Mercurial > repos > fmercuri > packmol_daimoners
diff template.j2 @ 2:bd6ee225b770 draft default tip
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| author | fmercuri |
|---|---|
| date | Wed, 23 Jun 2021 21:28:40 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template.j2 Wed Jun 23 21:28:40 2021 +0000 @@ -0,0 +1,42 @@ +# 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 %} +