Molecule to Reference Pharmacophore Alignment ============================================= The script *align_mols_to_ph4.py* overlays a set of input molecules with a given reference pharmacophore and outputs the molecules translated/rotated to the calculated alignment pose(s). **Synopsis** :program:`python` *align_mols_to_ph4.py* [-h] -r <file> -i <file> -o <file> [-n <integer>] [-x] [-d <float>] [-q] [-p] **Mandatory options** -r <file> Reference pharmacophore input file (\*.pml, \*.cdf) -i <file> Molecule input file -o <file> Aligned molecule output file **Other options** -h, --help Show help message and exit -n <integer> Number of top-ranked alignment solutions to output per molecule (default: best alignment solution only) -x Perform an exhaustive alignment search (default: false) -d <float> Minimum required RMSD between two consecutively output molecule alignment poses (default: 0.0) -q Disable progress output (default: false) -p Ignore feature orientations, feature position matching only (default: false) **Code** .. literalinclude:: /downloads/align_mols_to_ph4.py :language: python :linenos: :lines: 21- :download:`Download source file</downloads/align_mols_to_ph4.py>`