Search Java Classes and Packages
#Org.biojava.nbio.structure.io Classes and Interfaces - 89 results found.
| Name | Description | Type | Package | Framework |
| AbstractBean | a generic class that implements the toString method for a beanAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| AllChemCompProvider | A ChemComp provider that downloads and caches the components. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| AtomSite | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| AuditAuthor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| BondMaker | Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary | Class | org.biojava.nbio.structure.io | BioJava |
| CAConverter | Converts full atom representations to Calpha only ones. | Class | org.biojava.nbio.structure.io | BioJava |
| Cell | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ChargeAdder | Class | org.biojava.nbio.structure.io | BioJava | |
| ChemComp | A definition for a Chemical Component, as maintained by the wwPDB. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompAtom | stores these fields: _chem_comp_atom. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompBond | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ChemCompConsumer | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompDescriptor | Container object for _pdbx_chem_comp_descriptorSince:3. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompGroupFactory | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompProvider | Interface that is implemented by all classes that can provide ChemComp definitions. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| ChemCompTools | Some tools for working with chemical compounds. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ChemicalComponentDictionary | A representation of the Chemical Component Dictionary. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| CompoundFinder | Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. | Class | org.biojava.nbio.structure.io | BioJava |
| DatabasePDBremark | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DatabasePDBrev | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DatabasePdbrevRecord | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DownloadChemCompProvider | This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| Entity | A simple class to represent Entity records in mmCif filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntityPolySeq | Container for _entity_poly_seq recordsField Name mmCIF Data Item | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcGen | Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcNat | Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcSyn | PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| Exptl | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| FastaAFPChainConverter | A collection of static utilities to convert between AFPChains and FastaSequences. | Class | org.biojava.nbio.structure.io | BioJava |
| FastaStructureParser | Reads a protein sequence from a fasta file and attempts to match it to a 3D structure. | Class | org.biojava.nbio.structure.io | BioJava |
| FileConvert | Methods to convert a structure object into different file formats. | Class | org.biojava.nbio.structure.io | BioJava |
| FileDownloadUtils | Class | org.biojava.nbio.structure.io.util | BioJava | |
| FileParsingParameters | A class that configures parameters that can be sent to the PDB file parsers setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. | Class | org.biojava.nbio.structure.io | BioJava |
| GroupToSDF | Class | org.biojava.nbio.structure.io | BioJava | |
| LocalPDBDirectory | Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader. | Class | org.biojava.nbio.structure.io | BioJava |
| LocalPDBDirectory .FetchBehavior | Controls when the class should fetch files from the ftp serverAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
| LocalPDBDirectory .ObsoleteBehavior | Behaviors for when an obsolete structure is requested. | Class | org.biojava.nbio.structure.io | BioJava |
| MMcifConsumer | An interface for the events triggered by a MMcifParser. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMCIFFileReader | How to parse an mmCif file:public static void main(String[] args) throws Exception { | Class | org.biojava.nbio.structure.io | BioJava |
| MMCIFFileTools | Some tools for mmCIF file writing. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMcifParser | Interface that needs to be implemented by an MMcifParserSince:1. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| PDBBioAssemblyParser | Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit | Class | org.biojava.nbio.structure.io | BioJava |
| PDBFileParser | This class implements the actual PDB file parsing. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBFileReader | The wrapper class for parsing a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBParseException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBTemporaryStorageUtils | Internal use only. | Class | org.biojava.nbio.structure.io.util | BioJava |
| PDBTemporaryStorageUtils .LinkRecord | Temporary data storage for LINK records. | Class | org.biojava.nbio.structure.io.util | BioJava |
| PdbxChemCompDescriptor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxChemCompIdentifier | _pdbx_chem_comp_identifier. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxEntityNonPoly | A bean for the Pdbx_entity_nonpoly category. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxNonPolyScheme | A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxPolySeqScheme | A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxStructAssembly | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGen | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGenXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperList | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperListXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PolymerType | Enumerates the classification of polymers. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ReducedChemCompProvider | Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| Refine | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ResidueType | Enumerates the possible classifications of residues. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| SandboxStyleStructureProvider | The "Sandbox" style of organizing files is to have a directory structure like below, i. | Class | org.biojava.nbio.structure.io | BioJava |
| SeqRes2AtomAligner | Aligns the SEQRES residues to the ATOM residues. | Class | org.biojava.nbio.structure.io | BioJava |
| SiftsChainEntry | An entry in the chain-level SIFTS mapping between UniProt and the PDB. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsChainToUniprotMapping | A mapping between UniProt entries and PDB chains. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsEntity | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsMappingProvider | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsResidue | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsSegment | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsXMLParser | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SimpleMMcifConsumer | A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| SimpleMMcifParser | A simple mmCif file parserString file = "path/to/mmcif/file"; | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| SSBondImpl | A simple bean to store disulfide bridge information, the SSBOND records in the PDB files. | Class | org.biojava.nbio.structure.io | BioJava |
| Struct | a bean to contain the data of the _struct linesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructAsym | Contains the data for _struct_asymSince:1. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructConn | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructKeywords | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructNcsOper | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRef | A class to containt the _struct_ref field dataAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructRefSeq | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRefSeqDif | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructSite | Created by Matt on 11/1/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructSiteGen | Created by Matt on 10/31/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructureIOFile | StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureProvider | A class that can provide a protein structure object from somewhere. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureSequenceMatcher | A utility class with methods for matching ProteinSequences withAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
| Symmetry | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ZipChemCompProvider | This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |