#! /usr/local/bin/python import random # Import the module import folder # The 20 canonical amino acids aas = 'ACDEFGHIKLMNPQRSTVWY' # Initialize the protein folder -- very important! # side_length refers to the protein. E.g., in the 5x5 # model, side_length=5. side_length = 5 folder.init(side_length) for i in range(100): # Create a random polypeptide prot = ''.join([random.choice(aas) for i in range(side_length*side_length)]) # Fold it and retrieve its lowest-free-energy conformation, sid, and its # free energy of folding, dg. (sid, dg) = folder.foldProtein(prot) # Print them out print "%d\t%1.3f\t%s" % (sid, dg, prot)
def main():
prot = sys.argv[1]
folder.init(int(math.sqrt(len(prot))))
(sid, dg) = folder.fold(prot)
print sid, dg
import random, math, os, sys
# Import the modules
import folder, decoyfolder
#sys.path = [os.path.expanduser('~/research/lib')] + sys.path
#import translate
# The 20 canonical amino acids
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)])
def main(): prot = sys.argv[1] folder.init(int(math.sqrt(len(prot)))) (sid, dg) = folder.fold(prot) print sid, dg