spacr 0.0.20__py3-none-any.whl → 0.0.21__py3-none-any.whl

spacr/get_alfafold_structures.py

@@ -0,0 +1,72 @@
+import csv
+import os
+import requests
+
+def download_alphafold_structures(tsv_location, dst, version="4"):
+    # Create the destination directory if it does not exist
+    dst_pdb = os.path.join(dst,'pdb')
+    dst_cif = os.path.join(dst,'cif')
+    dst_pae = os.path.join(dst,'pae')
+    
+    if not os.path.exists(dst):
+        os.makedirs(dst)
+    if not os.path.exists(dst_pdb):
+        os.makedirs(dst_pdb)
+    if not os.path.exists(dst_cif):
+        os.makedirs(dst_cif)
+    if not os.path.exists(dst_pae):
+        os.makedirs(dst_pae)
+
+    failed_downloads = []  # List to keep track of failed downloads
+
+    # Open the TSV file and read entries
+    with open(tsv_location, 'r') as tsv_file:
+        reader = csv.DictReader(tsv_file, delimiter='\t')
+        for row in reader:
+            entry = row['Entry']
+            af_link = f"https://alphafold.ebi.ac.uk/files/AF-{entry}-F1-model_v{version}.pdb"
+            cif_link = f"https://alphafold.ebi.ac.uk/files/AF-{entry}-F1-model_v{version}.cif"
+            pae_link = f"https://alphafold.ebi.ac.uk/files/AF-{entry}-F1-predicted_aligned_error_v{version}.json"
+
+            try:
+                response_pdb = requests.get(af_link, stream=True)
+                response_cif = requests.get(cif_link, stream=True)
+                response_pae = requests.get(pae_link, stream=True)
+                if response_pdb.status_code == 200:
+                    
+                    # Save the PDB file
+                    with open(os.path.join(dst_pdb, f"AF-{entry}-F1-model_v{version}.pdb"), 'wb') as pdb_file:
+                        pdb_file.write(response_pdb.content)
+                    print(f"Downloaded: AF-{entry}-F1-model_v{version}.pdb")
+                    
+                    # Save the CIF file
+                    with open(os.path.join(dst_cif, f"AF-{entry}-F1-model_v{version}.cif"), 'wb') as cif_file:
+                        cif_file.write(response_cif.content)
+                    print(f"Downloaded: AF-{entry}-F1-model_v{version}.cif")
+                    
+                    # Save the PAE file
+                    with open(os.path.join(dst_pae, f"AF-{entry}-F1-predicted_aligned_error_v{version}.json"), 'wb') as pdb_file:
+                        pdb_file.write(response_pae.content)
+                    print(f"Downloaded: AF-{entry}-F1-predicted_aligned_error_v{version}.json")
+                    
+                else:
+                    # If the file could not be downloaded, record the entry
+                    failed_downloads.append(entry)
+                    print(f"Failed to download structure for: {entry}")
+            except Exception as e:
+                print(f"Error downloading structure for {entry}: {e}")
+                failed_downloads.append(entry)
+
+    # Save the list of failed downloads to a CSV file in the destination folder
+    if failed_downloads:
+        with open(os.path.join(dst, 'failed_downloads.csv'), 'w', newline='') as failed_file:
+            writer = csv.writer(failed_file)
+            writer.writerow(['Entry'])
+            for entry in failed_downloads:
+                writer.writerow([entry])
+        print(f"Failed download entries saved to: {os.path.join(dst, 'failed_downloads.csv')}")
+
+# Example usage:
+tsv_location = '/home/carruthers/Downloads/GT1_proteome/GT1_proteins_uniprot.tsv'  # Replace with the path to your TSV file containing a list of UniProt entries
+dst_folder = '/home/carruthers/Downloads/GT1_proteome'  # Replace with your destination folder
+download_alphafold_structures(tsv_location, dst_folder)

spacr/gui_mask_app.py

@@ -1,4 +1,4 @@
-import spacr, sys, ctypes, csv, matplotlib
+import sys, ctypes, matplotlib
 import tkinter as tk
 from tkinter import ttk, scrolledtext
 from ttkthemes import ThemedTk
@@ -16,11 +16,19 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, safe_literal_eval, clear_canvas, main_thread_update_function, create_dark_mode, set_dark_style, set_default_font, generate_fields, process_stdout_stderr
-from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv #, add_mask_gui_defaults
+from .gui_utils import ScrollableFrame, StdoutRedirector, clear_canvas, main_thread_update_function, create_dark_mode, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
+from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv#, toggle_advanced_settings
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
+def toggle_advanced_settings():
+    advanced = advanced_var.get()
+    for widget in advanced_widgets:
+        if advanced:
+            widget.grid()
+        else:
+            widget.grid_remove()
+
 @log_function_call
 def initiate_abort():
     global thread_control
@@ -73,7 +81,7 @@ def import_settings(scrollable_frame):
     
 @log_function_call
 def initiate_mask_root(width, height):
-    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
+    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, advanced_widgets, advanced_var
         
     theme = 'breeze'
     
@@ -87,7 +95,8 @@ def initiate_mask_root(width, height):
         style = ttk.Style(root)
         set_dark_style(style)
         
-    set_default_font(root, font_name="Arial", size=10)
+    style_text_boxes(style)
+    set_default_font(root, font_name="Arial", size=8)
     #root.state('zoomed')  # For Windows to maximize the window
     root.attributes('-fullscreen', True)
     root.geometry(f"{width}x{height}")
@@ -139,6 +148,10 @@ def initiate_mask_root(width, height):
     # Setup for user input fields (variables)
     variables = mask_variables()
     vars_dict = generate_fields(variables, scrollable_frame)
+    #del vars_dict['fps']
+
+    # Debugging: print vars_dict to ensure it is populated correctly
+    #print("vars_dict:", vars_dict)
     
     # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
     horizontal_container = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) #HORIZONTAL
@@ -167,21 +180,27 @@ def initiate_mask_root(width, height):
     q = Queue()
     sys.stdout = StdoutRedirector(console_output)
     sys.stderr = StdoutRedirector(console_output)
+
+    advanced_var = tk.BooleanVar()
+    advanced_checkbox = ttk.Checkbutton(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_checkbox.grid(row=46, column=1, pady=10, padx=10)
     
     # This is your GUI setup where you create the Run button
     run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run",command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=45, column=0, pady=10)
+    run_button.grid(row=45, column=0, pady=10, padx=10)
     
     abort_button = ttk.Button(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=45, column=1, pady=10)
+    abort_button.grid(row=45, column=1, pady=10, padx=10)
     
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="#333333", foreground="white")
-    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0))
-    
+    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+
     # Create the Import Settings button
     import_btn = tk.Button(root, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.pack(pady=20)
+    import_btn.pack(pady=20, padx=10)
+
     
+
     _process_console_queue()
     _process_fig_queue()
     create_dark_mode(root, style, console_output)
@@ -193,6 +212,7 @@ def initiate_mask_root(width, height):
 def gui_mask():
     global vars_dict, root
     root, vars_dict = initiate_mask_root(1000, 1500)
+    
     root.mainloop()
     
 if __name__ == "__main__":

spacr/gui_utils.py

@@ -14,6 +14,21 @@ except AttributeError:
 
 from .logger import log_function_call
 
+def set_default_font(root, font_name="Helvetica", size=12):
+    default_font = (font_name, size)
+    root.option_add("*Font", default_font)
+    root.option_add("*TButton.Font", default_font)
+    root.option_add("*TLabel.Font", default_font)
+    root.option_add("*TEntry.Font", default_font)
+
+def style_text_boxes(style):
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', background='#333333', foreground='#ffffff')
+    style.configure('TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#444444', foreground='#ffffff', font=('Helvetica', 12, 'bold'))
+    style.map('TButton',
+              background=[('active', '#555555'), ('disabled', '#222222')],
+              foreground=[('active', '#ffffff'), ('disabled', '#888888')])
+    style.configure('TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#2e2e2e', foreground='#ffffff')
+
 def read_settings_from_csv(csv_file_path):
     settings = {}
     with open(csv_file_path, newline='') as csvfile:
@@ -51,7 +66,7 @@ def disable_interactivity(fig):
         for handler_id in list(handlers.keys()):
             fig.canvas.mpl_disconnect(handler_id)
 
-def set_default_font(app, font_name="Arial Bold", size=10):
+def set_default_font_v1(app, font_name="Arial Bold", size=10):
     default_font = nametofont("TkDefaultFont")
     text_font = nametofont("TkTextFont")
     fixed_font = nametofont("TkFixedFont")
@@ -580,7 +595,7 @@ def measure_crop_wrapper(settings, q, fig_queue):
 
     try:
         print('start')
-        spacr.measure.measure_crop(settings=settings, annotation_settings={}, advanced_settings={})
+        spacr.measure.measure_crop(settings=settings)
     except Exception as e:
         errorMessage = f"Error during processing: {e}"
         q.put(errorMessage)  # Send the error message to the GUI via the queue