from pdb import Pdb from os import path import sys tmpDir = '.' daliFile = '1tenA.txt' myRefPdb = '1ten' myRefChain = 'A' myZ = 2. myTmpPath = './pdb' + myRefPdb + myRefChain v = True dali = Dali(refPdb=myRefPdb, refChain=myRefChain, tmpPath=myTmpPath, verbose=v) #dali.CallDali( dali.ReadFile(daliFile, verbose=v) dali.RemoveDissimilar(z=myZ) dali.GetSequenceFromPdb(tmpPath=myTmpPath, localPdb='', verbose=v, paranoid=False) dali.RemoveInternalHomologs(byOrganism=True, dropNoOrganism=True, orderBy='lali') dali.AlignToRef() dali.PrintAlignment() dali.CalculateEntropy(toPrint=True, filename='entropy_' + myRefPdb + myRefChain + '.dat') dali.PrintAnalogs() print('Number of sequences=', len(dali.analogs['aligned'].index))