iotbx.pdb
index
/net/chevy/raid1/nat/src/cctbx_project/iotbx/pdb/__init__.py

 
Package Contents
       
amino_acid_codes
atom_name_interpretation
atom_selection
cryst1_interpretation
crystal_symmetry_from_pdb
extract_rfactors_resolutions_sigma
fetch
hierarchy
hybrid_36
mining
mmcif
multimer_reconstruction
records
remark_290_interpretation
remark_2_interpretation
remark_3_interpretation
remediation (package)
rna_dna_detection
secondary_structure
tst_atom_name_interpretation
tst_atom_selection
tst_ext
tst_extract_rfactors_resolutions_sigma
tst_hierarchy
tst_mmcif
tst_mmcif_hierarchy
tst_ncs_groups_preprocessing
tst_pdb
tst_pdb_manipulation
tst_rna_dna_atom_names
tst_tls
xray_structure

 
Classes
       
__builtin__.object
Please_pass_string_or_None
combine_unique_pdb_files
header_date
join_fragment_files
pdb_input_from_any
pdb_input_mixin
read_scale_record
read_mtrix_record
residue_name_plus_atom_names_interpreter
rewrite_normalized
rna_dna_atom_names_interpretation

 
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(__builtin__.object)
     Methods defined here:
__init__(self, field)
Expected format: DD-MMM-YY
is_fully_defined(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class join_fragment_files(__builtin__.object)
     Methods defined here:
__init__(self, file_names)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pdb_input_from_any(__builtin__.object)
     Methods defined here:
__init__(self, file_name=None, source_info=<class 'iotbx.pdb.Please_pass_string_or_None'>, lines=None, pdb_id=None, raise_sorry_if_format_error=False)
file_content(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pdb_input_mixin(__builtin__.object)
     Methods defined here:
as_pdb_string(self, crystal_symmetry=<libtbx.AutoType object>, cryst1_z=<libtbx.AutoType object>, write_scale_records=True, append_end=False, atom_hetatm=True, sigatm=True, anisou=True, siguij=True, cstringio=None, link_records=<libtbx.AutoType object>, return_cstringio=<libtbx.AutoType object>)
special_position_settings(self, special_position_settings=None, weak_symmetry=False, min_distance_sym_equiv=0.5, u_star_tolerance=0)
write_pdb_file(self, file_name, open_append=False, crystal_symmetry=<libtbx.AutoType object>, cryst1_z=<libtbx.AutoType object>, write_scale_records=True, append_end=False, atom_hetatm=True, sigatm=True, anisou=True, siguij=True)
xray_structure_simple(self, crystal_symmetry=None, weak_symmetry=False, cryst1_substitution_buffer_layer=None, unit_cube_pseudo_crystal=False, fractional_coordinates=False, use_scale_matrix_if_available=True, min_distance_sym_equiv=0.5, non_unit_occupancy_implies_min_distance_sym_equiv_zero=True, scattering_type_exact=False, enable_scattering_type_unknown=False, atom_names_scattering_type_const=['PEAK', 'SITE'])
xray_structures_simple(self, one_structure_for_each_model=True, crystal_symmetry=None, weak_symmetry=False, cryst1_substitution_buffer_layer=None, unit_cube_pseudo_crystal=False, fractional_coordinates=False, min_distance_sym_equiv=0.5, non_unit_occupancy_implies_min_distance_sym_equiv_zero=True, use_scale_matrix_if_available=True, scattering_type_exact=False, enable_scattering_type_unknown=False, atom_names_scattering_type_const=['PEAK', 'SITE'])

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class read_mtrix_record(read_scale_record)
    
Method resolution order:
read_mtrix_record
read_scale_record
__builtin__.object

Methods defined here:
__init__(O, line, source_info='')

Data descriptors defined here:
coordinates_present
n
r
serial_number
t

 
class read_scale_record(__builtin__.object)
     Methods defined here:
__init__(O, line, source_info='')

Data descriptors defined here:
n
r
t

 
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)
ent_path_local_mirror(pdb_id, environ_key='PDB_MIRROR_PDB')
format_MTRIX_pdb_string(rotation_matrices, translation_vectors, serial_numbers=None, coordinates_present_flags=None)
MTRIX data sample
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
MTRIX1   1  1.000000  0.000000  0.000000        0.00000    1
MTRIX2   1  0.000000  1.000000  0.000000        0.00000    1
MTRIX3   1  0.000000  0.000000  1.000000        0.00000    1
MTRIX1   2  0.496590 -0.643597  0.582393        0.00000
MTRIX2   2  0.867925  0.376088 -0.324443        0.00000
MTRIX3   2 -0.010221  0.666588  0.745356        0.00000
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_link_records(link_list)
COLUMNS         DATA TYPE      FIELD           DEFINITION
-----------------------------------------------------------------------------
 1 -  6         Record name    "LINK  "
13 - 16         Atom           name1           Atom name.
17              Character      altLoc1         Alternate location indicator.
18 - 20         Residue name   resName1        Residue  name.
22              Character      chainID1        Chain identifier.
23 - 26         Integer        resSeq1         Residue sequence number.
27              AChar          iCode1          Insertion code.
43 - 46         Atom           name2           Atom name.
47              Character      altLoc2         Alternate location indicator.
48 - 50         Residue name   resName2        Residue name.
52              Character      chainID2        Chain identifier.
53 - 56         Integer        resSeq2         Residue sequence number.
57              AChar          iCode2          Insertion code.
60 - 65         SymOP          sym1            Symmetry operator atom 1.
67 - 72         SymOP          sym2            Symmetry operator atom 2.
74 - 78         Real(5.2)      Length          Link distance
format_scale_records(unit_cell=None, fractionalization_matrix=None, u=[0, 0, 0])
get_file_summary(pdb_in, hierarchy=None)
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, pdb_id=None, raise_sorry_if_format_error=False)
is_pdb_file(file_name)
is_pdb_mmcif_file(file_name)
make_atom_with_labels(result=None, 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)
merge_files_and_check_for_overlap(file_names, output_file, site_clash_cutoff=0.5, log=<open file '<stdout>', mode 'w'>)
pdb_input(file_name=None, source_info=<class 'iotbx.pdb.Please_pass_string_or_None'>, lines=None, pdb_id=None, raise_sorry_if_format_error=False)
quick_clash_check(file_name, site_clash_cutoff=0.5, out=<open file '<stdout>', mode 'w'>, show_outliers=5)
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)
show_file_summary(pdb_in, hierarchy=None, out=None)
systematic_chain_ids()
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>
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', 'OD2', 'WAT']
default_atom_names_scattering_type_const = ['PEAK', 'SITE']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
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(['A', 'AD', 'C', 'CD', 'G', 'GD', ...])
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>, 'ARG': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'ASN': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'ASP': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'CYS': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'GLN': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'GLU': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'GLY': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'HIS': <iotbx.pdb.atom_name_interpretation.interpreter object>, 'ILE': <iotbx.pdb.atom_name_interpretation.interpreter object>, ...}
rna_dna_atom_name_aliases = [('1D2', ' H21', 'G DG'), ("1D2'", " H2'", 'ANY'), ('1D2*', " H2'", 'ANY'), ('1D4', ' H41', 'C DC'), ("1D5'", " H5'", 'ANY'), ('1D5*', " H5'", 'ANY'), ('1D5M', ' H71', 'DT'), ('1D6', ' H61', 'A DA'), ('1H2', ' H21', 'G DG'), ("1H2'", " H2'", 'ANY'), ('1H2*', " H2'", 'ANY'), ('1H4', ' H41', 'C DC'), ("1H5'", " H5'", 'ANY'), ('1H5*', " H5'", 'ANY'), ('1H5M', ' H71', 'DT'), ('1H6', ' H61', 'A DA'), ('2D2', ' H22', 'G DG'), ("2D2'", "H2''", 'DA DC DG DT'), ('2D2*', "H2''", 'DA DC DG DT'), ('2D4', ' H42', 'C DC'), ...]
rna_dna_atom_names_backbone_aliases = {"1D2'": " H2'", '1D2*': " H2'", "1D5'": " H5'", '1D5*': " H5'", "1H2'": " H2'", '1H2*': " H2'", "1H5'": " H5'", '1H5*': " H5'", "2D2'": "H2''", '2D2*': "H2''", ...}
rna_dna_atom_names_backbone_reference_set = set([" C1'", " C2'", " C3'", " C4'", " C5'", " H1'", ...])
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', ...])