rdkit.ML.Descriptors.CompoundDescriptors module

descriptor calculator for compounds defined by a composition alone (only the composition is required)

class rdkit.ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator(simpleList, compoundList=None, dbName=None, dbTable='atomic_data', dbUser='sysdba', dbPassword='masterkey')

Bases: rdkit.ML.Descriptors.Descriptors.DescriptorCalculator

used for calculating descriptors

This is the central point for descriptor calculation

Notes

  • There are two kinds of descriptors this cares about:

    1. Simple Descriptors can be calculated solely using atomic descriptor values and the composition of the compound. The full list of possible simple descriptors is determined by the types of Calculator Methods (see below) and the contents of an atomic database.

      Simple Descriptors can be marked as nonZeroDescriptors. These are used to winnow out atom types where particular atomic descriptors are zero (usually indicating that the value is unknown)

      Simple Descriptors are maintained locally in the _simpleList_

    2. Compound Descriptors may rely upon more complicated computation schemes and descriptors for the compound as a whole (e.g. structural variables, etc.). The full list of compound descriptors is limitless. They are calculated using the _ML.Descriptors.Parser_ module.

      Compound Descriptors are maintained locally in the _compoundList_

  • This class has a some special methods which are labelled as Calculator Method These are used internally to take atomic descriptors and reduce them to a single simple descriptor value for a composition. They are primarily intended for internal use.

  • a composition vector is a list of 2-tuples: ‘[(atom1name,atom1Num),...]’ where atom1Num is the contribution of the atom to the stoichiometry of the compound. No assumption is made about the stoichiometries (i.e. they don’t have to be either integral or all sum to one).

BuildAtomDict()

builds the local atomic dict

We don’t want to keep around all descriptor values for all atoms, so this method takes care of only pulling out the descriptors in which we are interested.

Notes

  • this uses _chemutils.GetAtomicData_ to actually pull the data
CalcCompoundDescriptorsForComposition(compos='', composList=None, propDict={})

calculates all simple descriptors for a given composition

Arguments

  • compos: a string representation of the composition
  • composList: a composVect
  • propDict: a dictionary containing the properties of the composition as a whole (e.g. structural variables, etc.)

The client must provide either _compos_ or _composList_. If both are provided, _composList_ takes priority.

Returns
the list of descriptor values

Notes

  • when _compos_ is provided, this uses _chemutils.SplitComposition_ to split the composition into its individual pieces
CalcDescriptors(composVect, propDict)

calculates all descriptors for a given composition

Arguments

  • compos: a string representation of the composition
  • propDict: a dictionary containing the properties of the composition as a whole (e.g. structural variables, etc.). These are used to generate Compound Descriptors
Returns
the list of all descriptor values

Notes

  • this uses _chemutils.SplitComposition_ to split the composition into its individual pieces
CalcDescriptorsForComposition(composVect, propDict)

calculates all descriptors for a given composition

Arguments

  • compos: a string representation of the composition
  • propDict: a dictionary containing the properties of the composition as a whole (e.g. structural variables, etc.). These are used to generate Compound Descriptors
Returns
the list of all descriptor values

Notes

  • this uses _chemutils.SplitComposition_ to split the composition into its individual pieces
CalcSimpleDescriptorsForComposition(compos='', composList=None)

calculates all simple descriptors for a given composition

Arguments

  • compos: a string representation of the composition
  • composList: a composVect

The client must provide either _compos_ or _composList_. If both are provided, _composList_ takes priority.

Returns
the list of descriptor values

Notes

  • when _compos_ is provided, this uses _chemutils.SplitComposition_ to split the composition into its individual pieces
  • if problems are encountered because of either an unknown descriptor or atom type, a _KeyError_ will be raised.
DEV(desc, compos)

Calculator Method

average deviation of the descriptor values across the composition

Arguments

  • desc: the name of the descriptor
  • compos: the composition vector

Returns

a float
GetDescriptorNames()

returns a list of the names of the descriptors this calculator generates

MAX(desc, compos)

Calculator Method

maximum of the descriptor values across the composition

Arguments

  • desc: the name of the descriptor
  • compos: the composition vector

Returns

a float
MEAN(desc, compos)

Calculator Method

averages the descriptor values across the composition

Arguments

  • desc: the name of the descriptor
  • compos: the composition vector

Returns

a float
MIN(desc, compos)

Calculator Method

minimum of the descriptor values across the composition

Arguments

  • desc: the name of the descriptor
  • compos: the composition vector

Returns

a float
ProcessCompoundList()

Adds entries from the _compoundList_ to the list of _requiredDescriptors_

Each compound descriptor is surveyed. Any atomic descriptors it requires are added to the list of _requiredDescriptors_ to be pulled from the database.

ProcessSimpleList()

Handles the list of simple descriptors

This constructs the list of _nonZeroDescriptors_ and _requiredDescriptors_.

There’s some other magic going on that I can’t decipher at the moment.

SUM(desc, compos)

Calculator Method

sums the descriptor values across the composition

Arguments

  • desc: the name of the descriptor
  • compos: the composition vector

Returns

a float
rdkit.ML.Descriptors.CompoundDescriptors.GetAllDescriptorNames(db, tbl1, tbl2, user='sysdba', password='masterkey')

gets possible descriptor names from a database

Arguments

  • db: the name of the database to use
  • tbl1: the name of the table to be used for reading descriptor values
  • tbl2: the name of the table to be used for reading notes about the descriptors (descriptions of the descriptors if you like)
  • user: the user name for DB access
  • password: the password for DB access

Returns

a 2-tuple containing:

  1. a list of column names
  2. a list of column descriptors

Notes

  • this uses _Dbase.DbInfo_ and Dfunctionality for querying the database
  • it is assumed that tbl2 includes ‘property’ and ‘notes’ columns