.. index:: single: Pharmacophores; Input
           single: Pharmacophores; Output
           single: Pharmacophores; Processing
           single: Pharmacophores; Alignment
           single: Pharmacophores; Alignment Scoring
           single: Pharmacophore Features; Orientation Property
           single: Pharmacophore Features; Geometry Property
           single: Pharmacophore Features; Type Property
           single: Data Formats; PML
           single: Data Formats; CDF
           
Pharmacophore to Pharmacophore Alignment
========================================

The script *align_ph4s_to_ph4.py* overlays a set of input pharmacophores with a given reference pharmacophore and then writes the calculated alignment pose(s) to a specified output file.

**Synopsis**

  :program:`python` *align_ph4s_to_ph4.py* [-h] -r <file> -i <file> -o <file> [-s <file>] [-n <integer>] [-x] [-d <float>] [-Q] [-q] [-p]

**Mandatory options**

 -r <file>

    Reference pharmacophore input file (\*.pml, \*.cdf)

 -i <file>

    Pharmacophore input file (\*.pml, \*.cdf)

 -o <file>

    Aligned pharmacophore output file (\*.pml, \*.cdf)
  
**Other options**

 -h, --help

    Show help message and exit

 -s <file>

    Pharmacophore alignment score output file
    
 -n <integer>

    Number of top-ranked alignment solutions to output per input pharmacophore (default: best
    alignment solution only)

 -x

    Perform an exhaustive alignment search (default: false)

 -d <float>

    Minimum required score difference between two consecutively output pharmacophore alignment poses
    (default: 0.0)

 -Q

    If specified, only alignments where the positions of the features of the input pharmacophores lie strictly
    within the tolerance spheres of the reference pharmacophore features will be considered as being valid.
    Otherwise, alignments where the position of at least one feature of the aligned pairs lies within the tolerance
    sphere of the other feature are also valid (default: false)

 -q

    Disable progress output (default: false)

 -p

    Ignore feature orientations, feature position matching only (default: false)

**Code**

.. literalinclude:: /downloads/align_ph4s_to_ph4.py
   :language: python
   :linenos:
   :lines: 19-

:download:`Download source file</downloads/align_ph4s_to_ph4.py>`