Implement Command Line Interface (CLI)

[JanCBrammer]

No description provided.

[schatzsc]

Small GUI for stand-alone and web application for demonstration purpose would also be nice but not essential as long as we do not aim (yet) at a general and non-export audience

[schatzsc]

Here a short CLI which uses several different options for conversion of molfile into TUCAN string and vice versa, also allows control of implicit-to-explicit H conversion and graphical output via gravis https://robert-haas.github.io/gravis-docs/

Needs the following libraries:

import argparse
import sys
from pathlib import Path

Program initialization and command line interpretation

def get_command_line_parameters():
EXIT_SUCCESS = 0
EXIT_FAILURE = 1
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--file', help='input file: either v3000 molfile *.mol or textfile containing TUCAN string *.tcn', type=argparse.FileType('r'))
parser.add_argument('-m2m', '--molfile2molfile', help='Convert molfile to canonical molfile', action ='store_true')
parser.add_argument('-m2t', '--molfile2tucan', help='Convert molfile to canonical TUCAN string', action ='store_true')
parser.add_argument('-t2m', '--tucan2molfile', help='Convert TUCAN string to canonical molefile', action ='store_true')
parser.add_argument('-t2t', '--tucan2tucan', help='Convert TUCAN string to canonical TUCAN string', action ='store_true')
parser.add_argument('-i', '--i2e', help='Use implicit-to-explicit hydrogen conversion pre-processor', action ='store_true')
parser.add_argument('-g', '--plot_graph', help='Plot graph', action ='store_true')
args = parser.parse_args()
if not args.file:
print("\nno input file specified\n")
parser.print_usage()
sys.exit(EXIT_FAILURE)
path_to_file = Path().absolute()
filename = args.file.name
filepath = path_to_file/filename
conversion_direction = "m2t" # standard conversion mode
if args.molfile2molfile:
conversion_direction = "m2m"
if args.molfile2tucan:
conversion_direction = "m2t"
if args.tucan2molfile:
conversion_direction = "t2m"
if args.tucan2tucan:
conversion_direction = "t2t"
if args.i2e:
implicit_to_explicit_H = True
else:
implicit_to_explicit_H = False
if not args.plot_graph:
plotgraph = False
else:
plotgraph = True
return filepath, conversion_direction, implicit_to_explicit_H, plotgraph

Main program loop

filepath, conversion_direction, implicit_to_explicit_H, plot_graph = get_command_line_parameters()
print("\n"+'=' * 100)
print("\nTUCAN - A molecular identifier and descriptor for all domains of chemistry "+version)
print("\nJan Brammer (RWTH Aachen) and Ulrich Schatzschneider (Universität Würzburg) within NFDI4Chem")
print("\nCC BY-SA 06/2022\n")
print('=' * 100)
print("Processing file:", filepath)
print("Conversion mode:", conversion_mode[conversion_direction])
print('-' * 100)
if((conversion_direction == "m2m") and (filepath.suffix == ".mol")):
graph = graph_from_molfile(filepath, conversion_direction)
if(implicit_to_explicit_H == True):
graph = implicit_to_explicit_hydrogen_preprocessor(graph)
cgraph = canonicalize_molecule(graph, 0)
print(create_molfile(cgraph))
elif((conversion_direction == "m2t") and (filepath.suffix == ".mol")):
graph = graph_from_molfile(filepath, conversion_direction)
if(implicit_to_explicit_H == True):
graph = implicit_to_explicit_hydrogen_preprocessor(graph)
cgraph = canonicalize_molecule(graph, 0)
print(serialize_molecule(cgraph))
elif((conversion_direction == "t2m") and (filepath.suffix == ".tcn")):
graph = graph_from_tucan_string(filepath, conversion_direction)
cgraph = canonicalize_molecule(graph, 0)
print(create_molfile(cgraph))
elif((conversion_direction == "t2t") and (filepath.suffix == ".tcn")):
graph = graph_from_tucan_string(filepath, conversion_direction)
cgraph = canonicalize_molecule(graph, 0)
print(serialize_molecule(cgraph))
else:
raise IOError("Invalid combination of file format and program option")
print('-' * 100)
print_molecule_statistics(cgraph)
print('-' * 100)
if(plot_graph == True):
plot_graph_with_gravis(cgraph)

This is the end