/usr/lib/python2.7/dist-packages/chemfp/commandline/rdkit2fps.py is in python-chemfp 1.1p1-2.1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | # Copyright (c) 2010 Andrew Dalke Scientific, AB (Gothenburg, Sweden)
import sys
from .. import ParseError
from .. import argparse, io, rdkit, types
from . import cmdsupport
########### Configure the command-line parser
epilog = """\
This program guesses the input structure format based on the filename
extension. If the data comes from stdin, or the extension name us
unknown, then use "--in" to change the default input format. The
supported format extensions are:
File Type Valid FORMATs (use gz if compressed)
--------- ------------------------------------
SMILES smi, ism, can, smi.gz, ism.gz, can.gz
SDF sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz
"""
parser = argparse.ArgumentParser(
description="Generate FPS fingerprints from a structure file using RDKit",
epilog=epilog,
formatter_class=argparse.RawDescriptionHelpFormatter,
conflict_handler="resolve",
)
_base = rdkit._base
# --RDK and --morgan both have fpSize but argparse doesn't allow the
# same option in different groups. Especially with different defaults.
_base.add_argument_to_argparse("fpSize", parser)
rdk_group = parser.add_argument_group("RDKit topological fingerprints")
rdk_group.add_argument("--RDK", action="store_true",
help="generate RDK fingerprints (default)")
_base.add_argument_to_argparse("minPath", rdk_group)
_base.add_argument_to_argparse("maxPath", rdk_group)
_base.add_argument_to_argparse("nBitsPerHash", rdk_group)
_base.add_argument_to_argparse("useHs", rdk_group)
morgan_group = parser.add_argument_group("RDKit Morgan fingerprints")
morgan_group.add_argument("--morgan", action="store_true",
help="generate Morgan fingerprints")
_morgan = rdkit.RDKitMorganFingerprintFamily_v1
_morgan.add_argument_to_argparse("radius", morgan_group)
_morgan.add_argument_to_argparse("useFeatures", morgan_group)
_morgan.add_argument_to_argparse("useChirality", morgan_group)
_morgan.add_argument_to_argparse("useBondTypes", morgan_group)
torsion_group = parser.add_argument_group("RDKit Topological Torsion fingerprints")
torsion_group.add_argument("--torsions", action="store_true",
help="generate Topological Torsion fingerprints")
rdkit.RDKitTorsionFingerprintFamily_v1.add_argument_to_argparse(
"targetSize", torsion_group)
pair_group = parser.add_argument_group("RDKit Atom Pair fingerprints")
pair_group.add_argument("--pairs", action="store_true",
help="generate Atom Pair fingerprints")
rdkit.RDKitTorsionFingerprintFamily_v1.add_argument_to_argparse(
"minLength", pair_group)
rdkit.RDKitTorsionFingerprintFamily_v1.add_argument_to_argparse(
"maxLength", pair_group)
maccs_group = parser.add_argument_group("166 bit MACCS substructure keys")
maccs_group.add_argument(
"--maccs166", action="store_true", help="generate MACCS fingerprints")
substruct_group = parser.add_argument_group("881 bit substructure keys")
substruct_group.add_argument(
"--substruct", action="store_true", help="generate ChemFP substructure fingerprints")
rdmaccs_group = parser.add_argument_group("ChemFP version of the 166 bit RDKit/MACCS keys")
rdmaccs_group.add_argument(
"--rdmaccs", action="store_true", help="generate 166 bit RDKit/MACCS fingerprints")
parser.add_argument(
"--id-tag", metavar="NAME",
help="tag name containing the record id (SD files only)")
parser.add_argument(
"--in", metavar="FORMAT", dest="format",
help="input structure format (default guesses from filename)")
parser.add_argument(
"-o", "--output", metavar="FILENAME",
help="save the fingerprints to FILENAME (default=stdout)")
parser.add_argument(
"--errors", choices=["strict", "report", "ignore"], default="strict",
help="how should structure parse errors be handled? (default=strict)")
parser.add_argument(
"filenames", nargs="*", help="input structure files (default is stdin)")
def main(args=None):
args = parser.parse_args(args)
cmdsupport.mutual_exclusion(parser, args, "RDK",
("maccs166", "RDK", "substruct", "rdmaccs", "morgan",
"torsions", "pairs"))
if args.maccs166:
opener = types.get_fingerprint_family("RDKit-MACCS166")()
elif args.RDK:
fpSize = args.fpSize or rdkit.NUM_BITS
minPath = args.minPath
maxPath = args.maxPath
nBitsPerHash = args.nBitsPerHash
if maxPath < minPath:
parser.error("--minPath must not be greater than --maxPath")
useHs = args.useHs
opener = types.get_fingerprint_family("RDKit-Fingerprint")(
minPath=minPath,
maxPath=maxPath,
fpSize=fpSize,
nBitsPerHash=nBitsPerHash,
useHs=useHs)
elif args.substruct:
opener = types.get_fingerprint_family("ChemFP-Substruct-RDKit")()
elif args.rdmaccs:
opener = types.get_fingerprint_family("RDMACCS-RDKit")()
elif args.morgan:
opener = types.get_fingerprint_family("RDKit-Morgan")(
radius=args.radius,
fpSize=args.fpSize,
useFeatures=args.useFeatures,
useChirality=args.useChirality,
useBondTypes=args.useBondTypes)
elif args.torsions:
opener = types.get_fingerprint_family("RDKit-Torsion")(
fpSize=args.fpSize,
targetSize=args.targetSize)
elif args.pairs:
minLength = args.minLength
maxLength = args.maxLength
if maxLength < minLength:
parser.error("--minLength must not be greater than --maxLength")
opener = types.get_fingerprint_family("RDKit-AtomPair")(
fpSize=args.fpSize,
minLength=minLength,
maxLength=maxLength)
else:
raise AssertionError("Unknown fingerprinter")
if not rdkit.is_valid_format(args.format):
parser.error("Unsupported format specifier: %r" % (args.format,))
if not cmdsupport.is_valid_tag(args.id_tag):
parser.error("Invalid id tag: %r" % (args.id_tag,))
missing = cmdsupport.check_filenames(args.filenames)
if missing:
parser.error("Structure file %r does not exist" % (missing,))
metadata, reader = cmdsupport.read_multifile_structure_fingerprints(
opener, args.filenames, format=args.format,
id_tag=args.id_tag, aromaticity=None, errors=args.errors)
try:
io.write_fps1_output(reader, args.output, metadata)
except ParseError, err:
sys.stderr.write("ERROR: %s. Exiting." % (err,))
raise SystemExit(1)
if __name__ == "__main__":
main()
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