#============================================================*
#              test hinge joint creation                       *
#============================================================*

# 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 = 4 show
domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 4 show
domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 4 show
domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 4 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                           #
#--------------------------------------------------------------#

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 \
joint jnt1 bodies = { ground iq1_body }

joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true 

joint create  name = jnt2           \
              type = hinge          \
              domain = hc           \
              res = C[788]          \
              use = CA              \
              use_pca = true        \
              pca_res = C[783-795]  \
              axis = pca2           \
joint jnt2 bodies = { iq1_body iq2_body }
joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color show = true

#----------------------------------

#joint create  name = jnt2r          \
              type = universal      \
              domain = hc           \
              res = C[788]          \
              use = CA              \
              use_pca = true        \
              pca_res = C[783-795]  \
              axis1 = pca2          \
              axis2 = pca3          \
              pca_rot = 45
#joint jnt2r bodies = { iq1_body iq2_body }
#joint jnt2r color = [ 1 1 1 ] msize = 0.1 shading = color show = true


#----------------------------------

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
joint jnt3 bodies = { iq2_body iq3_body }
joint jnt3 color = [ 0 0 1 ] msize = 0.1 shading = color show = true 

#graphics background color = [ 1 1 1 ]


#----------------------------#
# 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 = [ 10 0 0 ]
simulation rsim add force = force1 body = iq3_body  time = { 0 1 }

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

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