Module _core_io_pdb_

bonding_distance_threshold( (str)element1, (str)element2) -> float :
    Get theshold distance below which two atoms are considered bonded. (1.2*covalent)
    

    C++ signature :
        double bonding_distance_threshold(std::string,std::string)

build_pose_as_is1( (FileData)fd, (Pose)pose, (ResidueTypeSet)residue_set, (AtomID_Map_T_bool_T)missing, (FileDataOptions)options) -> None :
    core/io/pdb/file_data.hh:397

    C++ signature :
        void build_pose_as_is1(core::io::pdb::FileData {lvalue},core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,core::id::AtomID_Map<bool> {lvalue},core::io::pdb::FileDataOptions)

build_pose_from_pdb_as_is( (Pose)pose, (ResidueTypeSet)residue_set, (str)filename, (std_istream)file_contents, (PDB_DReaderOptions)pdr_options) -> None :
    core/io/pdb/file_data.hh:389

    C++ signature :
        void build_pose_from_pdb_as_is(core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,std::string,std::istream {lvalue},core::io::pdb::PDB_DReaderOptions)

build_pose_from_pdb_as_is( (Pose)pose, (ResidueTypeSet)residue_set, (str)filename, (PDB_DReaderOptions)pdr_options) -> None :
    core/io/pdb/file_data.hh:380

    C++ signature :
        void build_pose_from_pdb_as_is(core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,std::string,core::io::pdb::PDB_DReaderOptions)

build_pose_from_pdb_as_is( (Pose)pose, (ResidueTypeSet)residue_set, (str)filename) -> None :
    core/io/pdb/file_data.hh:373

    C++ signature :
        void build_pose_from_pdb_as_is(core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,std::string)

build_pose_from_pdb_as_is( (Pose)pose, (str)filename, (PDB_DReaderOptions)pdr_options) -> None :
    Builds a pose into  <pose>, without repacking or optimizing
    hydrogens; using the full-atom ResidueTypeSet and a set of options.
    

    C++ signature :
        void build_pose_from_pdb_as_is(core::pose::Pose {lvalue},std::string,core::io::pdb::PDB_DReaderOptions)

build_pose_from_pdb_as_is( (Pose)pose, (str)filename) -> None :
    Builds a pose into  <pose>, without repacking or optimizing
    hydrogens; using the full-atom ResidueTypeSet
    

    C++ signature :
        void build_pose_from_pdb_as_is(core::pose::Pose {lvalue},std::string)

check_and_correct_sister_atom_based_on_chirality( (Residue)rsd, (str)sister1_name, (str)sister2_name, (str)parent_name, (str)outer_ref_name) -> None :
    core/io/pdb/file_data_fixup.hh:91

    C++ signature :
        void check_and_correct_sister_atom_based_on_chirality(boost::shared_ptr<core::conformation::Residue> {lvalue},std::string,std::string,std::string,std::string)

check_and_correct_sister_atom_based_on_outgroup( (Residue)rsd, (str)sister1_name, (str)sister2_name, (str)outgroup_name) -> None :
    core/io/pdb/file_data_fixup.hh:97

    C++ signature :
        void check_and_correct_sister_atom_based_on_outgroup(boost::shared_ptr<core::conformation::Residue> {lvalue},std::string,std::string,std::string)

check_and_correct_sister_atoms( (Residue)rsd) -> None :
    ///////////////////////////////////////////////////////////////////////////////////////
     due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms
      (like OP1 <--> OP2, or H41 <--> H42) in PDBs is totally wacky. This is an attempt to regularize...
      and it can actually make a difference since sometimes partial charges on sister hydrogens
      can be different. Right now only set up for nucleic acids, but could probably generalize.
    

    C++ signature :
        void check_and_correct_sister_atoms(boost::shared_ptr<core::conformation::Residue> {lvalue})

convert_atom_name( (str)res_name, (str)atom_name) -> str :
    core/io/pdb/file_data_fixup.hh:63

    C++ signature :
        std::string convert_atom_name(std::string,std::string)

convert_nucleic_acid_atom_name_to_standard( (AtomInformation)atom_info) -> None :
    core/io/pdb/file_data_fixup.hh:78

    C++ signature :
        void convert_nucleic_acid_atom_name_to_standard(core::io::pdb::AtomInformation {lvalue})

convert_nucleic_acid_atom_names_to_standard( (ResidueInformation)rinfo [, (bool)force_RNA=False]) -> None :
    This is a pretty good framework and could allow for other crazy nucleic acid atom name schemes.
    

    C++ signature :
        void convert_nucleic_acid_atom_names_to_standard(core::io::pdb::ResidueInformation {lvalue} [,bool=False])

convert_nucleic_acid_residue_info_to_standard( (object)rinfo [, (bool)force_RNA=False]) -> None :
    core/io/pdb/file_data_fixup.hh:65

    C++ signature :
        void convert_nucleic_acid_residue_info_to_standard(utility::vector1<core::io::pdb::ResidueInformation, std::allocator<core::io::pdb::ResidueInformation> > {lvalue} [,bool=False])

convert_res_name( (str)name) -> str :
    core/io/pdb/file_data_fixup.hh:60

    C++ signature :
        std::string convert_res_name(std::string)

dump_bfactor_pdb( (Pose)pose, (AtomID_Map_T_double_T)bfactor, (OStream)out [, (str)tag='1']) -> None :
    Writes  <pose>  bfactor data
    

    C++ signature :
        void dump_bfactor_pdb(core::pose::Pose,core::id::AtomID_Map<double>,std::ostream {lvalue} [,std::string='1'])

dump_connect_info( (Pose)pose, (OStream)out) -> None :
    dump_connect_info  Figure out CONECT  fields for PDB output -- atoms that are bonded in Rosetta but won't
    look that way to RASMOL or Pymol because of distance -- useful for centroid poses.
    

    C++ signature :
        void dump_connect_info(core::pose::Pose,std::ostream {lvalue})

dump_pdb( (Pose)pose, (str)filename [, (str)tag='1']) -> None :
    Writes the  <pose>  data to  <filename>
    example(s):
        dump_pdb(pose,'my_pose.pdb')
    See also:
        Pose
        Pose.dump_pdb
    

    C++ signature :
        void dump_pdb(core::pose::Pose,std::string [,std::string='1'])

dump_pdb( (Pose)pose, (OStream)out [, (str)tag='1']) -> None :
    Writes  <pose>  data
    

    C++ signature :
        void dump_pdb(core::pose::Pose,std::ostream {lvalue} [,std::string='1'])

dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask [, (str)tag='1']) -> None :
    Writes  <pose>  data
    

    C++ signature :
        void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool> [,std::string='1'])

dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask, (str)tag, (str)chain, (vector1_Size)resnums) -> None :
    Writes  <pose>  data
    

    C++ signature :
        void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool>,std::string,char,utility::vector1<unsigned long, std::allocator<unsigned long> >)

dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask, (int)atomno, (str)tag, (str)chain, (vector1_Size)resnums) -> None :
    Writes  <pose>  data
    

    C++ signature :
        void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool>,unsigned long {lvalue},std::string,char,utility::vector1<unsigned long, std::allocator<unsigned long> >)

dump_pdb_residue( (Residue)rsd, (OStream)out [, (int)start_atom_number=1]) -> None :
    Writes pdb data for the given residue, beginning from the given atom number
    

    C++ signature :
        void dump_pdb_residue(core::conformation::Residue,std::ostream {lvalue} [,unsigned long=1])

dump_pdb_residue( (Residue)rsd, (int)atom_number, (OStream)out) -> None :
    Writes pdb data for the given residue, incrementing atom_number counter
    

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

extract_scores( (Pose)pose, (str)filename, (OStream)out) -> None :
    core/io/pdb/pose_io.hh:155

    C++ signature :
        void extract_scores(core::pose::Pose,std::string,std::ostream {lvalue})

extract_scores( (Pose)pose, (object)out) -> None :
    Write  <pose>  Energies information into an output stream
    (e.g. the tail of a pdb file)
    

    C++ signature :
        void extract_scores(core::pose::Pose,utility::io::ozstream {lvalue})

fill_name_map( (object)name_map, (ResidueInformation)rinfo, (ResidueType)rsd_type, (FileDataOptions)options) -> None :
    core/io/pdb/file_data.hh:461

    C++ signature :
        void fill_name_map(boost::bimaps::bimap<std::string, std::string, mpl_::na, mpl_::na, mpl_::na> {lvalue},core::io::pdb::ResidueInformation,core::chemical::ResidueType,core::io::pdb::FileDataOptions)

fixup_rinfo_based_on_residue_type_set( (object)rinfos, (ResidueTypeSet)residue_set) -> None :
    core/io/pdb/file_data.hh:455

    C++ signature :
        void fixup_rinfo_based_on_residue_type_set(utility::vector1<core::io::pdb::ResidueInformation, std::allocator<core::io::pdb::ResidueInformation> > {lvalue},core::chemical::ResidueTypeSet)

flip_atom_xyz( (Residue)rsd, (str)sister1_name, (str)sister2_name) -> None :
    core/io/pdb/file_data_fixup.hh:102

    C++ signature :
        void flip_atom_xyz(boost::shared_ptr<core::conformation::Residue> {lvalue},std::string,std::string)

get_chirality_sign( (xyzVector_Real)xyz_sister1, (xyzVector_Real)xyz_sister2, (xyzVector_Real)xyz_parent, (xyzVector_Real)xyz_outer_ref) -> int :
    core/io/pdb/file_data_fixup.hh:110

    C++ signature :
        int get_chirality_sign(numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

get_closest_sister( (xyzVector_Real)xyz_sister1, (xyzVector_Real)xyz_sister2, (xyzVector_Real)xyz_outgroup) -> int :
    core/io/pdb/file_data_fixup.hh:115

    C++ signature :
        int get_closest_sister(numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)

is_NA( (str)res_name) -> bool :
    core/io/pdb/file_data_fixup.hh:71

    C++ signature :
        bool is_NA(std::string)

is_old_RNA( (str)res_name) -> bool :
    core/io/pdb/file_data_fixup.hh:69

    C++ signature :
        bool is_old_RNA(std::string)

is_potential_old_DNA( (str)res_name) -> bool :
    core/io/pdb/file_data_fixup.hh:67

    C++ signature :
        bool is_potential_old_DNA(std::string)

is_residue_type_recognized( (int)pdb_residue_index, (str)pdb_name, (object)rsd_type_list, (object)xyz, (map_string_Real)rtemp, (vector1_Size)UA_res_nums, (vector1_string)UA_res_names, (vector1_string)UA_atom_names, (vector1_xyzVector_Real)UA_coords, (vector1_Real)UA_temps, (FileDataOptions)options) -> bool :
    core/io/pdb/file_data.hh:422

    C++ signature :
        bool is_residue_type_recognized(unsigned long,std::string,utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >,std::map<std::string, numeric::xyzVector<double>, std::less<std::string>, std::allocator<std::pair<std::string const, numeric::xyzVector<double> > > >,std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > >,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<std::string, std::allocator<std::string> > {lvalue},utility::vector1<std::string, std::allocator<std::string> > {lvalue},utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},core::io::pdb::FileDataOptions)

is_residue_type_recognized( (int)pdb_residue_index, (str)pdb_name, (object)rsd_type_list, (object)xyz, (map_string_Real)rtemp, (vector1_Size)UA_res_nums, (vector1_string)UA_res_names, (vector1_string)UA_atom_names, (vector1_xyzVector_Real)UA_coords, (vector1_Real)UA_temps) -> bool :
    core/io/pdb/file_data.hh:409

    C++ signature :
        bool is_residue_type_recognized(unsigned long,std::string,utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >,std::map<std::string, numeric::xyzVector<double>, std::less<std::string>, std::allocator<std::pair<std::string const, numeric::xyzVector<double> > > >,std::map<std::string, double, std::less<std::string>, std::allocator<std::pair<std::string const, double> > >,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue},utility::vector1<std::string, std::allocator<std::string> > {lvalue},utility::vector1<std::string, std::allocator<std::string> > {lvalue},utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue})

missing_O2prime( (object)atoms) -> bool :
    core/io/pdb/file_data_fixup.hh:73

    C++ signature :
        bool missing_O2prime(utility::vector1<core::io::pdb::AtomInformation, std::allocator<core::io::pdb::AtomInformation> >)

pose_from_pose( (Pose)new_pose, (Pose)old_pose, (ResidueTypeSet)residue_set, (vector1_Size)residue_indices, (FileDataOptions)options) -> None :
    core/io/pdb/file_data.hh:451

    C++ signature :
        void pose_from_pose(core::pose::Pose {lvalue},core::pose::Pose,core::chemical::ResidueTypeSet,utility::vector1<unsigned long, std::allocator<unsigned long> >,core::io::pdb::FileDataOptions)

pose_from_pose( (Pose)new_pose, (Pose)old_pose, (ResidueTypeSet)residue_set, (vector1_Size)residue_indices) -> None :
    core/io/pdb/file_data.hh:443

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

pose_from_pose( (Pose)new_pose, (Pose)old_pose, (vector1_Size)residue_indices, (FileDataOptions)options) -> None :
    core/io/pdb/file_data.hh:436

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

pose_from_pose( (Pose)new_pose, (Pose)old_pose, (vector1_Size)residue_indices) -> None :
    core/io/pdb/file_data.hh:429

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

print_d( (str)format, (float)d) -> str :
    print double with format to string
    

    C++ signature :
        std::string print_d(char const*,double)

print_i( (str)format, (int)I) -> str :
    print int with format to string
    

    C++ signature :
        std::string print_i(char const*,int)

remap_names_on_geometry( (object)mapping, (ResidueInformation)rinfo, (ResidueType)rsd_type) -> None :
    Attempt to use element identity and connectivity to map atom names from the rinfo object onto the rsd_type object names.
    

    C++ signature :
        void remap_names_on_geometry(boost::bimaps::bimap<std::string, std::string, mpl_::na, mpl_::na, mpl_::na> {lvalue},core::io::pdb::ResidueInformation,core::chemical::ResidueType)

score_mapping( (object)mapping, (ResidueInformation)rinfo, (ResidueType)rsd_type) -> float :
    Scoring scheme for the heuristic PDB renaming
    

    C++ signature :
        double score_mapping(boost::bimaps::bimap<std::string, std::string, mpl_::na, mpl_::na, mpl_::na>,core::io::pdb::ResidueInformation,core::chemical::ResidueType)

sgn( (float)x) -> int :
    core/io/pdb/file_data_fixup.hh:104

    C++ signature :
        int sgn(double)

traced_dump_pdb( (Tracer)tr, (Pose)pose, (str)filename [, (str)tag='1']) -> None :
    dump_pdb depending on visibility of tracer
    

    C++ signature :
        void traced_dump_pdb(basic::Tracer,core::pose::Pose,std::string [,std::string='1'])

traced_dump_pdb( (Tracer)tr, (Pose)pose, (OStream)out [, (str)tag='1']) -> None :
    dump_pdb depending on visibility of tracer
    

    C++ signature :
        void traced_dump_pdb(basic::Tracer,core::pose::Pose,std::ostream {lvalue} [,std::string='1'])

write_additional_pdb_data( (OStream)out, (Pose)pose, (FileData)fd [, (bool)write_fold_tree=False]) -> None :
    Adds data to the end of a pdb that are not a standard part of the pdb format.
    

    C++ signature :
        void write_additional_pdb_data(std::ostream {lvalue},core::pose::Pose,core::io::pdb::FileData [,bool=False])