#============================================================*
#            test simulation of dna using cylinders          *
#============================================================*

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


# open pdb file
#--------------
database open name = dna  format = pdb  file = dna_bend.pdb 

# read molecule
#--------------
molecule read  database = dna name = m1  model = 1  type = dna 

# create domains 
#---------------
domain create helix = AB
# translate domain so that ground joint will be (0,0,0)
domain helix xform translation = [ 2.58377 -4.18649 -1.90172 ] 
#domain helix backbone color = [ 1 0 0 ] show = true
#domain helix bonds atoms = true  bond_color = element show = true

domain create dna_a = A
domain dna_a xform translation = [ 2.58377 -4.18649 -1.90172 ] 
domain dna_a backbone color = [ 1 0 0 ] width = 3 show = true
domain dna_a bonds atoms = false bond_color = element show = true

domain create dna_b = B
domain dna_b xform translation = [ 2.58377 -4.18649 -1.90172 ] 
domain dna_b backbone color = [ 0 1 0 ] width = 3 show = true
domain dna_b bonds atoms = false bond_color = element show = true


# create cylinders
#-----------------
solid create  name = cyl1  type = cylinder  \
              domain = helix                \
              region = A[6-16]B[156-166]    \
              color = [ 1 0 0 ]             \
              display = line                \
              show = true

solid create  name = cyl2  type = cylinder  \
              domain = helix                \
              region = A[16-26]B[146-156]   \
              allign = cyl1                 \
              allign_point = -1.0            \
              color = [ 0 1 0 ]             \
              display = line                \
              show = true

solid create  name = cyl3  type = cylinder  \
              domain = helix                \
              region = A[26-36]B[136-146]   \
              allign = cyl2                 \
              allign_point = 1.0           \
              color = [ 0 0 1 ]             \
              display = line                \
              show = true

solid create  name = cyl4  type = cylinder  \
              domain = helix                \
              region = A[36-46]B[126-136]   \
              allign = cyl3                 \
              allign_point = 1.0           \
              color = [ 0 1 1 ]             \
              display = line                \
              show = true

solid create  name = cyl5  type = cylinder  \
              domain = helix                \
              region = A[46-56]B[116-126]   \
              allign = cyl4                 \
              allign_point = 1.0           \
              color = [ 1 1 0 ]             \
              display = line                \
              show = true

# create bodies
#--------------
body create  name = ground    type = ground
body create  name = cyl1_body type = rigid  solid = cyl1
body create  name = cyl2_body type = rigid  solid = cyl2
body create  name = cyl3_body type = rigid  solid = cyl3
body create  name = cyl4_body type = rigid  solid = cyl4
body create  name = cyl5_body type = rigid  solid = cyl5


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

joint create  name = jnt1  type = ball  cylinder = cyl1  distance = 1.0
joint jnt1 color = [ 1 1 1 ] msize = 0.1 shading = color show = true
joint jnt1 bodies = { ground cyl1_body }

joint create  name = jnt2  type = ball cylinder = cyl2  distance = 0.0
joint jnt2 color = [ 1 0 0 ] msize = 0.1 shading = color show = true
joint jnt2 bodies = { cyl1_body cyl2_body }

joint create  name = jnt3  type = ball cylinder = cyl3  distance = 0.0
joint jnt3 color = [ 0 1 0 ] msize = 0.1 shading = color show = true
joint jnt3 bodies = { cyl2_body cyl3_body }

joint create  name = jnt4  type = ball  cylinder = cyl4  distance = 0.0
joint jnt4 color = [ 0 0 1 ] msize = 0.1 shading = color show = true
joint jnt4 bodies = { cyl3_body cyl4_body }

joint create  name = jnt5  type = ball  cylinder = cyl5  distance = 0.0
joint jnt5 color = [ 1 1 0 ] msize = 0.1 shading = color show = true
joint jnt5 bodies = { cyl4_body cyl5_body }


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

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


# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = cyl1_body
simulation rsim add body = cyl2_body
simulation rsim add body = cyl3_body
simulation rsim add body = cyl4_body
simulation rsim add body = cyl5_body

# add joints
#-----------
simulation rsim add joint = jnt1
simulation rsim add joint = jnt2
simulation rsim add joint = jnt3
simulation rsim add joint = jnt4
simulation rsim add joint = jnt5

# add forces
#-----------
force create  name = force1           \
              type = explicit         \
              point = [ 0 0 0 ]       \
              direction = [ 0 10 0 ]   \
              scale = 1.0

simulation rsim add force = force1    \
                    body = cyl5_body  \
                    time = { 0 1000 }

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

# step simulation
#----------------
#simulation rsim step = 500



graphics background color = [ 1 1 1 ]