added species.csv preproccessor to the cli

src/mechanalyzer/cli.py

@@ -4,6 +4,8 @@
 from .tools import compare_rates as compare_rates_
 from .tools import compare_thermo as compare_thermo_
 from .tools import pes_diagram_from_mess as pes_diagram_from_mess_
+from .tools import species_processer as species_processor_
+
 
 @click.group()
 def main():
@@ -576,3 +578,93 @@ def pes_diagram(
         labels,
         remove_fake,
         shift_energy)
+
+# preprocess-species
+@main.command()
+@click.option(
+    "-i",
+    "--input",
+    default="species.csv",
+    show_default=True,
+    help="Input species file name",
+)
+@click.option(
+    "-o",
+    "--output",
+    default="mod_species.csv",
+    show_default=True,
+    help="Output species file name",
+)
+@click.option(
+    "-s",
+    "--stereo",
+    default=False,
+    show_default=True,
+    help="add a stereochemical label to species inchis",
+)
+@click.option(
+    "-a",
+    "--amchi",
+    default=False,
+    show_default=True,
+    help="turn bad inchis into amchis",
+)
+@click.option(
+    "-c",
+    "--canonical",
+    default=False,
+    show_default=True,
+    help="add canonical enantiomer inchi to rows",
+)
+@click.option(
+    "-b",
+    "--hof-basis",
+    default=False,
+    show_default=True,
+    help="add cbh0, cbh1, and cbh2 heat-of-formation basis species",
+)
+@click.option(
+    "-u",
+    "--instability",
+    default=False,
+    show_default=True,
+    help="add instability product species",
+)
+@click.option(
+    "-g",
+    "--sort",
+    default=False,
+    show_default=True,
+    help="sort the mechanism by atom counts",
+)
+@click.option(
+    "-n",
+    "--ncpus",
+    default=1,
+    show_default=True,
+    help="number of cpus to use for tasks",
+)
+def preprocess_species(
+    input: str ="species.csv",
+    output: str = "mod_species.csv",
+    sort: bool = False,
+    stereo:  bool = False,
+    canonical: bool = False,
+    amchi: bool = False,
+    hof_basis: bool = False,
+    instability: bool = False,
+    ncpus: int = 1,
+):
+    """Preprocess species file by optionally adding stereochemical labels, 
+    canonical enantiomers inchis, amchis, heat-of-formation basis species,
+    instability products, and sorting."""
+    species_processor_.main(
+        input_fname=input,
+        output_fname=output,
+        sort=sort,
+        include_stereo=stereo,
+        include_canonical=canonical,
+        use_amchi=amchi,
+        expand_hof_basis=hof_basis,
+        expand_instability=instability,
+        ncpus=ncpus)

src/mechanalyzer/parser/new_spc.py

@@ -155,10 +155,10 @@ def parse_mech_spc_dct(file_str, quotechar="'", chk_ste=False,
         if idx == 0:
             headers = parse_first_line(line, quotechar=quotechar)
             if canon_ent and 'canon_enant_ich' not in headers:
-                print("Warning: user selected the 'canon_ent' option, but the"
-                      " field 'canon_enant_ich' is not in the CSV file.\n"
-                      "The canonical enantiomer will have to be calculated "
-                      "for every species, which might be slow.")
+                print("Determining canonical enantiomer for enantiomeric species,"
+                      "to prevent redundant computations. We recommend avoiding this"
+                      "slow-down by preprocessing the mechanism with\n"
+                      ">>> mechanalyzer preprocess-species -i species.csv -c True")
         else:
             cols = parse_line(line, idx, headers, quotechar=quotechar)
             if cols is not None:

src/mechanalyzer/tools/species_processer.py

@@ -0,0 +1,95 @@
+""" Modifies the species.csv file in ways:
+    Transform existing rows:
+    (0) adds inchis if only SMILES are present
+    (1) (optional)adds canonical enantiomer inchis to the species in the file csv
+        (the canonical enantiomer is which enantiomer will be used for calculations to
+        avoid reduandant calculations)
+    (2) (optional) adds stereochemistry to species in the file csv (chooses one enantiomer/diastereomer)
+        (see ste_mech script for expansion of all stereochemistry)
+    (3) (optional) sorts the species in the csv file by stoichiometries
+    (4) (optional) turns inchis into amchis that cannot be described by inchis (e.g., resonance)
+    Add new rows:
+    (5) (optional) adds required heat-of-formation basis species not present in csv file
+    (6) (optional) adds instability product species to the file csv
+"""
+
+import os
+import time
+from ioformat import pathtools
+from mechanalyzer import parser
+
+
+def main(
+        input_fname: str='species.csv',
+        output_fname: str='mod_species.csv',
+        sort: bool=False,
+        include_stereo: bool=False,
+        include_canonical: bool=False,
+        use_amchi: bool=False,
+        expand_hof_basis: bool=False,
+        expand_instability: bool=False,
+        ncpus: int=1,
+        ):
+    # Initialize the start time for script execution
+    t0 = time.time()
+    cwd = os.getcwd()
+
+    # Read input species file into a species dictionary and add
+    # necessary information like inchis if only smiles are present
+    # and useful information like inchikey
+    print(f'Reading species from {input_fname}...')
+    spc_str = pathtools.read_file(cwd, input_fname)
+    mech_spc_dct = parser.new_spc.parse_mech_spc_dct(spc_str)
+    new_mech_headers = ('smiles', 'inchi', 'inchikey', 'mult', 'charge')
+
+    # Add species that unstable will directly decompose into
+    if expand_instability:
+        print('Adding instability products to species dictionary...')
+        mech_spc_dct = parser.spc.add_instability_products(
+            mech_spc_dct, nprocs=ncpus, stereo=True)
+
+    # Convert inchis to amchis for species that cannot be represented by inchis
+    if use_amchi:
+        print('Converting InChIs to AMChIs where necessary...')
+        mech_spc_dct = parser.new_spc.mech_inchi_to_amchi(mech_spc_dct)
+
+    # Add a stereochemical label to any stereochemical species
+    if include_stereo:
+        print('Adding stereochemical information to species dictionary...')
+        mech_spc_dct = parser.spc.stereochemical_spc_dct(
+            mech_spc_dct, nprocs=ncpus, all_stereo=False)
+
+    # Sort the species dictionary, if requested
+    if sort:
+        print('Sorting species dictionary by atom count...')
+        mech_spc_dct = parser.spc.reorder_by_atomcount(
+            mech_spc_dct)
+
+    if include_canonical:
+        print('Adding canonical enantiomer InChIs to species dictionary...')
+        mech_spc_dct = parser.new_spc.add_canonical_enantiomer(
+            mech_spc_dct)
+        new_mech_headers += ('canon_enant_ich',)
+
+    # Add the thermochemical species to the species dictionary
+    if expand_hof_basis:
+        print('Adding heat-of-formation basis species to species dictionary...')
+        if not include_canonical:
+            mech_spc_dct = parser.new_spc.add_canonical_enantiomer(
+                mech_spc_dct, dummy=True)
+        # mech_spc_dct = parser.spc.add_heat_of_formation_basis(
+        #    mech_spc_dct, ref_schemes=('cbh0', 'cbh1'),
+        mech_spc_dct = parser.spc.add_heat_of_formation_basis(
+            mech_spc_dct, ref_schemes=('cbh0', 'cbh1', 'cbh2'),
+            nprocs=ncpus)
+
+    # Write the new species dictionary to a string
+    csv_str = parser.spc.csv_string(mech_spc_dct, new_mech_headers)
+
+    # Write the string to a file
+    pathtools.write_file(csv_str, cwd, output_fname)
+
+    # Compute script run time and print to screen
+    tf = time.time()
+    print(f'\nSuccess: {input_fname} has been processed an updated in {output_fname}.')
+    print(f'Time to complete: {tf-t0:.2f}')