Merge pull request #210 from OpenBioSim/feature_ion_template

Add function to create ions from AMBER templates
OpenBioSim · Jul 11, 2024 · 3c890c3 · 3c890c3
2 parents 633590a + a742357
commit 3c890c3
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Showing 7 changed files with 706 additions and 0 deletions.
diff --git a/corelib/src/libs/SireIO/biosimspace.cpp b/corelib/src/libs/SireIO/biosimspace.cpp
@@ -1589,6 +1589,68 @@ namespace SireIO
         return retval;
     }
 
+    Molecule createSodiumIon(const Vector &coords, const QString model, const PropertyMap &map)
+    {
+		// Strip all whitespace from the model name and convert to upper case.
+        auto _model = model.simplified().replace(" ", "").toUpper();
+
+        // Create a hash between the allowed model names and their templace files.
+        QHash<QString, QString> models;
+        models["TIP3P"] = getShareDir() + "/templates/ions/na_tip3p";
+        models["TIP4P"] = getShareDir() + "/templates/ions/na_tip4p";
+
+        // Make sure the user has passed a valid water model.
+        if (not models.contains(_model))
+        {
+            throw SireError::incompatible_error(QObject::tr("Unsupported AMBER ion model '%1'").arg(model), CODELOC);
+        }
+
+        // Extract the water model template path.
+        auto path = models[_model];
+
+        // Load the ion template.
+        auto ion_template = MoleculeParser::read(path + ".prm7", map);
+
+        // Extract the ion the template.
+        auto ion = ion_template[MolIdx(0)].molecule();
+
+        // Set the coordinates of the ion.
+        ion = ion.edit().atom(AtomIdx(0)).setProperty(map["coordinates"], coords).molecule().commit();
+
+        return ion;
+    }
+
+    Molecule createChlorineIon(const Vector &coords, const QString model, const PropertyMap &map)
+    {
+		// Strip all whitespace from the model name and convert to upper case.
+        auto _model = model.simplified().replace(" ", "").toUpper();
+
+        // Create a hash between the allowed model names and their templace files.
+        QHash<QString, QString> models;
+        models["TIP3P"] = getShareDir() + "/templates/ions/cl_tip3p";
+        models["TIP4P"] = getShareDir() + "/templates/ions/cl_tip4p";
+
+        // Make sure the user has passed a valid water model.
+        if (not models.contains(_model))
+        {
+            throw SireError::incompatible_error(QObject::tr("Unsupported AMBER ion model '%1'").arg(model), CODELOC);
+        }
+
+        // Extract the water model template path.
+        auto path = models[_model];
+
+        // Load the ion template.
+        auto ion_template = MoleculeParser::read(path + ".prm7");
+
+        // Extract the ion the template.
+        auto ion = ion_template[MolIdx(0)].molecule();
+
+        // Set the coordinates of the ion.
+        ion = ion.edit().atom(AtomIdx(0)).setProperty(map["coordinates"], coords).molecule().commit();
+
+        return ion;
+    }
+
     Vector cross(const Vector &v0, const Vector &v1)
     {
         double nx = v0.y() * v1.z() - v0.z() * v1.y();

diff --git a/corelib/src/libs/SireIO/biosimspace.h b/corelib/src/libs/SireIO/biosimspace.h
@@ -319,6 +319,38 @@ namespace SireIO
         const QHash<MolIdx, MolIdx> &molecule_mapping, const bool is_lambda1 = false,
         const PropertyMap &map0 = PropertyMap(), const PropertyMap &map1 = PropertyMap());
 
+    //! Create a sodium ion at the specified position.
+    /*! \param position
+            The position of the sodium ion.
+
+        \param model
+            The name of the water model.
+
+        \param map
+            A dictionary of user-defined molecular property names.
+
+        \retval sodium
+            The sodium ion.
+     */
+    SIREIO_EXPORT Molecule createSodiumIon(
+        const Vector &coords, const QString model, const PropertyMap &map = PropertyMap());
+
+    //! Create a chlorine ion at the specified position.
+    /*! \param position
+            The position of the chlorine ion.
+
+        \param model
+            The name of the water model.
+
+        \param map
+            A dictionary of user-defined molecular property names.
+
+        \retval chlorine
+            The chlorine ion.
+     */
+    SIREIO_EXPORT Molecule createChlorineIon(
+        const Vector &coords, const QString model, const PropertyMap &map = PropertyMap());
+
     Vector cross(const Vector &v0, const Vector &v1);
 } // namespace SireIO
 
@@ -332,6 +364,8 @@ SIRE_EXPOSE_FUNCTION(SireIO::setAmberWater)
 SIRE_EXPOSE_FUNCTION(SireIO::setGromacsWater)
 SIRE_EXPOSE_FUNCTION(SireIO::updateAndPreserveOrder)
 SIRE_EXPOSE_FUNCTION(SireIO::updateCoordinatesAndVelocities)
+SIRE_EXPOSE_FUNCTION(SireIO::createSodiumIon)
+SIRE_EXPOSE_FUNCTION(SireIO::createChlorineIon)
 
 SIRE_END_HEADER
 

diff --git a/corelib/templates/ions/cl_tip3p.prm7 b/corelib/templates/ions/cl_tip3p.prm7
@@ -0,0 +1,130 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 07/10/24  14:04:15
+%FLAG TITLE
+%FORMAT(20a4)
+
+%FLAG POINTERS
+%FORMAT(10I8)
+       1       1       0       0       0       0       0       0       0       0
+       1       1       0       0       0       0       0       0       1       0
+       0       0       0       0       0       0       0       0       1       0
+       0       0       0
+%FLAG ATOM_NAME
+%FORMAT(20a4)
+Cl- 
+%FLAG CHARGE
+%FORMAT(5E16.8)
+ -1.82223000E+01
+%FLAG ATOMIC_NUMBER
+%FORMAT(10I8)
+      17
+%FLAG MASS
+%FORMAT(5E16.8)
+  3.54500000E+01
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+       1
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+       1
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+       1
+%FLAG RESIDUE_LABEL
+%FORMAT(20a4)
+Cl- 
+%FLAG RESIDUE_POINTER
+%FORMAT(10I8)
+       1
+%FLAG BOND_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG BOND_EQUIL_VALUE
+%FORMAT(5E16.8)
+
+%FLAG ANGLE_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG ANGLE_EQUIL_VALUE
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_PERIODICITY
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_PHASE
+%FORMAT(5E16.8)
+
+%FLAG SCEE_SCALE_FACTOR
+%FORMAT(5E16.8)
+
+%FLAG SCNB_SCALE_FACTOR
+%FORMAT(5E16.8)
+
+%FLAG SOLTY
+%FORMAT(5E16.8)
+  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF
+%FORMAT(5E16.8)
+  9.24719470E+06
+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
+  1.14737423E+03
+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG ANGLES_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
+       0
+%FLAG HBOND_ACOEF
+%FORMAT(5E16.8)
+
+%FLAG HBOND_BCOEF
+%FORMAT(5E16.8)
+
+%FLAG HBCUT
+%FORMAT(5E16.8)
+
+%FLAG AMBER_ATOM_TYPE
+%FORMAT(20a4)
+Cl- 
+%FLAG TREE_CHAIN_CLASSIFICATION
+%FORMAT(20a4)
+M   
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+       0
+%FLAG IROTAT
+%FORMAT(10I8)
+       0
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII
+%FORMAT(5E16.8)
+  1.70000000E+00
+%FLAG SCREEN
+%FORMAT(5E16.8)
+  8.00000000E-01
+%FLAG ATOMS_PER_MOLECULE
+%FORMAT(10I8)
+       1
+%FLAG IPOL
+%FORMAT(1I8)
+       0
diff --git a/corelib/templates/ions/cl_tip4p.prm7 b/corelib/templates/ions/cl_tip4p.prm7
@@ -0,0 +1,130 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 07/10/24  14:04:34
+%FLAG TITLE
+%FORMAT(20a4)
+
+%FLAG POINTERS
+%FORMAT(10I8)
+       1       1       0       0       0       0       0       0       0       0
+       1       1       0       0       0       0       0       0       1       0
+       0       0       0       0       0       0       0       0       1       0
+       0       0       0
+%FLAG ATOM_NAME
+%FORMAT(20a4)
+Cl- 
+%FLAG CHARGE
+%FORMAT(5E16.8)
+ -1.82223000E+01
+%FLAG ATOMIC_NUMBER
+%FORMAT(10I8)
+      17
+%FLAG MASS
+%FORMAT(5E16.8)
+  3.54500000E+01
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+       1
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+       1
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+       1
+%FLAG RESIDUE_LABEL
+%FORMAT(20a4)
+Cl- 
+%FLAG RESIDUE_POINTER
+%FORMAT(10I8)
+       1
+%FLAG BOND_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG BOND_EQUIL_VALUE
+%FORMAT(5E16.8)
+
+%FLAG ANGLE_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG ANGLE_EQUIL_VALUE
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_FORCE_CONSTANT
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_PERIODICITY
+%FORMAT(5E16.8)
+
+%FLAG DIHEDRAL_PHASE
+%FORMAT(5E16.8)
+
+%FLAG SCEE_SCALE_FACTOR
+%FORMAT(5E16.8)
+
+%FLAG SCNB_SCALE_FACTOR
+%FORMAT(5E16.8)
+
+%FLAG SOLTY
+%FORMAT(5E16.8)
+  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF
+%FORMAT(5E16.8)
+  9.33304478E+06
+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
+  6.59809978E+02
+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG ANGLES_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+
+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
+       0
+%FLAG HBOND_ACOEF
+%FORMAT(5E16.8)
+
+%FLAG HBOND_BCOEF
+%FORMAT(5E16.8)
+
+%FLAG HBCUT
+%FORMAT(5E16.8)
+
+%FLAG AMBER_ATOM_TYPE
+%FORMAT(20a4)
+Cl- 
+%FLAG TREE_CHAIN_CLASSIFICATION
+%FORMAT(20a4)
+M   
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+       0
+%FLAG IROTAT
+%FORMAT(10I8)
+       0
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII
+%FORMAT(5E16.8)
+  1.70000000E+00
+%FLAG SCREEN
+%FORMAT(5E16.8)
+  8.00000000E-01
+%FLAG ATOMS_PER_MOLECULE
+%FORMAT(10I8)
+       1
+%FLAG IPOL
+%FORMAT(1I8)
+       0