F G I O S

F

finalizeStructure() - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

A generic function to be used at the end of all data addition to do required cleanup on the structure

G

getAltLocIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of location ids of the atoms.

getAtomIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of atom serial ids (_atom_site.id in mmCIF dictionary).

getbFactors() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the B-factors (temperature factors) of the atoms in Angstroms^2.

getBioassemblyName(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the name of the transformation for a bioassembly.

getChainIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of internal chain identifiers (asym_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.

getChainIndexListForTransform(int, int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the list of chain indices for the given transformation for the given bioassembly.

getChainNames() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of public chain identifiers (auth_ids in mmCIF dictionary), of length the number of chains (polymeric, non-polymeric and water) in the structure.

getChainsPerModel() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the number of chains (polymeric/non-polymeric/water) in each model.

getDepositionDate() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the deposition date of the structure as a string in ISO time standard format.

getEntityChainIndexList(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the chain indices for the entity specified by the index.

getEntityDescription(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the entity description (as defined in mmCIF dictionary) for the entity specified by the index.

getEntitySequence(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the sequence for the entity specified by the index.

getEntityType(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the entity type (polymer, non-polymer, water) for the entity specified by the index.

getExperimentalMethods() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the experimental methods as an array of strings.

getGroupAtomCharges(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the atom charges for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupAtomNames(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the atom names (e.g.

getGroupBondIndices(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the zero-based bond indices (in pairs) for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupBondOrders(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the bond orders for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupChemCompType(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the chemical component type for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupElementNames(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the IUPAC element names (e.g.

getGroupIds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing residue numbers (auth_seq_id in mmCIF dictionary) for each residue (group).

getGroupName(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the group name for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupSequenceIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the indices of groups (residues) in their corresponding sequences, obtainable through StructureDataInterface.getEntitySequence(int).

getGroupSingleLetterCode(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the single letter amino acid code or nucleotide code for the group specified in StructureDataInterface.getGroupTypeIndices().

getGroupsPerChain() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the number of groups (residues) in each chain.

getGroupTypeIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing indices to be used to obtain group level information, e.g.

getInsCodes() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the insertion codes (pdbx_PDB_ins_code in mmCIF dictionary) for each residue (group).

getInterGroupBondIndices() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the zero-based bond indices (in pairs) for the structure.

getInterGroupBondOrders() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array of bond orders (1,2,3) of inter-group bonds with length number of inter-group bonds

getMatrixForTransform(int, int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns a 4x4 transformation matrix for the given transformation for the given bioassembly.

getMmtfProducer() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns a string describing the producer of the MMTF file.

getMmtfVersion() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the MMTF version number (from the specification).

getNcsOperatorList() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the NCS operation matrix list.

getNumAtoms() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of atoms in the structure.

getNumAtomsInGroup(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of atoms in the group specified in StructureDataInterface.getGroupTypeIndices().

getNumBioassemblies() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of bioassemblies in this structure.

getNumBonds() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the total number of bonds in the structure

getNumChains() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of chains (for all models) in the structure.

getNumEntities() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of entities (as defined in mmCIF dictionary) in the structure

getNumGroups() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of groups (residues) in the structure that have experimentally determined 3D coordinates.

getNumModels() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of models in the structure.

getNumTransInBioassembly(int) - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the number of transformations in a given bioassembly.

getOccupancies() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the occupancy values of the atoms.

getReleaseDate() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the release date of the structure as a string in ISO time standard format.

getResolution() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the resolution of the dataset.

getRfree() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the Rfree of the dataset.

getRwork() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the Rwork of the dataset.

getSecStructList() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the secondary structure information for the structure as a list of integers

getSpaceGroup() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the space group of the structure.

getStructureId() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the identifier of the structure.

getTitle() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the title of the structure.

getUnitCell() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns the 6 floats that describe the unit cell.

getxCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the X coordinates of the atoms in Angstroms.

getyCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the Y coordinates of the atoms in Angstroms.

getzCoords() - Method in interface org.rcsb.mmtf.api.StructureDataInterface

Returns an array containing the Z coordinates of the atoms in Angstroms.

I

initStructure(int, int, int, int, int, String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Used before any additions to do any required pre-processing.

O

org.rcsb.mmtf.api - package org.rcsb.mmtf.api

APIs to accessing and passing on the data.

S

setAtomInfo(String, int, char, float, float, float, float, float, String, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the atom level information for a given atom.

setBioAssemblyTrans(int, int[], double[], String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets a single Bioassembly transformation to a structure.

setChainInfo(String, String, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the information for a given chain.

setEntityInfo(int[], String, String, String) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the entity level annotation for a chain(s).

setGroupBond(int, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets an intra-group bond.

setGroupInfo(String, int, char, String, int, int, char, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the information for a given group / residue with atomic data.

setHeaderInfo(float, float, float, String, String, String, String[]) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the header information.

setInterGroupBond(int, int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets an inter-group bond.

setModelInfo(int, int) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the number of chains for a given model.

setXtalInfo(String, float[], double[][]) - Method in interface org.rcsb.mmtf.api.StructureAdapterInterface

Sets the space group and unit cell information.

StructureAdapterInterface - Interface in org.rcsb.mmtf.api

Interface to inflate a given MMTF data source.

StructureDataInterface - Interface in org.rcsb.mmtf.api

An interface describing the data API.

F G I O S