"""
Geometry cutoffs configuration dialog for HBAT GUI.
This module provides a dialog for configuring molecular interaction
analysis parameters (distances, angles, etc.) without PDB fixing options.
"""
import tkinter as tk
from tkinter import messagebox, ttk
from typing import Any, Dict, Optional
from ..constants.parameters import (
AnalysisParameters,
ParameterRanges,
ParametersDefault,
)
[docs]
class GeometryCutoffsDialog:
"""Dialog for configuring comprehensive molecular interaction parameters.
Provides GUI interface for setting parameters for multiple interaction types:
- **Hydrogen Bonds:** Classical strong interactions (N/O-H···O/N)
- **Weak Hydrogen Bonds:** C-H···O interactions (important for binding)
- **Halogen Bonds:** C-X···A interactions (X = Cl, Br, I) with 150° default
- **π Interactions:** Multiple subtypes including:
- Hydrogen-π: C-H···π, N-H···π, O-H···π, S-H···π
- Halogen-π: C-Cl···π, C-Br···π, C-I···π
Uses tabbed interface to organize parameters by interaction type.
"""
[docs]
def __init__(
self, parent: tk.Tk, current_params: Optional[AnalysisParameters] = None
):
"""Initialize geometry cutoffs dialog.
:param parent: Parent window
:type parent: tk.Tk
:param current_params: Current analysis parameters
:type current_params: Optional[AnalysisParameters]
"""
self.parent = parent
self.current_params = current_params or AnalysisParameters()
self.result = None
# Create dialog window
self.dialog = tk.Toplevel(parent)
self.dialog.title("Geometry Cutoffs")
self.dialog.geometry("1200x600")
self.dialog.resizable(True, True)
# Make dialog modal
self.dialog.transient(parent)
self.dialog.grab_set()
# Initialize variables
self._init_variables()
# Create widgets
self._create_widgets()
# Center the dialog
self.dialog.update_idletasks()
x = (self.dialog.winfo_screenwidth() // 2) - (self.dialog.winfo_width() // 2)
y = (self.dialog.winfo_screenheight() // 2) - (self.dialog.winfo_height() // 2)
self.dialog.geometry(f"+{x}+{y}")
# Handle window closing
self.dialog.protocol("WM_DELETE_WINDOW", self._cancel)
# Set initial values
self.set_parameters(self.current_params)
def _init_variables(self):
"""Initialize tkinter variables with default values."""
self.analysis_mode = tk.StringVar(value=ParametersDefault.ANALYSIS_MODE)
self.covalent_factor = tk.DoubleVar(
value=ParametersDefault.COVALENT_CUTOFF_FACTOR
)
self.hb_distance = tk.DoubleVar(value=ParametersDefault.HB_DISTANCE_CUTOFF)
self.hb_angle = tk.DoubleVar(value=ParametersDefault.HB_ANGLE_CUTOFF)
self.da_distance = tk.DoubleVar(value=ParametersDefault.HB_DA_DISTANCE)
self.whb_distance = tk.DoubleVar(value=ParametersDefault.WHB_DISTANCE_CUTOFF)
self.whb_angle = tk.DoubleVar(value=ParametersDefault.WHB_ANGLE_CUTOFF)
self.whb_da_distance = tk.DoubleVar(value=ParametersDefault.WHB_DA_DISTANCE)
self.xb_distance = tk.DoubleVar(value=ParametersDefault.XB_DISTANCE_CUTOFF)
self.xb_angle = tk.DoubleVar(value=ParametersDefault.XB_ANGLE_CUTOFF)
self.pi_distance = tk.DoubleVar(value=ParametersDefault.PI_DISTANCE_CUTOFF)
self.pi_angle = tk.DoubleVar(value=ParametersDefault.PI_ANGLE_CUTOFF)
# Initialize π interaction subtype variables (needed for set_parameters)
self.pi_ccl_distance = None
self.pi_ccl_angle = None
self.pi_cbr_distance = None
self.pi_cbr_angle = None
self.pi_ci_distance = None
self.pi_ci_angle = None
self.pi_ch_distance = None
self.pi_ch_angle = None
self.pi_nh_distance = None
self.pi_nh_angle = None
self.pi_oh_distance = None
self.pi_oh_angle = None
self.pi_sh_distance = None
self.pi_sh_angle = None
# New interaction type variables
self.pi_pi_distance = tk.DoubleVar(
value=ParametersDefault.PI_PI_DISTANCE_CUTOFF
)
self.pi_pi_parallel_angle = tk.DoubleVar(
value=ParametersDefault.PI_PI_PARALLEL_ANGLE_CUTOFF
)
self.pi_pi_tshaped_angle_min = tk.DoubleVar(
value=ParametersDefault.PI_PI_TSHAPED_ANGLE_MIN
)
self.pi_pi_tshaped_angle_max = tk.DoubleVar(
value=ParametersDefault.PI_PI_TSHAPED_ANGLE_MAX
)
self.pi_pi_offset = tk.DoubleVar(value=ParametersDefault.PI_PI_OFFSET_CUTOFF)
self.carbonyl_distance = tk.DoubleVar(
value=ParametersDefault.CARBONYL_DISTANCE_CUTOFF
)
self.carbonyl_angle_min = tk.DoubleVar(
value=ParametersDefault.CARBONYL_ANGLE_MIN
)
self.carbonyl_angle_max = tk.DoubleVar(
value=ParametersDefault.CARBONYL_ANGLE_MAX
)
self.n_pi_distance = tk.DoubleVar(value=ParametersDefault.N_PI_DISTANCE_CUTOFF)
self.n_pi_sulfur_distance = tk.DoubleVar(
value=ParametersDefault.N_PI_SULFUR_DISTANCE_CUTOFF
)
self.n_pi_angle_min = tk.DoubleVar(value=ParametersDefault.N_PI_ANGLE_MIN)
self.n_pi_angle_max = tk.DoubleVar(value=ParametersDefault.N_PI_ANGLE_MAX)
# Store parameter values directly
self._param_values = {}
def _store_current_values(self):
"""Store current parameter values before switching categories."""
try:
self._param_values.update(
{
"hb_distance": (
self.hb_distance.get()
if hasattr(self, "hb_distance")
else ParametersDefault.HB_DISTANCE_CUTOFF
),
"hb_angle": (
self.hb_angle.get()
if hasattr(self, "hb_angle")
else ParametersDefault.HB_ANGLE_CUTOFF
),
"da_distance": (
self.da_distance.get()
if hasattr(self, "da_distance")
else ParametersDefault.HB_DA_DISTANCE
),
"whb_distance": (
self.whb_distance.get()
if hasattr(self, "whb_distance")
else ParametersDefault.WHB_DISTANCE_CUTOFF
),
"whb_angle": (
self.whb_angle.get()
if hasattr(self, "whb_angle")
else ParametersDefault.WHB_ANGLE_CUTOFF
),
"whb_da_distance": (
self.whb_da_distance.get()
if hasattr(self, "whb_da_distance")
else ParametersDefault.WHB_DA_DISTANCE
),
"xb_distance": (
self.xb_distance.get()
if hasattr(self, "xb_distance")
else ParametersDefault.XB_DISTANCE_CUTOFF
),
"xb_angle": (
self.xb_angle.get()
if hasattr(self, "xb_angle")
else ParametersDefault.XB_ANGLE_CUTOFF
),
"pi_distance": (
self.pi_distance.get()
if hasattr(self, "pi_distance")
else ParametersDefault.PI_DISTANCE_CUTOFF
),
"pi_angle": (
self.pi_angle.get()
if hasattr(self, "pi_angle")
else ParametersDefault.PI_ANGLE_CUTOFF
),
"covalent_factor": (
self.covalent_factor.get()
if hasattr(self, "covalent_factor")
else ParametersDefault.COVALENT_CUTOFF_FACTOR
),
"analysis_mode": (
self.analysis_mode.get()
if hasattr(self, "analysis_mode")
else ParametersDefault.ANALYSIS_MODE
),
}
)
# Store π interaction subtype values if they exist
pi_vars = [
"pi_ccl_distance",
"pi_ccl_angle",
"pi_cbr_distance",
"pi_cbr_angle",
"pi_ci_distance",
"pi_ci_angle",
"pi_ch_distance",
"pi_ch_angle",
"pi_nh_distance",
"pi_nh_angle",
"pi_oh_distance",
"pi_oh_angle",
"pi_sh_distance",
"pi_sh_angle",
"pi_pi_distance",
"pi_pi_parallel_angle",
"pi_pi_tshaped_angle_min",
"pi_pi_tshaped_angle_max",
"pi_pi_offset",
"carbonyl_distance",
"carbonyl_angle_min",
"carbonyl_angle_max",
"n_pi_distance",
"n_pi_sulfur_distance",
"n_pi_angle_min",
"n_pi_angle_max",
]
for var_name in pi_vars:
if hasattr(self, var_name):
var = getattr(self, var_name)
if var:
self._param_values[var_name] = var.get()
except tk.TclError:
pass # Variables destroyed, ignore
def _create_widgets(self) -> None:
"""Create and layout all parameter widgets with list selection interface.
:returns: None
:rtype: None
"""
# Main frame with padding
main_frame = ttk.Frame(self.dialog, padding="20")
main_frame.pack(fill=tk.BOTH, expand=True)
# Create container for content
content_frame = ttk.Frame(main_frame)
content_frame.pack(fill=tk.BOTH, expand=True, pady=(0, 15))
# Create paned window for list and content
paned = ttk.PanedWindow(content_frame, orient=tk.HORIZONTAL)
paned.pack(fill=tk.BOTH, expand=True)
# Left side - Category list
list_frame = ttk.Frame(paned, relief=tk.GROOVE, borderwidth=1)
paned.add(list_frame, weight=1)
# List label
ttk.Label(
list_frame, text="Parameter Categories", font=("TkDefaultFont", 10, "bold")
).pack(pady=(10, 5))
# Create listbox for categories
self.category_listbox = tk.Listbox(list_frame, selectmode=tk.SINGLE, height=10)
self.category_listbox.pack(fill=tk.BOTH, expand=True, padx=10, pady=(0, 10))
# Add categories
categories = [
"General Parameters",
"Hydrogen Bonds",
"Weak Hydrogen Bonds",
"Halogen Bonds",
"π Interactions",
"π-π Stacking",
"Carbonyl Interactions",
"n→π* Interactions",
]
for cat in categories:
self.category_listbox.insert(tk.END, cat)
# Bind selection event
self.category_listbox.bind("<<ListboxSelect>>", self._on_category_selected)
# Right side - Content area
self.content_container = ttk.Frame(paned)
paned.add(self.content_container, weight=3)
# Create scrollable area for content
self.content_canvas = tk.Canvas(self.content_container)
scrollbar = ttk.Scrollbar(
self.content_container, orient="vertical", command=self.content_canvas.yview
)
self.content_frame = ttk.Frame(self.content_canvas)
self.content_frame.bind(
"<Configure>",
lambda e: self.content_canvas.configure(
scrollregion=self.content_canvas.bbox("all")
),
)
self.content_canvas.create_window(
(0, 0), window=self.content_frame, anchor="nw"
)
self.content_canvas.configure(yscrollcommand=scrollbar.set)
# Enable mouse wheel scrolling
def _on_mousewheel(event):
self.content_canvas.yview_scroll(int(-1 * (event.delta / 120)), "units")
self.content_canvas.bind("<MouseWheel>", _on_mousewheel) # Windows
self.content_canvas.bind(
"<Button-4>", lambda e: self.content_canvas.yview_scroll(-1, "units")
) # Linux
self.content_canvas.bind(
"<Button-5>", lambda e: self.content_canvas.yview_scroll(1, "units")
) # Linux
# Pack canvas and scrollbar
self.content_canvas.pack(side=tk.LEFT, fill=tk.BOTH, expand=True)
scrollbar.pack(side=tk.RIGHT, fill=tk.Y)
# Store current content widget
self.current_content = None
# Select first category by default
self.category_listbox.selection_set(0)
self._on_category_selected(None)
# Buttons at bottom
button_frame = ttk.Frame(main_frame)
button_frame.pack(fill=tk.X, side=tk.BOTTOM)
ttk.Button(button_frame, text="OK", command=self._ok).pack(
side=tk.RIGHT, padx=(5, 0)
)
ttk.Button(button_frame, text="Cancel", command=self._cancel).pack(
side=tk.RIGHT
)
ttk.Button(
button_frame, text="Reset to Defaults", command=self._set_defaults
).pack(side=tk.LEFT, padx=(0, 5))
ttk.Button(
button_frame, text="Manage Presets...", command=self._open_preset_manager
).pack(side=tk.LEFT, padx=5)
def _create_general_parameters(self, parent):
"""Create general analysis parameters."""
group = ttk.LabelFrame(parent, text="General Parameters", padding=10)
group.pack(fill=tk.X, padx=10, pady=5)
# Analysis mode
ttk.Label(group, text="Analysis Mode:").grid(
row=0, column=0, sticky=tk.W, pady=2
)
stored_mode = self._param_values.get(
"analysis_mode", ParametersDefault.ANALYSIS_MODE
)
self.analysis_mode = tk.StringVar(value=stored_mode)
mode_frame = ttk.Frame(group)
mode_frame.grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
ttk.Radiobutton(
mode_frame,
text="Complete PDB Analysis",
variable=self.analysis_mode,
value="complete",
).pack(anchor=tk.W)
ttk.Radiobutton(
mode_frame,
text="Local Interactions Only",
variable=self.analysis_mode,
value="local",
).pack(anchor=tk.W)
# Covalent bond cutoff factor
ttk.Label(group, text="Covalent Bond Factor:").grid(
row=1, column=0, sticky=tk.W, pady=2
)
stored_factor = self._param_values.get(
"covalent_factor", ParametersDefault.COVALENT_CUTOFF_FACTOR
)
self.covalent_factor = tk.DoubleVar(value=stored_factor)
ttk.Scale(
group,
from_=ParameterRanges.MIN_COVALENT_FACTOR,
to=ParameterRanges.MAX_COVALENT_FACTOR,
variable=self.covalent_factor,
orient=tk.HORIZONTAL,
length=200,
).grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
# Value display
factor_label = ttk.Label(group, text="")
factor_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_factor_label(*args):
try:
factor_label.config(text=f"{self.covalent_factor.get():.2f}")
except tk.TclError:
pass # Widget destroyed, ignore
self.covalent_factor.trace("w", update_factor_label)
update_factor_label()
def _on_category_selected(self, event):
"""Handle category selection from list."""
selection = self.category_listbox.curselection()
if not selection:
return
# Store current values before switching
self._store_current_values()
# Clear current content
if self.current_content:
self.current_content.destroy()
# Create new content frame
self.current_content = ttk.Frame(self.content_frame, padding="20")
self.current_content.pack(fill=tk.BOTH, expand=True)
# Show appropriate content based on selection
category_index = selection[0]
if category_index == 0: # General Parameters
self._create_general_parameters(self.current_content)
elif category_index == 1: # Hydrogen Bonds
self._create_hydrogen_bond_parameters(self.current_content)
elif category_index == 2: # Weak Hydrogen Bonds
self._create_weak_hydrogen_bond_parameters(self.current_content)
elif category_index == 3: # Halogen Bonds
self._create_halogen_bond_parameters(self.current_content)
elif category_index == 4: # π Interactions
self._create_pi_interaction_parameters(self.current_content)
elif category_index == 5: # π-π Stacking
self._create_pi_pi_stacking_parameters(self.current_content)
elif category_index == 6: # Carbonyl Interactions
self._create_carbonyl_interaction_parameters(self.current_content)
elif category_index == 7: # n→π* Interactions
self._create_n_pi_interaction_parameters(self.current_content)
# Reset scroll position
self.content_canvas.yview_moveto(0)
def _create_hydrogen_bond_parameters(self, parent):
"""Create hydrogen bond parameter controls."""
group = ttk.LabelFrame(parent, text="Hydrogen Bond Parameters", padding=10)
group.pack(fill=tk.X, padx=10, pady=5)
# H...A distance
ttk.Label(group, text="H...A Distance (Å):").grid(
row=0, column=0, sticky=tk.W, pady=2
)
stored_dist = self._param_values.get(
"hb_distance", ParametersDefault.HB_DISTANCE_CUTOFF
)
self.hb_distance = tk.DoubleVar(value=stored_dist)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.hb_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
hb_dist_label = ttk.Label(group, text="")
hb_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_hb_dist(*args):
try:
hb_dist_label.config(text=f"{self.hb_distance.get():.1f}")
except tk.TclError:
pass
self.hb_distance.trace("w", update_hb_dist)
update_hb_dist()
# D-H...A angle
ttk.Label(group, text="D-H...A Angle (°):").grid(
row=1, column=0, sticky=tk.W, pady=2
)
stored_angle = self._param_values.get(
"hb_angle", ParametersDefault.HB_ANGLE_CUTOFF
)
self.hb_angle = tk.DoubleVar(value=stored_angle)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.hb_angle,
orient=tk.HORIZONTAL,
length=200,
).grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
hb_angle_label = ttk.Label(group, text="")
hb_angle_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_hb_angle(*args):
try:
hb_angle_label.config(text=f"{self.hb_angle.get():.0f}")
except tk.TclError:
pass
self.hb_angle.trace("w", update_hb_angle)
update_hb_angle()
# D...A distance
ttk.Label(group, text="D...A Distance (Å):").grid(
row=2, column=0, sticky=tk.W, pady=2
)
stored_da = self._param_values.get(
"da_distance", ParametersDefault.HB_DA_DISTANCE
)
self.da_distance = tk.DoubleVar(value=stored_da)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.da_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=2, column=1, sticky=tk.W, padx=10, pady=2)
da_dist_label = ttk.Label(group, text="")
da_dist_label.grid(row=2, column=2, sticky=tk.W, padx=5, pady=2)
def update_da_dist(*args):
try:
da_dist_label.config(text=f"{self.da_distance.get():.1f}")
except tk.TclError:
pass
self.da_distance.trace("w", update_da_dist)
update_da_dist()
def _create_weak_hydrogen_bond_parameters(self, parent):
"""Create weak hydrogen bond parameter controls for carbon donors."""
group = ttk.LabelFrame(
parent, text="Weak Hydrogen Bond Parameters (Carbon Donors)", padding=10
)
group.pack(fill=tk.X, padx=10, pady=5)
# WHB H...A distance
ttk.Label(group, text="H...A Distance (Å):").grid(
row=0, column=0, sticky=tk.W, pady=2
)
stored_whb_dist = self._param_values.get(
"whb_distance", ParametersDefault.WHB_DISTANCE_CUTOFF
)
self.whb_distance = tk.DoubleVar(value=stored_whb_dist)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.whb_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
whb_dist_label = ttk.Label(group, text="")
whb_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_whb_dist(*args):
try:
whb_dist_label.config(text=f"{self.whb_distance.get():.1f}")
except tk.TclError:
pass
self.whb_distance.trace("w", update_whb_dist)
update_whb_dist()
# WHB D-H...A angle
ttk.Label(group, text="D-H...A Angle (°):").grid(
row=1, column=0, sticky=tk.W, pady=2
)
stored_whb_angle = self._param_values.get(
"whb_angle", ParametersDefault.WHB_ANGLE_CUTOFF
)
self.whb_angle = tk.DoubleVar(value=stored_whb_angle)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.whb_angle,
orient=tk.HORIZONTAL,
length=200,
).grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
whb_angle_label = ttk.Label(group, text="")
whb_angle_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_whb_angle(*args):
try:
whb_angle_label.config(text=f"{self.whb_angle.get():.0f}")
except tk.TclError:
pass
self.whb_angle.trace("w", update_whb_angle)
update_whb_angle()
# WHB D...A distance
ttk.Label(group, text="D...A Distance (Å):").grid(
row=2, column=0, sticky=tk.W, pady=2
)
stored_whb_da = self._param_values.get(
"whb_da_distance", ParametersDefault.WHB_DA_DISTANCE
)
self.whb_da_distance = tk.DoubleVar(value=stored_whb_da)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.whb_da_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=2, column=1, sticky=tk.W, padx=10, pady=2)
whb_da_dist_label = ttk.Label(group, text="")
whb_da_dist_label.grid(row=2, column=2, sticky=tk.W, padx=5, pady=2)
def update_whb_da_dist(*args):
try:
whb_da_dist_label.config(text=f"{self.whb_da_distance.get():.1f}")
except tk.TclError:
pass
self.whb_da_distance.trace("w", update_whb_da_dist)
update_whb_da_dist()
def _create_halogen_bond_parameters(self, parent):
"""Create halogen bond parameter controls."""
group = ttk.LabelFrame(parent, text="Halogen Bond Parameters", padding=10)
group.pack(fill=tk.X, padx=10, pady=5)
# X...A distance
ttk.Label(group, text="X...A Distance (Å):").grid(
row=0, column=0, sticky=tk.W, pady=2
)
stored_xb_dist = self._param_values.get(
"xb_distance", ParametersDefault.XB_DISTANCE_CUTOFF
)
self.xb_distance = tk.DoubleVar(value=stored_xb_dist)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.xb_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
xb_dist_label = ttk.Label(group, text="")
xb_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_xb_dist(*args):
try:
xb_dist_label.config(text=f"{self.xb_distance.get():.1f}")
except tk.TclError:
pass
self.xb_distance.trace("w", update_xb_dist)
update_xb_dist()
# C-X...A angle
ttk.Label(group, text="C-X...A Angle (°):").grid(
row=1, column=0, sticky=tk.W, pady=2
)
stored_xb_angle = self._param_values.get(
"xb_angle", ParametersDefault.XB_ANGLE_CUTOFF
)
self.xb_angle = tk.DoubleVar(value=stored_xb_angle)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.xb_angle,
orient=tk.HORIZONTAL,
length=200,
).grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
xb_angle_label = ttk.Label(group, text="")
xb_angle_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_xb_angle(*args):
try:
xb_angle_label.config(text=f"{self.xb_angle.get():.0f}")
except tk.TclError:
pass
self.xb_angle.trace("w", update_xb_angle)
update_xb_angle()
def _create_pi_interaction_parameters(self, parent):
"""Create π interaction parameter controls."""
# General π interaction parameters
general_group = ttk.LabelFrame(
parent, text="General π Interaction Parameters", padding=10
)
general_group.pack(fill=tk.X, padx=10, pady=5)
# H...π distance
ttk.Label(general_group, text="H...π Distance (Å):").grid(
row=0, column=0, sticky=tk.W, pady=2
)
stored_pi_dist = self._param_values.get(
"pi_distance", ParametersDefault.PI_DISTANCE_CUTOFF
)
self.pi_distance = tk.DoubleVar(value=stored_pi_dist)
ttk.Scale(
general_group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.pi_distance,
orient=tk.HORIZONTAL,
length=200,
).grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
pi_dist_label = ttk.Label(general_group, text="")
pi_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_dist(*args):
try:
pi_dist_label.config(text=f"{self.pi_distance.get():.1f}")
except tk.TclError:
pass
self.pi_distance.trace("w", update_pi_dist)
update_pi_dist()
# D-H...π angle
ttk.Label(general_group, text="D-H...π Angle (°):").grid(
row=1, column=0, sticky=tk.W, pady=2
)
stored_pi_angle = self._param_values.get(
"pi_angle", ParametersDefault.PI_ANGLE_CUTOFF
)
self.pi_angle = tk.DoubleVar(value=stored_pi_angle)
ttk.Scale(
general_group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.pi_angle,
orient=tk.HORIZONTAL,
length=200,
).grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
pi_angle_label = ttk.Label(general_group, text="")
pi_angle_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_angle(*args):
try:
pi_angle_label.config(text=f"{self.pi_angle.get():.0f}")
except tk.TclError:
pass
self.pi_angle.trace("w", update_pi_angle)
update_pi_angle()
# π interaction subtype parameters
subtypes_group = ttk.LabelFrame(
parent, text="π Interaction Subtype Parameters", padding=10
)
subtypes_group.pack(fill=tk.X, padx=10, pady=5)
# Helper function to create parameter pair
def create_parameter_pair(
parent_frame,
row,
label_text,
dist_var_name,
angle_var_name,
dist_default,
angle_default,
):
# Get stored values or use defaults
stored_dist = self._param_values.get(dist_var_name, dist_default)
stored_angle = self._param_values.get(angle_var_name, angle_default)
# Distance parameter
ttk.Label(parent_frame, text=f"{label_text} Distance (Å):").grid(
row=row, column=0, sticky=tk.W, pady=2
)
dist_var = tk.DoubleVar(value=stored_dist)
setattr(self, dist_var_name, dist_var)
ttk.Scale(
parent_frame,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=dist_var,
orient=tk.HORIZONTAL,
length=150,
).grid(row=row, column=1, sticky=tk.W, padx=5, pady=2)
dist_label = ttk.Label(parent_frame, text="")
dist_label.grid(row=row, column=2, sticky=tk.W, padx=5, pady=2)
# Angle parameter
ttk.Label(parent_frame, text=f"{label_text} Angle (°):").grid(
row=row, column=3, sticky=tk.W, pady=2, padx=(20, 0)
)
angle_var = tk.DoubleVar(value=stored_angle)
setattr(self, angle_var_name, angle_var)
ttk.Scale(
parent_frame,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=angle_var,
orient=tk.HORIZONTAL,
length=150,
).grid(row=row, column=4, sticky=tk.W, padx=5, pady=2)
angle_label = ttk.Label(parent_frame, text="")
angle_label.grid(row=row, column=5, sticky=tk.W, padx=5, pady=2)
# Update functions
def update_dist(*args):
try:
dist_label.config(text=f"{dist_var.get():.1f}")
except tk.TclError:
pass
def update_angle(*args):
try:
angle_label.config(text=f"{angle_var.get():.0f}")
except tk.TclError:
pass
dist_var.trace("w", update_dist)
angle_var.trace("w", update_angle)
update_dist()
update_angle()
# Create all subtype parameters
create_parameter_pair(
subtypes_group,
0,
"C-Cl...π",
"pi_ccl_distance",
"pi_ccl_angle",
ParametersDefault.PI_CCL_DISTANCE_CUTOFF,
ParametersDefault.PI_CCL_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
1,
"C-Br...π",
"pi_cbr_distance",
"pi_cbr_angle",
ParametersDefault.PI_CBR_DISTANCE_CUTOFF,
ParametersDefault.PI_CBR_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
2,
"C-I...π",
"pi_ci_distance",
"pi_ci_angle",
ParametersDefault.PI_CI_DISTANCE_CUTOFF,
ParametersDefault.PI_CI_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
3,
"C-H...π",
"pi_ch_distance",
"pi_ch_angle",
ParametersDefault.PI_CH_DISTANCE_CUTOFF,
ParametersDefault.PI_CH_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
4,
"N-H...π",
"pi_nh_distance",
"pi_nh_angle",
ParametersDefault.PI_NH_DISTANCE_CUTOFF,
ParametersDefault.PI_NH_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
5,
"O-H...π",
"pi_oh_distance",
"pi_oh_angle",
ParametersDefault.PI_OH_DISTANCE_CUTOFF,
ParametersDefault.PI_OH_ANGLE_CUTOFF,
)
create_parameter_pair(
subtypes_group,
6,
"S-H...π",
"pi_sh_distance",
"pi_sh_angle",
ParametersDefault.PI_SH_DISTANCE_CUTOFF,
ParametersDefault.PI_SH_ANGLE_CUTOFF,
)
def _create_pi_pi_stacking_parameters(self, parent):
"""Create π-π stacking parameter controls."""
group = ttk.LabelFrame(parent, text="π-π Stacking Parameters", padding=10)
group.pack(fill=tk.X, padx=10, pady=5)
# Distance cutoff
dist_label = ttk.Label(group, text="Distance Cutoff (Å):")
dist_label.grid(row=0, column=0, sticky=tk.W, pady=2)
ToolTip(
dist_label,
"Maximum distance between aromatic ring centroids for π-π stacking interactions.\n"
"Typical range: 3.0-4.5 Å\n"
"• Parallel stacking: ~3.5-4.0 Å\n"
"• T-shaped stacking: ~3.5-4.5 Å\n"
"Based on McGaughey et al. (1998) and crystallographic data.",
)
self.pi_pi_distance.set(
self._param_values.get(
"pi_pi_distance", ParametersDefault.PI_PI_DISTANCE_CUTOFF
)
)
pi_pi_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.pi_pi_distance,
orient=tk.HORIZONTAL,
length=200,
)
pi_pi_scale.grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
pi_pi_scale,
"Adjust the maximum distance between aromatic ring centroids.\n"
"Lower values = stricter detection, higher values = more permissive.",
)
pi_pi_dist_label = ttk.Label(group, text="")
pi_pi_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_pi_dist(*args):
try:
pi_pi_dist_label.config(text=f"{self.pi_pi_distance.get():.1f}")
except tk.TclError:
pass
self.pi_pi_distance.trace("w", update_pi_pi_dist)
update_pi_pi_dist()
# Parallel angle cutoff
parallel_label = ttk.Label(group, text="Parallel Angle Cutoff (°):")
parallel_label.grid(row=1, column=0, sticky=tk.W, pady=2)
ToolTip(
parallel_label,
"Maximum angle between aromatic ring planes for parallel π-π stacking.\n"
"• 0° = perfectly parallel rings\n"
"• Typical cutoff: 20-30°\n"
"• Values >30° indicate T-shaped or edge-to-face interactions\n"
"Based on Hunter & Sanders (1990) π-π interaction classification.",
)
self.pi_pi_parallel_angle.set(
self._param_values.get(
"pi_pi_parallel_angle", ParametersDefault.PI_PI_PARALLEL_ANGLE_CUTOFF
)
)
parallel_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.pi_pi_parallel_angle,
orient=tk.HORIZONTAL,
length=200,
)
parallel_scale.grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
parallel_scale,
"Adjust angle tolerance for parallel stacking.\n"
"Lower values = more strict parallel geometry required.",
)
pi_pi_parallel_label = ttk.Label(group, text="")
pi_pi_parallel_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_pi_parallel(*args):
try:
pi_pi_parallel_label.config(
text=f"{self.pi_pi_parallel_angle.get():.0f}"
)
except tk.TclError:
pass
self.pi_pi_parallel_angle.trace("w", update_pi_pi_parallel)
update_pi_pi_parallel()
# T-shaped angle minimum
tmin_label = ttk.Label(group, text="T-shaped Angle Min (°):")
tmin_label.grid(row=2, column=0, sticky=tk.W, pady=2)
ToolTip(
tmin_label,
"Minimum angle between ring planes for T-shaped (edge-to-face) stacking.\n"
"• Typical range: 60-90°\n"
"• T-shaped geometry involves one ring edge interacting with another ring face\n"
"• Complementary to parallel stacking interactions\n"
"Based on Burley & Petsko (1985) aromatic interaction studies.",
)
self.pi_pi_tshaped_angle_min.set(
self._param_values.get(
"pi_pi_tshaped_angle_min", ParametersDefault.PI_PI_TSHAPED_ANGLE_MIN
)
)
tmin_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.pi_pi_tshaped_angle_min,
orient=tk.HORIZONTAL,
length=200,
)
tmin_scale.grid(row=2, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
tmin_scale,
"Adjust minimum angle for T-shaped interactions.\n"
"Higher values = more perpendicular geometry required.",
)
pi_pi_tmin_label = ttk.Label(group, text="")
pi_pi_tmin_label.grid(row=2, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_pi_tmin(*args):
try:
pi_pi_tmin_label.config(
text=f"{self.pi_pi_tshaped_angle_min.get():.0f}"
)
except tk.TclError:
pass
self.pi_pi_tshaped_angle_min.trace("w", update_pi_pi_tmin)
update_pi_pi_tmin()
# T-shaped angle maximum
ttk.Label(group, text="T-shaped Angle Max (°):").grid(
row=3, column=0, sticky=tk.W, pady=2
)
self.pi_pi_tshaped_angle_max.set(
self._param_values.get(
"pi_pi_tshaped_angle_max", ParametersDefault.PI_PI_TSHAPED_ANGLE_MAX
)
)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.pi_pi_tshaped_angle_max,
orient=tk.HORIZONTAL,
length=200,
).grid(row=3, column=1, sticky=tk.W, padx=10, pady=2)
pi_pi_tmax_label = ttk.Label(group, text="")
pi_pi_tmax_label.grid(row=3, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_pi_tmax(*args):
try:
pi_pi_tmax_label.config(
text=f"{self.pi_pi_tshaped_angle_max.get():.0f}"
)
except tk.TclError:
pass
self.pi_pi_tshaped_angle_max.trace("w", update_pi_pi_tmax)
update_pi_pi_tmax()
# Offset cutoff
ttk.Label(group, text="Offset Cutoff (Å):").grid(
row=4, column=0, sticky=tk.W, pady=2
)
self.pi_pi_offset.set(
self._param_values.get(
"pi_pi_offset", ParametersDefault.PI_PI_OFFSET_CUTOFF
)
)
ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.pi_pi_offset,
orient=tk.HORIZONTAL,
length=200,
).grid(row=4, column=1, sticky=tk.W, padx=10, pady=2)
pi_pi_offset_label = ttk.Label(group, text="")
pi_pi_offset_label.grid(row=4, column=2, sticky=tk.W, padx=5, pady=2)
def update_pi_pi_offset(*args):
try:
pi_pi_offset_label.config(text=f"{self.pi_pi_offset.get():.1f}")
except tk.TclError:
pass
self.pi_pi_offset.trace("w", update_pi_pi_offset)
update_pi_pi_offset()
def _create_carbonyl_interaction_parameters(self, parent):
"""Create carbonyl interaction parameter controls."""
group = ttk.LabelFrame(
parent, text="Carbonyl n→π* Interaction Parameters", padding=10
)
group.pack(fill=tk.X, padx=10, pady=5)
# Distance cutoff
carb_dist_label = ttk.Label(group, text="O···C Distance Cutoff (Å):")
carb_dist_label.grid(row=0, column=0, sticky=tk.W, pady=2)
ToolTip(
carb_dist_label,
"Maximum distance between lone pair donor oxygen and carbonyl carbon.\n"
"• Typical range: 2.8-3.2 Å\n"
"• Represents n→π* orbital interaction\n"
"• Distance based on crystallographic surveys of protein structures\n"
"• Critical for protein backbone stability and folding",
)
self.carbonyl_distance.set(
self._param_values.get(
"carbonyl_distance", ParametersDefault.CARBONYL_DISTANCE_CUTOFF
)
)
carb_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.carbonyl_distance,
orient=tk.HORIZONTAL,
length=200,
)
carb_scale.grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
carb_scale,
"Adjust O···C distance cutoff for carbonyl interactions.\n"
"Based on van der Waals radii and quantum mechanical calculations.",
)
carbonyl_dist_label = ttk.Label(group, text="")
carbonyl_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_carbonyl_dist(*args):
try:
carbonyl_dist_label.config(text=f"{self.carbonyl_distance.get():.1f}")
except tk.TclError:
pass
self.carbonyl_distance.trace("w", update_carbonyl_dist)
update_carbonyl_dist()
# Angle minimum
angle_min_label = ttk.Label(group, text="Bürgi-Dunitz Angle Min (°):")
angle_min_label.grid(row=1, column=0, sticky=tk.W, pady=2)
ToolTip(
angle_min_label,
"Minimum Bürgi-Dunitz approach angle for nucleophilic attack on carbonyl.\n"
"• Optimal angle: ~107° (tetrahedral trajectory)\n"
"• Range: 95-125° based on crystal structures\n"
"• Named after Bürgi & Dunitz (1983) crystallographic studies\n"
"• Represents stereoelectronically favored approach geometry",
)
self.carbonyl_angle_min.set(
self._param_values.get(
"carbonyl_angle_min", ParametersDefault.CARBONYL_ANGLE_MIN
)
)
angle_min_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.carbonyl_angle_min,
orient=tk.HORIZONTAL,
length=200,
)
angle_min_scale.grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
angle_min_scale,
"Adjust minimum Bürgi-Dunitz angle.\n"
"Based on ab initio calculations and crystallographic analysis.",
)
carbonyl_min_label = ttk.Label(group, text="")
carbonyl_min_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_carbonyl_min(*args):
try:
carbonyl_min_label.config(text=f"{self.carbonyl_angle_min.get():.0f}")
except tk.TclError:
pass
self.carbonyl_angle_min.trace("w", update_carbonyl_min)
update_carbonyl_min()
# Angle maximum
ttk.Label(group, text="Bürgi-Dunitz Angle Max (°):").grid(
row=2, column=0, sticky=tk.W, pady=2
)
self.carbonyl_angle_max.set(
self._param_values.get(
"carbonyl_angle_max", ParametersDefault.CARBONYL_ANGLE_MAX
)
)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.carbonyl_angle_max,
orient=tk.HORIZONTAL,
length=200,
).grid(row=2, column=1, sticky=tk.W, padx=10, pady=2)
carbonyl_max_label = ttk.Label(group, text="")
carbonyl_max_label.grid(row=2, column=2, sticky=tk.W, padx=5, pady=2)
def update_carbonyl_max(*args):
try:
carbonyl_max_label.config(text=f"{self.carbonyl_angle_max.get():.0f}")
except tk.TclError:
pass
self.carbonyl_angle_max.trace("w", update_carbonyl_max)
update_carbonyl_max()
def _create_n_pi_interaction_parameters(self, parent):
"""Create n→π* interaction parameter controls."""
group = ttk.LabelFrame(parent, text="n→π* Interaction Parameters", padding=10)
group.pack(fill=tk.X, padx=10, pady=5)
# Distance cutoff
n_pi_dist_label = ttk.Label(group, text="Distance Cutoff (Å):")
n_pi_dist_label.grid(row=0, column=0, sticky=tk.W, pady=2)
ToolTip(
n_pi_dist_label,
"Maximum distance between lone pair donor atom and aromatic ring centroid.\n"
"• Typical range: 3.0-4.0 Å for O/N donors\n"
"• Represents n→π* orbital interaction\n"
"• Common in protein-ligand and protein-protein interactions\n"
"• Important for molecular recognition and binding affinity",
)
self.n_pi_distance.set(
self._param_values.get(
"n_pi_distance", ParametersDefault.N_PI_DISTANCE_CUTOFF
)
)
n_pi_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.n_pi_distance,
orient=tk.HORIZONTAL,
length=200,
)
n_pi_scale.grid(row=0, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
n_pi_scale,
"Adjust distance cutoff for n→π* interactions.\n"
"Based on computational studies and structural databases.",
)
n_pi_dist_label = ttk.Label(group, text="")
n_pi_dist_label.grid(row=0, column=2, sticky=tk.W, padx=5, pady=2)
def update_n_pi_dist(*args):
try:
n_pi_dist_label.config(text=f"{self.n_pi_distance.get():.1f}")
except tk.TclError:
pass
self.n_pi_distance.trace("w", update_n_pi_dist)
update_n_pi_dist()
# Sulfur distance cutoff
sulfur_label = ttk.Label(group, text="Sulfur Distance Cutoff (Å):")
sulfur_label.grid(row=1, column=0, sticky=tk.W, pady=2)
ToolTip(
sulfur_label,
"Maximum distance for sulfur n→π* interactions (S···aromatic ring).\n"
"• Typically larger than O/N due to sulfur's larger atomic radius\n"
"• Range: 3.5-4.5 Å\n"
"• Important in cysteine-aromatic interactions\n"
"• Weaker than O/N interactions but geometrically significant",
)
self.n_pi_sulfur_distance.set(
self._param_values.get(
"n_pi_sulfur_distance", ParametersDefault.N_PI_SULFUR_DISTANCE_CUTOFF
)
)
sulfur_scale = ttk.Scale(
group,
from_=ParameterRanges.MIN_DISTANCE,
to=ParameterRanges.MAX_DISTANCE,
variable=self.n_pi_sulfur_distance,
orient=tk.HORIZONTAL,
length=200,
)
sulfur_scale.grid(row=1, column=1, sticky=tk.W, padx=10, pady=2)
ToolTip(
sulfur_scale,
"Adjust sulfur-aromatic distance cutoff.\n"
"Larger values account for sulfur's extended electron cloud.",
)
n_pi_sulfur_label = ttk.Label(group, text="")
n_pi_sulfur_label.grid(row=1, column=2, sticky=tk.W, padx=5, pady=2)
def update_n_pi_sulfur(*args):
try:
n_pi_sulfur_label.config(text=f"{self.n_pi_sulfur_distance.get():.1f}")
except tk.TclError:
pass
self.n_pi_sulfur_distance.trace("w", update_n_pi_sulfur)
update_n_pi_sulfur()
# Angle minimum
ttk.Label(group, text="Angle Min (°):").grid(
row=2, column=0, sticky=tk.W, pady=2
)
self.n_pi_angle_min.set(
self._param_values.get("n_pi_angle_min", ParametersDefault.N_PI_ANGLE_MIN)
)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.n_pi_angle_min,
orient=tk.HORIZONTAL,
length=200,
).grid(row=2, column=1, sticky=tk.W, padx=10, pady=2)
n_pi_min_label = ttk.Label(group, text="")
n_pi_min_label.grid(row=2, column=2, sticky=tk.W, padx=5, pady=2)
def update_n_pi_min(*args):
try:
n_pi_min_label.config(text=f"{self.n_pi_angle_min.get():.0f}")
except tk.TclError:
pass
self.n_pi_angle_min.trace("w", update_n_pi_min)
update_n_pi_min()
# Angle maximum
ttk.Label(group, text="Angle Max (°):").grid(
row=3, column=0, sticky=tk.W, pady=2
)
self.n_pi_angle_max.set(
self._param_values.get("n_pi_angle_max", ParametersDefault.N_PI_ANGLE_MAX)
)
ttk.Scale(
group,
from_=ParameterRanges.MIN_ANGLE,
to=ParameterRanges.MAX_ANGLE,
variable=self.n_pi_angle_max,
orient=tk.HORIZONTAL,
length=200,
).grid(row=3, column=1, sticky=tk.W, padx=10, pady=2)
n_pi_max_label = ttk.Label(group, text="")
n_pi_max_label.grid(row=3, column=2, sticky=tk.W, padx=5, pady=2)
def update_n_pi_max(*args):
try:
n_pi_max_label.config(text=f"{self.n_pi_angle_max.get():.0f}")
except tk.TclError:
pass
self.n_pi_angle_max.trace("w", update_n_pi_max)
update_n_pi_max()
[docs]
def get_parameters(self) -> AnalysisParameters:
"""Get current parameter values.
:returns: Current analysis parameters
:rtype: AnalysisParameters
"""
# Store current values first
self._store_current_values()
# Get values from stored parameters or current variables
def get_value(var_name, default_value):
if var_name in self._param_values:
return self._param_values[var_name]
elif hasattr(self, var_name):
var = getattr(self, var_name)
if var:
try:
return var.get()
except tk.TclError:
pass
return default_value
return AnalysisParameters(
hb_distance_cutoff=get_value(
"hb_distance", ParametersDefault.HB_DISTANCE_CUTOFF
),
hb_angle_cutoff=get_value("hb_angle", ParametersDefault.HB_ANGLE_CUTOFF),
hb_donor_acceptor_cutoff=get_value(
"da_distance", ParametersDefault.HB_DA_DISTANCE
),
whb_distance_cutoff=get_value(
"whb_distance", ParametersDefault.WHB_DISTANCE_CUTOFF
),
whb_angle_cutoff=get_value("whb_angle", ParametersDefault.WHB_ANGLE_CUTOFF),
whb_donor_acceptor_cutoff=get_value(
"whb_da_distance", ParametersDefault.WHB_DA_DISTANCE
),
xb_distance_cutoff=get_value(
"xb_distance", ParametersDefault.XB_DISTANCE_CUTOFF
),
xb_angle_cutoff=get_value("xb_angle", ParametersDefault.XB_ANGLE_CUTOFF),
pi_distance_cutoff=get_value(
"pi_distance", ParametersDefault.PI_DISTANCE_CUTOFF
),
pi_angle_cutoff=get_value("pi_angle", ParametersDefault.PI_ANGLE_CUTOFF),
# π interaction subtype parameters
pi_ccl_distance_cutoff=get_value(
"pi_ccl_distance", ParametersDefault.PI_CCL_DISTANCE_CUTOFF
),
pi_ccl_angle_cutoff=get_value(
"pi_ccl_angle", ParametersDefault.PI_CCL_ANGLE_CUTOFF
),
pi_cbr_distance_cutoff=get_value(
"pi_cbr_distance", ParametersDefault.PI_CBR_DISTANCE_CUTOFF
),
pi_cbr_angle_cutoff=get_value(
"pi_cbr_angle", ParametersDefault.PI_CBR_ANGLE_CUTOFF
),
pi_ci_distance_cutoff=get_value(
"pi_ci_distance", ParametersDefault.PI_CI_DISTANCE_CUTOFF
),
pi_ci_angle_cutoff=get_value(
"pi_ci_angle", ParametersDefault.PI_CI_ANGLE_CUTOFF
),
pi_ch_distance_cutoff=get_value(
"pi_ch_distance", ParametersDefault.PI_CH_DISTANCE_CUTOFF
),
pi_ch_angle_cutoff=get_value(
"pi_ch_angle", ParametersDefault.PI_CH_ANGLE_CUTOFF
),
pi_nh_distance_cutoff=get_value(
"pi_nh_distance", ParametersDefault.PI_NH_DISTANCE_CUTOFF
),
pi_nh_angle_cutoff=get_value(
"pi_nh_angle", ParametersDefault.PI_NH_ANGLE_CUTOFF
),
pi_oh_distance_cutoff=get_value(
"pi_oh_distance", ParametersDefault.PI_OH_DISTANCE_CUTOFF
),
pi_oh_angle_cutoff=get_value(
"pi_oh_angle", ParametersDefault.PI_OH_ANGLE_CUTOFF
),
pi_sh_distance_cutoff=get_value(
"pi_sh_distance", ParametersDefault.PI_SH_DISTANCE_CUTOFF
),
pi_sh_angle_cutoff=get_value(
"pi_sh_angle", ParametersDefault.PI_SH_ANGLE_CUTOFF
),
# New interaction parameters
pi_pi_distance_cutoff=get_value(
"pi_pi_distance", ParametersDefault.PI_PI_DISTANCE_CUTOFF
),
pi_pi_parallel_angle_cutoff=get_value(
"pi_pi_parallel_angle", ParametersDefault.PI_PI_PARALLEL_ANGLE_CUTOFF
),
pi_pi_tshaped_angle_min=get_value(
"pi_pi_tshaped_angle_min", ParametersDefault.PI_PI_TSHAPED_ANGLE_MIN
),
pi_pi_tshaped_angle_max=get_value(
"pi_pi_tshaped_angle_max", ParametersDefault.PI_PI_TSHAPED_ANGLE_MAX
),
pi_pi_offset_cutoff=get_value(
"pi_pi_offset", ParametersDefault.PI_PI_OFFSET_CUTOFF
),
carbonyl_distance_cutoff=get_value(
"carbonyl_distance", ParametersDefault.CARBONYL_DISTANCE_CUTOFF
),
carbonyl_angle_min=get_value(
"carbonyl_angle_min", ParametersDefault.CARBONYL_ANGLE_MIN
),
carbonyl_angle_max=get_value(
"carbonyl_angle_max", ParametersDefault.CARBONYL_ANGLE_MAX
),
n_pi_distance_cutoff=get_value(
"n_pi_distance", ParametersDefault.N_PI_DISTANCE_CUTOFF
),
n_pi_sulfur_distance_cutoff=get_value(
"n_pi_sulfur_distance", ParametersDefault.N_PI_SULFUR_DISTANCE_CUTOFF
),
n_pi_angle_min=get_value(
"n_pi_angle_min", ParametersDefault.N_PI_ANGLE_MIN
),
n_pi_angle_max=get_value(
"n_pi_angle_max", ParametersDefault.N_PI_ANGLE_MAX
),
covalent_cutoff_factor=get_value(
"covalent_factor", ParametersDefault.COVALENT_CUTOFF_FACTOR
),
analysis_mode=get_value("analysis_mode", ParametersDefault.ANALYSIS_MODE),
)
[docs]
def set_parameters(self, params: AnalysisParameters) -> None:
"""Set parameter values from AnalysisParameters object.
:param params: Analysis parameters to set
:type params: AnalysisParameters
"""
# Store values directly in our parameter storage
self._param_values.update(
{
"hb_distance": params.hb_distance_cutoff,
"hb_angle": params.hb_angle_cutoff,
"da_distance": params.hb_donor_acceptor_cutoff,
"whb_distance": params.whb_distance_cutoff,
"whb_angle": params.whb_angle_cutoff,
"whb_da_distance": params.whb_donor_acceptor_cutoff,
"xb_distance": params.xb_distance_cutoff,
"xb_angle": params.xb_angle_cutoff,
"pi_distance": params.pi_distance_cutoff,
"pi_angle": params.pi_angle_cutoff,
"pi_ccl_distance": params.pi_ccl_distance_cutoff,
"pi_ccl_angle": params.pi_ccl_angle_cutoff,
"pi_cbr_distance": params.pi_cbr_distance_cutoff,
"pi_cbr_angle": params.pi_cbr_angle_cutoff,
"pi_ci_distance": params.pi_ci_distance_cutoff,
"pi_ci_angle": params.pi_ci_angle_cutoff,
"pi_ch_distance": params.pi_ch_distance_cutoff,
"pi_ch_angle": params.pi_ch_angle_cutoff,
"pi_nh_distance": params.pi_nh_distance_cutoff,
"pi_nh_angle": params.pi_nh_angle_cutoff,
"pi_oh_distance": params.pi_oh_distance_cutoff,
"pi_oh_angle": params.pi_oh_angle_cutoff,
"pi_sh_distance": params.pi_sh_distance_cutoff,
"pi_sh_angle": params.pi_sh_angle_cutoff,
# New interaction parameters
"pi_pi_distance": params.pi_pi_distance_cutoff,
"pi_pi_parallel_angle": params.pi_pi_parallel_angle_cutoff,
"pi_pi_tshaped_angle_min": params.pi_pi_tshaped_angle_min,
"pi_pi_tshaped_angle_max": params.pi_pi_tshaped_angle_max,
"pi_pi_offset": params.pi_pi_offset_cutoff,
"carbonyl_distance": params.carbonyl_distance_cutoff,
"carbonyl_angle_min": params.carbonyl_angle_min,
"carbonyl_angle_max": params.carbonyl_angle_max,
"n_pi_distance": params.n_pi_distance_cutoff,
"n_pi_sulfur_distance": params.n_pi_sulfur_distance_cutoff,
"n_pi_angle_min": params.n_pi_angle_min,
"n_pi_angle_max": params.n_pi_angle_max,
"covalent_factor": params.covalent_cutoff_factor,
"analysis_mode": params.analysis_mode,
}
)
# Set values on existing variables if they exist
def safe_set(var_name, value):
if hasattr(self, var_name):
var = getattr(self, var_name)
if var:
try:
var.set(value)
except tk.TclError:
pass # Variable destroyed, ignore
safe_set("hb_distance", params.hb_distance_cutoff)
safe_set("hb_angle", params.hb_angle_cutoff)
safe_set("da_distance", params.hb_donor_acceptor_cutoff)
safe_set("whb_distance", params.whb_distance_cutoff)
safe_set("whb_angle", params.whb_angle_cutoff)
safe_set("whb_da_distance", params.whb_donor_acceptor_cutoff)
safe_set("xb_distance", params.xb_distance_cutoff)
safe_set("xb_angle", params.xb_angle_cutoff)
safe_set("pi_distance", params.pi_distance_cutoff)
safe_set("pi_angle", params.pi_angle_cutoff)
safe_set("pi_ccl_distance", params.pi_ccl_distance_cutoff)
safe_set("pi_ccl_angle", params.pi_ccl_angle_cutoff)
safe_set("pi_cbr_distance", params.pi_cbr_distance_cutoff)
safe_set("pi_cbr_angle", params.pi_cbr_angle_cutoff)
safe_set("pi_ci_distance", params.pi_ci_distance_cutoff)
safe_set("pi_ci_angle", params.pi_ci_angle_cutoff)
safe_set("pi_ch_distance", params.pi_ch_distance_cutoff)
safe_set("pi_ch_angle", params.pi_ch_angle_cutoff)
safe_set("pi_nh_distance", params.pi_nh_distance_cutoff)
safe_set("pi_nh_angle", params.pi_nh_angle_cutoff)
safe_set("pi_oh_distance", params.pi_oh_distance_cutoff)
safe_set("pi_oh_angle", params.pi_oh_angle_cutoff)
safe_set("pi_sh_distance", params.pi_sh_distance_cutoff)
safe_set("pi_sh_angle", params.pi_sh_angle_cutoff)
# New interaction parameters
safe_set("pi_pi_distance", params.pi_pi_distance_cutoff)
safe_set("pi_pi_parallel_angle", params.pi_pi_parallel_angle_cutoff)
safe_set("pi_pi_tshaped_angle_min", params.pi_pi_tshaped_angle_min)
safe_set("pi_pi_tshaped_angle_max", params.pi_pi_tshaped_angle_max)
safe_set("pi_pi_offset", params.pi_pi_offset_cutoff)
safe_set("carbonyl_distance", params.carbonyl_distance_cutoff)
safe_set("carbonyl_angle_min", params.carbonyl_angle_min)
safe_set("carbonyl_angle_max", params.carbonyl_angle_max)
safe_set("n_pi_distance", params.n_pi_distance_cutoff)
safe_set("n_pi_sulfur_distance", params.n_pi_sulfur_distance_cutoff)
safe_set("n_pi_angle_min", params.n_pi_angle_min)
safe_set("n_pi_angle_max", params.n_pi_angle_max)
safe_set("covalent_factor", params.covalent_cutoff_factor)
safe_set("analysis_mode", params.analysis_mode)
def _set_defaults(self):
"""Reset all parameters to default values."""
default_params = AnalysisParameters()
self.set_parameters(default_params)
[docs]
def reset_to_defaults(self) -> None:
"""Public method to reset parameters to defaults."""
self._set_defaults()
def _open_preset_manager(self):
"""Open the preset manager dialog."""
from .preset_manager_dialog import PresetManagerDialog
# Get current parameters
current_params = self.get_parameters()
# Open preset manager
dialog = PresetManagerDialog(self.dialog, current_params)
result = dialog.get_result()
if result:
# Apply the loaded preset
self._apply_preset_data(result)
messagebox.showinfo("Success", "Preset loaded successfully")
def _apply_preset_data(self, data: Dict[str, Any]) -> None:
"""Apply preset data to parameters."""
if "parameters" not in data:
raise ValueError("Invalid preset format: missing 'parameters' section")
params = data["parameters"]
# Apply hydrogen bond parameters
if "hydrogen_bonds" in params:
hb = params["hydrogen_bonds"]
self.hb_distance.set(
hb.get("h_a_distance_cutoff", ParametersDefault.HB_DISTANCE_CUTOFF)
)
self.hb_angle.set(
hb.get("dha_angle_cutoff", ParametersDefault.HB_ANGLE_CUTOFF)
)
self.da_distance.set(
hb.get("d_a_distance_cutoff", ParametersDefault.HB_DA_DISTANCE)
)
# Apply halogen bond parameters
if "halogen_bonds" in params:
xb = params["halogen_bonds"]
self.xb_distance.set(
xb.get("x_a_distance_cutoff", ParametersDefault.XB_DISTANCE_CUTOFF)
)
self.xb_angle.set(
xb.get("dxa_angle_cutoff", ParametersDefault.XB_ANGLE_CUTOFF)
)
# Apply π interaction parameters
if "pi_interactions" in params:
pi = params["pi_interactions"]
self.pi_distance.set(
pi.get("h_pi_distance_cutoff", ParametersDefault.PI_DISTANCE_CUTOFF)
)
self.pi_angle.set(
pi.get("dh_pi_angle_cutoff", ParametersDefault.PI_ANGLE_CUTOFF)
)
# Apply π interaction subtype parameters
self.pi_ccl_distance.set(
pi.get(
"ccl_pi_distance_cutoff", ParametersDefault.PI_CCL_DISTANCE_CUTOFF
)
)
self.pi_ccl_angle.set(
pi.get("ccl_pi_angle_cutoff", ParametersDefault.PI_CCL_ANGLE_CUTOFF)
)
self.pi_cbr_distance.set(
pi.get(
"cbr_pi_distance_cutoff", ParametersDefault.PI_CBR_DISTANCE_CUTOFF
)
)
self.pi_cbr_angle.set(
pi.get("cbr_pi_angle_cutoff", ParametersDefault.PI_CBR_ANGLE_CUTOFF)
)
self.pi_ci_distance.set(
pi.get("ci_pi_distance_cutoff", ParametersDefault.PI_CI_DISTANCE_CUTOFF)
)
self.pi_ci_angle.set(
pi.get("ci_pi_angle_cutoff", ParametersDefault.PI_CI_ANGLE_CUTOFF)
)
self.pi_ch_distance.set(
pi.get("ch_pi_distance_cutoff", ParametersDefault.PI_CH_DISTANCE_CUTOFF)
)
self.pi_ch_angle.set(
pi.get("ch_pi_angle_cutoff", ParametersDefault.PI_CH_ANGLE_CUTOFF)
)
self.pi_nh_distance.set(
pi.get("nh_pi_distance_cutoff", ParametersDefault.PI_NH_DISTANCE_CUTOFF)
)
self.pi_nh_angle.set(
pi.get("nh_pi_angle_cutoff", ParametersDefault.PI_NH_ANGLE_CUTOFF)
)
self.pi_oh_distance.set(
pi.get("oh_pi_distance_cutoff", ParametersDefault.PI_OH_DISTANCE_CUTOFF)
)
self.pi_oh_angle.set(
pi.get("oh_pi_angle_cutoff", ParametersDefault.PI_OH_ANGLE_CUTOFF)
)
self.pi_sh_distance.set(
pi.get("sh_pi_distance_cutoff", ParametersDefault.PI_SH_DISTANCE_CUTOFF)
)
self.pi_sh_angle.set(
pi.get("sh_pi_angle_cutoff", ParametersDefault.PI_SH_ANGLE_CUTOFF)
)
# Apply general parameters
if "general" in params:
gen = params["general"]
self.covalent_factor.set(
gen.get(
"covalent_cutoff_factor", ParametersDefault.COVALENT_CUTOFF_FACTOR
)
)
self.analysis_mode.set(
gen.get("analysis_mode", ParametersDefault.ANALYSIS_MODE)
)
def _ok(self):
"""Handle OK button - save settings and close."""
self.result = self.get_parameters()
self.dialog.destroy()
def _cancel(self):
"""Handle Cancel button - close without saving."""
self.result = None
self.dialog.destroy()
[docs]
def get_result(self) -> Optional[AnalysisParameters]:
"""Get the configured parameters.
:returns: Analysis parameters or None if cancelled
:rtype: Optional[AnalysisParameters]
"""
self.dialog.wait_window()
return self.result
