def run_gui(system, db=None):
import pele.gui.run as gr
gr.run_gui(system, db=db)
def draw(self, coordsl, index):
from OpenGL import GL,GLUT
coords=coordsl.reshape(coordsl.size/3,3)
#coords = coords.reshape(GMIN.getNAtoms, 3)
com=np.mean(coords, axis=0)
for xx in coords:
x = xx-com
GL.glPushMatrix()
GL.glTranslate(x[0],x[1],x[2])
GLUT.glutSolidSphere(0.3,30,30)
GL.glPopMatrix()
# get bond list from amber params
mol = readAmb.readAmberParam()
mol.populateBondConn()
# draw bonds
for atomPairs in mol.bondConn:
xyz1 = coords[atomPairs[0]-1] - com
xyz2 = coords[atomPairs[1]-1] - com
self.drawCylinder(xyz1, xyz2)
def createNEB(self, coords1, coords2):
pot = gminpot.GMINPotental(GMIN)
return NEB.NEB(coords1, coords2, pot, k = 100. ,nimages=20)
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(molSystem)
def run_gui(system):
import pele.gui.run as gr
gr.run_gui(system)
#print 'GMIN POTENTIAL'
#sys = AMBERSystem_GMIN('coords.prmtop', 'coords.inpcrd')
#sys.test_potential('coords.pdb')
# openmm potential is ~6x slower than gmin potential
print('OPENmm POTENTIAL')
sys = AMBERSystem_OpenMM('coords.prmtop', 'coords.inpcrd')
sys.test_potential('coords.pdb')
# create new database
from pele.storage import Database
dbcurr = sys.create_database()
# ------- TEST gui
from pele.gui import run as gr
gr.run_gui(sys, db=dbcurr)
# ------ Test potential
sys.test_potential('coords.pdb')
# ------ BH
start = time.clock()
sys.test_BH(dbcurr)
elapsed = (time.clock() - start)
print("time taken by BH = ", elapsed)
exit()
# ------- Connect runs
sys.test_connect(dbcurr)
# ------- Disconn graph
from pele.amber import amberSystem
# create new amber system
sys = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
#start the gui
from pele.gui import run as gr
gr.run_gui(sys)
import gmin_ as GMIN
from pele.potentials import GMINPotential
from pele.systems import LJCluster
import numpy as np
class GUPTASystem(LJCluster):
def __init__(self):
GMIN.initialize()
self.natoms = GMIN.getNAtoms()
super(GUPTASystem, self).__init__(self.natoms)
qp = self.params.structural_quench_params
qp["tol"]=1e-5
qp["maxErise"]=1e-5
qp["maxstep"]=0.1
qp["iprint"]=-1
qp["debug"]=False
neb = self.params.double_ended_connect.local_connect_params.NEBparams
neb["image_density"]=5
neb["adjustk_freq"]=5
def get_potential(self):
return GMINPotential(GMIN)
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(GUPTASystem)
from pele.amber.amberSystem import AMBERSystem
from pele.gui import run as gr
sysAmb = AMBERSystem('coords.prmtop', 'coords.inpcrd')
gr.run_gui(sysAmb, db="optimdb.sqlite")
from pele.amber import amberSystem
# create new amber system
system = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
database = system.create_database("optimdb.sqlite")
#start the gui
from pele.gui import run as gr
gr.run_gui(system, db=database)
from pele.amber import amberSystem
# create new amber system
sys = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
#start the gui
from pele.gui import run as gr
gr.run_gui(sys)
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def get_compare_exact(self, **kwargs):
return ExactMatchAACluster(self.aasystem,
accuracy=0.1,
tol=0.07,
**kwargs)
def get_mindist(self, **kwargs):
return MinPermDistAACluster(self.aasystem,
accuracy=0.1,
tol=0.07,
**kwargs)
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(PAPSystem, db="pap.sqlite")
from pele.amber import amberSystem
# create new amber system
system = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
database = system.create_database("optimdb.sqlite")
#start the gui
from pele.gui import run as gr
gr.run_gui(system, db=database)
#print 'GMIN POTENTIAL'
#sys = AMBERSystem_GMIN('coords.prmtop', 'coords.inpcrd')
#sys.test_potential('coords.pdb')
# openmm potential is ~6x slower than gmin potential
print 'OPENmm POTENTIAL'
sys = AMBERSystem_OpenMM('coords.prmtop', 'coords.inpcrd')
sys.test_potential('coords.pdb')
# create new database
from pele.storage import Database
dbcurr = sys.create_database()
# ------- TEST gui
from pele.gui import run as gr
gr.run_gui(sys, db=dbcurr)
# ------ Test potential
sys.test_potential('coords.pdb')
# ------ BH
start = time.clock()
sys.test_BH(dbcurr)
elapsed = (time.clock() - start)
print "time taken by BH = ", elapsed
exit()
# ------- Connect runs
sys.test_connect(dbcurr)
# ------- Disconn graph
water = create_pap()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.1
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
return system
def get_compare_exact(self, **kwargs):
return ExactMatchAACluster(self.aasystem, accuracy=0.1, tol=0.07, **kwargs)
def get_mindist(self, **kwargs):
return MinPermDistAACluster(self.aasystem,accuracy=0.1, tol=0.07, **kwargs)
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(PAPSystem, db="pap.sqlite")
# create new amber system
sysAmb = AMBERSystem('../../examples/amber/aladipep/coords.prmtop',
'../../examples/amber/aladipep/coords.inpcrd')
# load existing database
from pele.storage import Database
dbcurr = Database(db="../../examples/amber/aladipep/aladipep.db")
coords = sysAmb.get_random_configuration()
# aa = sysAmb.get_metric_tensor(coords)
# ------- TEST gui
from pele.gui import run as gr
gr.run_gui(sysAmb)
# ------ Test potential
sysAmb.test_potential("../../examples/amber/aladipep/coords.pdb")
# ------ BH
nsteps = 100
sysAmb.test_BH(dbcurr, nsteps)
exit()
# ------- Connect runs
sysAmb.test_connect(dbcurr)
# ------- Disconn graph
sysAmb.test_disconn_graph(dbcurr)
pot = GMINPotential(GMIN)
coords = pot.getCoords()
nrigid = coords.size / 6
print "I have %d water molecules in the system"%nrigid
print "The initial energy is", pot.getEnergy(coords)
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in xrange(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in xrange(nrigid):
self.draw_bonds.append((3*i, 3*i+1))
self.draw_bonds.append((3*i, 3*i+2))
return system
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(TIP4PSystem, db="tip4p_8.sqlite")
def run_gui(system):
import pele.gui.run as gr
gr.run_gui(system)
def run_gui(system, db=None):
import pele.gui.run as gr
gr.run_gui(system, db=db)
coords = pot.getCoords()
nrigid = old_div(coords.size, 6)
print("I have %d water molecules in the system" % nrigid)
print("The initial energy is", pot.getEnergy(coords))
water = tip4p.water()
system = RBTopology()
system.add_sites([deepcopy(water) for i in range(nrigid)])
self.potential = pot
self.nrigid = nrigid
self.render_scale = 0.3
self.atom_types = system.get_atomtypes()
self.draw_bonds = []
for i in range(nrigid):
self.draw_bonds.append((3 * i, 3 * i + 1))
self.draw_bonds.append((3 * i, 3 * i + 2))
return system
def get_potential(self):
return self.potential
if __name__ == "__main__":
import pele.gui.run as gr
gr.run_gui(TIP4PSystem, db="tip4p_8.sqlite")
if __name__ == "__main__":
# create new amber system
sysAmb = AMBERSystem('../../examples/amber/aladipep/coords.prmtop', '../../examples/amber/aladipep/coords.inpcrd')
# load existing database
from pele.storage import Database
dbcurr = Database(db="../../examples/amber/aladipep/aladipep.db")
coords = sysAmb.get_random_configuration()
# aa = sysAmb.get_metric_tensor(coords)
# ------- TEST gui
from pele.gui import run as gr
gr.run_gui(sysAmb)
# ------ Test potential
sysAmb.test_potential("../../examples/amber/aladipep/coords.pdb")
# ------ BH
nsteps = 100
sysAmb.test_BH(dbcurr, nsteps)
exit()
# ------- Connect runs
sysAmb.test_connect(dbcurr)
# ------- Disconn graph
sysAmb.test_disconn_graph(dbcurr)
def run_gui_disorder(L=10, dbname=None):
if dbname is None:
dbname = "xy_%dx%d.sqlite" %(L,L)
system = create_system(L=L, dbname=dbname)
db = system.create_database(dbname)
run_gui(system, db=db)
def rungui(system, db=None):
import pele.gui.run as gr
from pele.storage import Database
gr.run_gui(system, db=db)