aas = 'ACDEFGHIKLMNPQRSTVWY' # Initialize the protein folder -- very important! # side_length refers to the protein. E.g., in the 5x5 # model, side_length=5. if True: side_length = 5 prot_length = side_length*side_length folder.init(side_length) for i in range(10000): # Create a random polypeptide prot = ''.join([random.choice(aas) for xi in range(prot_length)]) # Fold it and retrieve its lowest-free-energy conformation, sid, and its # free energy of folding, dg. (sid, dg) = folder.fold(prot) # Print them out if dg < -3: print "%d\t%d\t%1.3f\t%s" % (i, sid, dg, prot) ''' print "sid g" for i in range(1): # Create a random polypeptide prot = ''.join([random.choice(aas) for i in range(prot_length)]) # Fold it and retrieve its lowest-free-energy conformation, sid, and its # free energy of folding, dg. (sid, dg) = folder.fold(prot) for j in range(50): G = folder.getEnergy(prot, j) # Print them out print "%d\t%1.3f\t%s" % (sid, dg, prot)
# Initialize the protein folder -- very important! # side_length refers to the protein. E.g., in the 5x5 # model, side_length=5. if True: print "****\nTesting folder module" side_length = 5 prot_length = side_length*side_length folder.init(side_length) for i in range(10000): # Create a random polypeptide prot = ''.join([random.choice(aas) for xi in range(prot_length)]) # Fold it and retrieve its lowest-free-energy conformation, sid, and its # free energy of folding, dg. (sid, dg) = folder.fold(prot) # Print them out if dg < -3: print "%d\t%d\t%1.3f\t%s" % (i, sid, dg, prot) sid = random.randint(0,1080) dg = -2 gene = folder.getSequenceForStructure(sid, dg) (new_sid, new_dg) = folder.fold(translate.Translate(gene)) assert(sid == new_sid and new_dg <= dg) if False: print "\n****\nTesting misfold module with compact lattice folder" side_length = 5 struct_id = 599 target_fraction_accurate = 0.85 ca_cost = 5
def main():
prot = sys.argv[1]
folder.init(int(math.sqrt(len(prot))))
(sid, dg) = folder.fold(prot)
print sid, dg
# Initialize the protein folder -- very important!
# side_length refers to the protein. E.g., in the 5x5
# model, side_length=5.
if True:
print "****\nTesting folder module"
side_length = 5
prot_length = side_length * side_length
folder.init(side_length)
for i in range(10000):
# Create a random polypeptide
prot = ''.join([random.choice(aas) for xi in range(prot_length)])
# Fold it and retrieve its lowest-free-energy conformation, sid, and its
# free energy of folding, dg.
(sid, dg) = folder.fold(prot)
# Print them out
if dg < -3:
print "%d\t%d\t%1.3f\t%s" % (i, sid, dg, prot)
sid = random.randint(0, 1080)
dg = -2
gene = folder.getSequenceForStructure(sid, dg)
(new_sid, new_dg) = folder.fold(translate.Translate(gene))
assert (sid == new_sid and new_dg <= dg)
if False:
print "\n****\nTesting misfold module with compact lattice folder"
side_length = 5
struct_id = 599
target_fraction_accurate = 0.85
ca_cost = 5
def main(): prot = sys.argv[1] folder.init(int(math.sqrt(len(prot)))) (sid, dg) = folder.fold(prot) print sid, dg