# Template for packmol in Galaxy
#  

tolerance {{ allparams.tolerance }}
nloop  {{ allparams.nloop }} 
maxit  {{ allparams.maxit }} 
seed  {{ allparams.seed }} 
filetype pdb 
output {{outfile}}

{% for struct in packmol_inputs %}
structure {{struct.file}}
# Galaxy datasetname - {{struct.datasetname}}
  number {{struct.structureparams.number}}
  radius {{struct.structureparams.radius}}
  resnumbers {{struct.structureparams.resnumbers}} 
{% for c in struct.structureparams.constraints_repeat %}
  {% if c.constraints.constraint == 'fixed' %}
   {% if c.constraints.center == 'Yes' %}
  center
   {% endif %}
  {{c.constraints.constraint}} {{c.constraints.x}} {{c.constraints.y}} {{c.constraints.z}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.g}}
  {% elif c.constraints.constraint == 'cube' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.d}}
  {% elif c.constraints.constraint == 'box' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.xmax}} {{c.constraints.ymax}} {{c.constraints.zmax}} 
  {% elif c.constraints.constraint == 'sphere' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
  {% elif c.constraints.constraint == 'ellipsoid' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} 
  {% elif c.constraints.constraint == 'plane' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
  {% elif c.constraints.constraint == 'cylinder' %}
  {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a1}} {{c.constraints.b1}} {{c.constraints.c1}} {{c.constraints.a2}} {{c.constraints.b2}} {{c.constraints.c2}} {{c.constraints.d}} {{c.constraints.l}}
  {% else %}
 unknowntype specified {{c.constraints}}
{% endif %}
{% endfor %}
end structure

{% endfor %}