Command Line Tool¶
MolVS comes with a simple command line tool that allows standardization and validation by typing molvs
at the
command line.
Standardization¶
See standardization help by typing molvs standardize -h
:
usage: molvs standardize [infile] [-i {smi,mol,sdf}] [-O <outfile>]
[-o {smi,mol,sdf}] [-: <smiles>]
positional arguments:
infile input filename
optional arguments:
-i {smi,mol,sdf}, --intype {smi,mol,sdf}
input filetype
-: <smiles>, --smiles <smiles>
input SMILES instead of file
-O <outfile>, --outfile <outfile>
output filename
-o {smi,mol,sdf}, --outtype {smi,mol,sdf}
output filetype
Validation¶
See validation help by typing molvs validate -h
:
usage: molvs validate [infile] [-i {smi,mol,sdf}] [-O <outfile>]
[-: <smiles>]
positional arguments:
infile input filename
optional arguments:
-i {smi,mol,sdf}, --intype {smi,mol,sdf}
input filetype
-: <smiles>, --smiles <smiles>
input SMILES instead of file
-O <outfile>, --outfile <outfile>
output filename
Examples¶
SMILES standardization:
$ molvs standardize -:"C[n+]1c([N-](C))cccc1"
CN=c1ccccn1C
Specifying an output format:
$ molvs standardize -:"[N](=O)(=O)O" -o mol
RDKit
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 0
1 4 1 0
M CHG 2 1 1 2 -1
M END
Using stdin:
$ echo "C[n+]1c([N-](C))cccc1" | molvs standardize
CN=c1ccccn1C
Specifying an input file:
$ molvs standardize example.mol
CN=c1ccccn1C
Specifying an output file:
$ molvs standardize example.mol -O output.smi
$ molvs standardize example.mol -O output.mol
$ molvs standardize example.mol -O output -o mol
Logging validations to stdout:
$ molvs validate -:"O=C([O-])c1ccccc1"
INFO: [NeutralValidation] Not an overall neutral system (-1)
Logging validations to a file:
$ molvs validate -:"O=C([O-])c1ccccc1" -O logs.txt