from colorama import Fore
from CHOMP import PDB, NewSystem, RotamerLibrary, RotamerGenerator, FasterPacker, SimulatedAnnealingPacker, ResidueGenerator
from chomp_setup import dunbrack_lib, energy_function, NewNeighborMap
from chomptools.design import DesignSystem, DesignEnergyGraph
#from chomptools.cplexpacker import CplexPacker
from time import time
from CHOMP import System
inputpdb = '2zta.pdb'
assert os.path.isfile(inputpdb)
from chomptools.design import Palette
### Load a protein normally
P = PDB(inputpdb)
P.RemoveHydrogens()
S = NewSystem(P)
print 'WT E', energy_function(S)
dimer = NewSystem(P)
S = System.Join(dimer)
print 'WT E', energy_function(S)
S.WritePDB('2zta_renum.pdb')
### Create a design palette
### TODO: make a version of the chomptools.design tools that
### identifies residues by ID and chain, rather than just ID
### this will facilitate the design of oligomers
dp = Palette(S)
dp.AddWT()
## Manually identified interface residues in PyMOL
## Use this line to freeze all non-interfacial resides
#dp.FreezeAll()
print Fore.GREEN
print 'DESIGN RESULTS'
print 'Chain A:', seqA
print 'Chain B:', seqB
if seqA == seqB:
print 'H**o-dimer!'
else:
print 'Hetero-dimer'
print Fore.RESET
### Let's rescore the redesigned output. It will vary a bit from the E that came out of
### combinatorial optimization. First, there is the usual source of deviation (neglect of
### small interactions in the EnergyGraph. Anoter source of small deviations is that when
### we create a system using CreateSystemFromRotamers coordinate precision is reduced to
### the precision of a PDB file.
score = energy_function(designedS)
print 'E =', score
open('designed.pdb', 'w').write(str(designedS))
open('designed.seq', 'w').write(designedS.GetSequence())
S.Label = 'Wild-type'
designedS.Label = 'Redesigned'
energy_function.CompareSystems(S, designedS)
for i in range(0, 10):
mp = MonteCarloPacker()
mp.SetTemperature(.1)
combo, E = mp.Pack(eg.pl, eg)
print 'Packer E', E
print 'Retest E', eg[combo]
print Fore.GREEN
print 'DESIGN RESULTS'
print 'Chain A:',seqA
print 'Chain B:',seqB
if seqA == seqB:
print 'H**o-dimer!'
else:
print 'Hetero-dimer'
print Fore.RESET
### Let's rescore the redesigned output. It will vary a bit from the E that came out of
### combinatorial optimization. First, there is the usual source of deviation (neglect of
### small interactions in the EnergyGraph. Anoter source of small deviations is that when
### we create a system using CreateSystemFromRotamers coordinate precision is reduced to
### the precision of a PDB file.
score = energy_function(designedS)
print 'E =', score
open('designed.pdb','w').write(str(designedS))
open('designed.seq','w').write(designedS.GetSequence())
S.Label = 'Wild-type'
designedS.Label = 'Redesigned'
energy_function.CompareSystems(S, designedS)
for i in range(0,10):
mp=MonteCarloPacker()
mp.SetTemperature(.1)
combo, E = mp.Pack(eg.pl, eg)
print 'Packer E',E
