Module _protocols_hybridization_

add_non_protein_cst( (Pose)pose, (Pose)tmpl, (float)self_cst_weight, (float)het_prot_cst_weight) -> None :
    protocols/hybridization/util.hh:80

    C++ signature :
        void add_non_protein_cst(core::pose::Pose {lvalue},core::pose::Pose {lvalue},double,double)

add_strand_pairs_cst( (Pose)pose, (vector1_pair_Size_Size)strand_pairs) -> None :
    protocols/hybridization/util.hh:77

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

apply_transformation( (Pose)mod_pose, (object)residue_list, (xyzMatrix_Real)R, (xyzVector_Real)preT, (xyzVector_Real)postT) -> None :
    protocols/hybridization/util.hh:148

    C++ signature :
        void apply_transformation(core::pose::Pose {lvalue},std::list<unsigned long, std::allocator<unsigned long> >,numeric::xyzMatrix<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

atom_map_valid_size( (Pose)pose, (AtomID_Map_T_core_id_AtomID_T)atom_map) -> int :
    protocols/hybridization/util.hh:99

    C++ signature :
        unsigned long atom_map_valid_size(core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>)

create_fragment_set( (Pose)pose, (int)len, (int)nfrag) -> FragSet :
    protocols/hybridization/util.hh:151

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> create_fragment_set(core::pose::Pose,unsigned long,unsigned long)

create_fragment_set_no_ssbias( (Pose)pose, (set_Size)user_pos, (int)len, (int)nfrag [, (str)force_ss='D']) -> FragSet :
    protocols/hybridization/util.hh:157

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> create_fragment_set_no_ssbias(core::pose::Pose,std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >,unsigned long,unsigned long [,char='D'])

create_fragment_set_no_ssbias( (Pose)pose, (int)len, (int)nfrag [, (str)force_ss='D']) -> FragSet :
    protocols/hybridization/util.hh:154

    C++ signature :
        boost::shared_ptr<core::fragment::FragSet> create_fragment_set_no_ssbias(core::pose::Pose,unsigned long,unsigned long [,char='D'])

discontinued_lower( (Pose)pose, (int)seqpos) -> bool :
    protocols/hybridization/util.hh:84

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

discontinued_upper( (Pose)pose, (int)seqpos) -> bool :
    protocols/hybridization/util.hh:82

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

downstream_residues_from_jump( (Pose)pose, (int)jump_number) -> object :
    protocols/hybridization/util.hh:86

    C++ signature :
        std::list<unsigned long, std::allocator<unsigned long> > downstream_residues_from_jump(core::pose::Pose,unsigned long)

generate_centroid_constraints( (Pose)pose, (object)templates, (vector1_Real)template_weights, (set_Size)ignore_res) -> None :
    protocols/hybridization/util.hh:66

    C++ signature :
        void generate_centroid_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose const>, std::allocator<boost::shared_ptr<core::pose::Pose const> > >,utility::vector1<double, std::allocator<double> >,std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >)

generate_fullatom_constraints( (Pose)pose, (object)templates, (vector1_Real)template_weights) -> None :
    protocols/hybridization/util.hh:71

    C++ signature :
        void generate_fullatom_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose const>, std::allocator<boost::shared_ptr<core::pose::Pose const> > >,utility::vector1<double, std::allocator<double> >)

get_gdtmm( (Pose)native, (Pose)pose, (SequenceAlignment)aln) -> float :
    protocols/hybridization/util.hh:162

    C++ signature :
        double get_gdtmm(core::pose::Pose {lvalue},core::pose::Pose {lvalue},boost::shared_ptr<core::sequence::SequenceAlignment> {lvalue})

get_num_residues_nonvirt( (Pose)pose) -> int :
    protocols/hybridization/util.hh:44

    C++ signature :
        unsigned long get_num_residues_nonvirt(core::pose::Pose)

get_num_residues_prot( (Pose)pose) -> int :
    protocols/hybridization/util.hh:45

    C++ signature :
        unsigned long get_num_residues_prot(core::pose::Pose)

get_superposition_transformation( (Pose)mod_pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map, (xyzMatrix_Real)R, (xyzVector_Real)preT, (xyzVector_Real)postT) -> None :
    protocols/hybridization/util.hh:141

    C++ signature :
        void get_superposition_transformation(core::pose::Pose,core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>,numeric::xyzMatrix<double> {lvalue},numeric::xyzVector<double> {lvalue},numeric::xyzVector<double> {lvalue})

natom_aligned( (Pose)pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map [, (float)distance_squared_threshold=4.0]) -> int :
    protocols/hybridization/util.hh:134

    C++ signature :
        unsigned long natom_aligned(core::pose::Pose {lvalue},core::pose::Pose,core::id::AtomID_Map<core::id::AtomID> [,double=4.0])

partial_align( (Pose)pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map, (object)residue_list [, (bool)iterate_convergence=False [, (vector1_Real)distance_thresholds=<rosetta.utility._utility_.vector1_Real object at 0x145507a68> [, (float)min_coverage=0.2]]]) -> None :
    protocols/hybridization/util.hh:118

    C++ signature :
        void partial_align(core::pose::Pose {lvalue},core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>,std::list<unsigned long, std::allocator<unsigned long> > [,bool=False [,utility::vector1<double, std::allocator<double> >=<rosetta.utility._utility_.vector1_Real object at 0x145507a68> [,double=0.2]]])

partial_align( (Pose)pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map, (bool)iterate_convergence, (vector1_Real)distance_thresholds, (float)min_coverage) -> None :
    protocols/hybridization/util.hh:108

    C++ signature :
        void partial_align(core::pose::Pose {lvalue},core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>,bool,utility::vector1<double, std::allocator<double> >,double)

renumber_with_pdb_info( (Loops)template_chunk, (Pose)template_pose) -> Loops :
    protocols/hybridization/util.hh:160

    C++ signature :
        protocols::loops::Loops renumber_with_pdb_info(protocols::loops::Loops {lvalue},boost::shared_ptr<core::pose::Pose const>)

setup_centroid_constraints( (Pose)pose, (object)templates, (vector1_Real)template_weights, (str)cen_cst_file, (set_Size)ignore_res_for_AUTO) -> None :
    protocols/hybridization/util.hh:53

    C++ signature :
        void setup_centroid_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose const>, std::allocator<boost::shared_ptr<core::pose::Pose const> > >,utility::vector1<double, std::allocator<double> >,std::string,std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >)

setup_fullatom_constraints( (Pose)pose, (object)templates, (vector1_Real)template_weights, (str)cen_cst_file, (str)fa_cst_file) -> None :
    protocols/hybridization/util.hh:60

    C++ signature :
        void setup_fullatom_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose const>, std::allocator<boost::shared_ptr<core::pose::Pose const> > >,utility::vector1<double, std::allocator<double> >,std::string,std::string)

setup_user_coordinate_constraints( (Pose)pose, (vector1_Size)reses_to_cst) -> None :
    protocols/hybridization/util.hh:74

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

update_atom_map( (Pose)pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map, (float)distance_squared_threshold) -> AtomID_Map_T_core_id_AtomID_T :
    protocols/hybridization/util.hh:126

    C++ signature :
        core::id::AtomID_Map<core::id::AtomID> update_atom_map(core::pose::Pose {lvalue},core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>,double)

all_chunks

Value:

rosetta.protocols.hybridization._protocols_hybridization_.AlignOption. all_chunks

random_chunk

Value:

rosetta.protocols.hybridization._protocols_hybridization_.AlignOption. random_chunk