Molalign examples


# align all mols in acd_search.sdf to coords of first mol
# by matching SMARTS C1CNc2ccccc2N1
./molalign -s "C1CNc2ccccc2N1" < acd_search.sdf [view] > acd_aligned.sdf [view]
# align all mols in acd_search.sdf to coords of first mol,
# then align to y axis
./molalign -s "C1CNc2ccccc2N1" -a y < acd_search.sdf [view] > acd_aligned2.sdf [view]
# align all mols in acd_search.sdf to coords of first mol
# getting SMARTS from first mol
./molalign -s "@sdf" < acd_search.sdf [view] > acd_aligned.sdf [view]
# align mols #2 thru #N in reaction.sdf to coords of first mol in sdf file
# using smarts O=COC
./molalign -s "O=COC" < reaction.sdf [view] > aligned3.sdf [view]
# align all mols in reaction.sdf,
# putting O=C (first two atoms of smarts) along x axis
./molalign -s "O=COC" -a x < reaction.sdf [view] > aligned4.sdf [view]
# align all mols in reaction.sdf to coords in reaction.rxn
# also output rxn product as mol #1 in output file
echo "END-OF-RDF-FILE" | cat reaction.rxn - reaction.sdf | \
./molalign -s "@rdf" -a rdf -p > aligned2.sdf [view]
# align all mols in reaction.sdf to coords in reaction.rxn
# matching O=COC in rxn and sdf.
# also output rxn product as mol #1 in output file
echo "END-OF-RDF-FILE" | cat reaction.rxn - reaction.sdf | \
./molalign -s "O=COC" -a rdf -p > aligned.sdf [view]