Package
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Description
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ccp.api.nmr
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Package for nmr spectroscopy
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ccp.api.nmr.NmrScreen
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Package NMR screening and metabolomics.
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ccp.api.nmr.NmrReference
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NMR reference information, such as chemical shift distributions.
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ccp.api.nmr.NmrExpPrototype
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Package for describing NMR experment prototypes, which could also be described as template descriptions.
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ccp.api.nmr.NmrEntry
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Entry of NMR data in databases, especially the BioMagResBank.
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ccp.api.nmr.NmrConstraint
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Nmr Constraints, used for structure generation. Includes constraints, constraint violations, and resonance-based structures ( e.g. CLOUDs).
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ccp.api.nmr.NmrCalc
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Nmr-related calculation tracking
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ccp.api.nmr.Nmr
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All data specific to NMR spectroscopy, including NMR experiments, analysis and assignments, constraint lists, shift lists, etc.
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ccp.api.molecule
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Package for molecule description, reference data, coordinates, etc.
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ccp.api.molecule.Validation
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Validation program output. Could be validation of structures, NMR data, ...
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ccp.api.molecule.Stereochemistry
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Reference description for types of stereochemistry.
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ccp.api.molecule.Molecule
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Covalent structure of molecules; sequence of linear poymers (DNA. RNA, and proteins).
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ccp.api.molecule.MolSystem
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Molecular system with various chains, their residues, atoms, interactions etc., independent of any coordinate set. Describes not the covalent structure of the molecule as such (given in the Molecule package), but the individual molecules and atoms and their role in context of the larger system. Attributes specific to X-ray, NMR or other techniques are given in other packages.
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ccp.api.molecule.MolStructure
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Three-dimensional structures and their atomic coordinates, corresponding to the ATOM and HETATM records in a PDB file.
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ccp.api.molecule.LabeledMolecule
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Package for describing isotope labeling of molecules
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ccp.api.molecule.ChemElement
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Chemical elements and isotopes.
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ccp.api.molecule.ChemCompLabel
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Package for standard substitution patterns under standard labeling schemes, e.g. for bacteria fed on 2-13C glycerol.
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ccp.api.molecule.ChemCompCoord
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Default or reference coordinates for ChemComps.
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ccp.api.molecule.ChemCompCharge
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DRAFT - backward compatibility of future versions not guaranteed.
Package for ChemComp partial charges, for different force fields.
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ccp.api.molecule.ChemComp
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Reference description of residues, molecules and molecule fragments, mainly topology and naming.
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ccp.api.lims
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Model package for (bio)chemical laboratory information management - sample production and tracking, experiments, target tracknig, ...
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ccp.api.lims.Target
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DRAFT - backward compatibility of future versions not guaranteed.
Molecular targets, in the bioinformatics sense of the word.
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ccp.api.lims.Sample
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DRAFT - backward compatibility of future versions not guaranteed.
Individual (laboratory) samples and information for tracking them.
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ccp.api.lims.RefSampleComponent
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DRAFT - backward compatibility of future versions not guaranteed.
Sample composition and description of the individual components. Includes information specific for certain biochemical techniques.
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ccp.api.lims.RefData
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Collection of reference data and spectra for RefSampleComponents.
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ccp.api.lims.Protocol
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DRAFT - backward compatibility of future versions not guaranteed.
Protocol
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ccp.api.lims.Location
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DRAFT - backward compatibility of future versions not guaranteed.
Storage location for samples.
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ccp.api.lims.Holder
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DRAFT - backward compatibility of future versions not guaranteed.
Description of sample containers and holders e.g. tubes, eppendorfs, 96-well plates, ...
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ccp.api.lims.Experiment
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DRAFT - backward compatibility of future versions not guaranteed.
Biochemical (or chemical) laboratory experiment.
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ccp.api.lims.ExpBlueprint
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DRAFT - backward compatibility of future versions not guaranteed.
Bioinformatical description of a molecular complex or system that is a target of investigation.
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ccp.api.lims.Crystallization
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ccp.api.lims.Classification
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Categorisations and systematic names usae din various contexts
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ccp.api.general
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Model packages for general data, not specific to any scientific area.
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ccp.api.general.Template
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Templates, i.e. abstract classes for general use in other parts of the data model.
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ccp.api.general.Taxonomy
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DRAFT - backward compatibility of future versions not guaranteed.
Biological organisms and their parts, including the description of sources for natural compounds.
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ccp.api.general.Method
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General descriptions of methods and protocols, for computation, laboratory procedures, and other purposes.
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ccp.api.general.KeywordDefinition
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Storage of keyword definitions - reference data.
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ccp.api.general.Instrument
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DRAFT - backward compatibility of future versions not guaranteed.
Laboratory instruments, robots, spectrometers, and similar machinery.
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ccp.api.general.DbRef
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DRAFT - backward compatibility of future versions not guaranteed.
References to external databases.
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ccp.api.general.DataLocation
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DRAFT - backward compatibility of future versions not guaranteed.
Package for storing file descriptors, file pointers and similar for external data files, such as iamges, binary data matrices, ...
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ccp.api.general.Citation
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DRAFT - backward compatibility of future versions not guaranteed.
Citation and litterature references.
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ccp.api.general.Annotation
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DRAFT - backward compatibility of future versions not guaranteed.
Annotation and additional information of (biopolymer) molecules at the residue level.
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ccp.api.general.Affiliation
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DRAFT - backward compatibility of future versions not guaranteed.
Individual people and organisations.
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