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feat(18): adopt the shared CLI helpers in screen.py #25

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Merged
tdudgeon merged 1 commit into from
Aug 11, 2026
Merged

feat(18): adopt the shared CLI helpers in screen.py #25

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25 changes: 10 additions & 15 deletions screen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
import traceback

import utils, rdkit_utils
from dm_job_utilities.cli import add_reporting_args
from dm_job_utilities.dm_log import DmLog

from rdkit import Chem
Expand Down Expand Up @@ -272,29 +273,24 @@ def main():

# Examples:
# python screen.py --smiles 'O=C(Nc1ccc(Cl)cc1)c1ccccn1' --input data/10000.smi --delimiter tab -o foo.smi\
# -d rdkit -m tanimoto
# --descriptor rdkit -m tanimoto
# python screen.py --queries-file data/10.smi --input data/10000.smi --delimiter tab --id-column 1 -o foo.smi \
# -d rdkit -m tanimoto --queries-delimiter tab --threshold 0.4
# --descriptor rdkit -m tanimoto --queries-delimiter tab --threshold 0.4

parser = argparse.ArgumentParser(description='screen')
rdkit_utils.add_common_molecule_io_args(parser, output_required=True)
add_reporting_args(parser)
# this Job has always defaulted to tab, and its manifest passes
# --delimiter only when the user sets it
parser.set_defaults(delimiter='\t')
inputs = parser.add_mutually_exclusive_group(required=True)
inputs.add_argument('-s', '--smiles', nargs='+', help="Query SMILES")
inputs.add_argument('--queries-file', help="File with query molecules")
parser.add_argument('--queries-delimiter', help="Delimiter for queries file (text format)")
parser.add_argument('--queries-read-header', action='store_true',
help="Does the queries file contain a header line (text format)")
parser.add_argument('-i', '--input', required=True, help="SMILES file with molecules to search")
parser.add_argument('--delimiter', default='\t', help="Delimiter")
parser.add_argument('--id-column', help="Column for name field (zero based integer for .smi, text for SDF)")
parser.add_argument('--mol-column', type=int, default=0,
help="Column index for molecule when using delineated text formats (zero based integer)")
parser.add_argument('--read-header', action='store_true', help="Read a header line with the field names")
parser.add_argument('-o', '--output', required=True, help="Output file as SMILES")
parser.add_argument('--write-header', action='store_true', help='Write a header line')
parser.add_argument('--read-records', default=100, type=int,
help="Read this many records to determine the fields that are present")

parser.add_argument('-d', '--descriptor', type=str.lower, choices=list(descriptors.keys()), default='rdkit',

parser.add_argument('--descriptor', type=str.lower, choices=list(descriptors.keys()), default='rdkit',
help='Descriptor or fingerprint type (default rdkit)')
parser.add_argument('-m', '--metric', type=str.lower, choices=list(metrics.keys()), default='tanimoto',
help='Similarity metric (default tanimoto)')
Expand All @@ -303,7 +299,6 @@ def main():
parser.add_argument("--alpha", type=float, default=1.0, help="Tversky alpha parameter")
parser.add_argument("--beta", type=float, default=0.0, help="Tversky beta parameter")
parser.add_argument("--nbits", type=int, default=None, help="Number of bits if using Morgan as bit vector e.g. 1024")
parser.add_argument("--interval", type=int, help="Reporting interval")

args = parser.parse_args()
DmLog.emit_event("screen: ", args)
Expand Down
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