Package org.openscience.cdk.smsd.filters
Class ChemicalFilters
- java.lang.Object
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- org.openscience.cdk.smsd.filters.ChemicalFilters
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@Deprecated public class ChemicalFilters extends Object
Deprecated.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.Class that ranks MCS final solution according to the chemical rules.- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
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Constructor Summary
Constructors Constructor 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.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static int
convertBondOrder(IBond bond)
Deprecated.Get bond order value asint
value.static int
convertBondStereo(IBond bond)
Deprecated.Get stereo value as integerstatic IBond.Order
convertOrder(double srcOrder)
Deprecated.Get bond order value asIBond.Order
.static IBond.Stereo
convertStereo(int stereoValue)
Deprecated.Get stereo value as Stereo enumList<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.
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Constructor Detail
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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- a: Bond energy,
- b: Fragment count,
- c: Stereo matches
- Parameters:
allMCS
-allAtomMCS
-firstSolution
-firstAtomMCS
-sourceMol
-targetMol
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Method Detail
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sortResultsByStereoAndBondMatch
public void sortResultsByStereoAndBondMatch() throws CDKException
Deprecated.Sort MCS solution by stereo and bond type matches.- Throws:
CDKException
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sortResultsByFragments
public void sortResultsByFragments()
Deprecated.Sort solution by ascending order of the fragment count.
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sortResultsByEnergies
public void sortResultsByEnergies() throws CDKException
Deprecated.Sort MCS solution by bond breaking energy.- Throws:
CDKException
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getSortedEnergy
public List<Double> getSortedEnergy()
Deprecated.Return sorted energy in ascending order.- Returns:
- sorted bond breaking energy
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getSortedFragment
public List<Integer> getSortedFragment()
Deprecated.Return sorted fragment in ascending order of the size.- Returns:
- sorted fragment count
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getStereoMatches
public List<Double> getStereoMatches()
Deprecated.Return Stereo matches in descending order.- Returns:
- sorted stereo matches
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convertOrder
public static IBond.Order convertOrder(double srcOrder)
Deprecated.Get bond order value asIBond.Order
.- Parameters:
srcOrder
- numerical bond order- Returns:
- the bond order type for the given numerical bond order
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convertBondOrder
public static int convertBondOrder(IBond bond)
Deprecated.Get bond order value asint
value.- Parameters:
bond
- TheIBond
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.
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convertBondStereo
public static int convertBondStereo(IBond bond)
Deprecated.Get stereo value as integer- Parameters:
bond
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convertStereo
public static IBond.Stereo convertStereo(int stereoValue)
Deprecated.Get stereo value as Stereo enum- Parameters:
stereoValue
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