CHEM.DB.DBPopulator2

Module DBPopulator2

Classes

DBPopulatorRun
Responsible for running the DBPopulator by first setting up all of the processors, iterators, etc.

DBPopulator
Script to read SDF or other molecule files and insert into the ChemDB non-redundantly.

SourceIteratorPreparer
Source table doesn't really have a parent.

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

ChemicalMixIteratorPreparer
Main outer loop iterator which does the actual walk through the molecule input stream which presumably hits one chemical mixture at a time.

Source2ChemicalMixIteratorPreparer
Called once per chemical mix.

AnnotationIteratorPreparer
Called once per source2chemicalmix.

ChemicalIteratorPreparer
Given a parent chemicalmix object, parse the isomeric SMILES string into components to identify individual chemicals to process.

MixtureComponentIteratorPreparer
Called once per chemical.

Isomer3DIteratorPreparer
Given a parent chemical object, call Corina to generate 3D isomer structures for processing.

ExternalIDProcessor
Figure out the molecule object's external ID value based on a specific SD tag name

FloatValueProcessor
If it's parseable as a numerical value, convert the annotation model's string value (svalue) into a float and store that in the fvalue field.

IsomerGenerator
Run Corina to generate isomers for the current chemical object.

MolStringProcessor
Convert the current object's attached mol attribute into a molecule string format, specified by the molFormat parameter (one of the OEChem constants, such as OEFormat_SDF), and save this string into the object's field named by the columnName parameter.

Functions

[hide private]

main()

Variables

[hide private]

DataColumns = ['can_smiles', 'chemaxon_logp', 'chiral_atoms', ...

Variables Details

[hide private]

DataColumns

Value:

['can_smiles', 'chemaxon_logp', 'chiral_atoms', 'chiral_bonds', 'entha
lpy', 'h_acceptors', 'h_donors', 'inchi', 'inchi_aux', 'molecular_form
ula', 'molecular_weight', 'name', 'num_atoms', 'num_c', 'num_h', 'num_
heavy_atoms', 'num_n', 'num_o', 'num_bonds', 'num_db_bonds', 'num_roto
rs', 'num_sg_bonds', 'oepassed_filter', 'rigid_segments', 'xlogp', 'za
p_area', 'zap_coulombic', 'zap_solvation', 'zap_total',]