#============================================================*
#         test surface transofrmation                        *
#============================================================*

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

# open pdb file
database open name =  neck_xform  format = pdb file =  ../../data/two_necks.pdb

# read molecule
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains
domain create hc = C
#domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 2 show
domain create iq1 = C[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
domain create iq2 = C[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
domain iq3 surface read format = pm file = sasa/camD_surf.pm
domain iq3 surface color = [ 0.3 0.3 1.0 ] render = color 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 group
joint create  name = jnt1   type = ball    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 

joint create  name = jnt2   type = ball    domain = hc    res = C[788]    use = CA
joint jnt2 bodies = { iq1_body iq2_body }
joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color show = true

joint create  name = jnt3   type = ball    domain = hc    res = C[814]    use = CA
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 random forces
#------------------
force create name = force1        \
             type = random        \
             mean = 0.0           \
             sd = 500.0           \
             seed = 147321        \
             scale = 0.1

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


# add directed forces
#--------------------
force create name = force2           \
             type = explicit         \
             point = [ 0 0 0 ]       \
             direction = [ 1 0 0 ]  \
             scale = 0.01

simulation rsim add force = force2    \
                    body = iq3_body   \
                    time = { 0 20 }


# initialize simulation
#----------------------
simulation rsim initialize
#simulation rsim momentum = off
simulation rsim time step = 0.02
simulation state save_frequency = 10 


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

graphics background color = [ 1 1 1 ]