Changeset 5a479d for src/Python

Timestamp:

Jan 24, 2024, 4:53:03 PM (21 months ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

d203d1e

Parents:

d083cc

git-author:

Frederik Heber <frederik.heber@…> (01/22/24 22:21:29)

git-committer:

Frederik Heber <frederik.heber@…> (01/24/24 16:53:03)

Message:

Added python actions to generate all graph6 strings.

• graph6 strings don't take permutations in the adjacency matrix into account. Hence, we are going through every permutation of non-hydrogens and generate the respective graph6 string.

Location:

src/Python

Files:

• PythonScripting_impl.hpp (modified) (2 diffs)
• getGraph6String.cpp (modified) (2 diffs)
• modules.hpp (modified) (2 diffs)

src/Python/PythonScripting_impl.hpp

@@ -110 +110 @@
       "returns list of elements over the nodes of the graph of the current selected set of atoms."
   );
+  boost::python::def< MoleCuilder::detail::stringVec() >(
+      "getAllGraph6Strings",
+      MoleCuilder::detail::module_getAllGraph6Strings,
+      "returns chemical graphs of the current selected set of atoms as graph6 representation with all non-hydrogen atom permutations."
+  );
+  boost::python::def< MoleCuilder::detail::stringVec() >(
+      "getAllElementListAsStrings",
+      MoleCuilder::detail::module_getAllElementListAsStrings,
+      "returns lists of elements over the nodes of the graph of the current selected set of atoms with all non-hydrogen atom permutations."
+  );
   boost::python::def< MoleCuilder::detail::doubleVec() >(
       "getBoundingBox",
@@ -183 +193 @@
       .def("__iter__", boost::python::iterator< std::vector< std::vector< double > > >())
       .def("__repr__", &MoleCuilder::PythonTypes::vec_item< std::vector< std::vector< double > > >::toStringRepr)
+  ;
+  // positions
+  boost::python::class_< std::vector< std::string > >("PythonType_stringVec")
+      .def("__len__", &std::vector< std::string >::size)
+      .def("clear", &std::vector< std::string >::clear)
+      .def("append", &MoleCuilder::PythonTypes::vec_item< std::vector< std::string > >::add,
+            boost::python::with_custodian_and_ward<1, 2>()) // let container keep value
+      .def("__getitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< std::string > >::get,
+           boost::python::return_value_policy<boost::python::copy_non_const_reference>())
+      .def("__setitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< std::string > >::set,
+           boost::python::with_custodian_and_ward<1,2>()) // to let container keep value
+      .def("__delitem__", &MoleCuilder::PythonTypes::vec_item< std::vector< std::string > >::del)
+      .def("__iter__", boost::python::iterator< std::vector< std::string > >())
+      .def("__repr__", &MoleCuilder::PythonTypes::vec_item< std::vector< std::string > >::toStringRepr)
   ;
 

src/Python/getGraph6String.cpp

@@ -39 +39 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
+#include <algorithm>
 #include <string>
 
+#include "Element/element.hpp"
 #include "Graph/Graph6Writer.hpp"
 #include "World.hpp"
@@ -68 +70 @@
   return output.str();
 }
+
+MoleCuilder::detail::stringVec MoleCuilder::detail::module_getAllGraph6Strings()
+{
+  /*
+   * Returns all graph6 representation by creating all permutations
+   * of the non-hydrogen atoms.
+   */
+  std::vector<const atom *> selected_atoms = World::getConstInstance().getSelectedAtoms();
+  // split set into hydrogen and non-hydrogen
+  const std::vector<const atom *>::iterator partitioner =
+    std::partition(selected_atoms.begin(), selected_atoms.end(), [](const atom * walker) { return walker->getElement().getAtomicNumber() != (atomicNumber_t)1; });
+  std::sort(selected_atoms.begin(), partitioner);
+  MoleCuilder::detail::stringVec returnlist;
+  do {
+    Graph6Writer writer(selected_atoms);
+    std::stringstream output;
+    writer.write_graph6(output);
+    returnlist.push_back(output.str());
+  } while(std::next_permutation(selected_atoms.begin(), partitioner));
+
+  return returnlist;
+}
+
+MoleCuilder::detail::stringVec MoleCuilder::detail::module_getAllElementListAsStrings()
+{
+  /*
+   * Returns non-hydrogen element lists by creating all permutations
+   * of the non-hydrogen atoms.
+   */
+  std::vector<const atom *> selected_atoms = World::getConstInstance().getSelectedAtoms();
+  // split set into non-hydrogen and hydrogen
+  const std::vector<const atom *>::iterator partitioner =
+    std::partition(selected_atoms.begin(), selected_atoms.end(), [](const atom * walker) { return walker->getElement().getAtomicNumber() != (atomicNumber_t)1; });
+  std::sort(selected_atoms.begin(), partitioner);
+  MoleCuilder::detail::stringVec returnlist;
+  do {
+    Graph6Writer writer(selected_atoms);
+    std::stringstream output;
+    writer.write_simple_elementlist(output);
+    returnlist.push_back(output.str());
+  } while(std::next_permutation(selected_atoms.begin(), partitioner));
+
+  return returnlist;
+}

src/Python/modules.hpp

@@ -31 +31 @@
 typedef std::vector<double> doubleVec;
 typedef std::vector< std::vector<double> > atomPositionsVec;
+typedef std::vector< std::string > stringVec;
 
 doubleVec module_getBoundingBox();
@@ -41 +42 @@
 std::string module_getGraph6String();
 std::string module_getElementListAsString();
+MoleCuilder::detail::stringVec module_getAllGraph6Strings();
+MoleCuilder::detail::stringVec module_getAllElementListAsStrings();
 
 } /* namespace detail */