pyrosetta_example

#Pyrosetta unsupported BuriedUnsatHbonds2 InterfaceHoles CavityVolume
pack_protocol = """<ROSETTASCRIPTS>
<SCOREFXNS>
  ### add Nov15 energy function with coordinate constraints
  <ScoreFunction name="NOV15" weights="beta" >
    <Reweight scoretype="coordinate_constraint" weight="1" />
  </ScoreFunction>
  <ScoreFunction name="VDW" weights="empty" >
    <Reweight scoretype="fa_atr" weight="1.0" />
  </ScoreFunction>
  ### ADDED FOR SCORING FILTERS
  <ScoreFunction name="TotalHydrophobic" weights="/home/fseeger/PPI_Benchmark/Design_Scripts/total_hydrophobic_weights.wts"/>
</SCOREFXNS>

<RESIDUE_SELECTORS>
    Layer name="core" select_core="true" use_sidechain_neighbors="false" core_cutoff="35" />  
    <Layer name="core" select_core="true" use_sidechain_neighbors="true" core_cutoff="3.6" />  
    ### select chain A
    <Chain name="chainA" chains="A"/>
    ### select chain B
    <Chain name="chainB" chains="B"/>
    ### select interface of chainB close within 8.0 A of chainA 
    <Neighborhood name="interface_chA" selector="chainB" distance="8.0"/>
    ### select interface of chainA close within 8.0 A of chainB 
    <Neighborhood name="interface_chB" selector="chainA" distance="8.0"/>
    ### select intersection of chain A and Chain B interface
    <And name="AB_interface" selectors="interface_chA,interface_chB" />
    ### select everything but the designable interface residues
    <Not name="Not_interface" selector="AB_interface" />
    ### select the core and the interface
    <And name="core_and_interface" selectors="core,AB_interface" /> 
    
    <InterfaceByVector name="interface_by_vec" cb_dist_cut="11" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="9" 
        grp1_selector="chainA" grp2_selector="chainB"/>
    <And name="core_and_interface_by_vec" selectors="interface_by_vec,core" />    


</RESIDUE_SELECTORS>

<SIMPLE_METRICS>
	<SelectedResiduesPyMOLMetric name="AB_interface" residue_selector="AB_interface" custom_type="AB_interface" />
    <SelectedResiduesPyMOLMetric name="core_and_interface" residue_selector="core_and_interface" custom_type="core_and_interface" />
    <SelectedResiduesPyMOLMetric name="interface_by_vec" residue_selector="interface_by_vec" custom_type="interface_by_vec" />
    <SelectedResiduesPyMOLMetric name="core_and_interface_by_vec" residue_selector="core_and_interface_by_vec" custom_type="core_and_interface_by_vec" />
</SIMPLE_METRICS>


<TASKOPERATIONS>
</TASKOPERATIONS>
<FILTERS>
</FILTERS>

<MOVERS>
    <RunSimpleMetrics name="run_metrics_selection" metrics="AB_interface,core_and_interface,interface_by_vec,core_and_interface_by_vec" prefix="" />
</MOVERS>

<PROTOCOLS>
    <Add mover="run_metrics_selection" />
</PROTOCOLS>
    <OUTPUT />
</ROSETTASCRIPTS>"""
task_design = rosetta_scripts.SingleoutputRosettaScriptsTask(pack_protocol)
# Syntax check via setup
logging.basicConfig(level=logging.WARN)
task_design.setup()
raw_input_pose = io.pose_from_file(filename="data/ZCON_37_N3_C1_2.pdb")
output_pose = task_design(raw_input_pose)
output_pose.scores