Package uk.ac.cam.ch.wwmm.opsin
Class NameToStructureConfig
- java.lang.Object
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- uk.ac.cam.ch.wwmm.opsin.NameToStructureConfig
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- All Implemented Interfaces:
java.lang.Cloneable
public class NameToStructureConfig extends java.lang.Object implements java.lang.Cloneable
Allows OPSIN to be configured e.g. enable processing of radicals Example usage: NameToStructureConfig n2sConfig = new NameToStructureConfig(); n2sconfig.setAllowRadicals(true); nts.parseChemicalName(chemicalName, n2sConfig) where nts is an instance of NameToStructure- Author:
- dl387
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Constructor Summary
Constructors Constructor Description NameToStructureConfig()
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
allowInterpretationOfAcidsWithoutTheWordAcid()
Are acids without the word "acid" interpretable e.g.NameToStructureConfig
clone()
static NameToStructureConfig
getDefaultConfigInstance()
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = falseboolean
isAllowRadicals()
Are radicals allowed? e.g.boolean
isDetailedFailureAnalysis()
Should OPSIN attempt reverse parsing to more accurately determine why parsing failedboolean
isOutputRadicalsAsWildCardAtoms()
Are radicals output as wildcard atoms e.g.void
setAllowRadicals(boolean allowRadicals)
Sets whether radicals allowed? e.g.void
setDetailedFailureAnalysis(boolean detailedFailureAnalysis)
Sets whether OPSIN should attempt reverse parsing to more accurately determine why parsing failedvoid
setInterpretAcidsWithoutTheWordAcid(boolean interpretAcidsWithoutTheWordAcid)
Sets whether acids without the word "acid" interpretable e.g.void
setOutputRadicalsAsWildCardAtoms(boolean outputRadicalsAsWildCardAtoms)
Should radicals be output as wildcard atoms e.g.void
setWarnRatherThanFailOnUninterpretableStereochemistry(boolean warnRatherThanFailOnUninterpretableStereochemistry)
Sets whether if OPSIN cannot understand the stereochemistry in a name whether OPSIN's result should be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)boolean
warnRatherThanFailOnUninterpretableStereochemistry()
If OPSIN cannot understand the stereochemistry in a name should OPSIN's result be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)
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Constructor Detail
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NameToStructureConfig
public NameToStructureConfig()
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
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Method Detail
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isAllowRadicals
public boolean isAllowRadicals()
Are radicals allowed? e.g. should fragments such as phenyl be interpretable- Returns:
- whether radicals are allowed
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setAllowRadicals
public void setAllowRadicals(boolean allowRadicals)
Sets whether radicals allowed? e.g. should fragments such as phenyl be interpretable
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isOutputRadicalsAsWildCardAtoms
public boolean isOutputRadicalsAsWildCardAtoms()
Are radicals output as wildcard atoms e.g. [*]CC for ethyl- Returns:
- whether radicals are output using explicit wildcard atoms
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setOutputRadicalsAsWildCardAtoms
public void setOutputRadicalsAsWildCardAtoms(boolean outputRadicalsAsWildCardAtoms)
Should radicals be output as wildcard atoms e.g. [*]CC for ethyl (as opposed to [CH2]C)
Note that if this is set to true InChIs cannot be generated- Parameters:
outputRadicalsAsWildCardAtoms
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isDetailedFailureAnalysis
public boolean isDetailedFailureAnalysis()
Should OPSIN attempt reverse parsing to more accurately determine why parsing failed- Returns:
- whether a more precise cause of failure should be determined if parsing fails
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setDetailedFailureAnalysis
public void setDetailedFailureAnalysis(boolean detailedFailureAnalysis)
Sets whether OPSIN should attempt reverse parsing to more accurately determine why parsing failed
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allowInterpretationOfAcidsWithoutTheWordAcid
public boolean allowInterpretationOfAcidsWithoutTheWordAcid()
Are acids without the word "acid" interpretable e.g. should "acetic" be interpretable- Returns:
- whether acids without the word "acid" should be interpretable
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setInterpretAcidsWithoutTheWordAcid
public void setInterpretAcidsWithoutTheWordAcid(boolean interpretAcidsWithoutTheWordAcid)
Sets whether acids without the word "acid" interpretable e.g. should "acetic" be interpretable- Parameters:
interpretAcidsWithoutTheWordAcid
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warnRatherThanFailOnUninterpretableStereochemistry
public boolean warnRatherThanFailOnUninterpretableStereochemistry()
If OPSIN cannot understand the stereochemistry in a name should OPSIN's result be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)- Returns:
- whether ignored stereochemistry is a warning (rather than a failure)
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setWarnRatherThanFailOnUninterpretableStereochemistry
public void setWarnRatherThanFailOnUninterpretableStereochemistry(boolean warnRatherThanFailOnUninterpretableStereochemistry)
Sets whether if OPSIN cannot understand the stereochemistry in a name whether OPSIN's result should be a warning and structure with incomplete stereochemistry, or should failure be returned (Default)- Parameters:
warnRatherThanFailOnUninterpretableStereochemistry
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getDefaultConfigInstance
public static NameToStructureConfig getDefaultConfigInstance()
Constructs a NameToStructureConfig with default settings: allowRadicals = false outputRadicalsAsWildCardAtoms = false detailedFailureAnalysis = false interpretAcidsWithoutTheWordAcid = false warnRatherThanFailOnUninterpretableStereochemistry = false
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clone
public NameToStructureConfig clone()
- Overrides:
clone
in classjava.lang.Object
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