Attribute
|
Type
|
Multiplicity
|
Description
|
calcIsoelectricPoint
|
Float
|
0..1
|
Calculated isoelectric point of molecule. The pI indicates the value of pH at which the net charge of the molecule would be neutralized, if the molecule would have a conformation with each amino acid fully exposed to the solvent. NB This is derived information, this should be moved when this gets developed.
|
commonNames
|
Line
|
0..*
|
List of molecule common names.
|
details
|
String
|
0..1
|
Free text, for notes, explanatory comments, etc.
|
empiricalFormula
|
Line
|
0..1
|
Derived. Empirical formula for molecule.
|
formalCharge
|
Int
|
1..1
|
Derived. Formal charge of molecule.
|
fragmentDetails
|
Text
|
0..1
|
Details on what (if anything) this Molecule is a fragment of).
|
functions
|
Line
|
0..*
|
Keywords describing functions for molecule. e.g. 'enzyme', 'structure', ...
|
hasNonStdChemComp
|
Boolean
|
1..1
|
Derived. Does molecule contain non-standard ChemComp? Note that this will be true whenever the molecule does not consist entirely of StdChemComps. Since only molTypes protein, DNA, and RNA have any StdChemComps at all, this attribute will be True but meaningless for any Molecule that contains ChemComps of other types.
|
hasNonStdChirality
|
Boolean
|
0..1
|
Derived. Does molecule contain ChemComp of non-standard chirality? Note that this will be true also when the Molecule contains a ChemComp where no StdChirality is defined.
|
isAromatic
|
Boolean
|
1..1
|
Derived. Does molecule contain aromatic groups?
|
isFinalised
|
Boolean
|
1..1
|
Non-finalised molecules may not have links to Samples etc.
Finalised molecules can no longer have residues added or removed.
Note that you can add MolResidues to non-finalised molecules even if they already have chains, but that you must make sure of adding new MolSystem.Residues as necessary.
|
isParamagnetic
|
Boolean
|
1..1
|
Derived. Does Molecule contain paramagnetic groups?
|
isStdCyclic
|
Boolean
|
0..1
|
Derived. Is Molecule a Std Cyclic polymer, i.e. a Std Linear polymer with a polymer-type link between the last and the first residue?
|
isStdLinear
|
Boolean
|
1..1
|
Derived. Is the molecule a standard linear polymer? A linear polymer must contain a linear sequence where MolResidues with successive serials are linked by linear polymer type links (linkCodes 'next' and 'prev').
Linear polymers may be heavily crosslinked but all the sequential links must be present and of the correct type. The component MolResidues may be of any type or a mixture of types (peptide, nucleotide, styrene monomers, ...) provided the 'next' and/or 'prev' links are present.
The following are not linear polymers:
- A strand of DNA with a break in the middle of the sequence numbering, even if the strand is circular.
- A protein with one peptide bond replaced by a bond going through an Aspartate side chain COOH.
- A glycoprotein.
- A linear polysaccharide.
|
keywords
|
Line
|
0..*
|
Keywords for searching molecule. e.g. 'DNA binding', 'receptor', 'Zinc finger'...
|
longName
|
Text
|
0..1
|
Long form of molecule name.
|
molType
|
MolType
|
0..1
|
Derived. molType of ChemComps making up Molecule. Possible values: 'protein', 'DNA', 'RNA', 'DNA/RNA', 'other'. The values are returned if *all* ChemComps are of the correct molType(s). 'other' is returned if the Molecule contains neither protein, not DNA, nor RNA ChemComps. If the Molecule contains a mixture of molTypes (except for DNA/RNA) the value is None (not set).
Note that the molType says nothing about how the ChemComps are linked, and that e.g. a Molecule of molType 'protein' need not contain a single peptide bond. If e.g. molType is 'protein' and isStdLinear' is True, on the other hand, the Molecule is a single unbroken polypeptide (which may or may not contain crosslinks).
|
molecularMass
|
Float
|
1..1
|
Derived. Molecular mass, in atomic units. This is the sum of the atomic weights of the atoms that form this molecule.
|
mutationDetails
|
Text
|
0..1
|
Details on mutations in the sequence (e.g. this is A54K relative to the wildtype).
|
name
|
Line
|
1..1
|
Name of Molecule. Used as key. Should be correct and informative, but may be an abbreviation or an acronym if the alternative is too long. Recommended e.g. NaCl, Lysozyme, Lac headpiece, morphine.
|
seqDetails
|
Text
|
0..1
|
Details, notes, comments etc. about the sequence.
|
seqLength
|
Int
|
1..1
|
Derived. Number of MolResidues in Molecule. For linear polymers equal to sequence length.
|
seqString
|
String
|
0..1
|
Derived. String holding sequence one-letter-codes with '*' for non-standard residues. The attribute is always defined, but is equal to the empty string except for linear polymers of defined molType. Note that one-letter codes are only defined for std ChemComps, which are only found for peptides and nucleotides, so the value for linear polymers of type 'other' is likely to be meaningless.
|
smiles
|
String
|
0..1
|
SMILES (Simplified Molecular Input Line Entry Specification) string describing molecule.
|
smilesType
|
SmilesType
|
0..1
|
Type of Smiles string in smiles attribute
|
stdSeqString
|
String
|
0..1
|
Derived. String holding sequence one-letter-codes with non-standard ChemComps replaced by one-letter-code of corresponding standard derivative, or by '*' if there is no standard derivative.
The attribute is always defined, but is equal to the empty string except for linear polymers of defined molType. Note that one-letter codes are only defined for std ChemComps, which are only found for peptides and nucleotides, so the value for linear polymers of type 'other' is likely to be meaningless.
|