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2
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1 # Template for packmol in Galaxy
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2 #
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3
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4 tolerance {{ allparams.tolerance }}
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5 nloop {{ allparams.nloop }}
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6 maxit {{ allparams.maxit }}
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7 seed {{ allparams.seed }}
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8 filetype pdb
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9 output {{outfile}}
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10
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11 {% for struct in packmol_inputs %}
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12 structure {{struct.file}}
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13 # Galaxy datasetname - {{struct.datasetname}}
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14 number {{struct.structureparams.number}}
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15 radius {{struct.structureparams.radius}}
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16 resnumbers {{struct.structureparams.resnumbers}}
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17 {% for c in struct.structureparams.constraints_repeat %}
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18 {% if c.constraints.constraint == 'fixed' %}
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19 {% if c.constraints.center == 'Yes' %}
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20 center
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21 {% endif %}
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22 {{c.constraints.constraint}} {{c.constraints.x}} {{c.constraints.y}} {{c.constraints.z}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.g}}
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23 {% elif c.constraints.constraint == 'cube' %}
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24 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.d}}
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25 {% elif c.constraints.constraint == 'box' %}
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26 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.xmin}} {{c.constraints.ymin}} {{c.constraints.zmin}} {{c.constraints.xmax}} {{c.constraints.ymax}} {{c.constraints.zmax}}
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27 {% elif c.constraints.constraint == 'sphere' %}
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28 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
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29 {% elif c.constraints.constraint == 'ellipsoid' %}
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30 {{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}}
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31 {% elif c.constraints.constraint == 'plane' %}
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32 {{c.constraints.placement}} {{c.constraints.constraint}} {{c.constraints.a}} {{c.constraints.b}} {{c.constraints.c}} {{c.constraints.d}}
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33 {% elif c.constraints.constraint == 'cylinder' %}
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34 {{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}}
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35 {% else %}
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36 unknowntype specified {{c.constraints}}
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37 {% endif %}
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38 {% endfor %}
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39 end structure
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40
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41 {% endfor %}
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42
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