CHEM.CombiCDB.MechanismPredictor.MechanismPredictor:
Given a mixture of molecules (usually a pair) and solvent /
reagent molecules if relevant, try finding the most reactive
electrons (higest occupied molecular orbital: HOMO) and most
accepting atom (lowest unoccupied molecular orbital: LUMO).
CHEM.CombiCDB.ReactionFormatter.ReactionCanonizer:
Given a reaction representation, encoded through one of OpenEye's
standard parsers (SMILES for SMIRKS, SDF for RDF), produce and canonize
a SMIRKS string output for each.
CHEM.CombiCDB.ReactionProcessor.ReactionProcessor:
Given a set of SMIRKS reactions and reactant molecules, generates as many
combinatorial products as possible by running every reactant permutation
through each reaction
Also includes a script to generate the output in a format easily inserted
into the application database.
CHEM.CombiCDB.SynthesisGenerator.SynthesisGenerator:
Given a set of starting reactant molecules and reagent objects
which can perform reactions on appropriate reactants, randomly
apply the reagents to the reactants in sequence (and parallel) to
generate a product that could conceivably be synthesized with such
components.
CHEM.Common.ChemicalDetail.ChemicalDetail:
Various utility methods for retrieving details for some chemical
from the database, usually keyed by the canonical SMILES
string.
CHEM.Common.ChemicalSearch.ChemicalSearch:
Given a SMILES string (and a limit on the results size), returns
the most similar fingerprints known by the fingerprint server
(specified in the Env.py file) as well as a similarity score
of each found fingerprint to the original search string.
CHEM.Common.IteratorFactory.IteratorFactory:
Abstract base class for all iterator factories.
CHEM.Common.Util.BoltzmannProbabilityWeight:
Functor which given an energy value, should provide a
proportional probability weight based on Boltzmann probability
distributions.
CHEM.Common.Util.Codec:
Throwaway class to "encrypt" and "decrypt"
strings since the rotor module got deprecated after Python 2.3.
CHEM.Common.Util.ProgressDots:
Clone of OEChem OEDots class, to add progress indicator to long
processes, without actually requiring OEChem as a dependency.
CHEM.DB.BaseDBPopulator.BaseDBPopulator:
Base class to take some kind of input data (probably a file),
iterate through it's contents and process it accordingly, possibly
calculating and formatting different values and then submitting
them for output (probably a database).
CHEM.DB.BaseDBPopulator.BaseDBPopulator:
Base class to take some kind of input data (probably a file),
iterate through it's contents and process it accordingly, possibly
calculating and formatting different values and then submitting
them for output (probably a database).
CHEM.DB.PubChemConvert.PubChemConvert:
Convert the contents of the input stream (probably database
dump), interpreted as a molecule file, into a molecule (SDF) file
with SD tags appropriate for PubChem.
CHEM.DB.rdb.BeautifulSoup.BeautifulSoup:
This parser knows the following facts about HTML:
* Some tags have no closing tag and should be interpreted as being
closed as soon as they are encountered.
CHEM.ML.FeatureRegression.FeatureRegression:
Given a list of feature dictionaries (sparse feature vectors)
representing different objects and a matching list of target values
to predict, assign values to each feature encountered to best
predict the target values.
CHEM.ML.Similarity.BaseSimilarity.BaseSimilarity:
Abstract base class for all similarity measure classes.
CHEM.ML.featureAnalysis.FeatureDictListToMatrix.FeatureDictListToMatrix:
Read the feature dict list of a molecule dataset (eg,
combinedFeatures.dict), and output selected(top,middle,bottom,or
random) number of features as a matrix according to the descending
order of features' frequences in the whole dataset.
CHEM.Structure.RMSDvsCorina.RMSDvsCorina:
Given a list of molecules, presumably with 3D coordinates, run
each through Corina to generate predicted 3D coordinates.
CHEM.Web.cgibin.BaseWeb.BaseWeb:
Common base class for web interface modules to supply some
standard setup, parameter extraction, file upload processing
methods, etc.
CHEM.Web.cgibin.BaseWeb.BaseWeb:
Common base class for web interface modules to supply some
standard setup, parameter extraction, file upload processing
methods, etc.
CHEM.DB.rdb.BeautifulSoup.BeautifulSoup:
This parser knows the following facts about HTML:
* Some tags have no closing tag and should be interpreted as being
closed as soon as they are encountered.
CHEM.ML.Util.FeatureDictReader:
Decodes data feature vectors (represented as index:value lines
in a text file) into string:value feature dictionary objects.
CHEM.ML.Util.FeatureDictWriter:
Utility class to encode data feature vectors (represented as
string:value feature dictionaries) into a plain text file
format.
CHEM.Kernel.Util.FeatureDictReader:
Utility class to dencode data feature vectors (represented as
index:count lines in a text file) into a string:count feature
dictionary objects.
CHEM.Kernel.Util.FeatureDictWriter:
Utility class to encode data feature vectors (represented as
string:count feature dictionaries) into a plain text file format,
that can then be re-read using the matching
"FeatureDictReader" class.
basestring:
Type basestring cannot be instantiated; it is the base for str
and unicode.