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Package: 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.
Classes
Data Types
Data Obj Types

Imported Packages:

ChemComp,   Molecule,   ccp.api.general.Citation,   ccp.api.general.DbRef,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.molecule.MolSystem:

MolStructure,   Validation,   cambridge.api.Dangle,   ccp.api.nmr.Nmr,   ccp.api.nmr.NmrCalc,   ccp.api.nmr.NmrConstraint,   ccp.api.nmr.NmrEntry,   ccp.api.nmr.NmrScreen,   ccpnmr.api.Analysis,   molsim.api.Symmetry,   utrecht.api.Haddock

Classes:

Class Description
Atom Atom in a specific location in a specific molecule in specific surroundings (Chain).

Atoms can *not* be deleted while they are linked to FixedAtomSets. If this is desired the fixedAtomSets link must be cleared first.
Chain A specific instance of a given molecule in a specific environment. E.g. one of the chains for a homodimer.

The Chain corresponds to a specific Molecule, but may differ in some ways.

Creating a Chain automatically creates the Residue and Atom objects corresponding to it.
ChainFragment Fragment of Chain with defined MolType for all residues. ChainFragments are generated automatically by the Chain initialiser function. See documentation of Chain.createChainFragments for a description of the normal way of dividing a Chain in ChainFragments.
ChainInteraction Interaction between two Chains in a MolSystem
MolSystem Molecular System - a set of potentially interacting chains. Describes all components of known molecular structure considered relevant for (typically) a structure determination. May include components of a complex, components in different states (e.g. free protein, free ligand, and protein and ligand bound in a complex), and also molecules that are not part of any interaction but are considered relevant (e.g. NMR-observable impurities in an Nmr study).
MolSystemLink Link between two ChemComps (bulding blocks) not already described in the Molecule description. Intended for intermolecular links, additional crosslinks, or links whose location was not known precisely when describing the Molecule. Disulfide bonds would be a good example for either category. Part of the description of MolSystem level additional links.
MolSystemLinkEnd LinkEnd, equivalent to ChemComp.LinkEnd. Part of the description of MolSystem level additional links. Note that the MolSeqLinkEnds defined in the Molecule corresponding to this Chain are also valid for the Chain, so that both need to be considered when describing the topology of the MolSystem
MolSystemSysName Systematic name of MolSystem according to namingSystem
NonCovalentBond NonCovalent bond, e.g. hydrogen bond, metal coordination bond
Residue A monomer part of a specific molecule in a specific environment (Chain)).
StructureGroup Group of Structure models. General purpose grouping mechanism for structures. May be from same or different generation cycles.

Data Obj Types:

Type Description
None

Data Types:

Type Description
None

Package guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00022
  Data Model Version 2.0.5
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 26 16:58:17 2012    from data model package  ccp.api.molecule.MolSystem   revision 1.46  
  Work done by the CCPN team.
www.ccpn.ac.uk