MMTF-PySpark
0.2.7
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A
add_neighbor() (AtomInteraction method)
add_point() (DistanceBox method)
AdvancedQuery (class in mmtfPyspark.webfilters.advancedQuery)
ALPHA_HELIX (DsspSecondaryStructure attribute)
AMINO_ACIDS21 (ProteinSequenceEncoder attribute)
AMINO_ACIDS_20 (PolymerComposition attribute)
AMINO_ACIDS_22 (PolymerComposition attribute)
angles (AtomInteraction attribute)
atom_counter (MmtfStructure attribute)
AtomInteraction (class in mmtfPyspark.interactions.atomInteraction)
B
BEND (DsspSecondaryStructure attribute)
BLAST (SequenceSimilarity attribute)
BlastCluster (class in mmtfPyspark.webfilters.blastCluster)
blosum62 (ProteinSequenceEncoder attribute)
blosum62_encode() (ProteinSequenceEncoder method)
BRIDGE (DsspSecondaryStructure attribute)
C
calc_coordination_geometry() (AtomInteraction method)
chain_counter (MmtfStructure attribute)
ChemicalStructureQuery (class in mmtfPyspark.webfilters.chemicalStructureQuery)
COIL (DsspSecondaryStructure attribute)
ColumnarStructure (class in mmtfPyspark.utils.columnarStructure)
ColumnarStructureX (class in mmtfPyspark.utils.columnarStructureX)
ContainsAlternativeLocations (class in mmtfPyspark.filters.containsAlternativeLocations)
ContainsDnaChain (class in mmtfPyspark.filters.containsDnaChain)
ContainsDProteinChain (class in mmtfPyspark.filters.containsDProteinChain)
ContainsDSaccharideChain (class in mmtfPyspark.filters.containsDSaccharideChain)
ContainsGroup (class in mmtfPyspark.filters.containsGroup)
ContainsLProteinChain (class in mmtfPyspark.filters.containsLProteinChain)
ContainsPolymerChainType (class in mmtfPyspark.filters.containsPolymerChainType)
ContainsRnaChain (class in mmtfPyspark.filters.containsRnaChain)
ContainsSequenceRegex (class in mmtfPyspark.filters.containsSequenceRegex)
convert_entity() (in module mmtfPyspark.utils.mmtfDecoder)
convert_group() (in module mmtfPyspark.utils.mmtfDecoder)
CoordinateGeometry (class in mmtfPyspark.interactions.coordinationGeometry)
CustomReportQuery (class in mmtfPyspark.webfilters.customReportQuery)
D
D_PEPTIDE_COOH_CARBOXY_TERMINUS (ContainsPolymerChainType attribute)
D_PEPTIDE_LINKING (ContainsPolymerChainType attribute)
D_PEPTIDE_NH3_AMINO_TERMINUS (ContainsPolymerChainType attribute)
D_SACCHARIDE (ContainsPolymerChainType attribute)
D_SACCHARIDE_14_and_14_LINKING (ContainsPolymerChainType attribute)
D_SACCHARIDE_14_and_16_LINKING (ContainsPolymerChainType attribute)
decode_entity_list() (in module mmtfPyspark.utils.mmtfDecoder)
decode_group_list() (in module mmtfPyspark.utils.mmtfDecoder)
DepositionDate (class in mmtfPyspark.filters.depositionDate)
DistanceBox (class in mmtfPyspark.utils.distanceBox)
distances (AtomInteraction attribute)
DNA_LINKING (ContainsPolymerChainType attribute)
DNA_OH_3_PRIME_TERMINUS (ContainsPolymerChainType attribute)
DNA_OH_5_PRIME_TERMINUS (ContainsPolymerChainType attribute)
DNA_STD_NUCLEOTIDES (PolymerComposition attribute)
download_full_mmtf_files() (in module mmtfPyspark.io.mmtfReader)
download_mmtf_files() (in module mmtfPyspark.io.mmtfReader)
download_reduced_mmtf_files() (in module mmtfPyspark.io.mmtfReader)
downsample() (in module mmtfPyspark.ml.datasetBalancer)
DsspSecondaryStructure (class in mmtfPyspark.utils.dsspSecondaryStructure)
E
ELECTRON_CRYSTALLOGRAPHY (ExperimentalMethods attribute)
ELECTRON_MICROSCOPY (ExperimentalMethods attribute)
ERP (ExperimentalMethods attribute)
EXACT (ChemicalStructureQuery attribute)
ExperimentalMethods (class in mmtfPyspark.filters.experimentalMethods)
EXTENDED (DsspSecondaryStructure attribute)
F
FIBER_DIFFRACTION (ExperimentalMethods attribute)
fit() (SparkMultiClassClassifier method)
(SparkRegressor method)
FLUORESCENCE_TRANSFER (ExperimentalMethods attribute)
G
get_alt_loc_list() (ColumnarStructure method)
get_angles() (CoordinateGeometry method)
get_as_object() (InteractionCenter method)
get_atom_name() (InteractionCenter method)
get_atom_names() (ColumnarStructure method)
get_atom_to_chain_indices() (ColumnarStructure method)
get_atom_to_group_indices() (ColumnarStructure method)
get_b_factors() (ColumnarStructure method)
get_blast_cluster() (BlastCluster method)
get_box_two() (DistanceBox method)
get_calpha_atom_indices() (ColumnarStructureX method)
get_calpha_coordinates() (ColumnarStructureX method)
get_center() (AtomInteraction method)
get_chain_ids() (ColumnarStructure method)
get_chain_name() (InteractionCenter method)
get_chain_names() (ColumnarStructure method)
get_chain_to_atom_indices() (ColumnarStructure method)
get_chain_to_entity_index() (ColumnarStructure method)
get_chain_to_group_indices() (ColumnarStructure method)
get_chem_comp_types() (ColumnarStructure method)
get_clamped_normalized_b_factors() (ColumnarStructureX method)
get_coordinates() (InteractionCenter method)
get_dataset() (groupInteractionExtractor method)
(in module mmtfPyspark.datasets.customReportService)
(in module mmtfPyspark.datasets.drugBankDataset)
(in module mmtfPyspark.datasets.jpredDataset)
(in module mmtfPyspark.datasets.pdbjMineDataset)
(in module mmtfPyspark.datasets.polymerSequenceExtractor)
(in module mmtfPyspark.datasets.secondaryStructureElementExtractor)
(in module mmtfPyspark.datasets.secondaryStructureExtractor)
(in module mmtfPyspark.datasets.secondaryStructureSegmentExtractor)
(in module mmtfPyspark.datasets.uniProt)
(in module mmtfPyspark.ml.pythonRDDToDataset)
get_distance() (CoordinateGeometry method)
get_distance_cutoff() (InteractionFilter method)
get_drug_links() (in module mmtfPyspark.datasets.drugBankDataset)
get_drug_target_links() (in module mmtfPyspark.datasets.drugBankDataset)
get_element() (InteractionCenter method)
get_elements() (ColumnarStructure method)
get_entity_indices() (ColumnarStructure method)
get_entity_types() (ColumnarStructure method)
get_full_dataset() (in module mmtfPyspark.datasets.g2sDataset)
get_group_name() (InteractionCenter method)
get_group_names() (ColumnarStructure method)
get_group_number() (InteractionCenter method)
get_group_numbers() (ColumnarStructure method)
get_group_to_atom_indices() (ColumnarStructure method)
get_group_types() (ColumnarStructure method)
get_indices() (ColumnarStructure method)
get_interactions() (AtomInteraction method)
(GroupInteractionExtractor method)
(LigandInteractionFingerprint method)
(PolymerInteractionFingerprint method)
get_length() (InteractionCenter method)
get_ligand_polymer_interactions() (InteractionFingerprinter method)
get_max_interactions() (InteractionFilter method)
get_min_interactions() (InteractionFilter method)
get_mmtf_full_path() (in module mmtfPyspark.io.mmtfReader)
get_mmtf_reduced_path() (in module mmtfPyspark.io.mmtfReader)
get_multiple_interactions_as_row() (AtomInteraction method)
get_neighbors() (DistanceBox method)
get_normalized_b_factor_cutoff() (InteractionFilter method)
get_normalized_b_factors() (ColumnarStructureX method)
(InteractionCenter method)
get_num_atoms() (ColumnarStructure method)
get_num_chains() (ColumnarStructure method)
get_num_groups() (ColumnarStructure method)
get_num_interactions() (AtomInteraction method)
get_num_models() (ColumnarStructure method)
get_occupancies() (ColumnarStructure method)
get_open_drug_links() (in module mmtfPyspark.datasets.drugBankDataset)
get_pair_interaction_schema() (AtomInteraction method)
get_pair_interactions() (GroupInteractionExtractor method)
get_pair_interactions_as_rows() (AtomInteraction method)
get_polymer_interactions() (InteractionFingerprinter method)
get_position_dataset() (in module mmtfPyspark.datasets.g2sDataset)
get_python_rdd() (in module mmtfPyspark.datasets.secondaryStructureExtractor)
get_schema() (AtomInteraction method)
get_sequence_position() (InteractionCenter method)
get_sequence_positions() (ColumnarStructure method)
get_struct_fields() (InteractionCenter method)
get_structure_chain_ids() (PiscesDownloader method)
get_structure_id() (AtomInteraction method)
get_swiss_models() (in module mmtfPyspark.datasets.swissModelDataset)
get_swiss_models_raw_data() (in module mmtfPyspark.datasets.swissModelDataset)
get_type() (InteractionCenter method)
get_variations() (in module mmtfPyspark.datasets.myVariantDataset)
get_word2vec_model() (ProteinSequenceEncoder method)
get_x_coords() (ColumnarStructure method)
get_y_coords() (ColumnarStructure method)
get_z_coords() (ColumnarStructure method)
getIntersection() (DistanceBox method)
group_counter (MmtfStructure attribute)
groupInteractionExtractor (class in mmtfPyspark.datasets.groupInteractionExtractor)
GroupInteractionExtractor (class in mmtfPyspark.interactions.groupInteractionExtractor)
I
INFRARED_SPECTROSCOPY (ExperimentalMethods attribute)
InteractionCenter (class in mmtfPyspark.interactions.interactionCenter)
InteractionFilter (class in mmtfPyspark.interactions.interactionFilter)
InteractionFingerprinter (class in mmtfPyspark.interactions.interactionFingerprinter)
is_polymer() (ColumnarStructure method)
is_prohibited_target_group() (InteractionFilter method)
is_query_atom_name() (InteractionFilter method)
is_query_element() (InteractionFilter method)
is_query_group() (InteractionFilter method)
is_target_atom_name() (InteractionFilter method)
is_target_element() (InteractionFilter method)
is_target_group() (InteractionFilter method)
L
L_PEPTIDE_COOH_CARBOXY_TERMINUS (ContainsPolymerChainType attribute)
L_PEPTIDE_LINKING (ContainsPolymerChainType attribute)
L_PEPTIDE_NH3_AMINO_TERMINUS (ContainsPolymerChainType attribute)
L_SACCHARIDE (ContainsPolymerChainType attribute)
L_SACCHARIDE_14_AND_14_LINKING (ContainsPolymerChainType attribute)
L_SACCHARIDE_14_AND_16_LINKING (ContainsPolymerChainType attribute)
LigandInteractionFingerprint (class in mmtfPyspark.interactions.ligandInteractionFingerprint)
M
main() (in module mmtfPyspark.ml.datasetClassifier)
(in module mmtfPyspark.ml.datasetRegressor)
mmtfPyspark (module)
mmtfPyspark.datasets (module)
mmtfPyspark.datasets.customReportService (module)
mmtfPyspark.datasets.drugBankDataset (module)
mmtfPyspark.datasets.g2sDataset (module)
mmtfPyspark.datasets.groupInteractionExtractor (module)
mmtfPyspark.datasets.jpredDataset (module)
mmtfPyspark.datasets.myVariantDataset (module)
mmtfPyspark.datasets.pdbjMineDataset (module)
mmtfPyspark.datasets.polymerSequenceExtractor (module)
mmtfPyspark.datasets.secondaryStructureElementExtractor (module)
mmtfPyspark.datasets.secondaryStructureExtractor (module)
mmtfPyspark.datasets.secondaryStructureSegmentExtractor (module)
mmtfPyspark.datasets.swissModelDataset (module)
mmtfPyspark.datasets.uniProt (module)
mmtfPyspark.filters (module)
mmtfPyspark.filters.containsAlternativeLocations (module)
mmtfPyspark.filters.containsDnaChain (module)
mmtfPyspark.filters.containsDProteinChain (module)
mmtfPyspark.filters.containsDSaccharideChain (module)
mmtfPyspark.filters.containsGroup (module)
mmtfPyspark.filters.containsLProteinChain (module)
mmtfPyspark.filters.containsPolymerChainType (module)
mmtfPyspark.filters.containsRnaChain (module)
mmtfPyspark.filters.containsSequenceRegex (module)
mmtfPyspark.filters.depositionDate (module)
mmtfPyspark.filters.experimentalMethods (module)
mmtfPyspark.filters.notFilter (module)
mmtfPyspark.filters.orFilter (module)
mmtfPyspark.filters.polymerComposition (module)
mmtfPyspark.filters.releaseDate (module)
mmtfPyspark.filters.resolution (module)
mmtfPyspark.filters.rFree (module)
mmtfPyspark.filters.rWork (module)
mmtfPyspark.filters.secondaryStructure (module)
mmtfPyspark.interactions (module)
mmtfPyspark.interactions.atomInteraction (module)
mmtfPyspark.interactions.coordinationGeometry (module)
mmtfPyspark.interactions.ExcludedLigandSets (module)
mmtfPyspark.interactions.groupInteractionExtractor (module)
mmtfPyspark.interactions.interactionCenter (module)
mmtfPyspark.interactions.interactionFilter (module)
mmtfPyspark.interactions.interactionFingerprinter (module)
mmtfPyspark.interactions.ligandInteractionFingerprint (module)
mmtfPyspark.interactions.polymerInteractionFingerprint (module)
mmtfPyspark.interactions.structureToAtomInteractions (module)
mmtfPyspark.io (module)
mmtfPyspark.io.mmtfReader (module)
mmtfPyspark.io.mmtfWriter (module)
mmtfPyspark.mappers (module)
mmtfPyspark.mappers.structureToBioassembly (module)
mmtfPyspark.mappers.structureToBiopython (module)
mmtfPyspark.mappers.structureToInteractingResidues (module)
mmtfPyspark.mappers.structureToPolymerChains (module)
mmtfPyspark.mappers.structureToPolymerSequences (module)
mmtfPyspark.mappers.structureToProteinDimers (module)
mmtfPyspark.mappers.structureToSecondaryStructureElements (module)
mmtfPyspark.mappers.structureToSecondaryStructureSegments (module)
mmtfPyspark.ml (module)
mmtfPyspark.ml.datasetBalancer (module)
mmtfPyspark.ml.datasetClassifier (module)
mmtfPyspark.ml.datasetRegressor (module)
mmtfPyspark.ml.proteinSequenceEncoder (module)
mmtfPyspark.ml.pythonRDDToDataset (module)
mmtfPyspark.ml.sequenceNgrammer (module)
mmtfPyspark.ml.sparkMultiClassClassifier (module)
mmtfPyspark.ml.sparkRegressor (module)
mmtfPyspark.utils (module)
mmtfPyspark.utils.columnarStructure (module)
mmtfPyspark.utils.columnarStructureX (module)
mmtfPyspark.utils.distanceBox (module)
mmtfPyspark.utils.dsspSecondaryStructure (module)
mmtfPyspark.utils.mmtfDecoder (module)
mmtfPyspark.utils.mmtfStructure (module)
mmtfPyspark.utils.structureToAllInteractions (module)
mmtfPyspark.utils.traverseStructureHierarchy (module)
mmtfPyspark.webfilters (module)
mmtfPyspark.webfilters.advancedQuery (module)
mmtfPyspark.webfilters.blastCluster (module)
mmtfPyspark.webfilters.chemicalStructureQuery (module)
mmtfPyspark.webfilters.customReportQuery (module)
mmtfPyspark.webfilters.pdbjMineSearch (module)
mmtfPyspark.webfilters.pisces (module)
mmtfPyspark.webfilters.sequenceSimilarity (module)
mmtfPyspark.webfilters.wildTypeQuery (module)
mmtfPyspark.webservices (module)
mmtfPyspark.webservices.advancedQueryService (module)
mmtfPyspark.webservices.piscesDownloader (module)
MmtfStructure (class in mmtfPyspark.utils.mmtfStructure)
model (ProteinSequenceEncoder attribute)
model_counter (MmtfStructure attribute)
N
NEUTRON_DIFFRACTION (ExperimentalMethods attribute)
ngram() (in module mmtfPyspark.ml.sequenceNgrammer)
NON_POLYMER (ContainsPolymerChainType attribute)
NotFilter (class in mmtfPyspark.filters.notFilter)
O
offset (DistanceBox attribute)
one_hot_encode() (ProteinSequenceEncoder method)
OrFilter (class in mmtfPyspark.filters.orFilter)
OTHER (ContainsPolymerChainType attribute)
overlapping_ngram_word2vec_encode() (ProteinSequenceEncoder method)
P
pass_data_on() (MmtfStructure method)
PdbjMineSearch (class in mmtfPyspark.webfilters.pdbjMineSearch)
PEPTIDE_LINKING (ContainsPolymerChainType attribute)
PI_HELIX (DsspSecondaryStructure attribute)
Pisces (class in mmtfPyspark.webfilters.pisces)
PiscesDownloader (class in mmtfPyspark.webservices.piscesDownloader)
PolymerComposition (class in mmtfPyspark.filters.polymerComposition)
PolymerInteractionFingerprint (class in mmtfPyspark.interactions.polymerInteractionFingerprint)
post_query() (in module mmtfPyspark.webservices.advancedQueryService)
POWDER_DIFFRACTION (ExperimentalMethods attribute)
print_all_data() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_bioassembly_data() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_chain_entity_group_atom_info() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_chain_group_info() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_chain_info() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_crystallographic_data() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_entity_info() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_metadata() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_mmtf_info() (in module mmtfPyspark.utils.traverseStructureHierarchy)
print_structure_data() (in module mmtfPyspark.utils.traverseStructureHierarchy)
properties (ProteinSequenceEncoder attribute)
property_encode() (ProteinSequenceEncoder method)
ProteinSequenceEncoder (class in mmtfPyspark.ml.proteinSequenceEncoder)
PSI_BLAST (SequenceSimilarity attribute)
Q
q3 (AtomInteraction attribute)
q3() (CoordinateGeometry method)
q4 (AtomInteraction attribute)
q4() (CoordinateGeometry method)
q5 (AtomInteraction attribute)
q5() (CoordinateGeometry method)
q6 (AtomInteraction attribute)
q6() (CoordinateGeometry method)
R
read_full_sequence_file() (in module mmtfPyspark.io.mmtfReader)
read_mmtf_files() (in module mmtfPyspark.io.mmtfReader)
read_reduced_sequence_file() (in module mmtfPyspark.io.mmtfReader)
read_sequence_file() (in module mmtfPyspark.io.mmtfReader)
recursive_index_decode() (in module mmtfPyspark.utils.mmtfDecoder)
ReleaseDate (class in mmtfPyspark.filters.releaseDate)
Resolution (class in mmtfPyspark.filters.resolution)
RESOLUTION_LIST (PiscesDownloader attribute)
RFree (class in mmtfPyspark.filters.rFree)
RNA_LINKING (ContainsPolymerChainType attribute)
RNA_OH_3_PRIME_TERMINUS (ContainsPolymerChainType attribute)
RNA_OH_5_PRIME_TERMINUS (ContainsPolymerChainType attribute)
RNA_STD_NUCLEOTIDES (PolymerComposition attribute)
run_length_decoder_numpy() (in module mmtfPyspark.utils.mmtfDecoder)
RWork (class in mmtfPyspark.filters.rWork)
S
SACCHARIDE (ContainsPolymerChainType attribute)
SecondaryStructure (class in mmtfPyspark.filters.secondaryStructure)
SEQ_ID_LIST (PiscesDownloader attribute)
SEQUENCE_COVERAGE_100 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_60 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_65 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_70 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_75 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_80 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_85 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_90 (WildTypeQuery attribute)
SEQUENCE_COVERAGE_95 (WildTypeQuery attribute)
SequenceSimilarity (class in mmtfPyspark.webfilters.sequenceSimilarity)
set_alt_loc_list() (MmtfStructure method)
set_atom_name() (InteractionCenter method)
set_center() (AtomInteraction method)
set_chain_name() (InteractionCenter method)
set_coordinates() (InteractionCenter method)
set_distance_cutoff() (InteractionFilter method)
set_element() (InteractionCenter method)
set_group_name() (InteractionCenter method)
set_group_number() (InteractionCenter method)
set_max_interactions() (InteractionFilter method)
set_min_interactions() (InteractionFilter method)
set_normalized_b_factor_cutoff() (InteractionFilter method)
set_normalized_b_factors() (InteractionCenter method)
set_prohibited_target_groups() (InteractionFilter method)
set_query_atom_names() (InteractionFilter method)
set_query_elements() (InteractionFilter method)
set_query_groups() (InteractionFilter method)
set_sequence_position() (InteractionCenter method)
set_structure_id() (AtomInteraction method)
set_target_atom_names() (InteractionFilter method)
set_target_elements() (InteractionFilter method)
set_target_groups() (InteractionFilter method)
set_type() (InteractionCenter method)
shifted_3gram_word2vec_encode() (ProteinSequenceEncoder method)
shifted_ngram() (in module mmtfPyspark.ml.sequenceNgrammer)
SIMILAR (ChemicalStructureQuery attribute)
SOLID_STATE_NMR (ExperimentalMethods attribute)
SOLUTION_NMR (ExperimentalMethods attribute)
SOLUTION_SCATTERING (ExperimentalMethods attribute)
SparkMultiClassClassifier (class in mmtfPyspark.ml.sparkMultiClassClassifier)
SparkRegressor (class in mmtfPyspark.ml.sparkRegressor)
StructureToAllInteractions (class in mmtfPyspark.utils.structureToAllInteractions)
StructureToAtomInteractions (class in mmtfPyspark.interactions.structureToAtomInteractions)
StructureToBioassembly (class in mmtfPyspark.mappers.structureToBioassembly)
StructureToBiopython (class in mmtfPyspark.mappers.structureToBiopython)
StructureToInteractingResidues (class in mmtfPyspark.mappers.structureToInteractingResidues)
StructureToPolymerChains (class in mmtfPyspark.mappers.structureToPolymerChains)
StructureToPolymerSequences (class in mmtfPyspark.mappers.structureToPolymerSequences)
StructureToProteinDimers (class in mmtfPyspark.mappers.structureToProteinDimers)
StructureToSecondaryStructureElements (class in mmtfPyspark.mappers.structureToSecondaryStructureElements)
StructureToSecondaryStructureSegments (class in mmtfPyspark.mappers.structureToSecondaryStructureSegments)
SUBSTRUCTURE (ChemicalStructureQuery attribute)
SUPERSTRUCTURE (ChemicalStructureQuery attribute)
T
THEORETICAL_MODEL (ExperimentalMethods attribute)
THREE_TEN_HELIX (DsspSecondaryStructure attribute)
to_mmtf_base64() (in module mmtfPyspark.io.mmtfWriter)
TURN (DsspSecondaryStructure attribute)
U
upsample() (in module mmtfPyspark.ml.datasetBalancer)
URL (PdbjMineSearch attribute)
(PiscesDownloader attribute)
W
WildTypeQuery (class in mmtfPyspark.webfilters.wildTypeQuery)
write_mmtf_files() (in module mmtfPyspark.io.mmtfWriter)
write_sequence_file() (in module mmtfPyspark.io.mmtfWriter)
X
X_RAY_DIFFRACTION (ExperimentalMethods attribute)