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))
