Example #1
0
 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
Example #2
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)
Example #3
0
                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)
Example #4
0
# 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)

Example #5
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)