#============================================================*
#                   test ball joints                         *
#============================================================*

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

# open pdb file
database open name = neck   format = pdb  file = neck_xform.pdb

# read protein molecule
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 create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show


#--------------------------------------------------------------#
#                      create bodies                           #
#--------------------------------------------------------------#
# 1st group
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 = ball  domain = hc  res = C[760]  use = CA \
              use_pca = true  pca_res = C[760-775] axis1 = pca1  axis2 = pca2 \
              axis3 = pca3 force_const1 = 1.0  force_const2 = 2.0 force_const3 = 2.0

joint create  name = jnt1   type = weld domain = hc  res = C[760]  use = CA

joint jnt1 bodies = { ground iq1_body }
joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 

# 2nd joint
#----------
joint create  name = jnt2   type = ball domain = hc  res = C[788]     use = CA  \
              use_pca = true  pca_res = C[783-795]  axis1 = pca1  axis2 = pca2  \
              axis3 = pca3 force_const1 = 1.0  force_const2 = 2.0 force_const3 = 2.0

joint jnt2 bodies = { iq1_body iq2_body }
joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color show = true


# 3rd joint
#----------
joint create  name = jnt3   type = ball    domain = hc    res = C[814]     use = CA \
              use_pca = true  pca_res = C[809-824]  axis1 = pca1  axis2 = pca2    \
              axis3 = pca3 force_const1 = 1.0  force_const2 = 2.0 force_const3 = 2.0
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 body = ground
simulation rsim add body = iq1_body
simulation rsim add body = iq2_body
simulation rsim add body = iq3_body


# add joints
#-----------
simulation rsim add joint = jnt1
simulation rsim add joint = jnt2
simulation rsim add joint = 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 = [ 2 0 0 ]   \
             scale = 1.0

simulation rsim add force = force1    \
                    body = iq3_body   \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize


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