add gyration radius for post processing

Signed-off-by: Conrad Huebler <[email protected]>
conradhuebler · Nov 9, 2023 · 85fc5b3 · 85fc5b3
1 parent 51487d3
commit 85fc5b3
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Showing 3 changed files with 46 additions and 0 deletions.
diff --git a/src/core/molecule.cpp b/src/core/molecule.cpp
@@ -793,6 +793,35 @@ Position Molecule::Centroid(bool protons, int fragment) const
     return GeometryTools::Centroid(getGeometryByFragment(fragment, protons));
 }
 
+Eigen::Vector3d Molecule::COM(bool protons, int fragment)
+{
+    // todo implement heavy and fragements ...
+    if (m_mass < 1)
+        CalculateMass();
+    Eigen::Vector3d com = { 0, 0, 0 };
+    for (int i = 0; i < m_geometry.size(); ++i) {
+        double mass = Elements::AtomicMass[m_atoms[i]];
+        com(0) += mass * m_geometry[i][0];
+        com(1) += mass * m_geometry[i][1];
+        com(2) += mass * m_geometry[i][2];
+    }
+    com(0) /= m_mass;
+    com(1) /= m_mass;
+    com(2) /= m_mass;
+    return com;
+}
+
+double Molecule::GyrationRadius(bool protons, int fragment)
+{
+    Eigen::Vector3d com = COM(protons, fragment);
+    double gyr = 0;
+    for (int i = 0; i < m_geometry.size(); ++i) {
+        gyr += ((com(0) - m_geometry[i][0]) * (com(0) - m_geometry[i][0]) + (com(0) - m_geometry[i][0]) * (com(0) - m_geometry[i][0]) + (com(0) - m_geometry[i][0]) * (com(0) - m_geometry[i][0]));
+    }
+    gyr /= double(m_geometry.size());
+    return gyr;
+}
+
 std::pair<int, Position> Molecule::Atom(int i) const
 {
     return std::pair<int, Position>(m_atoms[i], { m_geometry[i][0], m_geometry[i][1], m_geometry[i][2] });

diff --git a/src/core/molecule.h b/src/core/molecule.h
@@ -96,6 +96,8 @@ class Molecule
     Molecule getFragmentMolecule(int fragment) const;
 
     double CalculateDistance(int i, int j) const;
+    double GyrationRadius(bool hydrogen = true, int fragment = -1);
+
     Geometry getGeometry(const IntPair& pair, bool protons = true) const;
     Geometry getGeometry(std::vector<int> atoms, bool protons = true) const;
     Geometry getGeometryByFragment(int fragment, bool protons = true) const;
@@ -109,6 +111,7 @@ class Molecule
     bool setGeometryByFragment(const Geometry& geometry, int fragment, bool protons = true);
 
     Position Centroid(bool hydrogen = true, int fragment = -1) const;
+    Eigen::Vector3d COM(bool hydrogen = true, int fragment = -1);
     inline std::size_t AtomCount() const { return m_atoms.size(); }
     std::vector<int> Atoms() const { return m_atoms; }
     std::pair<int, Position> Atom(int i) const;

diff --git a/src/main.cpp b/src/main.cpp
@@ -819,6 +819,18 @@ int main(int argc, char **argv) {
                 Molecule mol = file.Next();
                 mol.writeXYZFile(outfile, Tools::RandomVector(0, mol.AtomCount()));
             }
+        } else if (strcmp(argv[1], "-gyration") == 0) {
+            FileIterator file(argv[2]);
+            int count = 1;
+            double sum = 0;
+
+            while (!file.AtEnd()) {
+                Molecule mol = file.Next();
+                double gyr = mol.GyrationRadius();
+                sum += gyr;
+                std::cout << ":: " << gyr << " " << sum / double(count) << std::endl;
+                count++;
+            }
         } else {
             bool centered = false;
             for (std::size_t i = 2; i < argc; ++i) {
@@ -838,6 +850,8 @@ int main(int argc, char **argv) {
                 mol.AnalyseIntermoleculeDistance();
                 std::cout << mol.Check() << std::endl
                           << std::endl;
+                std::cout << mol.COM().transpose() << std::endl;
+                std::cout << mol.GyrationRadius() << std::endl;
                 /*
                 Hessian hess("gfn2", UFFParameterJson);
                 hess.setMolecule(mol);