schrodinger.application.desmond.frag_snap module

schrodinger.application.desmond.frag_snap.get_aligned_coordinates_from_fragments(ct1, ct2, match1, match2, broken_bond_ct1, broken_bond_ct2)[source]

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

schrodinger.application.desmond.frag_snap.get_aligned_fragment_coords(fwt, fmut, matched1, matched2, map_orig2frag, coord)[source]

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

schrodinger.application.desmond.frag_snap.get_aligned_coordinates(ct1, ct2, matched_atom1, matched_atom2, broken_bond_ct2=[])[source]

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