#============================================================#
#   test hinge torques for peptide plane and sidechains.     #
#============================================================#

system echo = off
system verbose = false

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

# open pdb file
#--------------
database open name = db1  format = pdb  file = ../../data/neck_xform.pdb

# read molecule
#--------------
molecule read  name = m1   database = db1

# create helix domain
#--------------------
domain create helix = C
#domain helix backbone color = [ 1 1 1 ]  width = 3 show


# peptide/sidechain 1 
#--------------------
domain create d1 = C[783-784]  peptide = true
domain d1 bonds atoms = true atom_color = element \
                bond_color = [ 1 0 0 ]  render = line show
domain d1 backbone color = [ 1 0.61 0 ] planes = true  width = 2 show
#-----
domain create d2 = C[784]  sidechain_group = true
domain d2 bonds atoms = true atom_color = [ 1 0 0 ] bond_color = [ 0.5 0 0 ] show


# peptide/sidechain 2 
#--------------------
domain create d3 = C[784-785]  peptide = true
domain d3 bonds atoms = true atom_color = element  bond_color = element   \
          render = line  show
domain d3 backbone  color = [ 0 1 0 ]  planes = true  
#-----
domain create d4 = C[785]  sidechain_group = true
domain d4 bonds atoms = true atom_color = [ 0 1 0 ] bond_color = [ 0 0.5 0 ] show


# peptide/sidechain 3 
#--------------------
domain create d5 = C[785-786]  peptide = true
domain d5 bonds atoms = true atom_color = element  bond_color = element   \
          render = line  show
domain d5 backbone  color = [ 0 1 0 ]  planes = true
#-----
domain create d6 = C[786]  sidechain_group = true
domain d6 bonds atoms = true atom_color = [ 1 1 0 ] bond_color = [ 0.5 0.5 0 ] show


#--------------------------------------------------------------#
#                add rigid bodies                              #
#--------------------------------------------------------------#

body create  name = ground    type = ground
body create  name = d1b  type = rigid  domain = d1
body create  name = d2b  type = rigid  domain = d2
body create  name = d3b  type = rigid  domain = d3
body create  name = d4b  type = rigid  domain = d4
body create  name = d5b  type = rigid  domain = d5
body create  name = d6b  type = rigid  domain = d6

#--------------------------------------------------------------#
#                add joints                                    #
#--------------------------------------------------------------#

#----------- jnt 1 ---------------
joint create  name = jnt1  type = weld domain = d1  res = C[783] use = C
#joint create  name = jnt1  type = ball domain = d1  res = C[783] use = C
joint jnt1 color = [ 1 1 1 ] msize = 0.01 shading = color show = true
joint jnt1 bodies = { ground d1b }

#----------- jnt 2&3 ---------------
joint create  name = jnt2  type = hinge  position = d2:C[784]:N      \
              use_bond = true  bond = { d2:C[784]:CA  d1:C[784]:N }
joint jnt2 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt2 bodies = { d1b d2b }
joint jnt2 force_constant = 4.0 

joint create  name = jnt3  type = hinge  position = d3:C[784]:C      \
              use_bond = true  bond = { d2:C[784]:CA  d3:C[784]:C }
joint jnt3 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt3 bodies = { d2b d3b }
joint jnt3 force_constant = 4.0 

#----------- jnt 4 & 5 ---------------
joint create  name = jnt4  type = hinge  position = d4:C[785]:N      \
              use_bond = true  bond = { d3:C[785]:N  d4:C[785]:CA }
joint jnt4 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt4 bodies = { d3b d4b }
joint jnt4 force_constant = 4.0 

joint create  name = jnt5  type = hinge  position = d5:C[785]:C      \
              use_bond = true  bond = { d4:C[785]:CA  d5:C[785]:C }
joint jnt5 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt5 bodies = { d4b d5b }
joint jnt5 force_constant = 4.0 

#----------- jnt 6 & 7 ---------------
joint create  name = jnt6  type = hinge  position = d6:C[786]:N      \
              use_bond = true  bond = { d5:C[786]:N  d6:C[786]:CA }
joint jnt6 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt6 bodies = { d5b d6b }
joint jnt6 force_constant = 4.0 

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

simulation create name = rsim  type = rigid

simulation rsim add bodies = all
simulation rsim add joints = all
#simulation rsim print  bodies = true  joints = true


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


# add forces
#-----------
force create  name = force1              \
              type = explicit            \
              point = d6:C[786]:CB       \
              global_frame = true        \
              direction = [ 0 0 1 ]   \
              scale = 1.0

simulation rsim add force = force1     \
                    body = d6b        \
                    time = { 0 1000 }

force create  name = force2              \
              type = explicit            \
              point = d5:C[785]:O        \
              global_frame = true        \
              direction = [ 0 0 -1 ]     \
              scale = 1.0

simulation rsim add force = force2     \
                    body = d5b        \
                    time = { 0 1000 }

# initialize simulation
#----------------------
simulation rsim initialize
simulation rsim time step = 0.001


graphics  center  point = [ 1.32939 2.57201 2.19204 ]