#============================================================#
# test macros for dna modeling                               #
#============================================================#
system echo = off
system verbose = false

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

# open pdb file
#--------------
database open name = dna  format = pdb  file = ../data/dna_strand.pdb 

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

# create domains 
#---------------
domain create dna = CD

# dna domain macro
#-----------------
macro dnaDomain (id, seq, color)
  domain create dna${id} = ${seq}           
  domain dna${id} backbone color = ${color} show = true
  domain dna${id} atoms  color = ${color}  atom_names = { P }  show = true 
end macro

dnaDomain(1,  C[1-10]D[1-10],      [ 1 0 0 ])
dnaDomain(2,  C[10-19]D[10-19],    [ 0 1 0 ])

# create bodies
#--------------
body create  name = ground    type = ground

body create  type = rigid                    \
             names   = { dna1Body dna2Body } \
             domains = { dna1  dna2  }


# create joints
#--------------
variable k1 = 10.0
variable k2 = 10.0
variable k3 = 10.0


# dna joint macro
#-----------------
macro dnaJoint (i, j, pos, pca_res, rev_axis)
  joint create  name = dna${i}${j}Jnt  type = ball position = dna${j}:${pos} \
        use_pca = true  pca_domain = dna   pca_res = ${pca_res}              \
        axis1 = pca1  axis2 = pca2  reverse_axes = ${rev_axis}               \
        force_const1 = ${k1}  force_const2 = ${k2} force_const3 = ${k3}
  joint dna${i}${j}Jnt color = [ 1 1 1 ] msize = 0.1 shading = color \
        show_axes = true  show = true
  joint dna${i}${j}Jnt bodies = { dna${i}Body dna${j}Body }
end macro


# joint btw bodies dna1Body and dna2Body
#---------------------------------------
dnaJoint (1, 2, C[10]D[10], C[6-14]D[6-14], true)


graphics  center  point = [-0.872131 -0.311066 4.23767]