#============================================================*
#                test universal joints                       *
#============================================================*

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

# read molecule 
#--------------
database open name = neck   format = pdb  file = neck_xform.pdb
molecule read  name = protein  database = neck

# create domains
#---------------
domain create hc = C
domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 2 show
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 iq1h = C[760-788]
domain iq1h atoms color = [ 1 0 0 ] show

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
domain iq2 atoms color = [ 0 1 0 ] render = solid show
domain create iq2h = C[788-814]
domain iq2h atoms color = [ 0 1 0 ] render = line show

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show
domain iq3 atoms color = [ 0 0 1 ] render = solid show


# 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
body create  name = iq3_body  type = rigid   domain = iq3

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

# 1st joint 
# ---------
joint create  name = jnt1   type = universal domain = hc  res = C[760]  use = CA \
              use_pca = true pca_res = C[760-775]  axis1 = pca2  axis2 = pca3  \
              force_const1 = 20.0  force_const2 = 20.0
joint jnt1 bodies = { ground iq1_body }
#joint jnt1 color = [ 1 0 0 ] msize = 0.1 display = point shading = flat show = true 
joint jnt1 color = [ 1 0 0 ] msize = 0.1 width = 4 display = line shading = flat \
           show = true 
#joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = flat show = true 
#joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 


# 2nd joint 
# ---------
joint create  name = jnt2  type = universal  domain = hc  res = C[788]  use = CA  \
              use_pca = true  pca_res = C[783-795]  axis1 = pca2  axis2 = pca3  \ 
              force_const1 = 10.0  force_const2 = 20.0
joint jnt2 bodies = { iq1_body iq2_body }
#joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color display = line show = true
joint jnt2 color = [ 1 0 1 ] msize = 0.3 shading = flat show = true


# 3rd joint 
# ---------
joint create  name = jnt3  type = universal domain = hc  res = C[814]  use = CA  \
              use_pca = true  pca_res = C[809-824]  axis1 = pca2  axis2 = pca3 \
              force_const1 = 10.0  force_const2 = 20.0
joint jnt3 bodies = { iq2_body iq3_body }
joint jnt3 color = [ 0 0 1 ] msize = 0.1 shading = color show = true 

#----------------------------#
# create a rigid simulation  #
#----------------------------#

simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add bodies = { ground  iq1_body iq2_body iq3_body }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 jnt3 }

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

# add forces
#-----------
force create name = force1  type = explicit point = [ 0 0 0 ] direction = [ 1.5 0 0 ]  
simulation rsim add force = force1 body = iq3_body  time = { 0 5 }

# initialize simulation
#----------------------
simulation rsim initialize
simulation state save_frequency = 10

# step simulation
#----------------
#simulation rsim step = 200


graphics background color = [ 1 1 1 ]