Package Contents
		amino_acid_codes atom_name_interpretation atom_selection cryst1_interpretation crystal_symmetry_from_pdb extract_rfactors_resolutions_sigma hierarchy hybrid_36 records remark_290_interpretation remark_2_interpretation remark_3_interpretation tst_atom_name_interpretation tst_atom_selection tst_ext tst_extract_rfactors_resolutions_sigma tst_hierarchy tst_pdb tst_rna_dna_atom_names xray_structure

Classes
		__builtin__.object Please_pass_string_or_None combine_unique_pdb_files residue_name_plus_atom_names_interpreter rewrite_normalized rna_dna_atom_names_interpretation header_date read_scale_record   class Please_pass_string_or_None(__builtin__.object)       Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class combine_unique_pdb_files(__builtin__.object)       Methods defined here: __init__(self, file_names) report_non_unique(self, out=None, prefix='') Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class header_date       Methods defined here: __init__(self, field) Expected format: DD-MMM-YY is_fully_defined(self)   class read_scale_record       Methods defined here: __init__(self, line, source_info='')   class residue_name_plus_atom_names_interpreter(__builtin__.object)       Methods defined here: __init__(self, residue_name, atom_names, translate_cns_dna_rna_residue_names=None, return_mon_lib_dna_name=False) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class rewrite_normalized(__builtin__.object)       Methods defined here: __init__(self, input_file_name, output_file_name, keep_original_crystallographic_section=False, keep_original_atom_serial=False) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class rna_dna_atom_names_interpretation(__builtin__.object)       Methods defined here: __init__(self, residue_name, atom_names) mon_lib_names(self) unexpected_atom_names(self) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		StringIO(...) StringIO([s]) -- Return a StringIO-like stream for reading or writing common_residue_names_get_class(...) common_residue_names_get_class( (str)name [, (bool)consider_ccp4_mon_lib_rna_dna=False]) -> str :       C++ signature :         std::string common_residue_names_get_class(std::string [,bool=False]) encode_serial_number(width, value) format_cryst1_and_scale_records(crystal_symmetry=None, cryst1_z=None, write_scale_records=True, scale_fractionalization_matrix=None, scale_u=[0, 0, 0]) format_cryst1_record(crystal_symmetry, z=None) format_cryst1_sgroup(space_group_info) format_scale_records(unit_cell=None, fractionalization_matrix=None, u=[0, 0, 0]) hashlib_md5 = openssl_md5(...) Returns a md5 hash object; optionally initialized with a string header_year(record) hy36decode(...) hy36decode( (int)width, (str)s) -> int :       C++ signature :         int hy36decode(unsigned int,std::string) hy36encode(...) hy36encode( (int)width, (int)value) -> str :       C++ signature :         std::string hy36encode(unsigned int,int) hy36recode_width_4_all(...) hy36recode_width_4_all() -> int :       C++ signature :         unsigned int hy36recode_width_4_all() input(file_name=None, source_info=<class 'iotbx.pdb.Please_pass_string_or_None'>, lines=None) is_pdb_file(file_name) join_fragment_files(file_names) make_atom_with_labels(xyz=None, sigxyz=None, occ=None, sigocc=None, b=None, sigb=None, uij=None, siguij=None, hetero=None, serial=None, name=None, segid=None, element=None, charge=None, model_id=None, chain_id=None, resseq=None, icode=None, altloc=None, resname=None) resseq_decode(s) resseq_encode(value) rna_dna_atom_names_interpretation_core(...) rna_dna_atom_names_interpretation_core( (object)arg1) -> None :       C++ signature :         void rna_dna_atom_names_interpretation_core(boost::python::api::object {lvalue}) rna_dna_reference_residue_name(common_name) utils_base_256_ordinal(...) utils_base_256_ordinal( (str)s) -> int :       C++ signature :         long utils_base_256_ordinal(char const*)

Data
		Auto = <libtbx.AutoType object at 0x960390> cns_dna_rna_residue_names = {'ADE': 'A', 'CYT': 'C', 'GUA': 'G', 'THY': 'T', 'URI': 'U'} common_residue_names_amino_acid = ['GLY', 'ALA', 'VAL', 'LEU', 'ILE', 'MET', 'MSE', 'PRO', 'PHE', 'TRP', 'SER', 'THR', 'ASN', 'GLN', 'TYR', 'CYS', 'LYS', 'ARG', 'HIS', 'ASP', ...] common_residue_names_ccp4_mon_lib_rna_dna = ['AD ', 'AR ', 'CD ', 'CR ', 'GD ', 'GR ', 'TD ', 'UR ', ' AD', ' AR', ' CD', ' CR', ' GD', ' GR', ' TD', ' UR', 'Ad ', 'Ar ', 'Cd ', 'Cr ', ...] common_residue_names_element = ['ZN ', ' ZN', 'CA ', ' CA', 'MG ', ' MG', 'CL ', ' CL', 'NA ', ' NA', 'MN ', ' MN', 'K ', ' K', 'FE ', ' FE', 'CU ', ' CU', 'CD ', ' CD', ...] common_residue_names_rna_dna = ['A ', 'C ', 'G ', 'T ', 'U ', ' A', ' C', ' G', ' T', ' U', '+A ', '+C ', '+G ', '+T ', '+U ', ' +A', ' +C', ' +G', ' +T', ' +U', ...] common_residue_names_small_molecule = ['GOL', 'PO4', 'SO4'] common_residue_names_water = ['HOH', 'H2O', 'OH2', 'DOD', 'D2O', 'OD2', 'WAT', 'TIP'] default_atom_names_scattering_type_const = ['PEAK', 'SITE'] input_sections = ('unknown_section', 'title_section', 'remark_section', 'primary_structure_section', 'heterogen_section', 'secondary_structure_section', 'connectivity_annotation_section', 'miscellaneous_features_section', 'crystallographic_section', 'connectivity_section', 'bookkeeping_section') mon_lib_dna_rna_cif = set(['AD', 'AR', 'CD', 'CR', 'GD', 'GR', ...]) pdb_codes_fragment_files = '1bgl 1bgm\n1crp 1crr\n1f49 1gho\n1gix 1giy\n1j4z 1kp...d5c 3d5d\n3df1 3df2 3df3 3df4\n3f1e 3f1f 3f1g 3f1h\n' protein_atom_name_interpreters = {'ALA': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202a90>, 'ARG': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202ed0>, 'ASN': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202d90>, 'ASP': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202f50>, 'CYS': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202e50>, 'GLN': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202dd0>, 'GLU': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202f90>, 'GLY': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202a50>, 'HIS': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202f10>, 'ILE': <iotbx.pdb.atom_name_interpretation.interpreter object at 0x1202b90>, ...} rna_2p_3p_residue_names = set(['A2', 'A3', 'C2', 'C3', 'G2', 'G3', ...]) rna_2p_residue_names = set(['A2', 'C2', 'G2', 'U2']) rna_3p_residue_names = set(['A3', 'C3', 'G3', 'U3']) rna_dna_atom_names_reference_to_mon_lib_translation_dict = {" C1'": 'C1*', ' C2 ': 'C2', " C2'": 'C2*', " C3'": 'C3*', ' C4 ': 'C4', " C4'": 'C4*', ' C5 ': 'C5', " C5'": 'C5*', ' C6 ': 'C6', ' C7 ': 'C5M', ...} rna_dna_reference_residue_names = {'+A': '?A', '+C': '?C', '+G': '?G', '+T': 'DT', '+U': 'U', 'A': '?A', 'AD': 'DA', 'ADE': '?A', 'AR': 'A', 'C': '?C', ...} standard_rhombohedral_space_group_symbols = set(['R -3 :H', 'R -3 :R', 'R -3 c :H', 'R -3 c :R', 'R -3 m :H', 'R -3 m :R', ...])