%load_ext autoreload
%autoreload 2

import molsysmt as msm

Get sequence alignment

molecular_system_1 = msm.convert('pdb_id:181l', to_form='molsysmt.MolSys')
molecular_system_2 = msm.convert('pdb_id:1l17', to_form='molsysmt.MolSys')

msm.get(molecular_system_1, element='atom', selection='molecule_type=="protein"', n_groups=True)

162

msm.get(molecular_system_2, element='atom', selection='molecule_type=="protein"', n_groups=True)

164

msm.topology.get_sequence_alignment(molecular_system_1, selection='molecule_type=="protein"',
                                    reference_molecular_system=molecular_system_2, reference_selection='molecule_type=="protein"',
                                    prettyprint=True)

MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK--

MNVFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL

seq, seq_ref = msm.topology.get_sequence_alignment(molecular_system_1, selection='molecule_type=="protein"',
                                    reference_molecular_system=molecular_system_2, reference_selection='molecule_type=="protein"')

seq

'MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK--'

seq_ref

'MNVFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL'