#============================================================*
#                test for protein                            *
#============================================================*
system echo = off
system verbose = false

# set units
#----------
units
units scale  name = mass   uname = reducedMass   value = 10000.0

# read molecule 
#--------------
database open name = neck   format = pdb  file = ../../../data/neck_xform.pdb
molecule read  name = protein  database = neck
molecule protein  xform  rotation = [ 0 0 40 ] 

# create domains
#---------------
domain create hc = C
#domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 2 show
domain create d1 = C[783-795]

domain create iq1 = C[760-788]
#domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
#domain iq1 atoms color = [ 1 0 0 ] show

domain create iq2 = C[788-814]
#domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
#domain iq2 atoms color = [ 0 1 0 ] render = line show

domain iq2 pca  show = true


# create bodies from domains
#---------------------------
body create  name = ground    type = ground
body create  name = iq1_body  type = rigid   domain = iq1
body create  name = iq2_body  type = rigid   domain = iq2

# create joints 
#--------------

# 1st joint 
# ---------
joint create  name = jnt1   type = weld position = hc:C[760]:CA 
joint jnt1 bodies = { ground iq1_body }
joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 

# 2nd joint 
# ---------
variable k = 20
joint create  name = jnt2  type = ball  domain = hc  res = C[788]  use = CA  \
              force_const1 = ${k}  force_const2 = ${k} force_const3 = ${k}
joint jnt2 bodies = { iq1_body iq2_body }
joint jnt2 color = [ 1 0 1 ] msize = 0.05 shading = flat show = true


# create a rigid simulation
#--------------------------
simulation create name = rsim  type = rigid


# add bodies
#-----------
simulation rsim add bodies = { ground  iq1_body iq2_body }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 }


# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on

# add forces
#-----------
#force create name = force1  type = explicit point = [ 0.2 0 0 ] direction = [ 0 0 5 ]  
#simulation rsim add force = force1 body = iq2_body  time = { 0 1 }

force create name = force2  type = explicit torque = true \
      point = [ 0 0 0 ] direction = [ -0.82512 9.38027 3.36597 ]  
simulation rsim add force = force2 body = iq2_body  time = { 0 1 }



# initialize simulation
#----------------------
simulation rsim initialize
#simulation state save_frequency = 10
simulation rsim momentum = on 
simulation rsim time step = 0.005