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<paradocks> <!-- root node -->
<optimizer type="pso"> <!-- type of the optimizer (cpso as example) -->
<par val="150000"/> <!-- iterations -->
<par val="20"/> <!-- particle count -->
<par val="1"/> <!-- constricting inertia start -->
<par val="0.2"/> <!-- constricting inertia end -->
<par val="1"/> <!-- cognitive weight -->
<par val="3.4"/> <!-- social weight -->
<!-- the number of parameter is not restricted -->
<!-- but it has to be equal to the number of paramters which the optimizer expects -->
<fitness type="pscore"> <!-- type of the fitness function -->
<!-- protein input with coordinates and radius of the active site -->
<protein file="/home/rene/astex_diverse_set/1sq5/protein.mol2" x="53.7351" y="-41.3871" z="2.92896" rad="15"/>
<!-- arbitrary number of ligand files with index for multi mol2 files -->
<ligand file="/home/rene/astex_diverse_set/1sq5/ligand.mol2" idx="1"/>
<!-- random seed, 0 means seed with system time -->
<random seed="0"/>
<!-- number of consecutive runs -->
<runs val="30"/>
<!-- every run will create a outputfile -->
<!-- the name is prefix_protein_ligand_idx_run.xml -->
<!-- output during each iteration, posible values are: none, best, all -->
<iteration val="none"/>
<!-- structure output at the end, posible values are: best, all-->
<end val="best"/>
<!--prefix for the output files-->
<prefix val="./result"/>