Molalign command line help
usage: ./molalign -s SMARTS [-h] [-v] [-fs string] [-1 #] [-2 #] [-3 #] [-a sdf|rdf|x|y] [-o smi|sdf] [-p] [-v]
Reads on stdin:
(if -a rdf or -p or -s @rdf) an rdf file with product coords,
(if -a rdf or -p or -s @rdf) cat'ed to a unique file separator string
cat'ed to an sdf file with many product molecules.
Writes on stdout a sdf file of many product molecules
with coords rotated to conform to target (see -a).
REQUIRED:
-s SMARTS: SMARTS defining alignment atoms
or
-s "@sdf": SMARTS will be SMILES of first sdf molecule
or
-s "@rdf": SMARTS will be SMILES (or variants thereof) of first rdf product
Options:
-h: this brief help
-fs string: unique string marking end of rdf file (default END-OF-RDF-FILE)
-1 #: 1st atom in smarts (or in rdf if -s @rdf) to align (default=1)
-2 #: 2nd atom in smarts (or in rdf if -s @rdf) to align (default=2)
-3 #: 3rd atom in smarts (or in rdf if -s @rdf) to align (default=3)
-a: align to [rdf][sdf][x][y]
sdf: align to sdf first molecule coordinates (default)
rdf: align to rdf first product coordinates
x: align to x axis
y: align to y axis
-o: [smi][sdf] output file format
sdf : output sdf (default)
smi: output smiles
-p: include rdf product core in output sdf file (ignored unless -o sdf)
-v: diagnostic verbosity on stderr