Package CHEM :: Package CombiCDB :: Module MechanismModel

Module MechanismModel

Classes

ElectronArrow
Class / struct containing electron flow information for reaction mechanisms.

Functions

prepLabeledReactant(labeledReactant)
Assume reactant came out of a mechanism labeling run, in which case many atoms should have bogus formal charges in the 1000s range that should be converted to atom map indexes.

createNonIsoSmi(mol)
Generate a canonical SMILES representation of the molecule which does not include isomer (stereochemistry) information, but does retain atom-mapping needed for mechanism diagrams.

prepLabeledSmi(labeledSmi)
Back hack alterations made by the prepLabeledReactant function.

reactionProfileSupportsMechanism(reactionProfile)

generateMechanismPairs(reactants, reagent, reactionProfile, reactionProcessor=None, clearLabels=False)
Return pairs (2-ples) of molecules representing reactants and products after the mechanism arrows of the reactionProfile are applied to the given reactants.

clearMechanismLabels(mol)
Clear any labels used for mechanism specifications.

Function Details

[hide private]

prepLabeledReactant(labeledReactant)

Assume reactant came out of a mechanism labeling run, in which case many atoms should have bogus formal charges in the 1000s range that should be converted to atom map indexes. Any hydrogens participating in the mechanism must be assigned an artificial isotope number so that generation of an isomeric SMILES string will not just ignore them as implicit hydrogens.

createNonIsoSmi(mol)

Generate a canonical SMILES representation of the molecule which does not include isomer (stereochemistry) information, but does retain atom-mapping needed for mechanism diagrams.

Many of the mechanism steps done so far do not support stereochemistry, so better not to display stereochemistry information erroneously.

prepLabeledSmi(labeledSmi)

Back hack alterations made by the prepLabeledReactant function. In particular, those added an artificial isotope label to hydrogen atoms to force their appearance in the generated SMILES string. Once the SMILES string is ready, no need to keep the artificial label.

generateMechanismPairs(reactants, reagent, reactionProfile, reactionProcessor=None, clearLabels=False)

Return pairs (2-ples) of molecules representing reactants and products
after the mechanism arrows of the reactionProfile are applied to the given reactants.

reactionProcessor: Caller can supply their own reactionProcessor with modified attributes,
    otherise a default one will be used
clearLabels: If set, returned molecules will not have atom map and isotope labels
    which would normally be used to communicate to image renderer on where to draw arrows

clearMechanismLabels(mol)

Clear any labels used for mechanism specifications. In particular, clear (set to 0) all isotope and atom map indexes.