org.openscience.cdk.smsd.filters

Class ChemicalFilters

java.lang.Object

org.openscience.cdk.smsd.filters.ChemicalFilters

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

@Deprecated
public class ChemicalFilters
extends Object

Class that ranks MCS final solution according to the chemical rules.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol) Deprecated. This class has all the three chemical filters supported by the SMSD.

Method Summary

Methods

Modifier and Type	Method and Description
static int	convertBondOrder(IBond bond) Deprecated. Get bond order value as int value.
static int	convertBondStereo(IBond bond) Deprecated. Get stereo value as integer
static IBond.Order	convertOrder(double srcOrder) Deprecated. Get bond order value as IBond.Order.
static IBond.Stereo	convertStereo(int stereoValue) Deprecated. Get stereo value as Stereo enum
List<Double>	getSortedEnergy() Deprecated. Return sorted energy in ascending order.
List<Integer>	getSortedFragment() Deprecated. Return sorted fragment in ascending order of the size.
List<Double>	getStereoMatches() Deprecated. Return Stereo matches in descending order.
void	sortResultsByEnergies() Deprecated. Sort MCS solution by bond breaking energy.
void	sortResultsByFragments() Deprecated. Sort solution by ascending order of the fragment count.
void	sortResultsByStereoAndBondMatch() Deprecated. Sort MCS solution by stereo and bond type matches.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ChemicalFilters

public ChemicalFilters(List<Map<Integer,Integer>> allMCS,
               List<Map<IAtom,IAtom>> allAtomMCS,
               Map<Integer,Integer> firstSolution,
               Map<IAtom,IAtom> firstAtomMCS,
               IAtomContainer sourceMol,
               IAtomContainer targetMol)

Deprecated.

This class has all the three chemical filters supported by the SMSD. i.e ring matches, bond energy etc

1. a: Bond energy,
2. b: Fragment count,
3. c: Stereo matches

Parameters:

allMCS -

allAtomMCS -

firstSolution -

firstAtomMCS -

sourceMol -

targetMol -

Method Detail

sortResultsByStereoAndBondMatch

public void sortResultsByStereoAndBondMatch()
                                     throws CDKException

Deprecated.

Sort MCS solution by stereo and bond type matches.

Throws:

CDKException

sortResultsByFragments

public void sortResultsByFragments()

Deprecated.

Sort solution by ascending order of the fragment count.

sortResultsByEnergies

public void sortResultsByEnergies()
                           throws CDKException

Deprecated.

Sort MCS solution by bond breaking energy.

Throws:

CDKException

getSortedEnergy

public List<Double> getSortedEnergy()

Deprecated.

Return sorted energy in ascending order.

Returns:

sorted bond breaking energy

getSortedFragment

public List<Integer> getSortedFragment()

Deprecated.

Return sorted fragment in ascending order of the size.

Returns:

sorted fragment count

getStereoMatches

public List<Double> getStereoMatches()

Deprecated.

Return Stereo matches in descending order.

Returns:

sorted stereo matches

convertOrder

public static IBond.Order convertOrder(double srcOrder)

Deprecated.

Get bond order value as IBond.Order.

Parameters:

srcOrder - numerical bond order

Returns:

the bond order type for the given numerical bond order

convertBondOrder

public static int convertBondOrder(IBond bond)

Deprecated.

Get bond order value as int value.

Parameters:

bond - The IBond for which the order is returned.

Returns:

1 for a single bond, 2 for a double bond, 3 for a triple bond, 4 for a quadruple bond, and 0 for any other bond type.

convertBondStereo

public static int convertBondStereo(IBond bond)

Deprecated.

Get stereo value as integer

Parameters:

bond -

convertStereo

public static IBond.Stereo convertStereo(int stereoValue)

Deprecated.

Get stereo value as Stereo enum

Parameters:

stereoValue -