ndb_adapter package

Submodules

ndb_adapter.advanced_search_options module

class ndb_adapter.advanced_search_options.AdvancedSearchOptions(report_type: ndb_adapter.enums.ReportType = <ReportType.NDBStatus: <class 'ndb_adapter.search_report.NDBStatusReport'>>, statistics: bool = True)

Bases: object

Class needed for advanced search option parameters

get(stats: bool = False) → dict

Gets dictionary of advanced search options.

Parameters:stats (bool) – tells if dictionary should contain statistics Returns:dictionary with options Return type:dict

get_author()

Gets authors options

Returns:tuple of values Return type:(AndOr, str)

get_base()

Gets nucleic acid modification base options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_base_pair()

Gets RNA base pair interaction options

Returns:tuple of values Return type:(AndOr, BasePair)

get_base_pair_relative_freq()

Gets RNA base pair relative frequency interaction options

Returns:tuple of values Return type:(AndOr, BasePair, GreaterLower, float)

get_base_phosphate()

Gets RNA base phosphate interaction options

Returns:tuple of values Return type:(AndOr, BasePhosphate)

get_base_phosphate_relative_freq()

Gets RNA base phosphate relative frequency interaction options

Returns:tuple of values Return type:(AndOr, BasePhosphate, GreaterLower, float)

get_base_stack()

Gets RNA base stack interaction options

Returns:tuple of values Return type:(AndOr, BaseStack)

get_base_stack_relative_freq()

Gets RNA base stack relative frequency interaction options

Returns:tuple of values Return type:(AndOr, BaseStack, GreaterLower, float)

get_cell_a()

Gets cell a options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_alpha()

Gets cell alpha options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_b()

Gets cell b options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_beta()

Gets cell beta options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_c()

Gets cell c options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_gamma()

Gets cell gamma options

Returns:tuple of values Return type:(AndOr, GreaterLowerEqual, Optional[float])

get_cell_r_factor()

Gets cell r factor options

Returns:tuple of values Return type:(AndOr, RFactor)

get_cell_resolution()

Gets cell resolution options

Returns:tuple of values Return type:(AndOr, Optional[float])

get_conformation()

Gets nucleic acid conformation options

Returns:tuple of values Return type:(AndOr, ConformationType)

get_crystal_structure()

Gets tuple of crystal structure options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_dna()

Gets tuple of dna options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_drug()

Gets tuple of drug options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_drug_binding()

Gets tuple of drug binding options

Returns:tuple of values Return type:(AndOr, List[DrugBinding])

get_enzyme_binding()

Gets enzyme bindings functions options

Returns:tuple of values Return type:(AndOr, DnaRnaEither, AndOr, List[EnzymeFunction])

get_hairpin_loop_motif()

Gets RNA hairpin loop motif options

Returns:tuple of values Return type:(AndOr, List[HairpinLoopMotif])

get_hybrid()

Gets tuple of hybrid options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_internal_loop_motif()

Gets RNA internal loop motif options

Returns:tuple of values Return type:(AndOr, List[InternalLoopMotif])

get_ligand()

Gets tuple of ligand options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_ligand_id()

Gets tuple of ligand id options

Returns:tuple of values Return type:(AndOr, str)

get_ligand_name()

Gets tuple of ligand name options

Returns:tuple of values Return type:(AndOr, str)

get_na_features()

Gets nucleic acid features options

Returns:tuple of values Return type:(AndOr, AndOr, List[NaFeature])

get_na_pattern()

Gets nucleic acid sequence pattern options

Returns:tuple of values Return type:(AndOr, str)

get_ndb_id() → str

Gets NDB ID options

Returns:NDB ID Return type:str

get_nmr()

Gets nmr options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_nmr_restraints()

Gets nmr restraints available options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_non_redundant_list()

Gets RNA non redundant list cutoff options

Returns:tuple of values Return type:(AndOr, ResolutionCutoff)

get_oligo_seq_between()

Gets oligonucleotide between options

Returns:tuple of values Return type:(AndOr, Optional[int], Optional[int])

get_other_binding()

Gets other bindings functions options

Returns:tuple of values Return type:(AndOr, DnaRnaEither, AndOr, List[OtherFunction])

get_pdb_id() → str

Gets PDB ID options

Returns:PDB ID Return type:str

get_phosphate()

Gets nucleic acid modification phosphate options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_protein()

Gets tuple of protein options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_publication_year()

Gets year options

Returns:tuple of values Return type:(AndOr, str)

get_regulatory_binding()

Gets regulatory bindings functions options

Returns:tuple of values Return type:(AndOr, DnaRnaEither, AndOr, List[RegulatoryFunction])

get_released()

Gets released since date options

Returns:tuple of values Return type:(AndOr, Optional[date])

get_report_type() → ndb_adapter.enums.ReportType

Gets report type options

Returns:report type value Return type:ReportType

get_rna()

Gets tuple of rna options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_space_group()

Gets space group options

Returns:tuple of values Return type:(AndOr, SpaceGroup)

get_statistics() → bool

Gets advanced search if statistic

Returns:statistic true/false Return type:bool

get_strand_desc()

Gets nucleic acid strand description options

Returns:tuple of values Return type:(AndOr, List[StrandDescription])

get_structural_binding()

Gets structural bindings functions options

Returns:tuple of values Return type:(AndOr, DnaRnaEither, AndOr, List[StructuralFunction])

get_structure_factors()

Gets structure factor available options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

get_sugar()

Gets nucleic acid modification sugar options

Returns:tuple of values Return type:(AndOr, YesNoIgnore)

reset() → None

Reset advanced search options to defaults

Returns:None

set_author(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, author: str = '') → None

Sets authors in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• author (str) – authors string (default value = ‘’)

Returns:

None

set_base(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets nucleic acid modification base in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_base_pair(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_pair: ndb_adapter.enums.BasePair = <BasePair.Empty: ''>) → None

Sets RNA base pair interaction in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_pair (BasePair) – base pair interaction to set (default value = BasePair.Empty)

Returns:

None

set_base_pair_relative_freq(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_pair: ndb_adapter.enums.BasePair = <BasePair.Empty: ''>, gt_lt: ndb_adapter.enums.GreaterLower = <GreaterLower.GreaterEqual: 'gtEq'>, freq: float = 0.1) → None

Sets RNA base pair relative frequency interaction in options More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#relF

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_pair (BasePair) – base pair interaction to set (default value = BasePair.Empty)
• gt_lt (GreaterLower) – greater lower for relative frequency (default value = GreaterLower.GreaterEqual)
• freq (float) – relative frequency value (default value = 0.1)

Returns:

None

set_base_phosphate(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_phosphate: ndb_adapter.enums.BasePhosphate = <BasePhosphate.Empty: ''>) → None

Sets RNA base phosphate interaction in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_phosphate (BasePhosphate) – base phosphate interaction to set (default value = BasePhosphate.Empty)

Returns:

None

set_base_phosphate_relative_freq(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_phosphate: ndb_adapter.enums.BasePhosphate = <BasePhosphate.Empty: ''>, gt_lt: ndb_adapter.enums.GreaterLower = <GreaterLower.GreaterEqual: 'gtEq'>, freq: float = 0.1) → None

Sets RNA base phosphate relative frequency interaction in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#relF

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_phosphate (BasePhosphate) – base phosphate interaction to set (default value = BasePhosphate.Empty)
• gt_lt (GreaterLower) – greater lower for relative frequency (default value = GreaterLower.GreaterEqual)
• freq (float) – relative frequency value (default value = 0.1)

Returns:

None

set_base_stack(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_stack: ndb_adapter.enums.BaseStack = <BaseStack.Empty: ''>) → None

Sets RNA base stack interaction in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_stack (BaseStack) – base stack interaction to set (default value = BaseStack.Empty)

Returns:

None

set_base_stack_relative_freq(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, base_stack: ndb_adapter.enums.BaseStack = <BaseStack.Empty: ''>, gt_lt: ndb_adapter.enums.GreaterLower = <GreaterLower.GreaterEqual: 'gtEq'>, freq: float = 0.1) → None

Sets RNA base stack relative frequency interaction in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#relF

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• base_stack (BasePhosphate) – base phosphate interaction to set (default value = BaseStack.Empty)
• gt_lt (GreaterLower) – greater lower for relative frequency (default value = GreaterLower.GreaterEqual)
• freq (float) – relative frequency value (default value = 0.1)

Returns:

None

set_cell_a(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell a angstroms in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float a value in angstroms (default value = None)

Returns:

None

set_cell_alpha(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell alpha in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float alpha value (default value = None)

Returns:

None

set_cell_b(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell b angstroms in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float b value in angstroms (default value = None)

Returns:

None

set_cell_beta(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell beta in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float beta value (default value = None)

Returns:

None

set_cell_c(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell c angstroms in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float c value in angstroms (default value = None)

Returns:

None

set_cell_gamma(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, gt_lt_eq: ndb_adapter.enums.GreaterLowerEqual = <GreaterLowerEqual.Equal: 'eq'>, value: typing.Union[float, NoneType] = None) → None

Sets cell beta in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• gt_lt_eq (GreaterLowerEqual) – space group to choose (default value = .Empty)
• value (Optional[float]) – optional float gamma value (default value = None)

Returns:

None

set_cell_r_factor(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, r_factor: ndb_adapter.enums.RFactor = <RFactor.Empty: ''>) → None

Sets cell r factor in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• r_factor (RFactor) – r factor value in angstroms (default value = RFactor.Empty)

Returns:

None

set_cell_resolution(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, better_than: typing.Union[float, NoneType] = None) → None

Sets cell resolution angstroms in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• better_than (Optional[float]) – optional float resolution value in angstroms (default value = None)

Returns:

None

set_conformation(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, conformation: ndb_adapter.enums.ConformationType = <ConformationType.Empty: ''>) → None

Sets nucleic acid conformation in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• conformation (ConformationType) – conformation value (default value = ConformationType.Empty)

Returns:

None

set_crystal_structure(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets crystal structure in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_dna(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets dna in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_drug(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets drug in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_drug_binding(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *types: typing.List[ndb_adapter.enums.DrugBinding]) → None

Sets drug binding in options - to get it work ensure to call set_drug()!!!

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• types (List[DrugBinding]) – list of DrugBinding that should be in query, allowed as many as you want

Returns:

None

set_enzyme_binding(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, dna_rna_either: ndb_adapter.enums.DnaRnaEither = <DnaRnaEither.Either: 'EITHER'>, func_clause: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *functions: typing.List[ndb_adapter.enums.EnzymeFunction]) → None

Sets enzyme bindings functions in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• dna_rna_either (DnaRnaEither) – tells if it should be ‘dna’, ‘rna’ or ‘either’ in query (default value = .Either)
• func_clause (AndOr) – connector between functions in query
• functions (List[EnzymeFunction]) – list of EnzymeFunction that should be in query, allowed as many as you want

Returns:

None

set_hairpin_loop_motif(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *motifs: typing.List[ndb_adapter.enums.HairpinLoopMotif]) → None

Sets RNA hairpin loop motif in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#motif

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• motifs (List[HairpinLoopMotif]) – list of HairpinLoopMotif that should be in query, allowed as many as you want

Returns:

None

set_hybrid(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets hybrid in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_internal_loop_motif(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *motifs: typing.List[ndb_adapter.enums.InternalLoopMotif]) → None

Sets RNA internal loop motif in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#motif

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• motifs (List[InternalLoopMotif]) – list of InternalLoopMotif that should be in query, allowed as many as you want

Returns:

None

set_ligand(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets ligand in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_ligand_id(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, ligand_id: str = '') → None

Sets ligand id in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• ligand_id (str) – ligand ID (default value = ‘’)

Returns:

None

set_ligand_name(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, ligand_name: str = '') → None

Sets ligand name in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• ligand_name (str) – ligand name (default value = ‘’)

Returns:

None

set_na_features(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, func_clause: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *features: typing.List[ndb_adapter.enums.NaFeature]) → None

Sets nucleic acid features in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• func_clause (AndOr) – connector between features in query
• features (List[NaFeature]) – list of NaFeature that should be in query, allowed as many as you want

Returns:

None

set_na_pattern(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, pattern: str = '') → None

Sets nucleic acid sequence pattern in options.

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• pattern (str) – pattern value (default value = ‘’)

Returns:

None

set_ndb_id(ndb_id: str = '') → None

Sets NDB ID in options

Parameters:ndb_id (str) – NDB ID e.g. NA2326 (default value = ‘’) Returns:None

set_nmr(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets nmr in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_nmr_restraints(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets nmr restraints available in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_non_redundant_list(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, resolution: ndb_adapter.enums.ResolutionCutoff = <ResolutionCutoff.Empty: ''>) → None

Sets RNA non redundant list cutoff in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#nrl

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• resolution (ResolutionCutoff) – resolution value (default value = ResolutionCutoff.Empty)

Returns:

None

set_oligo_seq_between(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, from_len: typing.Union[int, NoneType] = None, to_len: typing.Union[int, NoneType] = None) → None

Sets oligonucleotide between “from_len” to “to_len” in options.

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• from_len (Optional[int]) – from oligonucleotide value (default value = None)
• to_len (Optional[int]) – to oligonucleotide value (default value = None)

Returns:

None

set_other_binding(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, dna_rna_either: ndb_adapter.enums.DnaRnaEither = <DnaRnaEither.Either: 'EITHER'>, func_clause: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *functions: typing.List[ndb_adapter.enums.OtherFunction]) → None

Sets other bindings functions in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• dna_rna_either (DnaRnaEither) – tells if it should be ‘dna’, ‘rna’ or ‘either’ in query (default value = .Either)
• func_clause (AndOr) – connector between functions in query
• functions (List[OtherFunction]) – list of OtherFunction that should be in query, allowed as many as you want

Returns:

None

set_pdb_id(pdb_id: str = '') → None

Sets PDB ID in options

Parameters:pdb_id (str) – PDB ID e.g. 4JRC (default value = ‘’) Returns:None

set_phosphate(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets nucleic acid modification phosphate in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_protein(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets protein in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_publication_year(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, year: str = '') → None

Sets authors in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• year (str) – year string (default value = ‘’)

Returns:

None

set_regulatory_binding(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, dna_rna_either: ndb_adapter.enums.DnaRnaEither = <DnaRnaEither.Either: 'EITHER'>, func_clause: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *functions: typing.List[ndb_adapter.enums.RegulatoryFunction]) → None

Sets regulatory bindings functions in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• dna_rna_either (DnaRnaEither) – tells if it should be ‘dna’, ‘rna’ or ‘either’ in query (default value = .Either)
• func_clause (AndOr) – connector between functions in query
• functions (List[RegulatoryFunction]) – list of RegulatoryFunction that should be in query, allowed as many as you want

Returns:

None

set_released(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, since_date: typing.Union[datetime.date, NoneType] = None) → None

Sets released since date in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• since_date (Optional[date]) – released since date (default value = None)

Returns:

None

set_report_type(report: ndb_adapter.enums.ReportType = <ReportType.NDBStatus: <class 'ndb_adapter.search_report.NDBStatusReport'>>) → None

Sets report type in search object

Parameters:report (ReportType) – report type to set Returns:None

set_rna(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets rna in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_space_group(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, space_group: ndb_adapter.enums.SpaceGroup = <SpaceGroup.Empty: ''>) → None

Sets space group in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• space_group (SpaceGroup) – space group to choose (default value = .Ignore)

Returns:

None

set_statistics(statistics: bool = True) → None

Sets if is statistics

Parameters:statistics (bool) – statistics value (default value = True) Returns:None

set_strand_desc(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *descriptions: typing.List[ndb_adapter.enums.StrandDescription]) → None

Sets nucleic acid strand description in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• descriptions (List[StrandDescription]) – list of StrandDescription that should be in query, allowed as many as you want

Returns:

None

set_structural_binding(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, dna_rna_either: ndb_adapter.enums.DnaRnaEither = <DnaRnaEither.Either: 'EITHER'>, func_clause: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, *functions: typing.List[ndb_adapter.enums.StructuralFunction]) → None

Sets structural bindings functions in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• dna_rna_either (DnaRnaEither) – tells if it should be ‘dna’, ‘rna’ or ‘either’ in query (default value = .Either)
• func_clause (AndOr) – connector between functions in query
• functions (List[StructuralFunction]) – list of StructuralFunction that should be in query, allowed as many as you want

Returns:

None

set_structure_factors(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets structure factor available in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

set_sugar(and_or: ndb_adapter.enums.AndOr = <AndOr.And: 'AND'>, yes_no_ignore: ndb_adapter.enums.YesNoIgnore = <YesNoIgnore.Ignore: 'Ignore'>) → None

Sets nucleic acid modification sugar in options

Parameters:

• and_or (AndOr) – tells if it should be ‘and’ or ‘or’ in query (default value = AndOr.And)
• yes_no_ignore (YesNoIgnore) – tells if it should ‘be’, ‘not be’ or ‘be ignored’ in query (default value = .Ignore)

Returns:

None

ndb_adapter.dna_search_options module

class ndb_adapter.dna_search_options.DnaSearchOptions

Bases: ndb_adapter.search_options.SearchOptions

Class for dna search options

get_structural_features() → ndb_adapter.enums.StructuralFeatures

Gets structural features options

Returns:structural feature Return type:StructuralFeatures

set_structural_features(feature: ndb_adapter.enums.StructuralFeatures = <StructuralFeatures.All: 'all'>) → None

Sets structural features in options

Parameters:feature (StructuralFeatures) – structural feature (default value = StructuralFeatures.All) Returns:None

ndb_adapter.enums module

class ndb_adapter.enums.AndOr

Bases: enum.Enum

Enum to handle “and”, “or” in query

Variables:

• And – and in query
• Or – or in query

And = <AndOr.And: 'AND'>

Or = <AndOr.Or: 'OR'>

class ndb_adapter.enums.BasePair

Bases: enum.Enum

Enum for base pair interaction options in query. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#bp

Variables:

• Empty – empty value in query
• CWW – (cis Watson-Crick/Watson-Crick) in query
• TWW – (trans Watson-Crick/Watson-Crick) in query
• CWH – (cis Watson-Crick/Hoogsteen) in query
• TWH – (trans Watson-Crick/Hoogsteen) in query
• CWS – (cis Watson-Crick/Sugar Edge) in query
• TWS – (trans Watson-Crick/Sugar Edge) in query
• CHH – (cis Hoogsteen/Hoogsteen) in query
• THH – (trans Hoogsteen/Hoogsteen) in query
• CHS – (cis Hoogsteen/Sugar Edge) in query
• THS – (trans Hoogsteen/Sugar Edge) in query
• CSS – (cis Sugar Edge/Sugar Edge) in query
• TSS – (trans Sugar Edge/Sugar Edge) in query

CHH = <BasePair.CHH: 'cHH'>

CHS = <BasePair.CHS: 'cHS'>

CSS = <BasePair.CSS: 'cSS'>

CWH = <BasePair.CWH: 'cWH'>

CWS = <BasePair.CWS: 'cWS'>

CWW = <BasePair.CWW: 'cWW'>

Empty = <BasePair.Empty: ''>

THH = <BasePair.THH: 'tHH'>

THS = <BasePair.THS: 'tHS'>

TSS = <BasePair.TSS: 'tSS'>

TWH = <BasePair.TWH: 'tWH'>

TWS = <BasePair.TWS: 'tWS'>

TWW = <BasePair.TWW: 'tWW'>

class ndb_adapter.enums.BasePhosphate

Bases: enum.Enum

Enum for base phosphate interaction in query. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#bph

Variables:

• Empty – empty values in query
• BPh_1 – 1BPh (base-phosphate position 1) in query
• BPh_2 – 2BPh (base-phosphate position 2) in query
• BPh_3 – 3BPh (base-phosphate position 3) in query
• BPh_4 – 4BPh (base-phosphate position 4) in query
• BPh_5 – 5BPh (base-phosphate position 5) in query
• BPh_6 – 6BPh (base-phosphate position 6) in query
• BPh_7 – 7BPh (base-phosphate position 7) in query
• BPh_8 – 8BPh (base-phosphate position 8) in query
• BPh_9 – 9BPh (base-phosphate position 9) in query
• BPh_0 – 0BPh (base-phosphate position 10) in query

BPh_0 = <BasePhosphate.BPh_0: '0BPh'>

BPh_1 = <BasePhosphate.BPh_1: '1BPh'>

BPh_2 = <BasePhosphate.BPh_2: '2BPh'>

BPh_3 = <BasePhosphate.BPh_3: '3BPh'>

BPh_4 = <BasePhosphate.BPh_4: '4BPh'>

BPh_5 = <BasePhosphate.BPh_5: '5BPh'>

BPh_6 = <BasePhosphate.BPh_6: '6BPh'>

BPh_7 = <BasePhosphate.BPh_7: '7BPh'>

BPh_8 = <BasePhosphate.BPh_8: '8BPh'>

BPh_9 = <BasePhosphate.BPh_9: '9BPh'>

Empty = <BasePhosphate.Empty: ''>

class ndb_adapter.enums.BaseStack

Bases: enum.Enum

Enum for base stack interaction in query. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#bs

Variables:

• Empty – empty value in query
• S_33 – s33 (stack, 3′ face on 3′ face) in query
• S_35 – s35 (stack, 3′ face on 5′ face) in query
• S_55 – s55 (stack, 5′ face on 5′ face) in query

Empty = <BaseStack.Empty: ''>

S_33 = <BaseStack.S_33: 's33'>

S_35 = <BaseStack.S_35: 's35'>

S_55 = <BaseStack.S_55: 's55'>

class ndb_adapter.enums.ConformationType

Bases: enum.Enum

Enum for conformation type in query

Variables:

• Empty – empty value in query
• All – all conformations in query
• A – A conformation in query
• B – B conformation in query
• RH – RH conformation in query
• T – T conformation in query
• U – U conformation in query
• Z – Z conformation in query

A = <ConformationType.A: 'A'>

All = <ConformationType.All: 'all'>

B = <ConformationType.B: 'B'>

Empty = <ConformationType.Empty: ''>

RH = <ConformationType.RH: 'RH'>

T = <ConformationType.T: 'T'>

U = <ConformationType.U: 'U'>

Z = <ConformationType.Z: 'Z'>

class ndb_adapter.enums.DnaRnaEither

Bases: enum.Enum

Enum to handle “dna”, “rna”, “either” in query

Variables:

• DNA – dna in query
• RNA – rna in query
• Either – either in query

DNA = <DnaRnaEither.DNA: 'DNA'>

Either = <DnaRnaEither.Either: 'EITHER'>

RNA = <DnaRnaEither.RNA: 'RNA'>

class ndb_adapter.enums.DrugBinding

Bases: enum.Enum

Enum to handle nucleic acid drug bindings options in query

Variables:

• Empty – empty value in query
• Intercalation – Intercalation in query
• OutsideBinder – Outside binder in query
• IntercalationCovalent – Intercalation, covalent in query
• OutsideBinderCovalent – Outside binder, covalent in query
• MajorGrooveBinder – Major groove binder in query
• MinorGrooveBinder – Minor groove binder in query
• MajorGrooveBinderCovalent – Major groove binder, covalent in query
• MinorGrooveBinderCovalent – Minor groove binder, covalent in query
• BisIntercalation – Bis-Intercalation in query
• DoubleMajorGrooveBinder – Double major groove binder in query
• DoubleMinorGrooveBinder – Double minor groove binder in query
• CovalentMetalBonds – Covalent metal bonds in query

BisIntercalation = <DrugBinding.BisIntercalation: 'Bis-Intercalation'>

CovalentMetalBonds = <DrugBinding.CovalentMetalBonds: 'Covalent Metal Bonds'>

DoubleMajorGrooveBinder = <DrugBinding.DoubleMajorGrooveBinder: 'Double Major Groove Binder'>

DoubleMinorGrooveBinder = <DrugBinding.DoubleMinorGrooveBinder: 'Double Minor Groove Binder'>

Empty = <DrugBinding.Empty: ''>

Intercalation = <DrugBinding.Intercalation: 'Intercalation'>

IntercalationCovalent = <DrugBinding.IntercalationCovalent: 'Intercalation, Covalent'>

IntercalationMajorGrooveBinder = <DrugBinding.IntercalationMajorGrooveBinder: 'Intercalation, Major Groove Binder'>

IntercalationMinorGrooveBinder = <DrugBinding.IntercalationMinorGrooveBinder: 'Intercalation, Minor Groove Binder'>

MajorGrooveBinder = <DrugBinding.MajorGrooveBinder: 'Major Groove Binder'>

MajorGrooveBinderCovalent = <DrugBinding.MajorGrooveBinderCovalent: 'Major Groove Binder, Covalent'>

MinorGrooveBinder = <DrugBinding.MinorGrooveBinder: 'Minor Groove Binder'>

MinorGrooveBinderCovalent = <DrugBinding.MinorGrooveBinderCovalent: 'Minor Groove Binder, Covalent'>

OutsideBinder = <DrugBinding.OutsideBinder: 'Outside binder'>

OutsideBinderCovalent = <DrugBinding.OutsideBinderCovalent: 'Outside binder, Covalent'>

class ndb_adapter.enums.EnzymeFunction

Bases: enum.Enum

Enum for enzyme function in query

Variables:

• Empty – empty value in query
• All – all functions in query
• Topoisomerase – topoisomerase function in query
• Synthetase – synthetase function in query
• Thrombin – thrombin function in query
• DNAPolymerase – DNA polymarase function in query
• DNAReverseTranscriptase – DNA polymerase / reverse transcriptase function in query
• DNAEndonuclease – DNA nuclease / endonucelase function in query
• DNAExonuclease – DNA nuclease / exonucelase function in query
• Glycosylase – glycosylase function in query
• Helicase – helicase function in query
• Kinase – kinase function in query
• Ligase – ligase function in query
• Lyase – lyase function in query
• MethylaseMethytransferase – methylase or methyltransferase function in query
• MRNACapping – mRNA capping function in query
• Phosphatase – phosphatase function in query
• Integrase – recombinase / integrase function in query
• Invertase – recombinase / invertase function in query
• Resolvase – recombinase / resolvase function in query
• Transposase – recombinase / transposase function in query
• RecombinaseOther – recombinase / other function in query
• RNAPolymerase – RNA polymerase function in query
• RNAEndonuclease – RNA nuclease / endonuclease function in query
• RNAExonuclease – RNA nuclease / exdonuclease function in query
• TRNAModifying – tRNA Modifying function in query
• Other – other function in query

All = <EnzymeFunction.All: 'ENZYME'>

DNAEndonuclease = <EnzymeFunction.DNAEndonuclease: 'DNA NUCLEASE/ENDONUCLEASE'>

DNAExonuclease = <EnzymeFunction.DNAExonuclease: 'DNA NUCLEASE/EXONUCLEASE'>

DNAPolymerase = <EnzymeFunction.DNAPolymerase: 'DNA POLYMERASE'>

DNAReverseTranscriptase = <EnzymeFunction.DNAReverseTranscriptase: 'DNA POLYMERASE/REVERSE TRANSCRIPTASE'>

Empty = <EnzymeFunction.Empty: ''>

Glycosylase = <EnzymeFunction.Glycosylase: 'GLYCOSYLASE'>

Helicase = <EnzymeFunction.Helicase: 'HELICASE'>

Integrase = <EnzymeFunction.Integrase: 'RECOMBINASE/INTEGRASE'>

Invertase = <EnzymeFunction.Invertase: 'RECOMBINASE/INVERTASE'>

Kinase = <EnzymeFunction.Kinase: 'KINASE'>

Ligase = <EnzymeFunction.Ligase: 'LIGASE'>

Lyase = <EnzymeFunction.Lyase: 'LYASE'>

MRNACapping = <EnzymeFunction.MRNACapping: 'MRNA CAPPING'>

MethylaseMethytransferase = <EnzymeFunction.MethylaseMethytransferase: 'METHYLASE OR METHYLTRANSFERASE'>

Other = <EnzymeFunction.Other: 'OTHER'>

Phosphatase = <EnzymeFunction.Phosphatase: 'PHOSPHATASE'>

RNAEndonuclease = <EnzymeFunction.RNAEndonuclease: 'RNA NUCLEASE/ENDONUCLEASE'>

RNAExonuclease = <EnzymeFunction.RNAExonuclease: 'RNA NUCLEASE/EXONUCLEASE'>

RNAPolymerase = <EnzymeFunction.RNAPolymerase: 'RNA POLYMERASE'>

RecombinaseOther = <EnzymeFunction.RecombinaseOther: 'RECOMBINASE/OTHER'>

Resolvase = <EnzymeFunction.Resolvase: 'RECOMBINASE/RESOLVASE'>

Synthetase = <EnzymeFunction.Synthetase: 'SYNTHETASE'>

TRNAModifying = <EnzymeFunction.TRNAModifying: 'TRNA MODIFYING'>

Thrombin = <EnzymeFunction.Thrombin: 'THROMBIN'>

Topoisomerase = <EnzymeFunction.Topoisomerase: 'TOPOISOMERASE'>

Transposase = <EnzymeFunction.Transposase: 'RECOMBINASE/TRANSPOSASE'>

class ndb_adapter.enums.ExpMethod

Bases: enum.Enum

Enum to handle experimental method in query

Variables:

• All – all in query
• XRAY – x-ray in query
• NMR – nmr in query

All = <ExpMethod.All: 'all'>

NMR = <ExpMethod.NMR: 'nmr'>

XRAY = <ExpMethod.XRAY: 'x-ray'>

class ndb_adapter.enums.GreaterLower

Bases: enum.Enum

Enum to handle “>=”, “<=” in query

Variables:

• GreaterEqual – >= in query
• LowerEqual – <= in query

GreaterEqual = <GreaterLower.GreaterEqual: 'gtEq'>

LowerEqual = <GreaterLower.LowerEqual: 'ltEq'>

class ndb_adapter.enums.GreaterLowerEqual

Bases: enum.Enum

Enum to handle “>=”, “<=”, “==” in query

Variables:

• GreaterEqual – >= in query
• LowerEqual – <= in query
• Equal – == in query

Equal = <GreaterLowerEqual.Equal: 'eq'>

GreaterEqual = <GreaterLowerEqual.GreaterEqual: 'gtEq'>

LowerEqual = <GreaterLowerEqual.LowerEqual: 'ltEq'>

class ndb_adapter.enums.HairpinLoopMotif

Bases: enum.Enum

Enum for hairpin loop motif in query

Variables:

• Empty – empty value in query
• All – all motifs in query
• TLoop – T-loop motif in query
• GNRA – GNRA motif in query
• UNCG – UNCG motif in query

All = <HairpinLoopMotif.All: 'All'>

Empty = <HairpinLoopMotif.Empty: ''>

GNRA = <HairpinLoopMotif.GNRA: 'GNRA'>

TLoop = <HairpinLoopMotif.TLoop: 'T-loop'>

UNCG = <HairpinLoopMotif.UNCG: 'UNCG'>

class ndb_adapter.enums.InternalLoopMotif

Bases: enum.Enum

Enum for internal loop motif in query

Variables:

• Empty – empty value in query
• All – all motifs in query
• SarcinRicin – Sarcin-ricin motif in query
• KinkTurn – Kink-turn motif in query
• CLoop – C-loop motif in query
• DoubleSheared – Double-sheared motif in query
• TripleSheared – Triple-sheared motif in query

All = <InternalLoopMotif.All: 'All'>

CLoop = <InternalLoopMotif.CLoop: 'C-loop'>

DoubleSheared = <InternalLoopMotif.DoubleSheared: 'Double-sheared'>

Empty = <InternalLoopMotif.Empty: ''>

KinkTurn = <InternalLoopMotif.KinkTurn: 'Kink-turn'>

SarcinRicin = <InternalLoopMotif.SarcinRicin: 'Sarcin-ricin'>

TripleSheared = <InternalLoopMotif.TripleSheared: 'Triple-sheared'>

class ndb_adapter.enums.NaFeature

Bases: enum.Enum

Enum for nucleic acid feature in query

Variables:

• Empty – empty value in query
• All – all features in query
• HairpinLoop – hairpin loop in query
• InternalLoop – internal loop in query
• Bulge – bulge in query
• Hammerhead – hammerhead in query
• ThreeWayJunction – three way junction in query
• FourWayJunction – four way (holliday) junction in query
• NonWatsonCrickBaseParing – non watson crick base paring in query
• MismatchBaseParing – mismatch base paring in query

All = <NaFeature.All: 'loop'>

Bulge = <NaFeature.Bulge: 'bulge'>

Empty = <NaFeature.Empty: ''>

FourWayJunction = <NaFeature.FourWayJunction: 'holliday_junction'>

HairpinLoop = <NaFeature.HairpinLoop: 'hairpin loop'>

Hammerhead = <NaFeature.Hammerhead: 'hammerhead'>

InternalLoop = <NaFeature.InternalLoop: 'internal loop'>

MismatchBaseParing = <NaFeature.MismatchBaseParing: 'mismat'>

NonWatsonCrickBaseParing = <NaFeature.NonWatsonCrickBaseParing: 'type_11_pair'>

ThreeWayJunction = <NaFeature.ThreeWayJunction: 'three_way_junction'>

class ndb_adapter.enums.OtherFunction

Bases: enum.Enum

Enum for other functions in query

Variables:

• Empty – empty value in query
• All – all functions in query
• Antibiotic – antibiotic function in query
• Antibody – antibody function in query
• Other – other function in query

All = <OtherFunction.All: 'OTHER'>

Antibiotic = <OtherFunction.Antibiotic: 'Antibiotic'>

Antibody = <OtherFunction.Antibody: 'Antibody'>

Empty = <OtherFunction.Empty: ''>

Other = <OtherFunction.Other: 'Other'>

class ndb_adapter.enums.Polymer

Bases: enum.Enum

Enums to handle polymer in query

Variables:

• All – all in query
• DNAOnly – DNA Only in query
• ProteinDNA – Protein DNA Complexes in query
• DrugDNA – Drug DNA Complexes in query
• HybridsChimera – Hybrids and Chimera in query
• PeptideNucleicAcid – Peptide Nucleic Acid / Mimetics in query

All = <Polymer.All: 'all'>

DNAOnly = <Polymer.DNAOnly: 'onlyDna'>

DrugDNA = <Polymer.DrugDNA: 'drugDna'>

HybridsChimera = <Polymer.HybridsChimera: 'hybNChimera'>

PeptideNucleicAcid = <Polymer.PeptideNucleicAcid: 'pepNucAcid'>

ProteinDNA = <Polymer.ProteinDNA: 'protDna'>

class ndb_adapter.enums.ProteinFunc

Bases: enum.Enum

Enums to handle protein function in query

Variables:

• All – all in query
• Enzymes – enzymes function in query
• Structural – structural function in query
• Regulatory – regulatory function in query
• Other – other function in query

All = <ProteinFunc.All: 'all'>

Enzymes = <ProteinFunc.Enzymes: 'enzymes'>

Other = <ProteinFunc.Other: 'other'>

Regulatory = <ProteinFunc.Regulatory: 'regulatory'>

Structural = <ProteinFunc.Structural: 'structural'>

class ndb_adapter.enums.RFactor

Bases: enum.Enum

Enum to handle R-factor in query

Variables:

• Empty – empty value in query
• R_10 – 0.10 in query
• R_15 – 0.15 in query
• R_20 – 0.20 in query
• R_25 – 0.25 in query
• R_30 – 0.30 in query
• R_35 – 0.35 in query

Empty = <RFactor.Empty: ''>

R_10 = <RFactor.R_10: '0.10'>

R_15 = <RFactor.R_15: '0.15'>

R_20 = <RFactor.R_20: '0.20'>

R_25 = <RFactor.R_25: '0.25'>

R_30 = <RFactor.R_30: '0.30'>

R_35 = <RFactor.R_35: '0.35'>

class ndb_adapter.enums.RegulatoryFunction

Bases: enum.Enum

Enum for regulatory functions in query

Variables:

• Empty – empty value in query
• All – all functions in query
• DnaRepairActivator – DNA repair activator function in query
• DnaRepairRepressor – DNA repair repressor function in query
• RecombinationActivator – recombination activator function in query
• RecombinationReporessor – recombination reporessor function in query
• ReplicationActivator – replication factor / activator function in query
• ReplicationReporessor – replication factor / reporessor function in query
• SpliceosomalProtein – spliceosomal protein function in query
• TranscriptionActivatorRepressor – transcription factor / activator and repressor function in query
• TranscriptionActivator – transcription factor / activator function in query
• TranscriptionCoactivator – transcription factor / coactivator function in query
• TranscriptionCorepressor – transcription factor / corepressor function in query
• TranscriptionElongation – transcription factor / elongation function in query
• Transcription – transcription factor in general in query
• TranscriptionReporessor – transcription factor / repressor function in query
• TranscriptionTermination – transcription factor / termination function in query
• TranslationElongation – translation factor / elongation function in query
• TranslationInitiator – translation factor / initiator function in query
• TranslationTermination – translation factor / termination function in query

All = <RegulatoryFunction.All: 'REGULATORY'>

DnaRepairActivator = <RegulatoryFunction.DnaRepairActivator: 'DNA Repair Activator'>

DnaRepairRepressor = <RegulatoryFunction.DnaRepairRepressor: 'DNA Repair Repressor'>

Empty = <RegulatoryFunction.Empty: ''>

RecombinationActivator = <RegulatoryFunction.RecombinationActivator: 'Recombination Activator'>

RecombinationReporessor = <RegulatoryFunction.RecombinationReporessor: 'Recombination Repressor'>

ReplicationActivator = <RegulatoryFunction.ReplicationActivator: 'Replication Factor/Activator'>

ReplicationReporessor = <RegulatoryFunction.ReplicationReporessor: 'Replication Factor/Repressor'>

SpliceosomalProtein = <RegulatoryFunction.SpliceosomalProtein: 'Spliceosomal Protein'>

Transcription = <RegulatoryFunction.Transcription: 'Transcription Factor/General'>

TranscriptionActivator = <RegulatoryFunction.TranscriptionActivator: 'Transcription Factor/Activator'>

TranscriptionActivatorRepressor = <RegulatoryFunction.TranscriptionActivatorRepressor: 'Transcription Factor/Activator And Repressor'>

TranscriptionCoactivator = <RegulatoryFunction.TranscriptionCoactivator: 'Transcription Factor/Coactivator'>

TranscriptionCorepressor = <RegulatoryFunction.TranscriptionCorepressor: 'Transcription Factor/Corepressor'>

TranscriptionElongation = <RegulatoryFunction.TranscriptionElongation: 'Transcription Factor/Elongation'>

TranscriptionReporessor = <RegulatoryFunction.TranscriptionReporessor: 'Transcription Factor/Repressor'>

TranscriptionTermination = <RegulatoryFunction.TranscriptionTermination: 'Transcription Factor/Termination'>

TranslationElongation = <RegulatoryFunction.TranslationElongation: 'Translation Factor/Elongation'>

TranslationInitiator = <RegulatoryFunction.TranslationInitiator: 'Translation Factor/Initiator'>

TranslationTermination = <RegulatoryFunction.TranslationTermination: 'Translation Factor/Termination'>

class ndb_adapter.enums.ReportType

Bases: enum.Enum

Enum representing advanced search report type - can be used to annotate return type of advanced search report

Variables:

• NDBStatus – NDB Status search report
• CellDimensions – Cell Dimensions search report
• Citation – Citation search report
• RefinementData – Refinement Data search report
• NABackboneTorsion – NA Backbone Torsion search report
• BasePairParameter – Base Pair Parameter search report
• BasePairStepParameter – Base Pair Step Parameter search report
• Descriptor – Descriptor search report
• Sequences – Sequences search report
• RNABasePairRelFreq – RNA 3D Base Pair Relative Frequency search report
• RNABasePhosphateRelFreq – RNA 3D Base Phosphate Relative Frequency search report
• RNABaseStackingRelFreq – RNA 3D Base Stacking Relative Frequency search report
• RNAMotif – RNA Motif search report

BasePairParameter = <ReportType.BasePairParameter: <class 'ndb_adapter.search_report.BasePairParameterReport'>>

BasePairStepParameter = <ReportType.BasePairStepParameter: <class 'ndb_adapter.search_report.BasePairStepParameterReport'>>

CellDimensions = <ReportType.CellDimensions: <class 'ndb_adapter.search_report.CellDimensionsReport'>>

Citation = <ReportType.Citation: <class 'ndb_adapter.search_report.CitationReport'>>

Descriptor = <ReportType.Descriptor: <class 'ndb_adapter.search_report.DescriptorReport'>>

NABackboneTorsion = <ReportType.NABackboneTorsion: <class 'ndb_adapter.search_report.NABackboneTorsionReport'>>

NDBStatus = <ReportType.NDBStatus: <class 'ndb_adapter.search_report.NDBStatusReport'>>

RNABasePairRelFreq = <ReportType.RNABasePairRelFreq: <class 'ndb_adapter.search_report.RNA3DBasePairRelFreqReport'>>

RNABasePhosphateRelFreq = <ReportType.RNABasePhosphateRelFreq: <class 'ndb_adapter.search_report.RNA3DBasePhosphateRelFreqReport'>>

RNABaseStackingRelFreq = <ReportType.RNABaseStackingRelFreq: <class 'ndb_adapter.search_report.RNA3DBaseStackingRelFreqReport'>>

RNAMotif = <ReportType.RNAMotif: <class 'ndb_adapter.search_report.RNA3DMotifReport'>>

RefinementData = <ReportType.RefinementData: <class 'ndb_adapter.search_report.RefinementDataReport'>>

Sequences = <ReportType.Sequences: <class 'ndb_adapter.search_report.SequencesReport'>>

class ndb_adapter.enums.ResolutionCutoff

Bases: enum.Enum

Enum to handle resolution cutoff options in query

Variables:

• All – all in query
• Empty – empty in query
• OneHalf – 1.5 in query
• Two – 2.0 in query
• TwoHalf – 2.5 in query
• Three – 3.0 in query
• ThreeHalf – 3.5 in query
• Four – 4.0 in query
• Twenty – 20.0 in query

All = <ResolutionCutoff.All: 'all'>

Empty = <ResolutionCutoff.Empty: ''>

Four = <ResolutionCutoff.Four: '4.0'>

OneHalf = <ResolutionCutoff.OneHalf: '1.5'>

Three = <ResolutionCutoff.Three: '3.0'>

ThreeHalf = <ResolutionCutoff.ThreeHalf: '3.5'>

Twenty = <ResolutionCutoff.Twenty: '20.0'>

Two = <ResolutionCutoff.Two: '2.0'>

TwoHalf = <ResolutionCutoff.TwoHalf: '2.5'>

class ndb_adapter.enums.RnaStructures

Bases: enum.Enum

Enum to handle rna structures option in query

Variables:

• All – all in query
• NonRedundant – no redundant in query

All = <RnaStructures.All: 'all'>

NonRedundant = <RnaStructures.NonRedundant: 'nr'>

class ndb_adapter.enums.RnaType

Bases: enum.Enum

Enum to handle rna type options in query

Variables:

• All – all in query
• TRNA – tRNA in query
• TRNAFrag – tRNA fragment in query
• Ribosome – Ribosome in query
• Ribozyme – Ribozyme in query
• Harpin – Hairpin Ribozyme in query
• Hammerhead – Hammerhead Ribozyme in query
• Group1Intron – Group I intron Ribozyme in query
• Group2Intron – Group II intron Ribozyme in query
• RnaseP – Rnase P Ribozyme in query
• Polymerase – Polymerase Ribozyme in query
• Ligase – Ligase Ribozyme in query
• Leadzyme – Leadzyme in query
• RibozymeFrag – Ribozyme fragment in query
• Virus – Virus in query
• ViralFrag – Viral fragment in query
• Riboswitch – Riboswitch in query
• RiboswitchFrag – Riboswitch fragment in query
• Aptamer – Aptamer in query
• Leadzyme – Leadzyme in query

All = <RnaType.All: 'all'>

Aptamer = <RnaType.Aptamer: 'aptamer'>

DoubleHelices = <RnaType.DoubleHelices: 'duplex'>

Group1Intron = <RnaType.Group1Intron: 'gr1In'>

Group2Intron = <RnaType.Group2Intron: 'gr2In'>

Hammerhead = <RnaType.Hammerhead: 'hammhd'>

Harpin = <RnaType.Harpin: 'hairpin'>

Leadzyme = <RnaType.Leadzyme: 'leadzyme'>

Ligase = <RnaType.Ligase: 'ligase'>

Polymerase = <RnaType.Polymerase: 'polymerase'>

QuadrupleHelices = <RnaType.QuadrupleHelices: 'quadruplexes'>

Ribosome = <RnaType.Ribosome: 'ribosome'>

Riboswitch = <RnaType.Riboswitch: 'riboswitch'>

RiboswitchFrag = <RnaType.RiboswitchFrag: 'riboswitchFr'>

Ribozyme = <RnaType.Ribozyme: 'ribozyme'>

RibozymeFrag = <RnaType.RibozymeFrag: 'ribozymeFr'>

RnaseP = <RnaType.RnaseP: 'rnase'>

SmallNucleotideFrag = <RnaType.SmallNucleotideFrag: 'singleStranded'>

TRNA = <RnaType.TRNA: 'trna'>

TRNAFrag = <RnaType.TRNAFrag: 'trnaFr'>

Telomerase = <RnaType.Telomerase: 'telomerase'>

TripleHelices = <RnaType.TripleHelices: 'triplexes'>

ViralFrag = <RnaType.ViralFrag: 'viralfr'>

Virus = <RnaType.Virus: 'virus'>

class ndb_adapter.enums.SpaceGroup

Bases: enum.Enum

Enum to handle space group in query

Variables:

• Empty – empty value in query
• B_2_21_2 – ‘B 2 21 2’ in query
• C_1_2_1 – ‘C 1 2 1’ in query
• C_2_2_2 – ‘C 2 2 2’ in query
• C_2_2_21 – ‘C 2 2 21’ in query
• F_2_2_2 – ‘F 2 2 2’ in query
• F_2_3 – ‘F 2 3’ in query
• F_4_3_2 – ‘F 4 3 2’ in query
• H_3 – ‘H 3’ in query
• H_3_2 – ‘H 3 2’ in query
• I_2_2_2 – ‘I 2 2 2’ in query
• I_2_3 – ‘I 2 3’ in query
• I_21_21_21 – ‘I 21 21 21’ in query
• I_21_3 – ‘I 21 3’ in query
• I_4 – ‘I 4’ in query
• I_4_2_2 – ‘I 4 2 2’ in query
• I_4_3_2 – ‘I 4 3 2’ in query
• I_41 – ‘I 41’ in query
• I_41_2_2 – ‘I 41 2 2’ in query
• P_minus1 – ‘P -1’ in query
• P_1 – ‘P 1’ in query
• P_1_1_21 – ‘P 1 1 21’ in query
• P_1_2_1 – ‘P 1 2 1’ in query
• P_2_2_21 – ‘P 2 2 21’ in query
• P_2_21_21 – ‘P 2 21 21’ in query
• P_2_3 – ‘P 2 3’ in query
• P_21_2_21 – ‘P 21 2 21’ in query
• P_21_21_2 – ‘P 21 21 2’ in query
• P_21_21_21 – ‘P 21 21 21’ in query
• P_21_3 – ‘P 21 3’ in query
• P_3 – ‘P 3’ in query
• P_3_1_2 – ‘P 3 1 2’ in query
• P_3_2_1 – ‘P 3 2 1’ in query
• P_31 – ‘P 31’ in query
• P_31_1_2 – ‘P 31 1 2’ in query
• P_31_2_1 – ‘P 31 2 1’ in query
• P_32 – ‘P 31’ in query
• P_32_1_2 – ‘P 31 1 2’ in query
• P_32_2_1 – ‘P 31 2 1’ in query
• P_4 – ‘P 4’ in query
• P_4_2_2 – ‘P 4 2 2’ in query
• P_4_21_2 – ‘P 4 21 2’ in query
• P_41 – ‘P 41’ in query
• P_41_2_2 – ‘P 41 2 2’ in query
• P_41_21_2 – ‘P 41 21 2’ in query
• P_42 – ‘P 42’ in query
• P_42_2_2 – ‘P 42 2 2’ in query
• P_42_21_2 – ‘P 42 21 2’ in query
• P_43 – ‘P 43’ in query
• P_43_2_2 – ‘P 43 2 2’ in query
• P_43_21_2 – ‘P 43 21 2’ in query
• P_6 – ‘P 6’ in query
• P_6_2_2 – ‘P 6 2 2’ in query
• P_61 – ‘P 61’ in query
• P_61_2_2 – ‘P 61 2 2’ in query
• P_62 – ‘P 62’ in query
• P_62_2_2 – ‘P 62 2 2’ in query
• P_63 – ‘P 63’ in query
• P_63_2_2 – ‘P 63 2 2’ in query
• P_64 – ‘P 64’ in query
• P_64_2_2 – ‘P 64 2 2’ in query
• P_65 – ‘P 65’ in query
• P_65_2_2 – ‘P 65 2 2’ in query
• R_3_2 – ‘R 3 2’ in query

B_2_21_2 = <SpaceGroup.B_2_21_2: 'B 2 21 2'>

C_1_2_1 = <SpaceGroup.C_1_2_1: 'C 1 2 1'>

C_2_2_2 = <SpaceGroup.C_2_2_2: 'C 2 2 2'>

C_2_2_21 = <SpaceGroup.C_2_2_21: 'C 2 2 21'>

Empty = <SpaceGroup.Empty: ''>

F_2_2_2 = <SpaceGroup.F_2_2_2: 'F 2 2 2'>

F_2_3 = <SpaceGroup.F_2_3: 'F 2 3'>

F_4_3_2 = <SpaceGroup.F_4_3_2: 'F 4 3 2'>

H_3 = <SpaceGroup.H_3: 'H 3'>

H_3_2 = <SpaceGroup.H_3_2: 'H 3 2'>

I_21_21_21 = <SpaceGroup.I_21_21_21: 'I 21 21 21'>

I_21_3 = <SpaceGroup.I_21_3: 'I 21 3'>

I_2_2_2 = <SpaceGroup.I_2_2_2: 'I 2 2 2'>

I_2_3 = <SpaceGroup.I_2_3: 'I 2 3'>

I_4 = <SpaceGroup.I_4: 'I 4'>

I_41 = <SpaceGroup.I_41: 'I 41'>

I_41_2_2 = <SpaceGroup.I_41_2_2: 'I 41 2 2'>

I_41_3_2 = <SpaceGroup.I_41_3_2: 'I 41 3 2'>

I_4_2_2 = <SpaceGroup.I_4_2_2: 'I 4 2 2'>

I_4_3_2 = <SpaceGroup.I_4_3_2: 'I 4 3 2'>

P_1 = <SpaceGroup.P_1: 'P 1'>

P_1_1_21 = <SpaceGroup.P_1_1_21: 'P 1 1 21'>

P_1_21_1 = <SpaceGroup.P_1_21_1: 'P 1 21 1'>

P_1_2_1 = <SpaceGroup.P_1_2_1: 'P 1 2 1'>

P_21_21_2 = <SpaceGroup.P_21_21_2: 'P 21 21 2'>

P_21_21_21 = <SpaceGroup.P_21_21_21: 'P 21 21 21'>

P_21_2_21 = <SpaceGroup.P_21_2_21: 'P 21 2 21'>

P_21_3 = <SpaceGroup.P_21_3: 'P 21 3'>

P_2_21_21 = <SpaceGroup.P_2_21_21: 'P 2 21 21'>

P_2_2_21 = <SpaceGroup.P_2_2_21: 'P 2 2 21'>

P_2_3 = <SpaceGroup.P_2_3: 'P 2 3'>

P_3 = <SpaceGroup.P_3: 'P 3'>

P_31 = <SpaceGroup.P_31: 'P 31'>

P_31_1_2 = <SpaceGroup.P_31_1_2: 'P 31 1 2'>

P_31_2_1 = <SpaceGroup.P_31_2_1: 'P 31 2 1'>

P_32 = <SpaceGroup.P_32: 'P 32'>

P_32_1_2 = <SpaceGroup.P_32_1_2: 'P 32 1 2'>

P_32_2_1 = <SpaceGroup.P_32_2_1: 'P 32 2 1'>

P_3_1_2 = <SpaceGroup.P_3_1_2: 'P 3 1 2'>

P_3_2_1 = <SpaceGroup.P_3_2_1: 'P 3 2 1'>

P_4 = <SpaceGroup.P_4: 'P 4'>

P_41 = <SpaceGroup.P_41: 'P 41'>

P_41_21_2 = <SpaceGroup.P_41_21_2: 'P 41 21 2'>

P_41_2_2 = <SpaceGroup.P_41_2_2: 'P 41 2 2'>

P_41_3_2 = <SpaceGroup.P_41_3_2: 'P 41 3 2'>

P_42 = <SpaceGroup.P_42: 'P 42'>

P_42_21_2 = <SpaceGroup.P_42_21_2: 'P 42 21 2'>

P_42_2_2 = <SpaceGroup.P_42_2_2: 'P 42 2 2'>

P_42_3_2 = <SpaceGroup.P_42_3_2: 'P 42 3 2'>

P_43 = <SpaceGroup.P_43: 'P 43'>

P_43_21_2 = <SpaceGroup.P_43_21_2: 'P 43 21 2'>

P_43_2_2 = <SpaceGroup.P_43_2_2: 'P 43 2 2'>

P_43_3_2 = <SpaceGroup.P_43_3_2: 'P 43 3 2'>

P_4_21_2 = <SpaceGroup.P_4_21_2: 'P 4 21 2'>

P_4_2_2 = <SpaceGroup.P_4_2_2: 'P 4 2 2'>

P_6 = <SpaceGroup.P_6: 'P 6'>

P_61 = <SpaceGroup.P_61: 'P 61'>

P_61_2_2 = <SpaceGroup.P_61_2_2: 'P 61 2 2'>

P_62 = <SpaceGroup.P_62: 'P 62'>

P_62_2_2 = <SpaceGroup.P_62_2_2: 'P 62 2 2'>

P_63 = <SpaceGroup.P_63: 'P 63'>

P_63_2_2 = <SpaceGroup.P_63_2_2: 'P 63 2 2'>

P_64 = <SpaceGroup.P_64: 'P 64'>

P_64_2_2 = <SpaceGroup.P_64_2_2: 'P 64 2 2'>

P_65 = <SpaceGroup.P_65: 'P 65'>

P_65_2_2 = <SpaceGroup.P_65_2_2: 'P 65 2 2'>

P_6_2_2 = <SpaceGroup.P_6_2_2: 'P 6 2 2'>

P_minus1 = <SpaceGroup.P_minus1: 'P -1'>

R_3_2 = <SpaceGroup.R_3_2: 'R 3 2'>

class ndb_adapter.enums.StrandDescription

Bases: enum.Enum

Enum for strand description in query

Variables:

• Empty – empty value in query
• DoubleHelix – double helix in query
• TripleHelix – triple helix in query
• QuadrupleHelix – quadruple helix in query

DoubleHelix = <StrandDescription.DoubleHelix: 'double helix'>

Empty = <StrandDescription.Empty: ''>

QuadrupleHelix = <StrandDescription.QuadrupleHelix: 'quadruple helix'>

TripleHelix = <StrandDescription.TripleHelix: 'triple helix'>

class ndb_adapter.enums.StructuralFeatures

Bases: enum.Enum

Enums to handle structural features in query

Variables:

• All – all in query
• SingleStranded – Single Stranded feature in query
• A_DNA – aDNA feature in query
• B_DNA – bDNA feature in query
• Z_DNA – zDNA feature in query
• OtherDoubleHelical – Other Double Helical Structures feature in query
• TripleHelices – Triple Helices feature in query
• QuadrupleHelices – Quadruple Helices feature in query

A_DNA = <StructuralFeatures.A_DNA: 'A'>

All = <StructuralFeatures.All: 'all'>

B_DNA = <StructuralFeatures.B_DNA: 'B'>

OtherDoubleHelical = <StructuralFeatures.OtherDoubleHelical: 'other'>

QuadrupleHelices = <StructuralFeatures.QuadrupleHelices: 'quadruple'>

SingleStranded = <StructuralFeatures.SingleStranded: 'single'>

TripleHelices = <StructuralFeatures.TripleHelices: 'triple'>

Z_DNA = <StructuralFeatures.Z_DNA: 'Z'>

class ndb_adapter.enums.StructuralFunction

Bases: enum.Enum

Enum for structural functions in query

Variables:

• Empty – empty value in query
• All – all functions in query
• Chromosomal – chromosomal function in query
• Histone – histone function in query
• HMG – hmg function in query
• Ribonucleoprotein – ribonucleoprotein function in query
• RibosomalProtein – ribosomal protein function in query
• SignalRecognitionParticle – signal recognition particle function in query
• TelomereBinding – telomere binding function in query
• ViralCoat – viral coat function in query

All = <StructuralFunction.All: 'STRUCTURAL'>

Chromosomal = <StructuralFunction.Chromosomal: 'Chromosomal'>

Empty = <StructuralFunction.Empty: ''>

HMG = <StructuralFunction.HMG: 'HMG'>

Histone = <StructuralFunction.Histone: 'Histone'>

Ribonucleoprotein = <StructuralFunction.Ribonucleoprotein: 'Ribonucleoprotein'>

RibosomalProtein = <StructuralFunction.RibosomalProtein: 'Ribosomal Protein'>

SignalRecognitionParticle = <StructuralFunction.SignalRecognitionParticle: 'Signal Recognition Particle'>

TelomereBinding = <StructuralFunction.TelomereBinding: 'Telomere Binding'>

ViralCoat = <StructuralFunction.ViralCoat: 'Viral Coat'>

class ndb_adapter.enums.YesNoIgnore

Bases: enum.Enum

Enum to handle “yes”, “no”, “ignore” in query

Variables:

• Yes – yes in query
• No – no in query
• Ignore – ignore in query

Ignore = <YesNoIgnore.Ignore: 'Ignore'>

No = <YesNoIgnore.No: 'N'>

Yes = <YesNoIgnore.Yes: 'Y'>

ndb_adapter.html_parser module

class ndb_adapter.html_parser.NDBHtmlParser

Bases: html.parser.HTMLParser

Class for html parse

analyze(data: str) → None

Function for analyze html structure

Parameters:data (str) – html string Returns:None

error(message: str)

Function for error messages

Parameters:message (str) – message string

find_all(name: str = None, after: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, before: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, params: dict = None) → typing.List[typing.Tag]

Function for get tree node matching criteria

Parameters:

• name (str) – node name (default value = None)
• after (Tag) – after node instance (default value = None)
• before (Tag) – before node instance (default value = None)
• params (dict) – node parameters (default value = None)

Returns:

searched nodes list

Return type:

List[Tag]

find_one(name: str = None, after: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, before: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, params: dict = None) → ndb_adapter.html_parser.Tag

Function for get tree node matching criteria

Parameters:

• name (str) – node name (default value = None)
• after (Tag) – after node instance (default value = None)
• before (Tag) – before node instance (default value = None)
• params (dict) – node parameters (default value = None)

Returns:

searched node

Return type:

‘Tag’

get_tree() → ndb_adapter.html_parser.Tag

Function for get tree top element

Return type:‘Tag’ Returns:Tree top

handle_data(data) → None

Function to handle data in tags

Parameters:data – data inside tag Returns:None

handle_endtag(tag) → None

Function to handle end tag and add to tree

Parameters:tag – tag ending Returns:None

handle_starttag(tag, attrs) → None

Function to handle start tag and add to stack of nodes

Parameters:

• tag – tag string
• attrs – attributes dictionary

Returns:

None

class ndb_adapter.html_parser.Tag(name: str, data: str = '', attrs: dict = None, parent: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, next_sib: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, prev_sib: typing.Union[ndb_adapter.html_parser.Tag, NoneType] = None, children: typing.List[typing.Tag] = None)

Bases: object

Class for handle html tags

add_child(child: ndb_adapter.html_parser.Tag) → None

To add child to tag

Parameters:child (Tag) – tag to add Returns:None

has_attr(params: dict) → bool

To check if tag has given attributes

Parameters:params (dict) – attributes to check Returns:True/False if there is attribute

next() → ndb_adapter.html_parser.Tag

Next tag

Returns:next tag Return type:Tag

next_data() → str

Next tag data

Returns:next tag data Return type:str

prev() → ndb_adapter.html_parser.Tag

Previous tag

Returns:previous tag Return type:Tag

prev_data() → str

Previous tag data

Returns:previous tag data Return type:str

ndb_adapter.ndb module

class ndb_adapter.ndb.NDB

Bases: ndb_adapter.ndb_base.NDBBase

Main class for search in NDB - all methods are static

static advanced_search(options: ndb_adapter.advanced_search_options.AdvancedSearchOptions = None) → ndb_adapter.search_result.AdvancedResult

Advanced search in NDB, if in options “stats= True” returns also statistics - works only in some search types. Default search “type= ReportType.NDBStatus”. Depending on ReportType you can annotate return type i.e. “result.report() # ReportType.NDBStatus”.

Parameters:options (AdvancedSearchOptions) – options for advanced search (default value = None) - clear AdvancedSearchOptions() Returns:search result { count -> int, report -> List[AdvancedReport], statistics -> Statistics } Return type:AdvancedResult

static dna_search(options: ndb_adapter.dna_search_options.DnaSearchOptions = None) → ndb_adapter.search_result.SimpleResult

Dna only search in NDB.

Parameters:options (DnaSearchOptions) – options for dna search (default value = None) - clear DnaSearchOptions() Returns:search simple result { count -> int, report -> List[SimpleReport] } Return type:SimpleResult

static download(structure_id: str, download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)
• structure_id (str) – structure NDB ID or PDB ID e.g. 4Z6C

Returns:

string or None

Return type:

str

static rna_search(options: ndb_adapter.rna_search_options.RnaSearchOptions = None) → ndb_adapter.search_result.SimpleResult

Rna only search in NDB.

Parameters:options (RnaSearchOptions) – options for rna search (default value = None) - clear RnaSearchOptions() Returns:search simple result { count -> int, report -> List[SimpleReport] } Return type:SimpleResult

static summary(structure_id: str) → ndb_adapter.summary_result.SummaryResult

Summary search in NDb

Parameters:structure_id (str) – structure NDB ID or PDB ID e.g. 4Z6C Returns:search summary result Return type:SummaryResult

ndb_adapter.ndb_base module

class ndb_adapter.ndb_base.NDBBase

Bases: object

Base class for NDB

Variables:

• siteUrl – ndb site url
• _advancedUrl – private advanced search url
• _summaryUrl – private summary url
• _dnaUrl – private dna search url
• _rnaUrl – private rna search url
• _chiralCorrectUrl – private chiral correct coordinates download url
• _nmrUrl – private nmr pdb coordinates download url
• _nmrMmCifUrl – private nmr mmcif coordinates download url
• _bioAssemblyCoordinateUrl – private bio assembly coordinates download url
• _mmCifUrl – private mmCIF coordinates download url
• _structureFactorsUrl – private structure factors download url
• _nmrRestraintsUrl – private nmr restraints download url
• _xmlCompleteUrl – private complete xml download url
• _xmlCoordinatesUrl – private coordinates only xml download url
• _xmlHeaderUrl – private header only xml download url

siteUrl = 'http://ndbserver.rutgers.edu'

ndb_adapter.ndb_download module

class ndb_adapter.ndb_download.DownloadHelper

Bases: object

Helper class for downloading form NDB

static download(structure_id: str, download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)
• structure_id (str) – structure NDB ID or PDB ID e.g. 4Z6C

Returns:

string or None

Return type:

str

Raises:

• AttributeError – when structure id is empty
• FileNotFoundError – when file is not present on server

static download_file(url: str) → _io.BytesIO

Function to download file and convert to BytesIO

Parameters:url (str) – file url Returns:file as BytesIO Return type:BytesIO

class ndb_adapter.ndb_download.DownloadType

Bases: enum.Enum

Enum for file download format

Variables:

• Pdb – Asymmetric Unit coordinates (pdb format, Unix compressed(.gz))
• Cif – Asymmetric Unit coordinates (cif format, Unix compressed(.gz))
• PdbBioAssembly – Biological Assembly coordinates
• PdbNmr – Coordinates (pdb format, Unix compressed(.gz))
• CifNmr – Coordinates (cif format, Unix compressed(.gz))
• CifStructureFactors – Structure Factors (cif format)
• CifNmrRestraints – NMR Restraints (cif format, Unix compressed(.gz))
• XmlComplete – XML | Complete with coordinates (xml format, GNU compressed(.gz))
• XmlCoordinates – XML | Coordinates only (xml format, GNU compressed(.gz))
• XmlHeader – XML | Header only (xml format, GNU compressed(.gz))

Cif = <DownloadType.Cif: <class 'ndb_adapter.ndb_download._Cif'>>

CifNmr = <DownloadType.CifNmr: <class 'ndb_adapter.ndb_download._CifNmr'>>

CifNmrRestraints = <DownloadType.CifNmrRestraints: <class 'ndb_adapter.ndb_download._CifNmrRestraints'>>

CifStructureFactors = <DownloadType.CifStructureFactors: <class 'ndb_adapter.ndb_download._CifStructureFactors'>>

Pdb = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>

PdbBioAssembly = <DownloadType.PdbBioAssembly: <class 'ndb_adapter.ndb_download._PdbBioAssembly'>>

PdbNmr = <DownloadType.PdbNmr: <class 'ndb_adapter.ndb_download._PdbNmr'>>

XmlComplete = <DownloadType.XmlComplete: <class 'ndb_adapter.ndb_download._XmlComplete'>>

XmlCoordinates = <DownloadType.XmlCoordinates: <class 'ndb_adapter.ndb_download._XmlCoordinates'>>

XmlHeader = <DownloadType.XmlHeader: <class 'ndb_adapter.ndb_download._XmlHeader'>>

ndb_adapter.report_parser module

ndb_adapter.report_parser.parse_advanced_search_report(text: str, text_stats: str, report_type: ndb_adapter.enums.ReportType) → ndb_adapter.search_result.AdvancedResult

To parse advanced search report from text to AdvancedResult

Parameters:

• text (str) – text to parse
• text_stats (str) – statistics text to parse
• report_type (ReportType) – type of report to parse

Returns:

advanced search result

Return type:

AdvancedResult

ndb_adapter.report_parser.parse_csv(table: typing.List[str], result_class: typing.Callable[[], AdvancedReport]) → typing.List[AdvancedReport]

To parse table of string as csv to list of AdvancedReport

Parameters:

• table (List[str]) – string table to parse
• result_class (Callable[[], AdvancedReport]) – class that init object before adding to results

Returns:

list of advanced report

Return type:

List[AdvancedReport]

ndb_adapter.report_parser.parse_search_report(html: str) → ndb_adapter.search_result.SimpleResult

To parse simple search report from html to SimpleResult

Parameters:html (str) – html string to parse Returns:simple search result Return type:SimpleResult

ndb_adapter.report_parser.parse_summary(html: str) → ndb_adapter.summary_result.SummaryResult

To parse summary search from html to SummaryResult

Parameters:html (str) – html string to parse Returns:summary search result Return type:SummaryResult

ndb_adapter.report_parser.parse_to_table(text: str) → typing.List[str]

To parse text to list of strings

Parameters:text – input string Returns:list of string Return type:List[str]

ndb_adapter.report_parser.parse_xls(file: _io.BytesIO) → typing.List[ndb_adapter.search_report.SimpleReport]

To parse xls file to list of Simplereport

Parameters:file (BytesIO) – file bytes to parse Returns:list of SimpleReport Return type:List[SimpleReport]

ndb_adapter.rna_search_options module

class ndb_adapter.rna_search_options.RnaSearchOptions

Bases: ndb_adapter.search_options.SearchOptions

Class for rna search options

get_non_redundant_list()

Gets non redundant list options

Returns:non redundant list Return type:(RnaStructures, ResolutionCutoff)

get_rna_type() → ndb_adapter.enums.RnaType

Gets rna type options

Returns:rna type Return type:RnaType

set_non_redundant_list(structures: ndb_adapter.enums.RnaStructures = <RnaStructures.All: 'all'>, resolution: ndb_adapter.enums.ResolutionCutoff = <ResolutionCutoff.All: 'all'>) → None

Sets non redundant list in options. More info: http://ndbserver.rutgers.edu/ndbmodule/ndb-help.html#nrl

Parameters:

• structures (RnaStructures) – rna structures type (default value = RnaStructures.All)
• resolution (ResolutionCutoff) – resolution cutoff (default value = ResolutionCutoff.All)

Returns:

None

set_rna_type(rna_type: ndb_adapter.enums.RnaType = <RnaType.All: 'all'>) → None

Sets rna type in options

Parameters:rna_type (RnaType) – rna type (default value = RnaType.All) Returns:None

ndb_adapter.search_options module

class ndb_adapter.search_options.SearchOptions(search_type: str)

Bases: object

Class for specific search options

get() → dict

Gets dictionary of options

Returns:dictionary options Return type:dict

get_experimental_method() → ndb_adapter.enums.ExpMethod

Gets experimental method options

Returns:experimental method Return type:ExpMethod

get_filter_text() → str

Gets filter text options

Returns:filter text Return type:str

get_polymer() → ndb_adapter.enums.Polymer

Gets polymer type options

Returns:polymer type Return type:Polymer

get_protein_func() → ndb_adapter.enums.ProteinFunc

Gets protein function options

Returns:protein function Return type:ProteinFunc

set_experimental_method(method: ndb_adapter.enums.ExpMethod = <ExpMethod.All: 'all'>) → None

Sets experimental method in options

Parameters:method (ExpMethod) – experimental method (default value = ExpMethod.All) Returns:None

set_filter_text(text: str) → None

Sets filter text in options. Use this option to narrow your results down considerably (>50% reduction) using any word seen in the results page. Eg: Any author name found in the right side.

Parameters:text (str) – filter text to be set Returns:None

set_polymer(polymer: ndb_adapter.enums.Polymer = <Polymer.All: 'all'>) → None

Sets polymer type in options

Parameters:polymer (Polymer) – polymer type (default value = Polymer.All) Returns:None

set_protein_func(protein: ndb_adapter.enums.ProteinFunc = <ProteinFunc.All: 'all'>) → None

Sets protein function in options

Parameters:protein (ProteinFunc) – protein function (default value = ProteinFunc.All) Returns:None

ndb_adapter.search_report module

class ndb_adapter.search_report.BasePairParameterReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for base pair parameter search report extending _AdvancedBaseReport

buckle

Gets advanced report structure buckle

Returns:buckle Return type:float

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

model_num

Gets advanced report structure model number

Returns:model number Return type:int

opening

Gets advanced report structure opening

Returns:opening Return type:float

pair_name

Gets advanced report structure pair name

Returns:pair name Return type:str

pair_num

Gets advanced report structure pair number

Returns:pair number Return type:int

propellor

Gets advanced report structure propellor

Returns:propellor Return type:float

static report_type() → str

shear

Gets advanced report structure shear

Returns:shear Return type:float

stagger

Gets advanced report structure stagger

Returns:stagger Return type:float

stretch

Gets advanced report structure stretch

Returns:stretch Return type:float

class ndb_adapter.search_report.BasePairStepParameterReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for base pair parameter search report extending _AdvancedBaseReport

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

helical_rise

Gets advanced report structure helical rise

Returns:helical rise Return type:float

helical_twist

Gets advanced report structure helical twist

Returns:helical twist Return type:float

inclination

Gets advanced report structure inclination

Returns:inclination Return type:float

model_num

Gets advanced report structure model number

Returns:model number Return type:int

static report_type() → str

rise

Gets advanced report structure rise

Returns:rise Return type:float

roll

Gets advanced report structure roll

Returns:roll Return type:float

shift

Gets advanced report structure shift

Returns:shift Return type:float

slide

Gets advanced report structure slide

Returns:slide Return type:float

step_name

Gets advanced report structure step name

Returns:step name Return type:str

step_num

Gets advanced report structure step number

Returns:step number Return type:int

tilt

Gets advanced report structure tilt

Returns:tilt Return type:float

tip

Gets advanced report structure tip

Returns:tip Return type:float

x_disp

Gets advanced report structure x displacement

Returns:x displacement Return type:float

y_disp

Gets advanced report structure y displacement

Returns:x displacement Return type:float

class ndb_adapter.search_report.CellDimensionsReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for cell dimensions search report extending _AdvancedBaseReport

cell_a

Gets advanced report structure cell a in angstroms

Returns:cell a Return type:float

cell_alpha

Gets advanced report structure cell alpha in degrees

Returns:alpha Return type:float

cell_b

Gets advanced report structure cell b in angstroms

Returns:cell b Return type:float

cell_beta

Gets advanced report structure cell beta in degrees

Returns:beta Return type:float

cell_c

Gets advanced report structure cell c in angstroms

Returns:cell c Return type:float

cell_gamma

Gets advanced report structure cell gamma in degrees

Returns:gamma Return type:float

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

static report_type() → str

space_group

Gets advanced report structure space group

Returns:space group Return type:float

class ndb_adapter.search_report.CitationReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for citation search report extending _AdvancedBaseReport

citation_authors

Gets advanced report structure citation authors

Returns:citation authors Return type:str

citation_title

Gets advanced report structure citation title

Returns:citation title Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

journal

Gets advanced report structure Journal

Returns:Journal Return type:str

pdb_id

Gets advanced report structure PDB ID

Returns:PDB ID Return type:str

pubmed_id

Gets advanced report structure pubmed ID

Returns:PDB ID Return type:str

static report_type() → str

year

Gets advanced report structure year

Returns:year Return type:int

class ndb_adapter.search_report.DescriptorReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for descriptor search report extending _AdvancedBaseReport

description

Gets advanced report structure description

Returns:description Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

static report_type() → str

class ndb_adapter.search_report.NABackboneTorsionReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for refinement data search report extending _AdvancedBaseReport

c3_o3_p_o5

Gets advanced report structure C3’-O3’-P-O5’

Returns:C3’-O3’-P-O5’ Return type:float

c4_c3_o3_p

Gets advanced report structure C4’-C3’-O3’-P

Returns:C4’-C3’-O3’-P Return type:float

c5_c4_c3_o3

Gets advanced report structure C5’-C4’-C3’-O3’

Returns:C5’-C4’-C3’-O3’ Return type:float

chain_id

Gets advanced report structure chain ID

Returns:chain ID Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

model_id

Gets advanced report structure model ID

Returns:model ID Return type:str

o3_p_o5_c5

Gets advanced report structure O3’-P-O5’-C5’

Returns:O3’-P-O5’-C5’ Return type:float

o4_c1_n1_9_c2_4

Gets advanced report structure O4’-C1’-N1-9-C2-4

Returns:O4’-C1’-N1-9-C2-4 Return type:float

o5_c5_c4_c3

Gets advanced report structure O5’-C5’-C4’-C3’

Returns:O5’-C5’-C4’-C3’ Return type:float

p_o5_c5_c4

Gets advanced report structure P-O5’-C5’-C4’

Returns:P-O5’-C5’-C4’ Return type:float

static report_type() → str

residue_name

Gets advanced report structure residue name

Returns:residue name Return type:str

residue_number

Gets advanced report structure residue number

Returns:residue number Return type:int

class ndb_adapter.search_report.NDBStatusReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for NDB status search report extending _AdvancedBaseReport

authors

Gets advanced report structure authors

Returns:authors Return type:str

deposition_date

Gets advanced report structure initial deposition date

Returns:initial deposition date Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

pdb_id

Gets advanced report structure PDB ID

Returns:PDB ID Return type:str

release_date

Gets advanced report structure NDB release date

Returns:release date Return type:str

static report_type() → str

title

Gets advanced report structure title

Returns:title Return type:str

class ndb_adapter.search_report.RNA3DBasePairRelFreqReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for RNA 3D Base Pair Relative Frequency Report search report extending _AdvancedBaseReport

chh

Gets advanced report relative cHH

Returns:relative cHH Return type:float

chs

Gets advanced report relative cHS

Returns:relative cHS Return type:float

css

Gets advanced report relative cSS

Returns:relative cSS Return type:float

cwh

Gets advanced report relative qWH

Returns:relative qWH Return type:float

cws

Gets advanced report relative cWS

Returns:relative cWS Return type:float

cww

Gets advanced report relative cWW

Returns:relative cWW Return type:float

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

pdb_id

Gets advanced report structure PDB

Returns:PDB ID Return type:str

static report_type() → str

thh

Gets advanced report relative tHH

Returns:relative tHH Return type:float

ths

Gets advanced report relative tHS

Returns:relative tHS Return type:float

tss

Gets advanced report relative tSS

Returns:relative tWS Return type:float

twh

Gets advanced report relative tWH

Returns:relative tWH Return type:float

tws

Gets advanced report relative tWS

Returns:relative tWS Return type:float

tww

Gets advanced report relative tWW

Returns:relative tWW Return type:float

class ndb_adapter.search_report.RNA3DBasePhosphateRelFreqReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for RNA 3D Base Phosphate Relative Frequency Report search report extending _AdvancedBaseReport

bph_0

Gets advanced report relative 0BPh

Returns:relative 0BPh Return type:float

bph_1

Gets advanced report relative 1BPh

Returns:relative 1BPh Return type:float

bph_2

Gets advanced report relative 2BPh

Returns:relative 2BPh Return type:float

bph_3

Gets advanced report relative 3BPh

Returns:relative 3BPh Return type:float

bph_4

Gets advanced report relative 4BPh

Returns:relative 4BPh Return type:float

bph_5

Gets advanced report relative 5BPh

Returns:relative 5BPh Return type:float

bph_6

Gets advanced report relative 6BPh

Returns:relative 6BPh Return type:float

bph_7

Gets advanced report relative 7BPh

Returns:relative 7BPh Return type:float

bph_8

Gets advanced report relative 8BPh

Returns:relative 8BPh Return type:float

bph_9

Gets advanced report relative 9BPh

Returns:relative 9BPh Return type:float

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

pdb_id

Gets advanced report structure PDB

Returns:PDB ID Return type:str

static report_type() → str

class ndb_adapter.search_report.RNA3DBaseStackingRelFreqReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for RNA 3D Base Stacking Relative Frequency Report search report extending _AdvancedBaseReport

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

pdb_id

Gets advanced report structure PDB

Returns:PDB ID Return type:str

static report_type() → str

s33

Gets advanced report structure relative s33

Returns:relative s33 Return type:float

s53

Gets advanced report structure relative s53

Returns:relative s53 Return type:float

s55

Gets advanced report structure relative s55

Returns:relative s55 Return type:float

class ndb_adapter.search_report.RNA3DMotifReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for RNA 3D Base Phosphate Relative Frequency Report search report extending _AdvancedBaseReport

annotation

Gets advanced report structure annotation

Returns:annotation Return type:str

common_name

Gets advanced report structure common name

Returns:common name Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

motif_id

Gets advanced report structure motif ID

Returns:motif ID Return type:str

pdb_id

Gets advanced report structure PDB

Returns:PDB ID Return type:str

static report_type() → str

class ndb_adapter.search_report.RefinementDataReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for refinement data search report extending _AdvancedBaseReport

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

higher_resolution

Gets advanced report structure higher resolution limit

Returns:higher resolution limit Return type:float

lower_resolution

Gets advanced report structure lower resolution limit

Returns:lower resolution limit Return type:float

r_free

Gets advanced report structure r free

Returns:r free Return type:float

r_obs

Gets advanced report structure r obs

Returns:r obs Return type:float

r_work

Gets advanced report structure r work

Returns:r work Return type:float

reflections

Gets advanced report structure reflections observed

Returns:reflections observed Return type:int

static report_type() → str

structure_ref

Gets advanced report structure refinement

Returns:structure refinement Return type:str

class ndb_adapter.search_report.SequencesReport(report: dict = None)

Bases: ndb_adapter.search_report._AdvancedBaseReport

Class for sequences search report extending _AdvancedBaseReport

description

Gets advanced report structure description

Returns:description Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

NOT WORKS ON THIS REPORT TYPE

static report_type() → str

sequence

Gets advanced report structure nucleic acid sequence

Returns:sequence Return type:str

class ndb_adapter.search_report.SimpleReport(report: dict = None)

Bases: object

Class for simple result report

authors

Gets simple report structure authors

Returns:authots Return type:str

citation_detail

Gets simple report structure citation title

Returns:citation detail Return type:str

citation_title

Gets simple report structure citation title

Returns:citation title Return type:str

classification

Gets simple report structure classification

Returns:classification Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from ndb

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

experimental_method

Gets simple report structure experimental method

Returns:experimental method Return type:str

get_dict() → dict

Gets simple report as dict

Returns:simple report dict Return type:dict

ndb_id

Gets simple report structure NDB ID

Returns:NDB ID Return type:str

pdb_id

Gets simple report structure PDB

Returns:PDB ID Return type:str

r_free

Gets simple report structure r free

Returns:r free Return type:float

r_work

Gets simple report structure r work

Returns:r work Return type:float

release_date

Gets simple report structure release date

Returns:release date Return type:str

resolution

Gets simple report structure resolution

Returns:resolution Return type:float

title

Gets simple report structure title

Returns:title Return type:str

class ndb_adapter.search_report.StatisticReport(report: dict = None)

Bases: object

Class for statistic search report

stats

Gets advanced report structure statistics

Returns:statistics Return type:str

ndb_adapter.search_result module

class ndb_adapter.search_result.AdvancedResult

Bases: ndb_adapter.search_result.SearchResult

Class for advanced search result

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → typing.List[str]

Download PDB files from NDB

Parameters:

• download_type (DownloadType) – files download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if files should be saved or not (default value = False)

Returns:

list of strings or None

Return type:

List[str]

get_report() → typing.List[AdvancedReport]

Gets advanced search results report list. You should annotate return type depending on ReportType.

Returns:list of advanced search reports Return type:List[AdvancedReport]

get_statistics() → ndb_adapter.statistics.Statistics

Get statistics of advanced search

Returns:statistics of advanced search

:rtype Statistics

set_statistics(report: list) → None

Sets statistic

Parameters:report (list) – report list to be parse as statistic Returns:None

statistics

Statistic report property gets report statistic

class ndb_adapter.search_result.SearchResult

Bases: object

Base class for search result

count

Search count property gets report count

get_count() → int

Gets search results count

Returns:search results count Return type:int

get_report() → list

Gets search results report

Returns:list of search results reports Return type:list

report

Search report property gets report list

set_count(count: int) → None

Sets result count

Parameters:count (int) – value to set as count Returns:None

set_report(report: list) → None

Sets result report list

Parameters:report (list) – list to be set as report Returns:None

class ndb_adapter.search_result.SimpleResult

Bases: ndb_adapter.search_result.SearchResult

Class for simple search result

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → typing.List[str]

Download PDB files from NDB

Parameters:

• download_type (DownloadType) – files download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if files should be saved or not (default value = False)

Returns:

list of strings or None

Return type:

List[str]

get_report() → typing.List[ndb_adapter.search_report.SimpleReport]

Gets search results report list

Returns:list of simple search reports Return type:List[SimpleReport]

ndb_adapter.statistics module

class ndb_adapter.statistics.Statistics

Bases: object

Class for search statistics

max

Gets max statistic dictionary

Returns:max statistics Return type:Dict[str, float]

mean

Gets mean statistic dictionary

Returns:mean statistics Return type:Dict[str, float]

min

Gets min statistic dictionary

Returns:min statistics Return type:Dict[str, float]

set_report(report: typing.List[ndb_adapter.search_report.StatisticReport]) → None

Sets statistic from report

Parameters:report (List[StatisticReport]) – list of statistic report Returns:None

std_dev

Gets standard deviation statistic dictionary

Returns:standard deviation statistics Return type:Dict[str, float]

ndb_adapter.summary_result module

class ndb_adapter.summary_result.SummaryResult

Bases: object

Class for summary results

cell_a

Gets summary result structure cell a angstroms value

Returns:structure cell a angstroms Return type:float

cell_alpha

Gets summary result structure cell alpha

Returns:structure cell alpha degrees Return type:Dict[str, float]

cell_b

Gets summary result structure cell b angstroms value

Returns:structure cell b angstroms Return type:float

cell_beta

Gets summary result structure cell beta

Returns:structure cell beta degrees Return type:float

cell_c

Gets structure cell c angstroms value of summary result

Returns:structure cell a angstroms Return type:float

cell_constants

Gets summary result structure cell constants as dict[str, float]

Returns:structure cell constants Return type:Dict[str, float]

cell_gamma

Gets summary result structure cell gamma

Returns:structure cell gamma degrees Return type:float

citation_authors

Gets summary result structure primary citation authors

Returns:primary citation authors Return type:str

citation_journal

Gets summary result structure primary citation journal

Returns:primary citation journal Return type:str

citation_pages

Gets summary result structure pages in primary citation

Returns:primary citation pages Return type:str

citation_pubmed_id

Gets summary result structure primary citation Pubmed ID

Returns:primary citation Pubmend ID Return type:str

citation_title

Gets summary result structure primary citation title

Returns:primary citation title Return type:str

citation_year

Gets summary result structure primary citation year

Returns:primary citation year Return type:str

description

Gets summary result structure description

Returns:description Return type:str

download(download_type: ndb_adapter.ndb_download.DownloadType = <DownloadType.Pdb: <class 'ndb_adapter.ndb_download._Pdb'>>, save: bool = False, target_dir: str = '') → str

Download PDB from NDB

Parameters:

• download_type (DownloadType) – file download type (default value is DownloadType.PDB)
• target_dir (str) – where to save file (default value is current dir)
• save (bool) – tells if file should be saved or not (default value = False)

Returns:

string or None

Return type:

str

experimental_method

Gets summary result structure experimental method

Returns:experimental method Return type:str

get_dict() → dict

Gets internal report dict

Returns:report as dictionary Return type:dict

ndb_id

Gets summary result structure NDB ID

Returns:NDB ID Return type:str

nucleic_acid_seq

Gets summary result structure nucleic acid sequences

Returns:structure nucleic acid sequences Return type:List[str]

nucleic_acid_seq_with_names

Gets summary result structure nucleic acid sequences with names

Returns:structure nucleic acid sequences with names Return type:List[Dict[str, str]]

pdb_id

Gets summary result structure PDB ID

Returns:PDB ID Return type:str

protein_seq

Gets summary result structure protein sequences

Returns:structure protein sequences Return type:List[str]

protein_seq_with_names

Gets summary result structure protein sequences with names

Returns:structure protein sequences with names Return type:List[Dict[str, str]]

refinement

Gets summary result structure refinement

Returns:refinement Return type:str

space_group

Gets summary result structure space group

Returns:space group Return type:str

title

Gets summary result structure title

Returns:title Return type:str

update(report: dict) → None

Update internal report

Parameters:report (dict) – extending report Returns:None

Module contents