,6 +50,9 @@ class AVOGADROQTGUI_EXPORT Molecule
   Q_OBJECT
 
 public:
+
+  QtPlugins::ConstraintsModel* constraints;
+
   /** Typedef for Atom class. */
   typedef Core::Molecule::AtomType AtomType;
 

avogadro/qtplugins/CMakeLists.txt

@@ -165,6 +165,9 @@ if(BUILD_GPL_PLUGINS)
   add_subdirectory(qtaim)
 endif()
 
+#kantundpeterpan
+add_subdirectory(constraints)
+
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${original_library_output_dir}")
 
 # Add all of the static plugins to the initialization file.

avogadro/qtplugins/constraints/CMakeLists.txt

@@ -0,0 +1,23 @@
+include_directories("${AvogadroLibs_SOURCE_DIR}/thirdparty")
+
+set(constraints
+  constraintsextension.cpp
+  constraintsdialog.cpp
+  constraintsmodel.cpp
+  constraint.cpp
+)
+
+set(constraints_uis
+  constraintsdialog.ui
+)
+
+avogadro_plugin(ConstraintsExtension
+  "Constraints extension"
+  ExtensionPlugin
+  constraintsextension.h
+  ConstraintsExtension
+  "${constraints}"
+  "${constraints_uis}"
+)
+
+target_link_libraries(ConstraintsExtension)

avogadro/qtplugins/constraints/constraint.cpp

@@ -0,0 +1,168 @@
+#include "constraint.h"
+
+namespace Avogadro {
+  namespace QtPlugins {
+
+    Constraint::Constraint(int type,
+                           int a,
+                           int b,
+                           int c,
+                           int d,
+                           double value,
+                           ConstraintsModel* model)
+    {
+      c_model = model;
+      ConstraintType = type;
+
+      //adjusting for 0 indexing
+      a = a-1;
+      b = b-1;
+      c = c-1;
+      d = d-1;
+
+      // store unique AtomIds
+
+      switch (ConstraintType)
+        {
+        case 0 ... 4:
+          // AtomA
+          Atoms << c_model->c_molecule->atomUniqueId(a);
+          break;
+
+        case 5:
+          //AtomA
+          Atoms << c_model->c_molecule->atomUniqueId(a);
+          //AtomB
+          Atoms << c_model->c_molecule->atomUniqueId(b);
+          break;
+
+        case 6:
+          //AtomA
+          Atoms << c_model->c_molecule->atomUniqueId(a);
+          //AtomB
+          Atoms << c_model->c_molecule->atomUniqueId(b);
+          //AtomC
+          Atoms << c_model->c_molecule->atomUniqueId(c);
+          break;
+
+        case 7:
+          //AtomA
+          Atoms << c_model->c_molecule->atomUniqueId(a);
+          //AtomB
+          Atoms << c_model->c_molecule->atomUniqueId(b);
+          //AtomC
+          Atoms << c_model->c_molecule->atomUniqueId(c);
+          //AtomD
+          Atoms << c_model->c_molecule->atomUniqueId(d);
+        }
+
+      ConstraintValue = value;
+
+    }
+
+    Constraint::~Constraint(){}
+
+    void Constraint::SetConstraintType(int type)
+    {
+      ConstraintType = type;
+    }
+
+    void Constraint::SetValue(double Value)
+    {
+      ConstraintValue = Value;
+    }
+
+    int Constraint::GetConstraintType() const
+    {
+      return ConstraintType;
+    }
+
+    double Constraint::GetConstraintValue() const
+    {
+      return ConstraintValue;
+    }
+
+    const Index Constraint::GetConstraintAtomA() const
+    {
+      if (Atoms.size() >= 1) //returned for all constraint types
+        {
+          return c_model->c_molecule->atomByUniqueId(Atoms[0]).index()+1;
+        }
+      else
+        {
+          return 0;
+        }
+    }
+
+    const Index Constraint::GetConstraintAtomB() const
+    {
+      if (Atoms.size() >= 2) //distance, angle and torsion constraints
+        {
+          return c_model->c_molecule->atomByUniqueId(Atoms[1]).index()+1;
+        }
+      else
+        {
+          return 0;
+        }
+    }
+
+    const Index Constraint::GetConstraintAtomC() const
+    {
+      if (Atoms.size() >= 3) //angle and torsion constraints
+        {
+          return c_model->c_molecule->atomByUniqueId(Atoms[2]).index()+1;
+        }
+      else
+        {
+          return 0;
+        }
+    }
+
+    const Index Constraint::GetConstraintAtomD() const
+    {
+      if (Atoms.size() >= 4) //torsion constraints only
+        {
+          return c_model->c_molecule->atomByUniqueId(Atoms[3]).index()+1;
+        }
+      else
+        {
+          return 0;
+        }
+    }
+
+    QJsonObject Constraint::toJson()
+    {
+      QJsonObject ConstraintJ;
+      ConstraintJ["type"] = GetConstraintType();
+      ConstraintJ["value"] = GetConstraintValue();
+
+      QJsonArray ConstraintAtoms;
+
+      switch (GetConstraintType())
+        {
+        case 0 ... 4:
+          ConstraintAtoms << static_cast<int>(GetConstraintAtomA());
+          break;
+        case 5:
+          ConstraintAtoms << static_cast<int>(GetConstraintAtomA())
+                          << static_cast<int>(GetConstraintAtomB());
+          break;
+        case 6:
+          ConstraintAtoms << static_cast<int>(GetConstraintAtomA())
+                          << static_cast<int>(GetConstraintAtomB())
+                          << static_cast<int>(GetConstraintAtomC());
+          break;
+        case 7:
+          ConstraintAtoms << static_cast<int>(GetConstraintAtomA())
+                          << static_cast<int>(GetConstraintAtomB())
+                          << static_cast<int>(GetConstraintAtomC())
+                          << static_cast<int>(GetConstraintAtomD());
+          break;
+        }
+
+      ConstraintJ.insert("atoms", ConstraintAtoms);
+
+      return ConstraintJ;
+    }
+  } //namespace QtPlugins
+}  //namespace Avogadro