Copy hydrocarbon files to hydrocarbon module in GhostFragment

.gitignore

@@ -32,6 +32,7 @@ __pycache__
 # These are directories used by IDEs for storing settings
 .idea/
 .vscode/
+.cache/
 
 # These are common Python virtual enviornment directory names
 venv/
@@ -55,4 +56,6 @@ toolchain.cmake
 
 install/
 .DS_Store
+.kdev4/
+GhostFragment.kdev4
 

src/ghostfragment/ghostfragment.cpp

@@ -20,6 +20,7 @@
 #include "screening/screening.hpp"
 #include "topology/topology.hpp"
 #include <ghostfragment/load_modules.hpp>
+#include "hydrocarbon/hydrocarbon.hpp"
 
 namespace ghostfragment {
 
@@ -29,6 +30,7 @@ void load_modules(pluginplay::ModuleManager& mm) {
     drivers::load_modules(mm);
     fragmenting::load_modules(mm);
     // screening::load_modules(mm);
+    hydrocarbon::load_modules(mm);
 
     capping::set_defaults(mm);
     topology::set_defaults(mm);

src/ghostfragment/hydrocarbon/hydrocarbon.hpp

@@ -0,0 +1,18 @@
+#pragma once
+#include <simde/simde.hpp>
+
+namespace ghostfragment::hydrocarbon {
+
+// chemist::Molecule hydrocarbon(int num_carbon);
+
+DECLARE_MODULE(MakeHydrocarbon);
+
+inline void load_modules(pluginplay::ModuleManager& mm) {
+    mm.add_module<MakeHydrocarbon>("Generate a straight chain alkane");
+}
+
+inline void set_defaults(pluginplay::ModuleManager& mm) {
+
+}
+
+} // namespace ghostfragment::hydrocarbon

tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.cpp → src/ghostfragment/hydrocarbon/make_hydrocarbon.cpp

@@ -14,8 +14,10 @@
  * limitations under the License.
  */
 
-#include "hydrocarbon.hpp"
 #include "position.hpp"
+#include "hydrocarbon.hpp"
+#include <simde/simde.hpp>
+#include <string>
 
 #define C_C_BOND 2.89
 #define H_C_BOND 2.06
@@ -26,8 +28,8 @@
 #define C_NPROTON 6
 #define H_NPROTON 1
 
-namespace testing {
-
+namespace ghostfragment::hydrocarbon {
+namespace {
 chemist::Molecule hydrocarbon(int num_carbon) {
     chemist::Molecule m;
 
@@ -90,5 +92,26 @@ chemist::Molecule hydrocarbon(int num_carbon) {
 
     return m;
 }
+}
+
+const auto mod_desc = R"(
+Hydrocarbon Chain Generator
+---------------------------
+)";
+
+MODULE_CTOR(MakeHydrocarbon) {
+    description(mod_desc);
+    satisfies_property_type<simde::MoleculeFromString>();
+}
 
-} // namespace testing
+MODULE_RUN(MakeHydrocarbon) {
+    const std::string& num_carbon_string = std::get<0>(simde::MoleculeFromString::unwrap_inputs(inputs));
+
+    auto hc = hydrocarbon(std::stoi(num_carbon_string));
+
+    auto rv = results();
+
+    return simde::MoleculeFromString::wrap_results(rv, hc);
+}
+
+}

tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.cpp → src/ghostfragment/hydrocarbon/position.cpp

@@ -15,8 +15,9 @@
  */
 
 #include "position.hpp"
+#include <cmath>
 
-namespace testing {
+namespace ghostfragment::hydrocarbon {
 
 std::array<float, 3> position_carbon(const std::vector<float>& source_coords,
                                      float carbon_bond, int num,
@@ -112,4 +113,4 @@ std::array<float, 3> position_hydrogen(const std::vector<float>& source_coords,
     return coords;
 }
 
-} // namespace testing
+} // namespace ghostfragment::hydrocarbon

tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/position.hpp → src/ghostfragment/hydrocarbon/position.hpp

@@ -16,10 +16,9 @@
 
 #pragma once
 #include <array>
-#include <cmath>
 #include <vector>
 
-namespace testing {
+namespace ghostfragment::hydrocarbon {
 
 std::array<float, 3> position_carbon(const std::vector<float>& source_coords,
                                      float carbon_bond, int num,
@@ -28,4 +27,4 @@ std::array<float, 3> position_carbon(const std::vector<float>& source_coords,
 std::array<float, 3> position_hydrogen(const std::vector<float>& source_coords,
                                        int flag, int num, float hydrogen_bond,
                                        float angle_deg);
-} // namespace testing
+} // namespace ghostfragment::hydrocarbon

tests/cxx/unit_tests/ghostfragment/testing/hydrocarbon/hydrocarbon.hpp

@@ -19,13 +19,12 @@
 #include <chemist/chemical_system/molecule/molecule.hpp>
 #include <chemist/fragmenting/fragmented_nuclei.hpp>
 #include <chemist/topology/connectivity_table.hpp>
+#include <ghostfragment/hydrocarbon/hydrocarbon.hpp>
 #include <cstdlib>
 #include <string>
 
 namespace testing {
 
-chemist::Molecule hydrocarbon(int num_carbon);
-
 inline auto hydrocarbon_connectivity(std::size_t N) {
     // Probably a better way, but this works
     const auto n_atoms = hydrocarbon(N).size();