Removed allow violations option as it is not needed anymore

prospr/core/core_module.cpp

@@ -36,10 +36,10 @@ PYBIND11_MODULE(prospr_core, m) {
   /* Protein class definition. */
   py::class_<Protein>(m, "Protein")
       .def(py::init<const std::string, int, const std::string,
-                    std::map<std::string, int>, bool, bool &>(),
+                    std::map<std::string, int>, bool &>(),
            "Protein constructor", py::arg("sequence"), py::arg("dim") = 2,
            py::arg("model") = "HP", py::arg("bond_values") = bond_values,
-           py::arg("bond_symmetry") = true, py::arg("allow_violations") = false)
+           py::arg("bond_symmetry") = true)
       .def_property_readonly("solutions_checked",
                              &Protein::get_solutions_checked)
       .def_property_readonly("aminos_placed", &Protein::get_aminos_placed)

prospr/core/src/protein.cpp

@@ -33,7 +33,6 @@ Protein::Protein(const Protein &other) {
   this->bond_values = other.bond_values;
   this->weighted_amino_acids = other.weighted_amino_acids;
   this->max_weights = other.max_weights;
-  this->allow_violations = other.allow_violations;
 
   /* Create new AminoAcid objects for all amino acids. */
   AminoAcid *new_aa;
@@ -61,8 +60,7 @@ Protein::Protein(const Protein &other) {
 
 /* Construct a new Protein. */
 Protein::Protein(std::string sequence, int dim, std::string model,
-                 std::map<std::string, int> bond_values, bool bond_symmetry,
-                 bool allow_violations) {
+                 std::map<std::string, int> bond_values, bool bond_symmetry) {
   this->sequence = sequence;
   space = {};
   cur_len = 0;
@@ -72,7 +70,6 @@ Protein::Protein(std::string sequence, int dim, std::string model,
   score = 0;
   solutions_checked = 0;
   aminos_placed = 0;
-  this->allow_violations = allow_violations;
 
   /* Deduct what model to use, or apply custom one. */
   if (model == "HP") {
@@ -301,7 +298,7 @@ void Protein::place_amino(int move, bool track) {
   last_pos[abs(move) - 1] += move / abs(move);
 
   /* Check for illegal folds. */
-  if (!allow_violations && space.count(last_pos) > 0)
+  if (space.count(last_pos) > 0)
     throw std::runtime_error("Protein folded onto itself..");
 
   /* Place amino acid on new (valid) position. */

prospr/core/src/protein.hpp

@@ -29,7 +29,7 @@ class Protein {
   /* Construct a new Protein. */
   Protein(std::string sequence, int dim = 2, std::string model = "HP",
           std::map<std::string, int> bond_values = {},
-          bool bond_symmetry = true, bool allow_violations = false);
+          bool bond_symmetry = true);
 
   /* Overload assignment operator for assignments. */
   Protein &operator=(const Protein &other);
@@ -113,7 +113,6 @@ class Protein {
   std::uint64_t aminos_placed;
   std::uint64_t solutions_checked;
   std::vector<AminoAcid *> amino_acids;
-  bool allow_violations;
 
   /* Change score according to the already performed addition or removal
    * of the given move.