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Python API Documentation


    
See Also: Documentation for Data Model
Quick Guide to CCP software
Overview of Python API

Directly Contained packages:

Package Description
cambridge Programs from the University of Cambridge (outside CCPN)
ccp CCP Data Model for biochemistry, macromolecular structure and bioinformatics.
ccpnmr Data modelling specifically for use in the CcpNmr suite of programs, rather than for general use.
memops Modelling for the memops framework, generally applicable to any data model from any field.
molsim Data Model for molecular simulation and related areas
utrecht Programs from Utrecht University


All Contained packages:

cambridge contains:

Package Description
cambridge.api.Dangle Data for the CcpNmr Dangle program, for predicting torsion angles from shifts.

ccp contains:

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

ccpnmr contains:

Package Description
ccpnmr.api.NameMapping Data for mappings between atom and residue names in various systems, for use with the CcpNmr format conversion programs.
ccpnmr.api.AnalysisProfile Analysis user profile data
ccpnmr.api.Analysis Data for the CcpNmr Analysis program, mainly about screen graphics and program state.

memops contains:

Package Description
memops.api.Implementation The memops implementation - the basic machinery that makes the various subroutine libraries function.
memops.api.AccessControl Packge for access control information

molsim contains:

Package Description
molsim.api.Symmetry Molecular symmetry description and restraint
molsim.api.AnnealProtocol Data model for annealing protocols

utrecht contains:

Package Description
utrecht.api.Haddock Haddock-specific data


Package guid:

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