A description of the command line interface can be obtained by executing
smartsopt with no arguments.
prompt> smartsopt
will generate the following output:
SMARTSOpt v1.1 SMARTS Pattern Optimizer
OpenEye Scientific Software, December 2005
usage: smartsopt [options] <smafile> [outfile]
options: -h Preserve first atom during reordering
-i Assume isomeric primitives always match
-I Assume isomeric primitives don't match
-a Aromatic atoms and bonds must be aromatic
-A Aliphatic atoms must be aliphatic
-B Aliphatic bonds must be aliphatic
-r Only ring bonds can match in rings
-j Allow matching of implicit hydrogens
Command line options are distinguished from filenames by having
a `-' prefix. Options can appear anywhere on the command line,
i.e. before, after or in between filenames. When incompatible
options are specified the last one given on the command line takes effect.
The first filename given on the command line is taken to be the input
SMARTS file, and the optional second filename is treated as the
output SMARTS file. A minus character may be used in place of the
input filename to specify that the input is to be read from standard
input, stdin, and in place of the output filename to specify that the
output is to be written to standard output, stdout. If only one
filename is specified on the command line, the output is written to
stdout by default.
- -h
- This option ensures that the first atom of the input SMARTS
pattern is kept as the first atom of the output SMARTS pattern. This
is useful, for example, in optimizing patterns to be used as recursive
SMARTS or in atom typing. By default, smartsopt assumes the pattern
will be used in substructure searching, and is free to arbitrarily
reorder atom and bond expressions for improved search speed.
- -i
- Generates SMARTS patterns that assume that isomeric primitives,
such as isotopes, atom chirality or bond stereo chemistry always match.
It is often known in advance that the database to be searched contains
absolute canonical SMILES, in which case an isomeric pattern will always
fail. This option transforms a substructure query assuming these
primitives always match, allowing an enantiomeric parent to be found.
- -I
- Generates SMARTS patterns that assume that isomeric primitives,
such as isotopes, atom chirality or bond stereo chemistry never match.
It is often known in advance that the database to be searched contains
absolute canonical SMILES, in which case an isomeric pattern will always
fail. This option simplifies the pattern when this is the case.
- -a
- This option requires that atoms and bonds that are aromatic
in the input file, must be aromatic in the matched molecule. Because
a substructure query only specifies part of a molecule, a Kekulé
substructure that is aromatic in the query may match molecules in
which that substructure is aliphatic, typically by substitution and
or non-neutral charge states.
- -A
- This option requires that atoms that are non-aromatic in
the query, must be non-aromatic in the matched molecule. Because
a substructure query only specifies part of a molecule, a Kekulé
substructure that is aliphatic in the query may match molecules in
which that substructure is aromatic, typically by substitution and
or non-neutral charge states.
- -B
- This option requires that bonds that are non-aromatic in
the query, must be non-aromatic in the matched molecule.
- -r
- This option requires that acyclic bonds in the query must
be acyclic in the matched molecule.
