Least RMSD align

%load_ext autoreload
%autoreload 2

import molsysmt as msm

molsys_1 = msm.convert('181l', to_form='molsysmt.MolSys',
                       selection='molecule_type=="protein"')
molsys_2 = msm.convert('1l17', to_form='molsysmt.MolSys',
                       selection='molecule_type=="protein"')

msm.convert(molsys_1, 'string:amino_acids_1')

'MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK'

msm.convert(molsys_2, 'string:amino_acids_1')

'MNVFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL'

molsys_2on1 = msm.structure.least_rmsd_align(molsys_2, reference_molecular_system=molsys_1)

MOLSYSMT WARNING | BiopythonDeprecationWarning: The attribute 'target_end_gap_score' was renamed to 'end_insertion_score'. This was done to be consistent with the
AlignmentCounts object returned by the .counts method of an Alignment object.

MOLSYSMT WARNING | BiopythonDeprecationWarning: The attribute 'query_end_gap_score' was renamed to 'end_deletion_score'. This was done to be consistent with the
AlignmentCounts object returned by the .counts method of an Alignment object.

msm.view([molsys_1, molsys_2on1])