Module _protocols_ligand_docking_

add_ligand_conditionally( (Ligand_info)ligand_info, (object)ligands, (int)heavy_atom_number) -> None :
    protocols/ligand_docking/Rotate.hh:155

    C++ signature :
        void add_ligand_conditionally(protocols::ligand_docking::Ligand_info,utility::vector1<protocols::ligand_docking::Ligand_info, std::allocator<protocols::ligand_docking::Ligand_info> > {lvalue},unsigned long)

append_automorphic_rmsd( (int)ligand_residue_id, (__CPP_Job__)job, (Pose)before, (Pose)after, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:114

    C++ signature :
        void append_automorphic_rmsd(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,core::pose::Pose,std::string)

append_interface_deltas( (int)jump_id, (__CPP_Job__)job, (Pose)after, (__CPP_ScoreFunction__)scorefxn, (str)prefix, (object)normalization_function) -> None :
    protocols/ligand_docking/ligand_scores.hh:53

    C++ signature :
        void append_interface_deltas(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction>,std::string,boost::shared_ptr<protocols::qsar::scoring_grid::ScoreNormalization>)

append_interface_deltas( (int)jump_id, (__CPP_Job__)job, (Pose)after, (__CPP_ScoreFunction__)scorefxn, (str)prefix) -> None :
    append interface_delta scores
    

    C++ signature :
        void append_interface_deltas(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction>,std::string)

append_ligand_RMSD( (int)jump_id, (__CPP_Job__)job, (Pose)before, (Pose)after, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:96

    C++ signature :
        void append_ligand_RMSD(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,core::pose::Pose,std::string)

append_ligand_grid_scores( (int)jump_id, (__CPP_Job__)job, (Pose)after, (str)prefix, (object)normalization_function) -> None :
    protocols/ligand_docking/ligand_scores.hh:79

    C++ signature :
        void append_ligand_grid_scores(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,std::string,boost::shared_ptr<protocols::qsar::scoring_grid::ScoreNormalization>)

append_ligand_grid_scores( (int)jump_id, (__CPP_Job__)job, (Pose)after, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:70

    C++ signature :
        void append_ligand_grid_scores(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,std::string)

append_ligand_travel( (int)jump_id, (__CPP_Job__)job, (Pose)before, (Pose)after, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:62

    C++ signature :
        void append_ligand_travel(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,core::pose::Pose,std::string)

append_multi_residue_ligand_RMSD( (int)jump_id, (__CPP_Job__)job, (Pose)before, (Pose)after, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:105

    C++ signature :
        void append_multi_residue_ligand_RMSD(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,core::pose::Pose,std::string)

append_radius_of_gyration( (int)jump_id, (__CPP_Job__)job, (Pose)before, (str)prefix) -> None :
    protocols/ligand_docking/ligand_scores.hh:87

    C++ signature :
        void append_radius_of_gyration(unsigned long,boost::shared_ptr<protocols::jd2::Job>,core::pose::Pose,std::string)

apply_rotate( (__CPP_RigidBodyMover__)mover, (Pose)pose, (xyzVector_Real)center, (int)jump_id, (vector1_Size)tag_along_chains) -> None :
    protocols/ligand_docking/Rotate.hh:149

    C++ signature :
        void apply_rotate(boost::shared_ptr<protocols::rigid::RigidBodyMover>,core::pose::Pose {lvalue},numeric::xyzVector<double>,unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >)

check_RMSD( (Ligand_info)ligand, (int)heavy_atom_number, (object)ligands) -> bool :
    protocols/ligand_docking/Rotate.hh:141

    C++ signature :
        bool check_RMSD(protocols::ligand_docking::Ligand_info,unsigned long,utility::vector1<protocols::ligand_docking::Ligand_info, std::allocator<protocols::ligand_docking::Ligand_info> >)

check_score( (Ligand_info)ligand, (int)heavy_atom_number) -> bool :
    Convenience Functions for use with Rotate
    

    C++ signature :
        bool check_score(protocols::ligand_docking::Ligand_info,unsigned long)

constrain_ligand_torsions( (Pose)pose, (float)stddev_degrees [, (bool)constrain_all_torsions_equally=True]) -> None :
    Call get_ligand_torsion_constraints() for all non-polymer residues
    and add the resulting constraints to the Pose.
    

    C++ signature :
        void constrain_ligand_torsions(core::pose::Pose {lvalue},double [,bool=True])

find_attach_pt( (int)jump_id, (object)interface, (Pose)pose) -> int :
    protocols/ligand_docking/MinimizeBackbone.hh:130

    C++ signature :
        unsigned long find_attach_pt(unsigned long,protocols::ligand_docking::ligand_options::Interface,core::pose::Pose)

find_peptide_attach_pt( (int)start, (int)stop, (map_Size_Size)jump_to_attach) -> int :
    protocols/ligand_docking/MinimizeBackbone.hh:137

    C++ signature :
        unsigned long find_peptide_attach_pt(int,int,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)

find_unconnected_residues( (Pose)pose, (int)start, (int)end) -> vector1_Size :
    protocols/ligand_docking/LigandDesign.hh:78

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > find_unconnected_residues(core::pose::Pose,unsigned long,unsigned long)

frac_atoms_within( (Residue)rsd1, (Residue)rsd2, (vector1_Real)cutoffs, (vector1_Real)fractions_out) -> None :
    Without superimposing, automorphically computes the fraction of atoms
    in these residues that are within the given cutoff(s) of each other.
    

    C++ signature :
        void frac_atoms_within(core::conformation::Residue,core::conformation::Residue,utility::vector1<double, std::allocator<double> >,utility::vector1<double, std::allocator<double> > {lvalue})

generate_unique_name([  (str)input_name='']) -> str :
    protocols/ligand_docking/AddHydrogen.hh:54

    C++ signature :
        std::string generate_unique_name([ std::string=''])

get_distribution( (str)distribution_str) -> Distribution :
    protocols/ligand_docking/DistributionMap.hh:79

    C++ signature :
        protocols::ligand_docking::Distribution get_distribution(std::string)

get_incomplete_connections( (Residue)residue) -> vector1_Size :
    protocols/ligand_docking/LigandDesign.hh:77

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > get_incomplete_connections(boost::shared_ptr<core::conformation::Residue const>)

get_ligand_seqpos( (Pose)pose) -> vector1_Size :
    simple function to scan the pose for all ligand residues
    

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > get_ligand_seqpos(core::pose::Pose)

get_ligand_torsion_constraints( (Pose)pose, (int)rsd_no, (float)stddev_degrees, (object)csts_out, (bool)constrain_all_torsions_equally) -> None :
    Produce dihedral restraints for all chi angles in the specified
    residue, from chi_rotamers() if available, and from the rotamer library otherwise.
    

    C++ signature :
        void get_ligand_torsion_constraints(core::pose::Pose {lvalue},unsigned long,double,utility::vector1<boost::shared_ptr<core::scoring::constraints::Constraint>, std::allocator<boost::shared_ptr<core::scoring::constraints::Constraint> > > {lvalue},bool)

get_rb_atr_and_rep_scores( (object)grid, (Pose)pose, (int)begin, (int)end) -> pair_int_int :
    a cleaner implementation of rb_grid_score_atr_rep
    

    C++ signature :
        std::pair<int, int> get_rb_atr_and_rep_scores(core::grid::CartGrid<int>,core::pose::Pose,unsigned long,unsigned long)

grid_rotamer_trials( (object)grid, (Pose)pose, (int)rsd_no [, (int)min_score=0]) -> None :
    Try all rotamers for the specified residue and install the first one
    that minimizes the grid score.  Only tested with ligand residues w/ a conformer library.
    

    C++ signature :
        void grid_rotamer_trials(core::grid::CartGrid<int>,core::pose::Pose {lvalue},unsigned long [,int=0])

grid_rotamer_trials_atr_rep( (object)grid, (Pose)pose, (int)rsd_no) -> None :
    Try all rotamers for the specified residue and install the first one
    that minimizes the repulsive score, breaking ties by the attractive score.
    Only tested with ligand residues w/ a conformer library.
    

    C++ signature :
        void grid_rotamer_trials_atr_rep(core::grid::CartGrid<int>,core::pose::Pose {lvalue},unsigned long)

grid_score( (object)grid, (Residue)rsd [, (int)max_score=9999]) -> int :
    Sum the grid values for all heavy atoms in the residue
    

    C++ signature :
        int grid_score(core::grid::CartGrid<int>,core::conformation::Residue [,int=9999])

grid_score_atr_rep( (object)grid, (Residue)rsd, (int)atr_out, (int)rep_out [, (int)max_rep=9999]) -> None :
    Sum the grid values for all heavy atoms in the residue
    

    C++ signature :
        void grid_score_atr_rep(core::grid::CartGrid<int>,core::conformation::Residue,int {lvalue},int {lvalue} [,int=9999])

grow( (Pose), (int)start, (int)end) -> bool :
    protocols/ligand_docking/LigandDesign.hh:73

    C++ signature :
        bool grow(core::pose::Pose,unsigned long,unsigned long)

has_incomplete_connections( (Pose)pose, (int)start, (int)end) -> bool :
    protocols/ligand_docking/LigandDesign.hh:74

    C++ signature :
        bool has_incomplete_connections(core::pose::Pose,unsigned long,unsigned long)

make_atr_rep_grid( (Pose)pose, (xyzVector_Real)center) -> object :
    Make a grid around the specified point with attractive (negative)
    and repulsive (positive) values for the protein backbone.
    

    C++ signature :
        boost::shared_ptr<core::grid::CartGrid<int> > make_atr_rep_grid(core::pose::Pose,numeric::xyzVector<double>)

make_atr_rep_grid_without_ligand( (Pose)pose, (xyzVector_Real)center, (int)ligand_chain_id_to_exclude) -> object :
    Make a grid around the specified point with attractive (negative)
    and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude
    

    C++ signature :
        boost::shared_ptr<core::grid::CartGrid<int> > make_atr_rep_grid_without_ligand(core::pose::Pose,numeric::xyzVector<double>,unsigned long)

make_atr_rep_grid_without_ligands( (Pose)pose, (xyzVector_Real)center, (vector1_Size)ligand_chain_ids_to_exclude) -> object :
    Make a grid around the specified point with attractive (negative)
    and repulsive (positive) values for all heavy atoms not in ligand_chain_ids_to_exclude
    

    C++ signature :
        boost::shared_ptr<core::grid::CartGrid<int> > make_atr_rep_grid_without_ligands(core::pose::Pose,numeric::xyzVector<double>,utility::vector1<unsigned long, std::allocator<unsigned long> >)

move_ligand_neighbor_to_desired_position( (str)chain, (xyzVector_Real)desired_position, (Pose)pose) -> None :
    Move the neighbor atom of the specified chain to the desired_position
    

    C++ signature :
        void move_ligand_neighbor_to_desired_position(std::string,numeric::xyzVector<double>,core::pose::Pose {lvalue})

move_ligand_to_desired_centroid( (int)jump_id, (xyzVector_Real)desired_centroid, (Pose)pose) -> None :
    Move the center of the object(s) downstream of jump_id to the desired_centroid
    

    C++ signature :
        void move_ligand_to_desired_centroid(unsigned long,numeric::xyzVector<double>,core::pose::Pose {lvalue})

move_ligand_to_desired_centroid( (str)chain, (xyzVector_Real)desired_centroid, (Pose)pose) -> None :
    Move the center of specified chain to the desired_centroid
    

    C++ signature :
        void move_ligand_to_desired_centroid(std::string,numeric::xyzVector<double>,core::pose::Pose {lvalue})

passes_filters( (Pose)pose, (int)start, (int)end) -> bool :
    protocols/ligand_docking/LigandDesign.hh:75

    C++ signature :
        bool passes_filters(core::pose::Pose,unsigned long,unsigned long)

random_connection( (Residue)residue) -> int :
    protocols/ligand_docking/LigandDesign.hh:76

    C++ signature :
        unsigned long random_connection(boost::shared_ptr<core::conformation::Residue const>)

rb_grid_rotamer_trials_atr_rep( (object)grid, (Pose)pose, (int)begin, (int)end) -> None :
    protocols/ligand_docking/grid_functions.hh:82

    C++ signature :
        void rb_grid_rotamer_trials_atr_rep(core::grid::CartGrid<int>,core::pose::Pose {lvalue},unsigned long,unsigned long)

rb_grid_score_atr_rep( (object)grid, (Pose)pose, (int)begin, (int)end, (int)atr_out, (int)rep_out [, (int)max_rep=9999]) -> None :
    Sum the grid values for all heavy atoms in the residue
    

    C++ signature :
        void rb_grid_score_atr_rep(core::grid::CartGrid<int>,core::pose::Pose,unsigned long,unsigned long,int {lvalue},int {lvalue} [,int=9999])

reorder_with_first_non_mobile_as_root( (FoldTree)f, (object)interface, (Pose)pose) -> None :
    protocols/ligand_docking/MinimizeBackbone.hh:124

    C++ signature :
        void reorder_with_first_non_mobile_as_root(boost::shared_ptr<core::kinematics::FoldTree>,protocols::ligand_docking::ligand_options::Interface,core::pose::Pose {lvalue})

restrain_ligand_nbr_atom( (int)lig_id, (float)stddev_Angstroms, (Pose)pose) -> Constraint :
    protocols/ligand_docking/TetherLigand.hh:66

    C++ signature :
        boost::shared_ptr<core::scoring::constraints::Constraint const> restrain_ligand_nbr_atom(unsigned long,double,core::pose::Pose {lvalue})

restrict_to_protein_residues( (object)interface, (Pose)pose) -> None :
    protocols/ligand_docking/MinimizeBackbone.hh:118

    C++ signature :
        void restrict_to_protein_residues(protocols::ligand_docking::ligand_options::Interface {lvalue},core::pose::Pose)

rotamers_for_trials( (Pose)pose, (int)rsd_no, (object)conformers_out) -> None :
    Internal helper function for rotamer trials;  fills conformers_out.
    

    C++ signature :
        void rotamers_for_trials(core::pose::Pose {lvalue},unsigned long,utility::vector1<boost::shared_ptr<core::conformation::Residue>, std::allocator<boost::shared_ptr<core::conformation::Residue> > > {lvalue})

select_best_poses( (object)scores_in, (object)scores_out [, (float)to_keep=0.05]) -> None :
    Trims scores_in based on ligand_is_touching (if present) and
    then by total_score.
    

    C++ signature :
        void select_best_poses(utility::vector1<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > >, std::allocator<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > > > >,utility::vector1<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > >, std::allocator<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > > > > {lvalue} [,double=0.05])

select_best_poses( (AtomTreeDiff)atdiff, (object)scores_out [, (float)to_keep=0.05]) -> None :
    Selects the best ligand docking results from a silent file
    and appends their scores to the supplied list.
    

    C++ signature :
        void select_best_poses(core::import_pose::atom_tree_diffs::AtomTreeDiff,utility::vector1<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > >, std::allocator<std::pair<std::string, std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > > > > > {lvalue} [,double=0.05])

select_best_poses( (AtomTreeDiff)atdiff, (set_string)tags_out) -> None :
    Convenience wrapper: selects the best ligand docking results
    from a silent file and appends their tags to the supplied set.
    

    C++ signature :
        void select_best_poses(core::import_pose::atom_tree_diffs::AtomTreeDiff,std::set<std::string, std::less<std::string>, std::allocator<std::string> > {lvalue})

torsion_constraints_from_chi_rotamers( (int)rsd_no, (int)chino, (ResidueType)rsdtype) -> Constraint :
    Produce an ambiguous dihedral restraint for the specified chi angle,
    assuming that ResidueType.chi_rotamers() lists (all) energetic minima.
    

    C++ signature :
        boost::shared_ptr<core::scoring::constraints::Constraint> torsion_constraints_from_chi_rotamers(unsigned long,unsigned long,core::chemical::ResidueType)

torsion_constraints_from_rotamers( (int)rsd_no, (int)chino, (object)rsds, (float)stddev_degrees) -> Constraint :
    Produce an ambiguous dihedral restraint for the specified chi angle,
    assuming that the provided conformations represent (all) energetic minima.
    

    C++ signature :
        boost::shared_ptr<core::scoring::constraints::Constraint> torsion_constraints_from_rotamers(unsigned long,unsigned long,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,double)

Gaussian

Value:

rosetta.protocols.ligand_docking._protocols_ligand_docking_.Distributi on.Gaussian

Uniform

Value:

rosetta.protocols.ligand_docking._protocols_ligand_docking_.Distributi on.Uniform