moleculekit.tools.sequencestructuralalignment module#

moleculekit.tools.sequencestructuralalignment.sequenceStructureAlignment(mol, ref, molseg=None, refseg=None, molsel='all', refsel='all', maxalignments=10, nalignfragment=1)#

Aligns two structures by their longests sequences alignment

Parameters:

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

  • ref (Molecule) – The reference Molecule to which we want to align

  • molseg (str | None) – The segment of mol we want to align

  • refseg (str | None) – The segment of ref we want to align to

  • molsel (str | ndarray) – The atom selection of mol we want to align. Can be a selection string, a boolean mask, or an integer index array. Defaults to “all”.

  • refsel (str | ndarray) – The atom selection of ref we want to align to. Can be a selection string, a boolean mask, or an integer index array. Defaults to “all”.

  • maxalignments (int) – The maximum number of alignments we want to produce

  • nalignfragment (int) – The number of fragments used for the alignment.

Returns:

  • 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], …]