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protocols::motifs::Motif Member List

This is the complete list of members for protocols::motifs::Motif, including all inherited members.

apply_check(core::pose::Pose const &pose, Size const pos) const protocols::motifs::Motifvirtual
backward_check(core::conformation::Residue const &check_res) const protocols::motifs::Motifvirtual
backward_jump() const protocols::motifs::Motifinline
backward_jump_protocols::motifs::Motifprivate
basebaseAtomIDsprotocols::motifs::Motifprivatestatic
build_inverted_rotamers(core::pose::Pose &pose, Size const motif_anchor_position, bool use_forward, Size rotamer_build_position=0) const protocols::motifs::Motifvirtual
build_rotamers(core::pose::Pose &pose, Size const rotamer_build_position, bool use_forward, Size const ex_, bool res2=false) const protocols::motifs::Motifvirtual
clone() const protocols::motifs::Motif
forward_check(core::conformation::Residue const &check_res) const protocols::motifs::Motifvirtual
forward_jump() const protocols::motifs::Motifinline
forward_jump_protocols::motifs::Motifprivate
has_path() const protocols::motifs::Motifinline
has_path_protocols::motifs::Motifprivate
has_remark() const protocols::motifs::Motifinline
has_remark_protocols::motifs::Motifprivate
Motif(std::string const resname1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, std::string const resname2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3, core::kinematics::Jump const &orientation)protocols::motifs::Motif
Motif(core::pose::Pose const &pose, Size const pdb_residue_position_1, char const pdb_chain_id1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, Size const pdb_residue_position_2, char const pdb_chain_id2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3)protocols::motifs::Motif
Motif(core::pose::Pose const &pose, Size const pdb_residue_position_1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, Size const pdb_residue_position_2, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3)protocols::motifs::Motif
Motif(core::conformation::Residue const &res1, core::conformation::Residue const &res2)protocols::motifs::Motif
Motif(core::conformation::Residue const &res1, core::conformation::Residue const &res2, utility::vector1< Size > const res2_atoms)protocols::motifs::Motif
Motif(std::string const resname1, std::string const res1_atom1, std::string const res1_atom2, std::string const res1_atom3, std::string const res2_atom1, std::string const res2_atom2, std::string const res2_atom3, core::kinematics::Jump const &orientation)protocols::motifs::Motif
Motif(Motif const &src)protocols::motifs::Motif
motifAtomIDsprotocols::motifs::Motifprivatestatic
operator<<(std::ostream &os, Motif const &mot)protocols::motifs::Motiffriend
path() const protocols::motifs::Motifinline
path_protocols::motifs::Motifprivate
place_atom(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, core::conformation::Atom &atm, bool one_three=true, std::string const atomtype="C1*") const protocols::motifs::Motifvirtual
place_atom(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, core::conformation::Atom &atm, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, Size const &atomtype, bool one_three=true) const protocols::motifs::Motifvirtual
place_atom_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, core::conformation::Atom &atm, bool one_three=true, std::string const atomtype="C1*") const protocols::motifs::Motifvirtual
place_atom_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, core::conformation::Atom &atm, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, Size const &atomtype, bool one_three=true) const protocols::motifs::Motifvirtual
place_atoms(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, utility::vector1< std::string > const &atoms, bool one_three=true) const protocols::motifs::Motifvirtual
place_atoms(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, utility::vector1< Size > const &atoms, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const protocols::motifs::Motifvirtual
place_atoms_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, utility::vector1< std::string > const &atoms, bool one_three=true) const protocols::motifs::Motifvirtual
place_atoms_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, utility::vector1< Size > const &atoms, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const protocols::motifs::Motifvirtual
place_residue(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool one_three=true) const protocols::motifs::Motifvirtual
place_residue(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const protocols::motifs::Motifvirtual
place_residue_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, bool one_three=true) const protocols::motifs::Motifvirtual
place_residue_(core::conformation::Residue const &fixed, core::conformation::Residue &mobile, bool forward, Size const &res2_atom1_index_in, Size const &res2_atom2_index_in, Size const &res2_atom3_index_in, bool one_three=true) const protocols::motifs::Motifvirtual
print(std::ostream &os) const protocols::motifs::Motifvirtual
print() const protocols::motifs::Motifvirtual
remark() const protocols::motifs::Motifinline
remark_protocols::motifs::Motifprivate
res1_atom1_index() const protocols::motifs::Motifinline
res1_atom1_index_protocols::motifs::Motifprivate
res1_atom1_int() const protocols::motifs::Motifinline
res1_atom1_int_protocols::motifs::Motifprivate
res1_atom1_name() const protocols::motifs::Motifinline
res1_atom1_name_protocols::motifs::Motifprivate
res1_atom2_index() const protocols::motifs::Motifinline
res1_atom2_index_protocols::motifs::Motifprivate
res1_atom2_int() const protocols::motifs::Motifinline
res1_atom2_int_protocols::motifs::Motifprivate
res1_atom2_name() const protocols::motifs::Motifinline
res1_atom2_name_protocols::motifs::Motifprivate
res1_atom3_index() const protocols::motifs::Motifinline
res1_atom3_index_protocols::motifs::Motifprivate
res1_atom3_int() const protocols::motifs::Motifinline
res1_atom3_int_protocols::motifs::Motifprivate
res1_atom3_name() const protocols::motifs::Motifinline
res1_atom3_name_protocols::motifs::Motifprivate
res2_atom1_index() const protocols::motifs::Motifinline
res2_atom1_index_protocols::motifs::Motifprivate
res2_atom1_int() const protocols::motifs::Motifinline
res2_atom1_int_protocols::motifs::Motifprivate
res2_atom1_name() const protocols::motifs::Motifinline
res2_atom1_name_protocols::motifs::Motifprivate
res2_atom2_index() const protocols::motifs::Motifinline
res2_atom2_index_protocols::motifs::Motifprivate
res2_atom2_int() const protocols::motifs::Motifinline
res2_atom2_int_protocols::motifs::Motifprivate
res2_atom2_name() const protocols::motifs::Motifinline
res2_atom2_name_protocols::motifs::Motifprivate
res2_atom3_index() const protocols::motifs::Motifinline
res2_atom3_index_protocols::motifs::Motifprivate
res2_atom3_int() const protocols::motifs::Motifinline
res2_atom3_int_protocols::motifs::Motifprivate
res2_atom3_name() const protocols::motifs::Motifinline
res2_atom3_name_protocols::motifs::Motifprivate
restype_name1() const protocols::motifs::Motifinline
restype_name1_protocols::motifs::Motifprivate
restype_name2() const protocols::motifs::Motifinline
restype_name2_protocols::motifs::Motifprivate
store_path(std::string const &path_in)protocols::motifs::Motif
store_remark(std::string const &remark_in)protocols::motifs::Motif
~Motif()protocols::motifs::Motifvirtual