Module _protocols_docking_

calc_CA_Irmsd( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
    calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms
    

    C++ signature :
        double calc_CA_Irmsd(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)

calc_Fnat( (Pose)pose, (str)list_file, (vector1_int)movable_jumps) -> float :
    Calculates the fraction of native contacts from the given native contacts pair list
    

    C++ signature :
        double calc_Fnat(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> >)

calc_Fnat( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
    Calculates the fraction of native contacts recovered between the input and native pose.  A native-contact is defined
    as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure
    

    C++ signature :
        double calc_Fnat(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)

calc_Fnonnat( (Pose)pose, (str)list_file, (vector1_int)movable_jumps) -> float :
    Calculates the fraction of non-native contacts from the given native contacts pari list
    

    C++ signature :
        double calc_Fnonnat(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> >)

calc_Fnonnat( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
    Calculates the fraction of non-native contacts recovered between the input and native pose.  A native-contact is defined
    as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact
    

    C++ signature :
        double calc_Fnonnat(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)

calc_Irmsd( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
    Calculates the all-atom RMSD of all residues within 5A of the interface at superposition along those same atoms
    

    C++ signature :
        double calc_Irmsd(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)

calc_Lrmsd( (Pose)pose, (Pose)native_pose, (vector1_int)movable_jumps) -> float :
    Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner
    

    C++ signature :
        double calc_Lrmsd(core::pose::Pose,core::pose::Pose,utility::vector1<int, std::allocator<int> >)

calc_interaction_energy( (Pose)pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
    Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other
    

    C++ signature :
        double calc_interaction_energy(core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)

calc_res_contact( (Residue)rsd1, (Residue)rsd2, (float)dist_cutoff) -> bool :
    protocols/docking/metrics.hh:66

    C++ signature :
        bool calc_res_contact(boost::shared_ptr<core::conformation::Residue>,boost::shared_ptr<core::conformation::Residue>,double)

setup_foldtree( (Pose)pose, (int)cutpoint, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
    protocols/docking/util.hh:96

    C++ signature :
        void setup_foldtree(core::pose::Pose,unsigned long,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})

setup_foldtree( (Pose)pose, (int)cutpoint, (vector1_int)movable_jumps) -> None :
    Sets up a docking fold tree based on user-specified chains for the first and second partner
    

    C++ signature :
        void setup_foldtree(core::pose::Pose {lvalue},unsigned long,utility::vector1<int, std::allocator<int> > {lvalue})

setup_foldtree( (Pose)pose, (object)partner_to_chains, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
    protocols/docking/util.hh:81

    C++ signature :
        void setup_foldtree(core::pose::Pose,std::map<unsigned long, utility::vector1<unsigned long, std::allocator<unsigned long> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, utility::vector1<unsigned long, std::allocator<unsigned long> > > > >,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})

setup_foldtree( (Pose)pose, (object)partner_to_chains, (vector1_int)movable_jumps) -> None :
    Sets up a docking fold tree based on a map of which chains
    are part of which partner
    

    C++ signature :
        void setup_foldtree(core::pose::Pose {lvalue},std::map<unsigned long, utility::vector1<unsigned long, std::allocator<unsigned long> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, utility::vector1<unsigned long, std::allocator<unsigned long> > > > >,utility::vector1<int, std::allocator<int> > {lvalue})

setup_foldtree( (Pose)pose, (int)interface_id, (object)db_session, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
    protocols/docking/util.hh:65

    C++ signature :
        void setup_foldtree(core::pose::Pose,unsigned long,boost::shared_ptr<utility::sql_database::session>,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})

setup_foldtree( (Pose)pose, (int)interface_id, (object)db_session, (vector1_int)movable_jumps) -> None :
    Sets up a docking fold tree based on looking up the
    interface in a database
    

    C++ signature :
        void setup_foldtree(core::pose::Pose {lvalue},unsigned long,boost::shared_ptr<utility::sql_database::session>,utility::vector1<int, std::allocator<int> > {lvalue})

setup_foldtree( (Pose)pose, (str)partner_chainID, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
    protocols/docking/util.hh:47

    C++ signature :
        void setup_foldtree(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})

setup_foldtree( (Pose)pose, (str)partner_chainID, (vector1_int)movable_jumps) -> None :
    Sets up a docking fold tree based on user-specified chains for the first and second partner
    

    C++ signature :
        void setup_foldtree(core::pose::Pose {lvalue},std::string,utility::vector1<int, std::allocator<int> > {lvalue})