kappa += (100. - 40.) / 90000.
if (p != 0 or iter != 0):
FTSM.setConstraint(PHI,
PSI,
phi=z[p][0],
psi=z[p][1],
kappa=kappa,
forcefield=ff)
# UPDATE FREE SPACE
# USE FIRST SYSTEM TO GET M
# USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES
# FROM TARGETS
zp0 = z[p][0]
z[p][0] -= (kappa / gamma) * dt * (FTSM.M(x[p], PHI, PHI) *
(z[p][0] - y[p].dihedral(PHI)) +
FTSM.M(x[p], PHI, PSI) *
(z[p][1] - y[p].dihedral(PSI)))
z[p][1] -= (kappa / gamma) * dt * (FTSM.M(x[p], PSI, PHI) *
(zp0 - y[p].dihedral(PHI)) +
FTSM.M(x[p], PSI, PSI) *
(z[p][1] - y[p].dihedral(PSI)))
# UPDATE CARTESIAN
prop[p][0].propagate(scheme="velocityscale",
steps=1,
dt=dt,
forcefield=ff,
params={'T0': 300})
io.plotVector(proparray[0][0],stringgraph,S, rangex=[-numpy.pi, 0], rangey=[-100*numpy.pi/180, numpy.pi])
# SET THE STATE BACK TO THE ORIGINAL PDB
#io.readPDBPos(physarray[0][0], "examples/alanSolStates/alanC7axial_wb5_min_eq.pdb")
dt = 1.0
for iter in range(0, 100000): # NUMBER OF FTSM ITERATIONS
for workpt in range(0, numpoints): # LOOPING OVER POINTS
if (iter >= 10000 and iter <= 100000):
kappa += (100.-40.)/90000.
# UPDATE FREE SPACE
# USE FIRST SYSTEM TO GET M
# USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES
# FROM TARGETS
M = FTSM.M(physarray[workpt][0], PHI_DIHEDRAL, PSI_DIHEDRAL)
#print "DIFFERENCE: ", S[workpt][0]-physarray[workpt][1].phi(PHI_DIHEDRAL), " " , S[workpt][1]-physarray[workpt][1].phi(PSI_DIHEDRAL)
S[workpt][0] -= (kappa/gamma)*M*dt*(S[workpt][0]-physarray[workpt][1].phi(PHI_DIHEDRAL))
S[workpt][1] -= (kappa/gamma)*M*dt*(S[workpt][1]-physarray[workpt][1].phi(PSI_DIHEDRAL))
# UPDATE CARTESIAN
# Dr. Izaguirre: I have checked and this constraint
# is correct. The energy is harmonic, but the force (the gradient)
# is not harmonic. In fact it is exactly what is in the paper.
proparray[workpt][0].propagate(scheme="LangevinImpulse", steps=1, dt=dt, forcefield=ff)
proparray[workpt][1].propagate(scheme="LangevinImpulse", steps=1, dt=dt, forcefield=ff)
# My own function which sets phi and psi for individual force objects
# Saves performance since I only change 'angle', I don't want to define
# all new force objects by changing params.
for iter in range(0, numsteps): # NUMBER OF FTSM ITERATIONS
for p in range(0, numpoints): # LOOPING OVER POINTS
if (iter >= 15000):# and iter <= 100000):
kappa += (100.-40.)/90000.
if (p != 0 or iter != 0):
FTSM.setConstraint(PHI, PSI, phi=z[p][0], psi=z[p][1], kappa=kappa, forcefield=ff)
# UPDATE FREE SPACE
# USE FIRST SYSTEM TO GET M
# USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES
# FROM TARGETS
zp0 = z[p][0]
z[p][0] -= (kappa/gamma)*dt*(FTSM.M(x[p], PHI, PHI)*(z[p][0]-y[p].dihedral(PHI)) + FTSM.M(x[p], PHI, PSI)*(z[p][1] - y[p].dihedral(PSI)))
z[p][1] -= (kappa/gamma)*dt*(FTSM.M(x[p], PSI, PHI)*(zp0-y[p].dihedral(PHI)) + FTSM.M(x[p], PSI, PSI)*(z[p][1] - y[p].dihedral(PSI)))
# My own function which sets phi and psi for individual force objects
# Saves performance since I only change 'angle', I don't want to define
# all new force objects by changing params.
#if (iter != 0 or p != 0):
# FTSM.setConstraint(phi=z[p][0], psi=z[p][1], kappa=kappa, forcefield=ff)
# UPDATE CARTESIAN
# Dr. Izaguirre: I have checked and this constraint
# is correct. The energy is harmonic, but the force (the gradient)
# is not harmonic. In fact it is exactly what is in the paper.
prop[p][0].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300})
prop[p][1].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300})
# My own function which sets phi and psi for individual force objects
kappa += kappaincr
if (iter != 0):
FTSM.setConstraint(PHI,
PSI,
phi=z_p[0],
psi=z_p[1],
kappa=kappa,
forcefield=ff)
# UPDATE FREE SPACE
# USE FIRST SYSTEM TO GET M
# USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES
# FROM TARGETS
zp0 = z_p[0]
z_p[0] -= (kappa /
gamma) * dt * (FTSM.M(x, PHI, PHI) *
(z_p[0] - y.angle(PHI)) + FTSM.M(x, PHI, PSI) *
(z_p[1] - y.angle(PSI)))
z_p[1] -= (kappa /
gamma) * dt * (FTSM.M(x, PSI, PHI) *
(zp0 - y.angle(PHI)) + FTSM.M(x, PSI, PSI) *
(z_p[1] - y.angle(PSI)))
# UPDATE CARTESIAN
# Dr. Izaguirre: I have checked and this constraint
# is correct. The energy is harmonic, but the force (the gradient)
# is not harmonic. In fact it is exactly what is in the paper.
prop[0].propagate(scheme="velocityscale",
steps=1,
dt=dt,
forcefield=ff,
