Added embedding mouse detection

docs/index.html

@@ -20,14 +20,15 @@ <h1>protein-visualizer</h1>
                 through deep learning.</p>
             <img src="demo_run.png" alt="Demonstration of running the visualizer"/>
             <h2>How does it work?</h2>
-            <p>This interactive visualizer uses a deep learning model to identify functional and structural clusters within
+            <p>This interactive visualizer uses a neural network to identify functional and structural clusters within
             a protein by calculating embeddings, numerical expressions of each amino acid. The high-dimensional
             data is then transformed into 2D in order to easily interpret the possible functional components of a
-            protein. Next, a different deep learning model uses both the 3D structure and amino acid sequence to predict
+            protein. Next, a graph convolutional network uses both the 3D structure and amino acid sequence to predict
             Gene Ontology (GO) annotations that describe the molecular function of the protein. Through
             Gradient-weighted Class Activation Mapping (GradCAM), the program can calculate how much each amino
             acid contributed to each GO prediction and subsequently allow for the identification of functional residues.</p>
-            <p><b>Note:</b> All of the data (except for 3D structure) shown in this program is generated through machine
+            <p>This program was written entirely with Python, using Pyglet as an OpenGL interface.</p>
+            <p><b>Disclaimer:</b> All of the data (except for 3D structure) shown in this program is generated through machine
             learning and thus cannot be verified to be completely accurate. It is recommended to double-check
                 the predicted functions through experimental sources </p>
 
@@ -75,7 +76,8 @@ <h2>Controls</h2>
         </section>
         <section id="Code">
             <h1>Code</h1>
-            All of the code is available under the MIT license on the <a href="https://github.com/kiwijuice56/protein-visualizer">protein-visualizer GitHub repository.</a>
+            <p>All of the code is available under the MIT license on the <a href="https://github.com/kiwijuice56/protein-visualizer">protein-visualizer GitHub repository.</a>
+            Feel free to take any part of the code to expand or transform, just make sure you keep the attributions to ProSE and DeepFRI!
         </section>
         <section id="Attribution">
             <h1>Attribution</h1>

gui/user_interface.py

@@ -67,7 +67,9 @@ def on_mouse_scroll(self, x, y, scroll_x, scroll_y):
 
     def on_mouse_motion(self, x, y, dx, dy):
         prev_hl_idx = self.hl_idx
-        self.hl_idx = self.pdb_renderer.hovered_residue
+        self.hl_idx = self.embedding_renderer.hovered_residue
+        if self.hl_idx == -1:
+            self.hl_idx = self.pdb_renderer.hovered_residue
 
         if not prev_hl_idx == -1:
             self.protein.residues[prev_hl_idx].highlighted = False

main.py

@@ -50,6 +50,9 @@
 
 @window.event
 def on_draw():
+    embedding_renderer.detect_mouse()
+    pdb_renderer.detect_mouse()
+
     # Draw the 3D protein
     pdb_renderer.draw()
 

renderers/embedding_renderer.py

@@ -83,6 +83,9 @@ def __init__(self, protein, window, bounding_box=None, point_size=8):
         # Define the pyglet vertex list
         self.vertices = None
         self.outline_vertices = None
+        self.id_vertices = None
+
+        self.hovered_residue = -1
 
         # Default to full-screen render
         self.bounding_box = []
@@ -148,10 +151,15 @@ def set_bounding_box(self, bounding_box):
             ('c4B', self.GRID_LINE_COLOR * (len(grid_points) // 2))
         )
 
+        rgb_id = [[(i >> 16) & 255, (i >> 8) & 255, i & 255] for i in range(1, len(self.scaled_points) // 2 + 1)]
         self.vertices = pyglet.graphics.vertex_list(
             len(self.protein.embedding_points) // 2,
             ('v2f', self.scaled_points),
             ('c4B', np.zeros(len(self.protein.embedding_points) // 2 * 4, dtype=np.byte)))
+        self.id_vertices = pyglet.graphics.vertex_list(
+            len(self.protein.embedding_points) // 2,
+            ('v2f', self.scaled_points),
+            ('c3B', [x for xs in rgb_id for x in xs]))
         self.update_colors()
 
     def update_colors(self, start=0, end=-1):
@@ -166,6 +174,39 @@ def update_colors(self, start=0, end=-1):
             self.vertices.colors[i * 4: i * 4 + 3] = self.protein.residues[i].color
             self.vertices.colors[i * 4 + 3] = self.POINT_OPACITY
 
+    def detect_mouse(self):
+        glClearColor(*[0] * 4)
+        glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
+        glEnable(GL_SCISSOR_TEST)
+        glDisable(GL_POINT_SMOOTH)
+
+        glScissor(*self.bounding_box)
+
+        glLoadIdentity()
+        glDisable(GL_DEPTH_TEST)
+        glEnable(GL_BLEND)
+        glOrtho(0, self.window.width, 0, self.window.height, 0, 1000)
+
+        if self.camera.updated:
+            self.set_bounding_box(self.bounding_box)
+            self.camera.updated = False
+
+        glPointSize(int(self.point_size * 2.0))
+        self.id_vertices.draw(pyglet.gl.GL_POINTS)
+
+        read = (GLubyte * 3)(0)
+        glReadPixels(self.camera.input_handler.x, self.camera.input_handler.y, 1, 1, GL_RGB, GL_UNSIGNED_BYTE, read)
+        selected_id = sum([read[i] << (8 * (2 - i)) for i in range(3)])
+        if not selected_id == 0:
+            self.hovered_residue = selected_id - 1
+        else:
+            self.hovered_residue = -1
+
+        # Clean up
+        glDisable(GL_SCISSOR_TEST)
+        glDisable(GL_DEPTH_TEST)
+        glDisable(GL_BLEND)
+
     def draw(self):
         glEnable(GL_SCISSOR_TEST)
         glEnable(GL_POINT_SMOOTH)

renderers/pdb_renderer.py

@@ -191,17 +191,13 @@ def set_bounding_box(self, bounding_box):
         self.bounding_box = bounding_box
         self.camera.input_handler.bounding_box = bounding_box
 
-    def draw(self):
+    def detect_mouse(self):
         glClearColor(*[0] * 4)
         glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
-        glEnable(GL_POINT_SMOOTH)
-        glEnable(GL_SCISSOR_TEST)
-
         glLoadIdentity()
         glMatrixMode(GL_PROJECTION)
         gluPerspective(self.FOV, self.window.width / float(self.window.height), self.Z_NEAR, self.Z_FAR)
         self.camera.draw()
-
         glScissor(*self.bounding_box)
 
         glPointSize(int(1.5 * self.point_size))
@@ -217,9 +213,14 @@ def draw(self):
         else:
             self.hovered_residue = -1
 
-        glClearColor(*[c / 255.0 for c in self.BACKGROUND_COLOR])
+    def draw(self):
+        glClearColor(*[0] * 4)
         glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
+        glEnable(GL_POINT_SMOOTH)
+        glEnable(GL_SCISSOR_TEST)
         glEnable(GL_LINE_SMOOTH)
+        glEnable(GL_BLEND)
+        glScissor(*self.bounding_box)
 
         glLoadIdentity()
         glMatrixMode(GL_PROJECTION)