module#, ref, molseg=None, refseg=None, molsel='all', refsel='all', maxalignments=10, nalignfragment=1)#

Aligns two structures by their longests sequences alignment

  • mol (Molecule object) – The Molecule we want to align

  • ref (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], …]