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Improvements to the way failures are handled and state saving #44

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Merged
merged 3 commits into from
Oct 4, 2023
Merged

Improvements to the way failures are handled and state saving #44

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116f36c
Added a file to note every failure that happened during the running o…
MilitaoLucas Oct 2, 2023
d3359eb
Fixed Failures and added a json with the mc_scores for it to be able …
MilitaoLucas Oct 2, 2023
0ec9d26
Added --failure_directory argument
MilitaoLucas Oct 3, 2023
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40 changes: 27 additions & 13 deletions ...lti_component_hydrogen_bond_propensity/multi_component_hydrogen_bond_propensity_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import argparse
import tempfile
import subprocess
import json

import matplotlib

Expand Down Expand Up @@ -313,7 +314,7 @@ def make_mc_report(identifier, results, directory, diagram_file, chart_file):
launch_word_processor(output_file)


def main(structure, work_directory, library, csdrefcode):
def main(structure, work_directory, failure_directory, library, csdrefcode):
# This loads up the CSD if a refcode is requested, otherwise loads the structural file supplied
if csdrefcode:
try:
Expand All @@ -334,6 +335,7 @@ def main(structure, work_directory, library, csdrefcode):
coformer_files = glob.glob(os.path.join(library, '*.mol2'))
tempdir = tempfile.mkdtemp()
mc_dictionary = {}
failures = []

# for each coformer in the library, make a pair file for the api/coformer and run a HBP calculation
for i, f in enumerate(coformer_files):
Expand All @@ -343,22 +345,33 @@ def main(structure, work_directory, library, csdrefcode):
crystal = crystal_reader[0]

directory = os.path.join(os.path.abspath(work_directory), crystal.identifier)

try:
propensities, donors, acceptors = propensity_calc(crystal, directory)
coordination_scores = coordination_scores_calc(crystal, directory)
pair_output(crystal.identifier, propensities, donors, acceptors, coordination_scores, directory)
mc_dictionary[coformer_name] = get_mc_scores(propensities, crystal.identifier)

except RuntimeError:
print("Propensity calculation failure for %s!" % coformer_name)
mc_dictionary[coformer_name] = ["N/A", "N/A", "N/A", "N/A", "N/A", crystal.identifier]
if os.path.exists(os.path.join(directory, "success.json")):
with open(os.path.join(directory, "success.json"), "r") as file:
tloaded = json.load(file)
mc_dictionary[coformer_name] = tloaded
else:
try:
propensities, donors, acceptors = propensity_calc(crystal, directory)
coordination_scores = coordination_scores_calc(crystal, directory)
pair_output(crystal.identifier, propensities, donors, acceptors, coordination_scores, directory)
with open(os.path.join(directory, "success.json"), "w") as file:
tdata = get_mc_scores(propensities, crystal.identifier)
json.dump(tdata, file)
mc_dictionary[coformer_name] = get_mc_scores(propensities, crystal.identifier)
print(get_mc_scores(propensities, crystal.identifier))
except RuntimeError:
print("Propensity calculation failure for %s!" % coformer_name)
mc_dictionary[coformer_name] = ["N/A", "N/A", "N/A", "N/A", "N/A", crystal.identifier]
failures.append(coformer_name)

# Make sense of the outputs of all the calculations
mc_hbp_screen = sorted(mc_dictionary.items(), key=lambda e: 0 if e[1][0] == 'N/A' else e[1][0], reverse=True)
diagram_file = make_diagram(api_molecule, work_directory)
chart_file = make_mc_chart(mc_hbp_screen, directory, api_molecule)
make_mc_report(structure, mc_hbp_screen, work_directory, diagram_file, chart_file)
if failure_directory is not None:
with open(os.path.join(failure_directory, 'failures.txt'), 'w', encoding='utf-8', newline='') as file:
file.write('\n'.join(map(str, failures)))


if __name__ == '__main__':
Expand Down Expand Up @@ -396,9 +409,10 @@ def main(structure, work_directory, library, csdrefcode):
parser.add_argument('-c', '--coformer_library', type=str,
help='the directory of the desired coformer library',
default=ccdc_coformers_dir)
parser.add_argument('-f', '--failure_directory', type=str,
help='The location where the failures file should be generated')

args = parser.parse_args()

refcode = False

if not os.path.isfile(args.input_structure):
Expand All @@ -413,4 +427,4 @@ def main(structure, work_directory, library, csdrefcode):
if not os.path.isdir(args.coformer_library):
parser.error('%s - library not found.' % args.coformer_library)

main(args.input_structure, args.directory, args.coformer_library, refcode)
main(args.input_structure, args.directory, args.failure_directory, args.coformer_library, refcode)