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Package: ChemComp


    Reference description of residues, molecules and molecule fragments, mainly topology and naming.
Classes
Data Types
Data Obj Types

Imported Packages:

ChemElement,   Stereochemistry,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.molecule.ChemComp:

ChemCompCharge,   ChemCompCoord,   ChemCompLabel,   LabeledMolecule,   MolStructure,   MolSystem,   Molecule,   ccp.api.nmr.Nmr,   ccp.api.nmr.NmrReference,   ccpnmr.api.Analysis,   ccpnmr.api.AnalysisProfile,   ccpnmr.api.NameMapping

Classes:

Class Description
AbstractChemAtom Atom in topology sense. E.g. Arg CB.

The AbstractChemAtoms within a ChemComp comprise all atomds (including link atoms) contained in any form of the ChemComp. The ChemCompVars then select the appropriate subset of AbstractChemAtoms. Bonds, angles, Stereochemistry etc. are relevant only for the ChemCompVars that contain all AbstractChemAtoms involved.

ChemAtom names are (should be) IUPAC and follow from the nature of the ChemComp. LinkAtom names (should) reflect the linkCode of the LinkEnd they are part of; the recommended style is that a LinkEnd with a linkCode 'prev' should have link atoms named 'prev_1' for the LinkAtom partaking in the bond and 'prev_2' for the other LinkAtom.
AtomSysName 'sysName' is the systematic name for the ChemAtom or ChemAtomSet with name 'atomName' and subType atomSubType according to the naming system 'namingSystem'. 'atomName' and atomSubTypecan be used to identify the ChemAtom(Set) involved.
ChemAngle Angle between chemAtoms. Serrves as definition for reference.
ChemAtom Atom, in the sense of a part of a toplogical description of a ChemComp. ChemAtoms, unlike LinkAtoms, are part of the ChemComp itself.
ChemAtomSet Group of chem atoms that may form a pseudoatom. A ChemAtomSet may consist of either other ChemAtomSets or of ChemAtoms, but not both. All ChemAtomSets are relevant for all ChemCompVars, but they (or some of the ChemAtomSets they consist of) may contain fewer or even no atoms in some ChemCompVars.
ChemBond Bond between chemAtoms. Defines topology of ChemCompVars
ChemComp Chemical Component. E.g. GLU (glutamate). Describes the topology of templates that serve as building block for molecules. The ChemComp holds information valid for all toploigical variants, as well as all Atoms, Bonds, Angles etc. for the different ChemCompVars (e.g. 'start','protonated'; 'end','deprotonated', etc.). For this reason the Atoms, Bonds etc. linked to do not form a consistent set.
ChemCompSysName ChemComp systematic name class. Gives systematic names applicable to a set of ChemCompVars. Some naming systems have only one systematic name for all ChemCompVars, others have different names for different sets.
ChemCompVar ChemComp with a given chain location (for polymers) or sybstitution/lin king pattern (for non-polymers) and a given topological variant. Topological variants are e.g. protonation states, and in general topological variations that can change over time for a given molecule. For Polymers topological variations (defined through the descriptor attribute) also include linking patterns in addition to those that make up the linear polymer links.

A Polymer ChemComp is any ChemComp with at least one ChemCompVar with  linking 'start', 'middle', or 'end'.  
If linking is 'start', there must be a 'next' link but no 'prev' link
if linking is 'end' there must be a 'prev' link but no 'next' link
if linking is 'middle' there must be both a 'next' and 'a prev'
if linking is neither there must be neither a 'next' nor a 'prev' link
if linking is 'none' and the ChemComp is not a linear polymer, there must be no links at all.
If there are no links, liking must be 'none'

The relevant constraints are placed on ChemCompVar and LinkEnd.
ChemTorsion Tosrion angle between four ChenmAtoms. Serves as definition for reference.
ChemTorsionSysName Systematic name of ChemTorsion accordign to NamingSystem
LinkAtom Atom used to specify LinkEnds. Serves as a placeholder for ChemAtoms that are not part of the present ChemComp but of other ChemComps linked to it. As such allows the definition of bonds, Torsions, Stereochemistry etc. involving ChemAtoms from several ChemComps. The key element in the definition of LinkEnds.
LinkEnd Describes one end of link to other ChemComp.
linkAtoms[0] and chemAtoms[0] must be included in the same set of chemCompVars. linkAtoms[1] and chemAtoms[1] must be included in the same set of ChemCompVars as linkAtoms[0] or in a subset of it.

There are constraints on the linkEnd, linkEnd.linkCode, ChemCompVar and ChemCompVar.linking (see ChemCompVar documentation). To satisfy the constraints the LinkEnd must be created after the ChemCompVars are created and linked to the correct AbstractChemAtoms.
NamingSystem ChemComp naming system. Serves as container for ChemComp and Atom/AtomSet systematic names. May be defined relative to a reference, in which case only names that differ from those in the reference are given explicitly
NonStdChemComp ChemComp that is not a standard ChemComp, but may or may not be derived from one.
StdChemComp Standard ChemComp, or ChemComp that has a one-letter Code (unique within the molType). In practice one of the twenty standard amino acids or the four standrad DNA or RNA bases
Stereochemistry The stereochemistry attribute in combination with the AbstractChemAtoms and their order in the link define the stereochemistry of the atoms.  

Data Obj Types:

Type Description
None

Data Types:

Type Description
AtomChirality IUPAC chirality for Atom. Values are 'R', 'S', 'unknown'.
BondStereochemistry IUPAC bond stereochemistry. Values are 'E', 'Z', 'unknown' (for 'not applicable')
BondType Bond types enumeration
ChemCompLinking Tag for describing a ChemCompVar, more precisely (part of) substitution pattern..
The default values are those that are legal for linear polymers. They are:
'start' (protein N-terminal or RNA/DNA 5' end)
'end' (protein C-terminal or RNA/DNA 3' end)
'middle' (protein RNA or DNA non-terminal redidue)
'none' not substituted.
Note that for e.g. Cysteines there might be other substitution sites that would be distinguished in the descriptor.

'any' is not a legal value for ChemCompVars, but is used in other contexts to indicate information that is relevant to any ChemCompVar in a ChemComp

For ChemComps other than parts of linear polymers, values 'start', 'middle', 'end' are illegal, and other values could be chosen. ChemCompLinking should be used to describe substitution pattern
MolType Basic Molecule Type of ChemComp.

'protein', 'DNA', 'RNA','otherpolymer' are all classes of *linear* polymers. 'nonpolymer' stands for anything that is not part of a *linear* polymer, including e.g. sugars.
ThreeLetterCode Chemical Component three-letter code, as used in PDB.
TwelveLetterCode Twelve letter code for ChemComp

Package guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:51_00046
  Data Model Version 2.0.5
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  Work done by the CCPN team.
www.ccpn.ac.uk