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Alex-AMCAlex-AMC
committedAug 20, 2024
Initial Commit of Surface Charge Script SCI-1315
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‎scripts/surface_charge/_surface_charge_calculator.py

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#
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# This script can be used for any purpose without limitation subject to the
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# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
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#
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# This permission notice and the following statement of attribution must be
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# included in all copies or substantial portions of this script.
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#
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# The following line states a licence feature that is required to show this script in Mercury and Hermes script menus.
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# Created 18/08/2024 by Alex Moldovan
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# ccdc-licence-features not-applicable
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import os
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import warnings
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from typing import List, Tuple
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import numpy as np
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from ccdc.io import CrystalReader
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from ccdc.particle import Surface
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from ccdc.utilities import HTMLReport
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class SurfaceCharge:
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def __init__(self, crystal, use_existing_charges: bool = False):
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if use_existing_charges:
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# if crystal.molecule.assign_partial_charges() is False:
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# warnings.warn(f"Gasteiger charges could not be assigned to molecule: {crystal.identifier}",
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# RuntimeWarning)
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raise NotImplementedError("Use existing charges instead. Current implementation only supports Gasteiger.")
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self.crystal = crystal
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self.surface = None
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self._surface_charge = None
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def calculate_surface_charge(self, hkl: Tuple[int, int, int], offset: float):
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self.surface = Surface(self.crystal, miller_indices=hkl, offset=offset)
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if self.surface.slab.assign_partial_charges():
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self._surface_charge = np.round(np.sum([atom.partial_charge for atom in self.surface.surface_atoms]), 3)
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return
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warnings.warn(f"Gasteiger charges could not be assigned to molecule: {self.crystal.identifier}",
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RuntimeWarning)
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self._surface_charge = np.nan
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@property
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def surface_charge(self):
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if self._surface_charge is None:
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raise ValueError("Surface charge calculation not yet calculated, run calculate_surface_charge()")
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return self._surface_charge
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@property
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def surface_charge_per_area(self):
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return self.surface_charge / self.surface.descriptors.projected_area
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class SurfaceChargeController:
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def __init__(self, structure: str, hkl_and_offsets: List[Tuple[int, int, int, float]],
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output_directory: str = None, use_existing_charges: bool = False):
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self.surface_charges_per_area = []
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self.surface_charges = []
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self.projected_area = []
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self.crystal = None
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if output_directory is None:
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output_directory = os.getcwd()
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self.output_directory = output_directory
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self.structure = structure
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self._surfaces = None
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self.get_structure()
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self.identifier = self.crystal.identifier
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self._surfaces = hkl_and_offsets
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self.use_existing_charges = use_existing_charges
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def get_structure(self):
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if "." not in self.structure:
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self.crystal = CrystalReader('CSD').crystal(self.structure)
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elif ".mol2" in self.structure:
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self.crystal = CrystalReader(self.structure)[0]
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else:
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raise IOError(" \n ERROR : Please supply ref code mol2")
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@property
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def surfaces(self):
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if self._surfaces:
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return self._surfaces
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def calculate_surface_charge(self):
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for surface in self.surfaces:
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charges = SurfaceCharge(crystal=self.crystal, use_existing_charges=self.use_existing_charges)
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charges.calculate_surface_charge(hkl=surface[:3], offset=surface[3])
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self.surface_charges.append(charges.surface_charge)
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self.projected_area.append(charges.surface.descriptors.projected_area)
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self.surface_charges_per_area.append(charges.surface_charge_per_area)
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def make_report(self):
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html_content = self.generate_html_table()
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output_file = os.path.join(self.output_directory, self.identifier + "_surface_charge.html")
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with HTMLReport(file_name=output_file,
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ccdc_header=True, append=False, embed_images=False,
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report_title=f'Surface Charge Calculations - {self.identifier}') as self.report:
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self.report.write(html_content)
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print(f"Results saved to {output_file}")
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def generate_html_table(self):
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# HTML Table Header
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html = """
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<html>
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<head>
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<title>Calculation Results</title>
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<style>
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table { width: 100%; border-collapse: collapse; }
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th, td { border: 1px solid black; padding: 8px; text-align: center; }
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th { background-color: #f2f2f2; }
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</style>
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</head>
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<body>
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<h2>Calculation Results</h2>
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<table>
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<tr>
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<th>hkl</th>
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<th>Offset</th>
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<th>Projected Area</th>
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<th>Surface Charge</th>
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<th>Surface Charge per Projected Area</th>
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</tr>
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"""
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# HTML Table Rows
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for i, (h, k, l, offset) in enumerate(self.surfaces):
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hkl = "{" + f"{h}, {k}, {l}" + "}"
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html += f"""
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<tr>
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<td>{hkl}</td>
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<td>{offset:.2f}</td>
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<td>{self.projected_area[i]:.3f}</td>
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<td>{self.surface_charges[i]:.3f}</td>
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<td>{self.surface_charges_per_area[i]:.4f}</td>
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</tr>
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"""
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# HTML Table Footer
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html += """
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</table>
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</body>
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</html>
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"""
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return html

‎scripts/surface_charge/surface_charge.py

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#
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# This script can be used for any purpose without limitation subject to the
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# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
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#
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# This permission notice and the following statement of attribution must be
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# included in all copies or substantial portions of this script.
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#
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# The following line states a licence feature that is required to show this script in Mercury and Hermes script menus.
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# Created 18/08/2024 by Alex Moldovan (https://orcid.org/0000-0003-2776-3879)
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import os
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import sys
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import tkinter as tk
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from tkinter import ttk, messagebox, filedialog
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from ccdc.utilities import ApplicationInterface
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from _surface_charge_calculator import SurfaceChargeController
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class SurfaceChargeGUI:
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def __init__(self, initial_file_path=None):
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self.root = tk.Tk()
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self.root.title("Surface Charge Calculator")
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try:
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photo = tk.PhotoImage(file=os.path.join(os.path.dirname(__file__), 'assets/csd-python-api-logo.png'))
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self.root.wm_iconphoto(False, photo)
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except FileNotFoundError:
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print("Could not find icon file for app.")
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except Exception as e:
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print("Unable to load icon")
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print(e) # This doesn't seem to work with X11 port forwarding 🤷‍♀️
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# Disable window resizing
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self.root.resizable(False, False)
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self.initial_file_path = initial_file_path
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self.create_string_file_inputs()
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self.create_input_fields()
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self.create_buttons()
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self.create_treeview()
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self.create_directory_selection()
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self.configure_grid() # Ensure grid configuration
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if self.initial_file_path:
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self.handle_initial_file_path(self.initial_file_path)
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def handle_initial_file_path(self, file_path):
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"""Handles the initial file path by disabling the input fields and setting the file path."""
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self.file_var.set(file_path) # Set the provided file path
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self.string_var.set("") # Clear the string input
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# Disable the input fields
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self.string_entry.config(state='disabled')
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self.file_entry.config(state='readonly')
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self.browse_button.config(state='disabled')
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def configure_grid(self):
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self.root.grid_rowconfigure(8, weight=1)
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self.root.grid_rowconfigure(9, weight=0)
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self.root.grid_rowconfigure(10, weight=0)
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self.root.grid_columnconfigure(0, weight=1)
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self.root.grid_columnconfigure(1, weight=1)
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self.root.grid_columnconfigure(2, weight=1)
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self.root.grid_columnconfigure(3, weight=1)
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self.root.grid_columnconfigure(4, weight=1)
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self.root.grid_columnconfigure(5, weight=1)
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self.root.grid_columnconfigure(6, weight=1)
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self.root.grid_columnconfigure(7, weight=1)
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def create_string_file_inputs(self):
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tk.Label(self.root, text="Structure").grid(row=0, column=0, columnspan=2, sticky='w')
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tk.Label(self.root, text="Refcode:").grid(row=1, column=0, padx=5, pady=5, sticky='e')
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self.string_var = tk.StringVar()
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self.string_entry = tk.Entry(self.root, textvariable=self.string_var, validate="key",
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validatecommand=(self.root.register(self.on_string_input), "%P"))
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self.string_entry.grid(row=1, column=1, padx=5, pady=5, columnspan=2, sticky='ew')
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tk.Label(self.root, text="Select File:").grid(row=2, column=0, padx=5, pady=5, sticky='e')
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self.file_var = tk.StringVar()
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self.file_entry = tk.Entry(self.root, textvariable=self.file_var, state='readonly')
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self.file_entry.grid(row=2, column=1, padx=5, pady=5, columnspan=2, sticky='ew')
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self.browse_button = tk.Button(self.root, text="Browse", command=self.browse_file)
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self.browse_button.grid(row=2, column=3, padx=5, pady=5, sticky='ew')
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def on_string_input(self, input_value):
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if input_value.strip():
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self.browse_button.config(state='disabled')
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else:
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self.browse_button.config(state='normal')
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return True
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def create_input_fields(self):
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tk.Label(self.root, text="Select hkl and offset").grid(row=3, column=0, columnspan=2, sticky='w')
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input_frame = tk.Frame(self.root)
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input_frame.grid(row=4, column=0, columnspan=8, padx=5, pady=5, sticky='ew')
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input_frame.grid_columnconfigure(0, weight=1)
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input_frame.grid_columnconfigure(1, weight=1)
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input_frame.grid_columnconfigure(2, weight=1)
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input_frame.grid_columnconfigure(3, weight=1)
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input_frame.grid_columnconfigure(4, weight=1)
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input_frame.grid_columnconfigure(5, weight=1)
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input_frame.grid_columnconfigure(6, weight=1)
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input_frame.grid_columnconfigure(7, weight=1)
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tk.Label(input_frame, text="h:").grid(row=0, column=0, padx=2, pady=5, sticky='e')
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tk.Label(input_frame, text="k:").grid(row=0, column=2, padx=2, pady=5, sticky='e')
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tk.Label(input_frame, text="l:").grid(row=0, column=4, padx=2, pady=5, sticky='e')
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tk.Label(input_frame, text="offset:").grid(row=0, column=6, padx=2, pady=5, sticky='e')
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self.h_var = tk.IntVar()
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self.spin_h = tk.Spinbox(input_frame, from_=-9, to=9, width=2, textvariable=self.h_var)
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self.spin_h.grid(row=0, column=1, padx=2, pady=5, sticky='ew')
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self.k_var = tk.IntVar()
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self.spin_k = tk.Spinbox(input_frame, from_=-9, to=9, width=2, textvariable=self.k_var)
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self.spin_k.grid(row=0, column=3, padx=2, pady=5, sticky='ew')
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self.l_var = tk.IntVar()
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self.spin_z = tk.Spinbox(input_frame, from_=-9, to=9, width=2, textvariable=self.l_var)
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self.spin_z.grid(row=0, column=5, padx=2, pady=5, sticky='ew')
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self.offset_var = tk.DoubleVar()
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self.entry_offset = tk.Entry(input_frame, width=10, textvariable=self.offset_var)
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self.entry_offset.grid(row=0, column=7, padx=2, pady=5, sticky='ew')
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def create_buttons(self):
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self.add_button = tk.Button(self.root, text="Add Surface", command=self.add_combination)
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self.add_button.grid(row=5, column=0, columnspan=2, pady=10, sticky='ew')
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self.delete_button = tk.Button(self.root, text="Delete Selected", command=self.delete_combination)
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self.delete_button.grid(row=5, column=2, pady=5, sticky='ew')
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self.reset_button = tk.Button(self.root, text="Reset Fields", command=self.reset_fields)
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self.reset_button.grid(row=5, column=3, pady=5, sticky='ew')
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self.create_directory_selection()
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def create_directory_selection(self):
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tk.Label(self.root, text="Output Directory:").grid(row=9, column=0, padx=5, pady=5, sticky='e')
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self.dir_var = tk.StringVar(value=os.getcwd()) # Default to current working directory
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self.dir_entry = tk.Entry(self.root, textvariable=self.dir_var, state='readonly', width=50)
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self.dir_entry.grid(row=9, column=1, padx=5, pady=5, columnspan=3, sticky='ew')
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self.browse_dir_button = tk.Button(self.root, text="Browse", command=self.select_directory)
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self.browse_dir_button.grid(row=9, column=4, padx=5, pady=5, sticky='ew')
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self.calculate_button = tk.Button(self.root, text="Calculate", command=self.calculate)
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self.calculate_button.grid(row=10, column=0, columnspan=5, pady=10, sticky='ew')
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def select_directory(self):
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selected_dir = filedialog.askdirectory(initialdir=self.dir_var.get(), title="Select Output Directory")
157+
if selected_dir:
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self.dir_var.set(selected_dir)
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def create_treeview(self):
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tk.Label(self.root, text="Current Selections").grid(row=7, column=0, padx=5, pady=5, columnspan=8,
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sticky='w')
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self.combination_tree = ttk.Treeview(self.root, columns=("h", "k", "l", "Offset"), show='headings')
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self.combination_tree.grid(row=8, column=0, columnspan=8, padx=10, pady=10, sticky='nsew')
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self.combination_tree.heading("h", text="h")
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self.combination_tree.heading("k", text="k")
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self.combination_tree.heading("l", text="l")
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self.combination_tree.heading("Offset", text="Offset")
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self.combination_tree.column("h", width=50, anchor=tk.CENTER)
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self.combination_tree.column("k", width=50, anchor=tk.CENTER)
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self.combination_tree.column("l", width=50, anchor=tk.CENTER)
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self.combination_tree.column("Offset", width=100, anchor=tk.CENTER)
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def browse_file(self):
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file_path = filedialog.askopenfilename(filetypes=[("mol2 files", "*.mol2")])
179+
if file_path:
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self.file_var.set(file_path)
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def add_combination(self):
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try:
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h = self.h_var.get()
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k = self.k_var.get()
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l = self.l_var.get()
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if (h, k, l) == (0, 0, 0):
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messagebox.showerror("Invalid input", "Please enter valid integers for h, k, l and a float for offset.")
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return
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offset = self.offset_var.get()
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combination = (h, k, l, offset)
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if not self.is_duplicate(combination):
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self.combination_tree.insert('', tk.END, values=combination)
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else:
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messagebox.showwarning("Duplicate Entry", "This hkl and offset already exists.")
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except tk.TclError:
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messagebox.showerror("Invalid input", "Please enter valid integers for h, k, l and a float for offset.")
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def is_duplicate(self, combination):
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combination_converted = tuple((str(i) for i in combination))
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for row_id in self.combination_tree.get_children():
202+
row_values = self.combination_tree.item(row_id, 'values')
203+
if tuple(row_values) == combination_converted:
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return True
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return False
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def delete_combination(self):
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selected_item = self.combination_tree.selection()
209+
if selected_item:
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self.combination_tree.delete(selected_item)
211+
else:
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messagebox.showwarning("No selection", "Please select a surface to delete.")
213+
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def reset_fields(self):
215+
self.h_var.set(0)
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self.k_var.set(0)
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self.l_var.set(0)
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self.offset_var.set(0.0)
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self.string_var.set("")
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self.file_var.set("")
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self.browse_button.config(state='normal')
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def calculate(self):
224+
string_input = self.string_var.get().strip()
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file_input = self.file_var.get().strip()
226+
if not (string_input or file_input):
227+
tk.messagebox.showerror("Input Error", "Please provide a refcode or select a file.")
228+
return
229+
230+
if not self.combination_tree.get_children():
231+
tk.messagebox.showerror("Selection Error", "There must be at least one surface in the list.")
232+
return
233+
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items = self.combination_tree.get_children()
235+
data = []
236+
for item in items:
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values = self.combination_tree.item(item, 'values')
238+
try:
239+
h = int(values[0])
240+
k = int(values[1])
241+
l = int(values[2])
242+
offset = float(values[3])
243+
data.append((h, k, l, offset))
244+
except ValueError as e:
245+
print(f"Error converting data: {e}")
246+
continue
247+
if string_input:
248+
input_string = string_input # Use string input if available
249+
elif file_input:
250+
input_string = file_input
251+
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output_dir = self.dir_var.get()
253+
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surface_charge_controller = SurfaceChargeController(structure=input_string, output_directory=output_dir,
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hkl_and_offsets=data)
256+
surface_charge_controller.calculate_surface_charge()
257+
surface_charge_controller.make_report()
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self.root.destroy()
259+
260+
261+
if __name__ == "__main__":
262+
if len(sys.argv) > 3 and sys.argv[3].endswith(".m2a"):
263+
mercury = ApplicationInterface()
264+
run_from_mercury = True
265+
input_structure = mercury.input_mol2_file
266+
app = SurfaceChargeGUI(initial_file_path=input_structure)
267+
app.root.mainloop()
268+
else:
269+
app = SurfaceChargeGUI()
270+
app.root.mainloop()

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