Module frag_snap

Send each connected fragment pairs for snapcore coordinates.
If the fragments have less than three atoms and contain no
dummy atoms, generate snapcore coordinates.  If case of stereo failure
or phase exeception, return None for coordinate array.

ct1: Structure from first molecule
ct2: Structure from second molecule
matched1: list of matched atom indices in ct1
matched2: list of matched atom indices in ct2
broken_bond_ct1: list of bond tuples
broken_bond_ct2: list of bond tuples
return: tuple of snapped core coordinates for ct1 and ct2
        if no failure, otherwise None for failed snapcore

fwt: fragment Structure from first molecule
fmut: fragment Structure from second molecule
matched1: list of matched atom indices in fwt
matched2: list of matched atom indices in fmut
map_orig2frag: dictionary mapping original atom indices to fragment indices
coord: original coordinates returned by mut_ct.getXYZ(), if snapcore  is possible
       aligned coordinates of fmut atoms are copied
return: False if alignment failed otherwise True

wrapper for PhpAlignCore
ct1: first Structure
ct2: second Structure
matched_atom1: list of mateched atom in ct1
matched_atom2: list of mateched atom in ct2
broken_bond_ct2: list of broken bonds in ct2
return: numpy array of aligned coordinates for ct2 atoms
        if successful, otherwise None