Module _core_conformation_

add_lower_terminus_type_to_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
    core/conformation/util.hh:151

    C++ signature :
        void add_lower_terminus_type_to_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)

add_upper_terminus_type_to_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
    core/conformation/util.hh:158

    C++ signature :
        void add_upper_terminus_type_to_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)

add_variant_type_to_conformation_residue( (Conformation)conformation, (VariantType)variant_type, (int)seqpos) -> None :
    Construct a variant of an existing conformation residue.
    

    C++ signature :
        void add_variant_type_to_conformation_residue(core::conformation::Conformation {lvalue},core::chemical::VariantType,unsigned long)

annotated_atom_graph_from_conformation( (Conformation)conformation, (object)pg, (xyzVector_Real)additional_point) -> int :
    create a pointgraph which consists of 1 node for every atom, plus 1 additional node which will be added as the last node.  The index of the additional node is returned
    

    C++ signature :
        unsigned long annotated_atom_graph_from_conformation(core::conformation::Conformation,boost::shared_ptr<core::graph::UpperEdgeGraph<core::conformation::AtomGraphVertexData, core::conformation::AtomGraphEdgeData> >,numeric::xyzVector<double>)

atom_graph_from_conformation( (Conformation)conformation, (object)pg) -> None :
    core/conformation/AtomGraph.hh:31

    C++ signature :
        void atom_graph_from_conformation(core::conformation::Conformation,boost::shared_ptr<core::graph::UpperEdgeGraph<core::conformation::AtomGraphVertexData, core::conformation::AtomGraphEdgeData> >)

atom_id_to_named_atom_id( (AtomID)atom_id, (Residue)rsd) -> NamedAtomID :
    core/conformation/util.hh:350

    C++ signature :
        core::id::NamedAtomID atom_id_to_named_atom_id(core::id::AtomID,core::conformation::Residue)

build_chemical_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
    build a sub atom-tree for a chemical edge and attach it to main atom-tree
    

    C++ signature :
        void build_chemical_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})

build_jump_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
    build a sub atom-tree for a jump edge and attach it to main atom-tree
    

    C++ signature :
        void build_jump_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})

build_polymer_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
    build a sub atom-tree for a polymer edge and attach it to main atom-tree
    

    C++ signature :
        void build_polymer_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})

build_residue_tree( (object)residues, (Residue)rsd, (FoldTree)fold_tree, (object)atom_ptr) -> None :
    build_residue_tree function that uses the foldtree info
    also used in build_tree to build the residue tree for the root residue
    

    C++ signature :
        void build_residue_tree(utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::kinematics::tree::Atom>, std::allocator<boost::shared_ptr<core::kinematics::tree::Atom> > > {lvalue})

build_residue_tree( (int)root_atomno, (Residue)rsd, (object)atom_ptr, (bool)root_atom_is_jump_atom) -> None :
    build the tree of atoms for this residue, anchored at root_atomno
    

    C++ signature :
        void build_residue_tree(int,core::conformation::Residue,utility::vector1<boost::shared_ptr<core::kinematics::tree::Atom>, std::allocator<boost::shared_ptr<core::kinematics::tree::Atom> > > {lvalue},bool)

build_tree( (FoldTree)fold_tree, (object)residues, (object)atom_pointer) -> None :
    core/conformation/util.hh:179

    C++ signature :
        void build_tree(core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})

change_cys_state( (int)index, (str)cys_type_name3, (Conformation)conf) -> bool :
    Replace a CYS with a CYD or vice-versa for changing disulfide bonds.
    [in] index Position of the residue to replace.
    [in] cys_type_name3 The 3-letter name of the cys type to use: either CYS
     or CYD.
    [inout] conf The conformation to modify
    true if the replacement was successful, false otherwise.
    

    C++ signature :
        bool change_cys_state(unsigned long,std::string,core::conformation::Conformation {lvalue})

char_valid_as_torsion_bin( (str)torbin) -> bool :
    returns true if the input character represents a valid torsion bin
    

    C++ signature :
        bool char_valid_as_torsion_bin(char)

cis_omega_torsion_bin( (ppo_torsion_bin)torbin) -> bool :
    core/conformation/ppo_torsion_bin.hh:43

    C++ signature :
        bool cis_omega_torsion_bin(core::conformation::ppo_torsion_bin)

copy_residue_coordinates_and_rebuild_missing_atoms( (Residue)source_rsd, (Residue)target_rsd, (Conformation)conformation) -> None :
    Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.
    

    C++ signature :
        void copy_residue_coordinates_and_rebuild_missing_atoms(core::conformation::Residue,core::conformation::Residue {lvalue},core::conformation::Conformation)

copy_residue_coordinates_and_rebuild_missing_atoms( (Residue)source_rsd, (Residue)target_rsd, (Conformation)conformation, (bool)preserve_only_sidechain_dihedrals) -> None :
    Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.
    If preserve_only_sidechain_dihedrals is true, then this function only copies mainchain coordinates,
    and rebuilds all sidechain coordinates from scratch, setting side-chain dihedrals based on the source residue.
    Otherwise, if false, it copies all the atoms that it can from the source residue, then rebuilds the rest.
    Vikram K. Mulligan (vmullig@uw.edu)
    

    C++ signature :
        void copy_residue_coordinates_and_rebuild_missing_atoms(core::conformation::Residue,core::conformation::Residue {lvalue},core::conformation::Conformation,bool)

disulfide_bonds( (Conformation)conformation, (vector1_pair_Size_Size)disulfides) -> None :
    Generate a list of all disulfide bonds in the conformation
    

    C++ signature :
        void disulfide_bonds(core::conformation::Conformation,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > {lvalue})

form_disulfide( (Conformation)conformation, (int)lower_res, (int)upper_res) -> None :
    Introduce cysteines at the specified location and define a disulfide bond between them.
    Does not do the repacking & minimization required to place the disulfide correctly.
    

    C++ signature :
        void form_disulfide(core::conformation::Conformation {lvalue},unsigned long,unsigned long)

form_disulfide_helper( (Conformation)conformation, (int)lower_res, (ResidueTypeSet)restype_set) -> None :
    Helper function for the form_disulfide function.
    This function ensures that as a residue is mutated to a disulfide-bonding residue type,
    all other variant types are preserved; it is used to avoid code duplication.
    Vikram K. Mulligan, Baker laboratory (vmullig@uw.edu)
    

    C++ signature :
        void form_disulfide_helper(core::conformation::Conformation {lvalue},unsigned long,boost::shared_ptr<core::chemical::ResidueTypeSet const>)

get_anchor_and_root_atoms( (Residue)anchor_rsd, (Residue)root_rsd, (Edge)edge, (int)anchor_atomno, (int)root_atomno) -> None :
    Use this routine to deduce atom indices of connect atoms in the tree
    

    C++ signature :
        void get_anchor_and_root_atoms(core::conformation::Residue,core::conformation::Residue,core::kinematics::Edge,unsigned long {lvalue},unsigned long {lvalue})

get_anchor_atomno( (Residue)rsd, (int)dir) -> int :
    get anchor atom to which the atom-tree of next residue in the edge is attached.
    

    C++ signature :
        int get_anchor_atomno(core::conformation::Residue,int)

get_anchor_atomno( (Residue)anchor_rsd, (int)seqpos, (FoldTree)fold_tree) -> int :
    Get the atom-index of the atom to which the residue at position seqpos should be anchored.
    

    C++ signature :
        int get_anchor_atomno(core::conformation::Residue,unsigned long,core::kinematics::FoldTree)

get_chemical_root_and_anchor_atomnos( (Residue)rsd_anchor, (Residue)rsd_root, (int)anchor_atom_no, (int)root_atom_no) -> None :
    core/conformation/util.hh:308

    C++ signature :
        void get_chemical_root_and_anchor_atomnos(core::conformation::Residue,core::conformation::Residue,unsigned long {lvalue},unsigned long {lvalue})

get_root_atomno( (Residue)rsd, (int)dir) -> int :
    core/conformation/util.hh:251

    C++ signature :
        int get_root_atomno(core::conformation::Residue,int)

get_root_residue_root_atomno( (Residue)rsd, (FoldTree)fold_tree) -> int :
    core/conformation/util.hh:257

    C++ signature :
        unsigned long get_root_residue_root_atomno(core::conformation::Residue,core::kinematics::FoldTree)

get_torsion_bin( (float)phi, (float)psi [, (float)omega=180]) -> ppo_torsion_bin :
    determine the torsion bin for a given phi/psi/omega combination, assuming that omega is 180 if not specified
    Amelie Stein (amelie.stein@ucsf.edu)
    @date Wed May  2 11:18:29 PDT 2012
    

    C++ signature :
        core::conformation::ppo_torsion_bin get_torsion_bin(double,double [,double=180])

idealize_hydrogens( (Residue)res, (Conformation)conf) -> None :
    core/conformation/Residue.functions.hh:27

    C++ signature :
        void idealize_hydrogens(core::conformation::Residue {lvalue},core::conformation::Conformation)

idealize_position( (int)seqpos, (Conformation)conformation) -> None :
    Idealize backbone and sidechain at seqpos
    

    C++ signature :
        void idealize_position(unsigned long,core::conformation::Conformation {lvalue})

insert_ideal_bonds_at_polymer_junction( (int)seqpos, (Conformation)conformation) -> None :
    Sets the two bond angles and the bond length across the junction, rebuilds dependent atoms (eg O,H)
    

    C++ signature :
        void insert_ideal_bonds_at_polymer_junction(unsigned long,core::conformation::Conformation {lvalue})

insert_ideal_mainchain_bonds( (int)seqpos, (Conformation)conformation) -> None :
    core/conformation/util.hh:72

    C++ signature :
        void insert_ideal_mainchain_bonds(unsigned long,core::conformation::Conformation {lvalue})

insert_residue_into_atom_tree( (Residue)new_rsd, (FoldTree)fold_tree, (object)residues, (AtomTree)atom_tree) -> None :
    Inserts/ appends new residue subtree into an existing atomtree
    The foldtree must already have been changed to reflect the new residue
    The sequence position of the new residue is deduced from new_rsd.seqpos()
    This function handles renumbering of the atomtree if necessary
    

    C++ signature :
        void insert_residue_into_atom_tree(core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})

is_disulfide_bond( (Conformation)conformation, (int)residueA_pos, (int)residueB_pos) -> bool :
    Find whether there is a disulfide defined between two residues
    

    C++ signature :
        bool is_disulfide_bond(core::conformation::Conformation,unsigned long,unsigned long)

is_ideal_position( (int)seqpos, (Conformation)conformation [, (float)theta_epsilon=0.005 [, (float)D_epsilon=0.02]]) -> bool :
    Return true if position contains an ideal geometry up to some epsilon
    s seqpos - sequence position
    s conformation - conformation object
    s theta_epsilon - permitted deviation from ideal bond angles, in Radians
    s D_epsilon - permitted deviation from ideal bond length
    @remarks conformation is needed for context of polymer nbrs
    

    C++ signature :
        bool is_ideal_position(unsigned long,core::conformation::Conformation [,double=0.005 [,double=0.02]])

map_char_to_torsion_bin( (str)torbin) -> ppo_torsion_bin :
    returns the torsion bin that the input character represents
    

    C++ signature :
        core::conformation::ppo_torsion_bin map_char_to_torsion_bin(char)

map_string_to_torsion_bin_string( (str)torstring) -> object :
    convert a string of characters into a vector of the internally recognized ppo_torsion_bin enumeration
    @throws utility::excn::EXCN_MsgException if any of the input characters in this string are invalid
    

    C++ signature :
        utility::vector0<core::conformation::ppo_torsion_bin, std::allocator<core::conformation::ppo_torsion_bin> > map_string_to_torsion_bin_string(std::string)

map_torsion_bin_to_char( (ppo_torsion_bin)torbin) -> str :
    convert a torsion bin to a character s.t. that character can be converted back to a torsion bin
    

    C++ signature :
        char map_torsion_bin_to_char(core::conformation::ppo_torsion_bin)

named_atom_id_to_atom_id( (NamedAtomID)atom_id, (Residue)rsd) -> AtomID :
    core/conformation/util.hh:364

    C++ signature :
        core::id::AtomID named_atom_id_to_atom_id(core::id::NamedAtomID,core::conformation::Residue)

orient_residue_for_ideal_bond( (Residue)moving_rsd, (ResidueConnection)moving_connection, (Residue)fixed_rsd, (ResidueConnection)fixed_connection, (Conformation)conformation [, (bool)lookup_bond_length=False]) -> None :
    core/conformation/util.hh:59

    C++ signature :
        void orient_residue_for_ideal_bond(core::conformation::Residue {lvalue},core::chemical::ResidueConnection,core::conformation::Residue,core::chemical::ResidueConnection,core::conformation::Conformation [,bool=False])

promote_sameresidue_child_of_jump_atom( (Edge)edge, (object)residues, (AtomTree)atom_tree) -> None :
    Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list
    

    C++ signature :
        void promote_sameresidue_child_of_jump_atom(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})

promote_sameresidue_child_of_jump_atom( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
    Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list
    

    C++ signature :
        void promote_sameresidue_child_of_jump_atom(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> >)

remap_cis_omega_torsion_bins_to_trans( (ppo_torsion_bin)torbin) -> ppo_torsion_bin :
    core/conformation/ppo_torsion_bin.hh:40

    C++ signature :
        core::conformation::ppo_torsion_bin remap_cis_omega_torsion_bins_to_trans(core::conformation::ppo_torsion_bin)

remove_lower_terminus_type_from_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
    core/conformation/util.hh:165

    C++ signature :
        void remove_lower_terminus_type_from_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)

remove_upper_terminus_type_from_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
    core/conformation/util.hh:172

    C++ signature :
        void remove_upper_terminus_type_from_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)

remove_variant_type_from_conformation_residue( (Conformation)conformation, (VariantType)variant_type, (int)seqpos) -> None :
    Construct a non-variant of an existing conformation residue.
    

    C++ signature :
        void remove_variant_type_from_conformation_residue(core::conformation::Conformation {lvalue},core::chemical::VariantType,unsigned long)

replace_conformation_residue_copying_existing_coordinates( (Conformation)conformation, (int)seqpos, (ResidueType)new_rsd_type) -> None :
    core/conformation/util.hh:132

    C++ signature :
        void replace_conformation_residue_copying_existing_coordinates(core::conformation::Conformation {lvalue},unsigned long,core::chemical::ResidueType)

replace_residue_in_atom_tree( (Residue)new_rsd, (FoldTree)fold_tree, (object)residues, (AtomTree)atom_tree) -> None :
    Helper function for conformation routines
    

    C++ signature :
        void replace_residue_in_atom_tree(core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})

residue_point_graph_from_conformation( (Conformation)conformation, (UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T)pg) -> None :
    core/conformation/PointGraph.hh:43

    C++ signature :
        void residue_point_graph_from_conformation(core::conformation::Conformation,core::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> {lvalue})

set_chi_according_to_coordinates( (Residue)rotamer) -> None :
    rotamer chi-update from coords useful for building rotamers from coordinates
    

    C++ signature :
        void set_chi_according_to_coordinates(core::conformation::Residue {lvalue})

setup_corresponding_atoms( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Residue)rsd1, (Residue)rsd2) -> None :
    set up a map to match mainchain atoms from residue1 to residue2
    

    C++ signature :
        void setup_corresponding_atoms(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Residue,core::conformation::Residue)

show_atom_tree( (Atom)atom, (Conformation)conf, (OStream)os) -> None :
    core/conformation/util.hh:125

    C++ signature :
        void show_atom_tree(core::kinematics::tree::Atom,core::conformation::Conformation,std::ostream {lvalue})

stub_id_to_named_stub_id( (StubID)stub_id, (Residue)rsd) -> NamedStubID :
    core/conformation/util.hh:370

    C++ signature :
        core::id::NamedStubID stub_id_to_named_stub_id(core::id::StubID,core::conformation::Residue)

write_kinemage_header( (OStream)ostr, (int)kin_number, (str)title, (xyzVector_Real)ctr) -> None :
    core/conformation/ResidueKinWriter.hh:41

    C++ signature :
        void write_kinemage_header(std::ostream {lvalue},unsigned long,std::string,numeric::xyzVector<double>)

AUTOMATIC

Value:

rosetta.core.conformation._core_conformation_.Strategy.AUTOMATIC

NAIVE

Value:

rosetta.core.conformation._core_conformation_.Strategy.NAIVE

OCTREE

Value:

rosetta.core.conformation._core_conformation_.Strategy.OCTREE

STRIPEHASH

Value:

rosetta.core.conformation._core_conformation_.Strategy.STRIPEHASH

THREEDGRID

Value:

rosetta.core.conformation._core_conformation_.Strategy.THREEDGRID

n_ppo_torsion_bins

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.n_ppo_to rsion_bins

ppo_torbin_A

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_A

ppo_torbin_B

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_B

ppo_torbin_E

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_E

ppo_torbin_G

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_G

ppo_torbin_U

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_U

ppo_torbin_X

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_X

ppo_torbin_a

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_a

ppo_torbin_b

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_b

ppo_torbin_e

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_e

ppo_torbin_g

Value:

rosetta.core.conformation._core_conformation_.ppo_torsion_bin.ppo_torb in_g