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xml_relax_after_ligMPNN.py
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165 lines (143 loc) · 6.62 KB
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XML_BSITE_REPACK_MIN = """
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="scorefxn_full" weights="beta_genpot">
<Reweight scoretype="coordinate_constraint" weight="0.5"/>
<Reweight scoretype="atom_pair_constraint" weight="0.3" />
</ScoreFunction>
<ScoreFunction name="scorefxn_soft" weights="beta_genpot_soft">
<Reweight scoretype="coordinate_constraint" weight="1.0"/>
<Reweight scoretype="fa_rep" weight="0.2"/>
<Reweight scoretype="atom_pair_constraint" weight="0.5" />
</ScoreFunction>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Index name="repack_res" resnums="{0}"/>
<Not name="fix_res" selector="repack_res"/>
<Chain name="chB" chains="B"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="dont_repack" selector="fix_res">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="repack_selected_res" selector="repack_res">
<RestrictToRepackingRLT/>
</OperateOnResidueSubset>
#
<InitializeFromCommandline name="init"/>
<ExtraRotamersGeneric name="ex1ex2" ex1="1" ex2="1"/>
</TASKOPERATIONS>
<FILTERS>
<ScoreType name="totalscore" scorefxn="scorefxn_full" threshold="9999999" confidence="1"/>
<ResidueCount name="nres" confidence="1" />
<CalculatorFilter name="res_totalscore" confidence="1" equation="SCORE/NRES" threshold="9999999">
<Var name="SCORE" filter_name="totalscore" />
<Var name="NRES" filter_name="nres" />
</CalculatorFilter>
<Ddg name="ddg" threshold="9999999" jump="1" repeats="1" repack="1" repack_bound="true" repack_unbound="true" relax_unbound="false" scorefxn="scorefxn_full"/>
ContactMolecularSurface name="cms" target_selector="chB" binder_selector="repack_res"/>
<ContactMolecularSurface name="cms" target_selector="chB" binder_selector="repack_res" use_rosetta_radii="true"/>
</FILTERS>
<MOVERS>
<AddConstraints name="add_ca_csts" >
<CoordinateConstraintGenerator name="coord_cst_gen" ca_only="true" native="true" align_reference="true"/>
</AddConstraints>
<ConstraintSetMover name="add_lig_d_csts" add_constraints="1" cst_file="{1}" />
<ConstraintSetMover name="rm_lig_d_csts" cst_file="none" />
<RemoveConstraints name="rm_csts" constraint_generators="coord_cst_gen"/>
<PackRotamersMover name="repack" scorefxn="scorefxn_full" task_operations="init,ex1ex2,repack_selected_res,dont_repack"/>
<PackRotamersMover name="repack_soft" scorefxn="scorefxn_soft" task_operations="init,ex1ex2,repack_selected_res,dont_repack"/>
MinMover name="min_full" bb="1" chi="1" jump="0" scorefxn="scorefxn_full"/>
<MinMover name="min_full" bb="1" chi="1" jump="ALL" scorefxn="scorefxn_full"/>
<MinMover name="min_soft" bb="1" chi="1" jump="ALL" scorefxn="scorefxn_soft"/>
</MOVERS>
<PROTOCOLS>
<Add mover="add_ca_csts"/>
<Add mover="add_lig_d_csts"/>
<Add mover="repack_soft"/>
<Add mover="min_soft"/>
<Add mover="repack"/>
<Add mover="min_full"/>
<Add mover="rm_csts"/>
<Add mover="rm_lig_d_csts"/>
Add filter="OH_hbond"/>
Add filter="HH_hbond"/>
Add filter="NE1_hbond"/>
Add filter="NZ_hbond"/>
<Add filter="ddg"/>
<Add filter="cms"/>
<Add filter="res_totalscore"/>
<Add filter="totalscore"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
"""
XML_BSITE_FASTRELAX = """
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="scorefxn_full" weights="beta_genpot">
<Reweight scoretype="coordinate_constraint" weight="0.5"/>
<Reweight scoretype="atom_pair_constraint" weight="0.5" />
</ScoreFunction>
<ScoreFunction name="scorefxn_soft" weights="beta_genpot_soft">
<Reweight scoretype="coordinate_constraint" weight="1.0"/>
<Reweight scoretype="fa_rep" weight="0.2"/>
<Reweight scoretype="atom_pair_constraint" weight="0.5" />
</ScoreFunction>
<ScoreFunction name="scorefxn_nocst" weights="beta_genpot">
<Reweight scoretype="coordinate_constraint" weight="0.0"/>
<Reweight scoretype="atom_pair_constraint" weight="0.0" />
</ScoreFunction>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Index name="repack_res" resnums="{0}"/>
<Not name="fix_res" selector="repack_res"/>
<Chain name="chB" chains="B"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="dont_repack" selector="fix_res">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="repack_selected_res" selector="repack_res">
<RestrictToRepackingRLT/>
</OperateOnResidueSubset>
#
<InitializeFromCommandline name="init"/>
<ExtraRotamersGeneric name="ex1ex2" ex1="1" ex2="1"/>
</TASKOPERATIONS>
<FILTERS>
<ScoreType name="totalscore" scorefxn="scorefxn_full" threshold="9999999" confidence="1"/>
<ResidueCount name="nres" confidence="1" />
<CalculatorFilter name="res_totalscore" confidence="1" equation="SCORE/NRES" threshold="999999">
<Var name="SCORE" filter_name="totalscore" />
<Var name="NRES" filter_name="nres" />
</CalculatorFilter>
<Ddg name="ddg_after_relax_cst" threshold="99999" jump="1" repeats="1" repack="1" repack_bound="true" repack_unbound="true" relax_unbound="false" scorefxn="scorefxn_full"/>
<Ddg name="ddg" threshold="99999" jump="1" repeats="1" repack="1" repack_bound="true" repack_unbound="true" relax_unbound="false" scorefxn="scorefxn_nocst"/>
ContactMolecularSurface name="cms" target_selector="chB" binder_selector="repack_res"/>
<ContactMolecularSurface name="cms" target_selector="chB" binder_selector="repack_res" use_rosetta_radii="true"/>
</FILTERS>
<MOVERS>
<AddConstraints name="add_ca_csts" >
<CoordinateConstraintGenerator name="coord_cst_gen" ca_only="true" native="true" align_reference="true"/>
</AddConstraints>
<ConstraintSetMover name="add_lig_d_csts" add_constraints="1" cst_file="{1}"/>
<ConstraintSetMover name="rm_lig_d_csts" cst_file="none"/>
<RemoveConstraints name="rm_csts" constraint_generators="coord_cst_gen"/>
<FastRelax name="fastrelax_cst" scorefxn="scorefxn_full" task_operations="init,ex1ex2,repack_selected_res,dont_repack" repeats="1" cst_file="{1}" />
<FastRelax name="fastrelax_nocst" scorefxn="scorefxn_nocst" task_operations="init,ex1ex2,repack_selected_res,dont_repack" repeats="1" />
</MOVERS>
<PROTOCOLS>
<Add mover="add_ca_csts"/>
<Add mover="add_lig_d_csts"/>
<Add mover="fastrelax_cst"/>
<Add mover="rm_csts"/>
<Add mover="rm_lig_d_csts"/>
<Add filter="ddg_after_relax_cst"/>
<Add mover="fastrelax_nocst"/>
<Add filter="ddg"/>
<Add filter="cms"/>
<Add filter="res_totalscore"/>
<Add filter="totalscore"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
"""