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)

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.

Parameters

• 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

Returns

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)

Parameters

• 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=[])

Wrapper for PhpAlignCore

Parameters

• 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

Returns

numpy array of aligned coordinates for ct2 atoms if successful, otherwise None