CDPL.Chem.BemisMurckoAnalyzer Class Reference

Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains. More...

Inheritance diagram for CDPL.Chem.BemisMurckoAnalyzer:

Public Member Functions
None	__init__ ()
	Constructs the BemisMurckoAnalyzer instance.
None	__init__ (BemisMurckoAnalyzer analyzer)
	Initializes a copy of the BemisMurckoAnalyzer instance analyzer. More...
BemisMurckoAnalyzer	assign (BemisMurckoAnalyzer gen)
	Replaces the current state of self with a copy of the state of the BemisMurckoAnalyzer instance gen. More...
None	stripHydrogens (bool strip)
	Specifies whether hydrogen atoms shall be stripped from the input before the decomposition. More...
bool	hydrogensStripped ()
	Tells whether hydrogen atoms are stripped from the input before the decomposition. More...
None	analyze (MolecularGraph molgraph)
	Performs the Bemis-Murcko decomposition of the molecular graph molgraph. More...
FragmentList	getRingSystems ()
	Returns the perceived ring systems of the input molecular graph. More...
FragmentList	getSideChains ()
	Returns the side chains (acyclic substituents) of the input molecular graph. More...
FragmentList	getLinkers ()
	Returns the linker fragments connecting different ring systems of the input molecular graph. More...
FragmentList	getFrameworks ()
	Returns the Bemis-Murcko frameworks of the input molecular graph (union of ring systems and linkers). More...

Properties
	hydrogenStripping = property(hydrogensStripped, stripHydrogens)
	ringSystems = property(getRingSystems)
	sideChains = property(getSideChains)
	linkers = property(getLinkers)
	frameworks = property(getFrameworks)

Detailed Description

Decomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains.

After calling analyze() the four constituent fragment sets can be queried separately via getRingSystems(), getLinkers(), getFrameworks() and getSideChains(). The framework of a molecule is the union of all ring systems together with the linker chains that connect them; side chains are the remaining acyclic substituents. Hydrogen atoms can optionally be stripped from the input.

See also

[BEMU]

Since

1.1

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.BemisMurckoAnalyzer.__init__

(

BemisMurckoAnalyzer

analyzer

)

Initializes a copy of the BemisMurckoAnalyzer instance analyzer.

Parameters

analyzer

The BemisMurckoAnalyzer instance to copy.

Member Function Documentation

assign()

BemisMurckoAnalyzer CDPL.Chem.BemisMurckoAnalyzer.assign

(

BemisMurckoAnalyzer

gen

)

Replaces the current state of self with a copy of the state of the BemisMurckoAnalyzer instance gen.

Parameters

gen	The BemisMurckoAnalyzer instance to copy.

Returns

self

stripHydrogens()

None CDPL.Chem.BemisMurckoAnalyzer.stripHydrogens

(

bool

strip

)

Specifies whether hydrogen atoms shall be stripped from the input before the decomposition.

Parameters

strip

If True, hydrogens are removed prior to analysis.

hydrogensStripped()

bool CDPL.Chem.BemisMurckoAnalyzer.hydrogensStripped

(

)

Tells whether hydrogen atoms are stripped from the input before the decomposition.

Returns

True if hydrogens are stripped, and False otherwise.

analyze()

None CDPL.Chem.BemisMurckoAnalyzer.analyze

(

MolecularGraph

molgraph

)

Performs the Bemis-Murcko decomposition of the molecular graph molgraph.

After this call the four fragment sets produced by the decomposition are available via getRingSystems(), getLinkers(), getFrameworks() and getSideChains().

Parameters

molgraph

The molecular graph to decompose.

getRingSystems()

FragmentList CDPL.Chem.BemisMurckoAnalyzer.getRingSystems

(

)

Returns the perceived ring systems of the input molecular graph.

Returns

A reference to the list of ring-system fragments.

getSideChains()

FragmentList CDPL.Chem.BemisMurckoAnalyzer.getSideChains

(

)

Returns the side chains (acyclic substituents) of the input molecular graph.

Returns

A reference to the list of side-chain fragments.

getLinkers()

FragmentList CDPL.Chem.BemisMurckoAnalyzer.getLinkers

(

)

Returns the linker fragments connecting different ring systems of the input molecular graph.

Returns

A reference to the list of linker fragments.

getFrameworks()

FragmentList CDPL.Chem.BemisMurckoAnalyzer.getFrameworks

(

)

Returns the Bemis-Murcko frameworks of the input molecular graph (union of ring systems and linkers).

Returns

A reference to the list of framework fragments.