Source code for octadist.octadist_cli

# OctaDist  Copyright (C) 2019  Rangsiman Ketkaew et al.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

import argparse
import os
import sys

import octadist
from .octadist_gui import run_gui
from octadist.src.io import is_xyz, get_coord_xyz, extract_octa


[docs]def check_file(file): """ Check if input file is exist or not. Parameters ---------- file : str Input file name. Returns ------- file : str Input file name. """ exist = os.path.isfile(file) if exist: return file else: print(f"File not found: {file}") sys.exit(1)
[docs]def find_coord(file): """ Find atomic symbols and atomic coordinates of structure. Parameters ---------- file : str Input file name. Returns ------- atom : list Atomic symbols. coord : list Atomic coordinates. """ if file.endswith(".xyz"): if is_xyz(file): atom, coord = get_coord_xyz(file) else: print(f"File type of input file is not supported: {file}") sys.exit(1) else: print(f"File type of input file is not supported: {file}") sys.exit(1) atom = list(filter(None, atom)) return atom, coord
[docs]def calc_param(coord): """ Calculate octahedral distortion parameters. Parameters ---------- coord : array_like Atomic coordinates of octahedral structure. Returns ------- computed : dict Computed parameters: zeta, delta, sigma, theta. """ dist = octadist.CalcDistortion(coord) computed = {"zeta": dist.zeta, "delta": dist.delta, "sigma": dist.sigma, "theta": dist.theta} return computed
[docs]def run_cli(): """ OctaDist command-line interface (CLI). This function has been implemented by entry points function in setuptools package. """ description = """\ Octahedral Distortion Calculator: A tool for computing octahedral distortion parameters in coordination complex. For more details, please visit https://octadist.github.io. """ epilog = f"Rangsiman Ketkaew\tUpdated on {octadist.__release__}\tE-mail: {octadist.__email__}" parser = argparse.ArgumentParser( prog="octadist_cli", description=description, formatter_class=argparse.RawDescriptionHelpFormatter, epilog=epilog, ) # input/output parser.add_argument( "-i", "--inp", action="store", type=str, metavar="INPUT", help="Input structure in .xyz format", ) parser.add_argument("-f", "--format", action="store_true", help="Show formatted output summary") # octahedron parameters parser.add_argument( "-r", "--ref-index", type=int, metavar="REF_CENTER_ATOM", dest="ref_index", default=0, help="Index of the reference center atom. Default to 0", ) parser.add_argument( "-c", "--cutoff", type=float, metavar="CUTOFF_DIST", dest="cutoff", default=2.8, help="Cutoff distance (in Angstroms) for determining octahedron. Default to 2.8", ) parser.add_argument( "-s", "--save", action="store", type=str, metavar="OUTPUT", help="Save formatted output to text file, " "please specify name of OUTPUT file without '.txt' extension", ) parser.add_argument( "-p", "--par", type=str, nargs="+", choices=["zeta", "delta", "sigma", "theta"], metavar="PARAMETER", help="Select which the parameter (zeta, delta, sigma, theta) to show", ) parser.add_argument( "--show", type=str, nargs="+", choices=["atom", "coord"], metavar="MOL", help="Show atomic symbol (atom) and atomic coordinate (coord) of octahedral structure", ) parser.add_argument( "-g", "--gui", action="store_true", help="launch OctaDist GUI (this option is the same as 'octadist' command", ) parser.add_argument("-a", "--about", action="store_true", help="Show program info") parser.add_argument("-v", "--version", action="version", version=octadist.__version__) args = parser.parse_args() if len(sys.argv) == 1: parser.print_help() sys.exit(1) if args.about: print("\nOctaDist Program info") print("=====================") print(f"- Name\t\t=\t{octadist.__title__}") print(f"- Author\t=\t{octadist.__author__}") print(f"- Version\t=\t{octadist.__version__}") print(f"- Revision\t=\t{octadist.__revision__}") print(f"- Release\t=\t{octadist.__release__}") print(f"- Description\t=\t{octadist.__description__}") print(f"- E-mail\t=\t{octadist.__email__}") print(f"- Document\t=\t{octadist.__doc__}") print(f"- Website\t=\t{octadist.__website__}") print(f"- Reference\t=\t{octadist.__ref__}. " + f"{octadist.__doi__}") sys.exit(1) # in case GUI is requested if args.gui: run_gui() sys.exit(1) atom_coord = {} computed = {} if not args.inp: print("No input file specified") sys.exit(1) # check if file is correct file = check_file(args.inp) atom, coord = find_coord(file) atom, coord = extract_octa(atom, coord, args.ref_index, args.cutoff) if len(atom) < 7: print( "Extracted octahedron is incomplete. Please adjust cutoff distance, e.g., increase the value, to fix the issue." ) sys.exit(1) atom_coord = {"atom": atom, "coord": coord} computed = calc_param(coord) # get only basename of file from path basename = os.path.basename(args.inp) # print unformatted output if not args.format: for v in computed.values(): print(f"{v:12.8f}") # print formatted output else: for k, v in computed.items(): print(f"{k}\t=\t{v:12.8f}") # print atom and coord if args.show: for key in args.show: print(atom_coord[key]) # save result if args.save: with open(args.save + ".txt", "w") as f: f.write("Octahedral distortion parameters\n") f.write("--------------------------------\n") f.write(f"File: {basename}\n") for k, v in computed.items(): f.write(f"{k}\t=\t{v:12.8f}\n") f.write(f"\nComputed by OctaDist {octadist.__version__}\n") f.close() print(f"\nOutput file has been saved to {os.path.realpath(f.name)}")
if __name__ == "__main__": run_cli()