Package CHEM :: Package DB :: Module ReactDBPopulator

Module ReactDBPopulator

Classes

ReactDBPopulator
Script to read SDF or other (reaction) molecule files and insert into the ReactDB as specific (level 3) reaction_steps.

ReactionSynthesisIteratorPreparer
Reaction synthesis table doesn't really have a parent.

ReactionStepIteratorPreparer
Main outer loop iterator which does the actual walk through the (reaction) molecule input stream which presumably hits one reaction molecule at a time.

AnnotationTypeIteratorPreparer
Called once per reaction_step.

ReactionStepAnnotationIteratorPreparer
Called once per reaction step annotation.

ComponentTypeAnnotationIteratorPreparer
Called once per reaction_step.

ChemicalAnnotationIteratorPreparer
Called once per reaction_step_chemical to generate a parent chemical record for a new reaction component.

ReactionStepChemicalAnnotationIteratorPreparer
Called once per reaction step chemical (as annotations).

ComponentTypeIteratorPreparer
Called once per reaction_step.

ChemicalComponentIteratorPreparer
Called once per reaction_step_chemical to generate a parent chemical record for a new reaction component.

ReactionStepChemicalComponentIteratorPreparer
Called once per reaction step chemical (as a reaction component).

ReactionFileIteratorPreparer
Called once, should just produce one item for the input file the script is working on

Functions

[hide private]

main(argv)
Main method, callable from command line

Variables

[hide private]

DEFAULT_REAGENT_ID = -1

DEFAULT_REACTION_SYNTHESIS_ID = -1

DataColumns = ["reaction_smirks",]