Aligns two structures by their longests sequences alignment
Molecule object) – The Molecule we want to align
Molecule object) – The reference Molecule to which we want to align
molseg (str) – The segment of mol we want to align
refseg (str) – The segment of ref we want to align to
maxalignments (int) – The maximum number of alignments we want to produce
nalignfragment (int) – The number of fragments used for the alignment.
mols (list) – A list of Molecules each containing a different alignment.
masks (list) – A list of boolean mask pairs of which atoms were aligned. [[molmask1, refmask1], [molmask2, refmask2], …]