def __init__(self, T = 300, ff = 'ecepp3', st = 1, libdir = 'SMMP/'):
self.setTemperature(T)
if ff == 'ecepp3':
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.ientyp=0
elif ff == 'ecepp2':
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 1
smmp.epar_l.epsd = 0
smmp.epar_l.ientyp=0
elif ff == 'flex':
smmp.epar_l.flex = 1
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.ientyp=0
smmp.epar_l.tesgrd = 0
smmp.isolty.itysol = st
smmp.init_energy(libdir)
self.__objects = []
self.__boxSize = 10
smmp.updchois.upchswitch = 0
smmp.updchois.rndord = 0
smmp.updchois.bgsprob = 0
else:
it=smmp.var_i.ityvr[i]
if it == 3:
print >>out, nursvr(i), ':', name, ':', smmp.var_r.vlvr[i] * crd, ' &'
def zimmer(self):
first = smmp.mol_i.irsml1[self.__id] - 1
last = smmp.mol_i.irsml2[self.__id]
nrs = smmp.mol_i.irsml2[smmp.mol_i.ntlml - 1] - 1
smmp.zimmer(last)
return smmp.zimme.zimm[first:last]
def __len__(self):
return smmp.mol_i.irsml2[self.__id] - smmp.mol_i.irsml1[self.__id] + 1
if __name__ == "__main__":
libdir = 'SMMP/'
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.tesgrd = 0
smmp.isolty.itysol = 0
smmp.init_energy(libdir)
p1 = Protein('EXAMPLES/1bdd.pdb')
for i in p1.atoms():
print i
print p1.getDihedral('phi', 11)
it = smmp.var_i.ityvr[i]
if it == 3:
print >> out, nursvr(
i), ':', name, ':', smmp.var_r.vlvr[i] * crd, ' &'
def zimmer(self):
first = smmp.mol_i.irsml1[self.__id] - 1
last = smmp.mol_i.irsml2[self.__id]
nrs = smmp.mol_i.irsml2[smmp.mol_i.ntlml - 1] - 1
smmp.zimmer(last)
return smmp.zimme.zimm[first:last]
def __len__(self):
return smmp.mol_i.irsml2[self.__id] - smmp.mol_i.irsml1[self.__id] + 1
if __name__ == "__main__":
libdir = 'SMMP/'
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.tesgrd = 0
smmp.isolty.itysol = 0
smmp.init_energy(libdir)
p1 = Protein('EXAMPLES/1bdd.pdb')
for i in p1.atoms():
print i
print p1.getDihedral('phi', 11)
# muca.py
#
# Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
# Jan H. Meinke, Sandipan Mohanty
#
import sys
sys.path.append('../..')
import smmp, universe, protein
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.ientyp = 0
smmp.isolty.itysol = 0
smmp.init_energy('./SMMP/')
smmp.mol_i.ntlml=0
smmp.sgrnd(31433)
smmp.updchois.upchswitch = 0
smmp.updchois.rndord = 0
smmp.updchois.bgsprob = 0.3
smmp.init_lund()
p = protein.Protein('../enkefa.seq', '../enkefa.var')
smmp.multicanonical.mulcan_par(100000, 500, 1000, -12, 20, 1.0, 0)
#smmp.multicanonical.mulcan_sim(100, 100000, 10, 1000, -12, 20, 1.0, 0)
#!/usr/bin/env python
# muca.py
#
# Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
# Jan H. Meinke, Sandipan Mohanty
#
import sys
sys.path.append('../..')
import smmp, universe, protein
smmp.epar_l.flex = 0
smmp.epar_l.sh2 = 0
smmp.epar_l.epsd = 0
smmp.epar_l.ientyp = 0
smmp.isolty.itysol = 0
smmp.init_energy('./SMMP/')
smmp.mol_i.ntlml = 0
smmp.sgrnd(31433)
smmp.updchois.upchswitch = 0
smmp.updchois.rndord = 0
smmp.updchois.bgsprob = 0.3
smmp.init_lund()
p = protein.Protein('../enkefa.seq', '../enkefa.var')
smmp.multicanonical.mulcan_par(100000, 500, 1000, -12, 20, 1.0, 0)
#smmp.multicanonical.mulcan_sim(100, 100000, 10, 1000, -12, 20, 1.0, 0)