Merge branch 'master' into develop

docs/source/quickstart.rst

@@ -75,6 +75,9 @@ all keep track of exactly.
     p_2d.solutions_checked
     >>> 0
 
+    p_2d.aminos_placed
+    >>> 1
+
     p_2d.bond_values
     >>> {"HH": -1}
 

prospr/__init__.py

@@ -1,5 +1,6 @@
 from prospr_core import AminoAcid, Protein, depth_first, depth_first_bnb
 from .datasets import load_vanEck250, load_vanEck1000
+from .visualize import plot_protein
 
 __all__ = [
     "AminoAcid",
@@ -8,4 +9,5 @@
     "depth_first_bnb",
     "load_vanEck250",
     "load_vanEck1000",
+    "plot_protein",
 ]

prospr/core/core_module.cpp

@@ -43,6 +43,8 @@ PYBIND11_MODULE(prospr_core, m) {
                 py::arg("bond_symmetry")=true)
         .def_property_readonly("solutions_checked",
             &Protein::get_solutions_checked)
+        .def_property_readonly("aminos_placed",
+            &Protein::get_aminos_placed)
         .def_property_readonly("cur_len", &Protein::get_cur_len)
         .def_property_readonly("dim", &Protein::get_dim)
         .def_property_readonly("bond_values", &Protein::get_bond_values)

prospr/core/src/depth_first_bnb.cpp

@@ -17,7 +17,7 @@
 /* Returns true if the branch cannot produce a better score. */
 bool prune_branch(Protein* protein, int max_length, int no_neighbors,
         int move, int best_score) {
-    protein->place_amino(move);
+    protein->place_amino(move, false);
 
     int cur_len = protein->get_cur_len();
     int cur_score = protein->get_score();

prospr/core/src/protein.cpp

@@ -22,6 +22,7 @@ Protein::Protein(std::string sequence, int dim, std::string model,
     last_pos.assign(dim, 0);
     score = 0;
     solutions_checked = 0;
+    aminos_placed = 0;
 
     /* Deduct what model to use, or apply custom one. */
     if (model == "HP") {
@@ -94,6 +95,7 @@ Protein::Protein(std::string sequence, int dim, std::string model,
     if (sequence.size() != 0) {
         space[last_pos] = amino_acids[0];
         cur_len++;
+        aminos_placed++;
     }
 }
 
@@ -147,6 +149,11 @@ int Protein::get_solutions_checked() {
     return solutions_checked;
 }
 
+/* Returns the number of amino acids placed. */
+int Protein::get_aminos_placed() {
+    return aminos_placed;
+}
+
 /* Returns if the amino acid at the given index is weighted. */
 bool Protein::is_weighted(int index) {
     return weighted_amino_acids.find(sequence[index]) != std::string::npos;
@@ -176,6 +183,7 @@ void Protein::reset() {
     last_move = 0;
     score = 0;
     solutions_checked = 0;
+    aminos_placed = 0;
 
     space[last_pos] = amino_acids[0];
 }
@@ -227,9 +235,13 @@ void Protein::place_amino(int move, bool track) {
 
     cur_len++;
 
-    /* Update number of found solutions. */
-    if (track && cur_len == (int)sequence.size()) {
-        solutions_checked++;
+    /* Update number of found solutions and amino acids placed. */
+    if (track) {
+        aminos_placed++;
+
+        if (cur_len == (int)sequence.size()) {
+            solutions_checked++;
+        }
     }
 }
 

prospr/core/src/protein.hpp

@@ -50,6 +50,9 @@ class Protein {
         /* Returns the number of performed changes. */
         int get_solutions_checked();
 
+        /* Returns the number of amino acids placed. */
+        int get_aminos_placed();
+
         /* Returns if the amino acid at the given index is weighted. */
         bool is_weighted(int index);
 
@@ -91,6 +94,7 @@ class Protein {
         int last_move;
         std::vector<int> last_pos;
         int score;
+        int aminos_placed;
         int solutions_checked;
         std::vector<AminoAcid*> amino_acids;
 

setup.py

@@ -12,7 +12,7 @@
 from setuptools import setup
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 
-__version__ = "0.2a4"
+__version__ = "0.2a5"
 
 # Define core module extension.
 ext_modules = [
@@ -43,7 +43,7 @@
     packages=["prospr"],
     package_data={"prospr": ["data/*/*.csv"]},
     platforms=["any"],
-    python_requires=">=3.6",
+    python_requires=">=3.9",
     zip_safe=False,
     install_requires=[
         "matplotlib",

tests/core/test_depth_first.py

@@ -30,10 +30,14 @@ def test_protein_2d_depth_first(self, protein_2d):
         """
         p = depth_first(protein_2d)
         assert p.score == -3
+        assert p.solutions_checked == 1000
+        assert p.aminos_placed == 1574
 
     def test_protein_3d_depth_first(self, protein_3d):
         """
         Test if a 3D protein is folded correctly using depth_first search.
         """
         p = depth_first(protein_3d)
         assert p.score == -4
+        assert p.solutions_checked == 186455
+        assert p.aminos_placed == 235818

tests/core/test_depth_first_bnb.py

@@ -30,10 +30,14 @@ def test_protein_2d_depth_first_bnb(self, protein_2d):
         """
         p = depth_first_bnb(protein_2d)
         assert p.score == -3
+        assert p.solutions_checked == 4
+        assert p.aminos_placed == 53
 
     def test_protein_3d_depth_first_bnb(self, protein_3d):
         """
         Test if a 3D protein is folded correctly using depth_first_bnb search.
         """
         p = depth_first_bnb(protein_3d)
         assert p.score == -4
+        assert p.solutions_checked == 5
+        assert p.aminos_placed == 49368

tests/core/test_protein.py

@@ -33,6 +33,7 @@ def test_protein_2d_generation(self, protein_2d):
         assert protein_2d.last_pos == [0, 0]
         assert protein_2d.score == 0
         assert protein_2d.solutions_checked == 0
+        assert protein_2d.aminos_placed == 1
 
     def test_protein_3d_generation(self, protein_3d):
         """Test if a 3D protein is generated correctly."""
@@ -44,32 +45,37 @@ def test_protein_3d_generation(self, protein_3d):
         assert protein_3d.last_pos == [0, 0, 0]
         assert protein_3d.score == 0
         assert protein_3d.solutions_checked == 0
+        assert protein_3d.aminos_placed == 1
 
     def test_protein_2d_place_moves(self, protein_2d):
         """Test if a 2D protein can move in all directions."""
         assert protein_2d.cur_len == 1
         moves = [1, 2, -1, -1, -2]
         scores = [0, 0, -1, -1, -1]
+        track_placed = [1, 0, 1, 0, 1]
 
         for i, m in enumerate(moves):
-            protein_2d.place_amino(m)
+            protein_2d.place_amino(m, track=bool(track_placed[i]))
             assert protein_2d.hash_fold() == moves[: i + 1]
             assert protein_2d.cur_len == len(moves[: i + 1]) + 1
             assert protein_2d.last_move == m
             assert protein_2d.score == scores[i]
+            assert protein_2d.aminos_placed == 1 + sum(track_placed[: i + 1])
 
     def test_protein_3d_place_moves(self, protein_3d):
         """Test if a 3D protein can move in all directions."""
         assert protein_3d.cur_len == 1
         moves = [1, 2, -1, 3, -2, -1, -3]
         scores = [0, 0, -1, -1, -1, -1, -2]
+        track_placed = [1, 0, 1, 0, 1, 0, 1]
 
         for i, m in enumerate(moves):
-            protein_3d.place_amino(m)
+            protein_3d.place_amino(m, track=bool(track_placed[i]))
             assert protein_3d.hash_fold() == moves[: i + 1]
             assert protein_3d.cur_len == len(moves[: i + 1]) + 1
             assert protein_3d.last_move == m
             assert protein_3d.score == scores[i]
+            assert protein_3d.aminos_placed == 1 + sum(track_placed[: i + 1])
 
     def test_protein_2d_undo_moves(self, protein_2d):
         """Test if a 2D protein can remove amino acids in all directions."""