public class NameToStructureConfig
extends java.lang.Object
implements java.lang.Cloneable
Constructor and Description |
---|
NameToStructureConfig()
Constructs a NameToStructureConfig with default settings:
allowRadicals = false
outputRadicalsAsWildCardAtoms = false
detailedFailureAnalysis = false
interpretAcidsWithoutTheWordAcid = false
warnRatherThanFailOnUninterpretableStereochemistry = false
|
Modifier and Type | Method and 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 = false
|
boolean |
isAllowRadicals()
Are radicals allowed? e.g.
|
boolean |
isDetailedFailureAnalysis()
Should OPSIN attempt reverse parsing to more accurately determine why parsing failed
|
boolean |
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 failed
|
void |
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)
|
public NameToStructureConfig()
public boolean isAllowRadicals()
public void setAllowRadicals(boolean allowRadicals)
public boolean isOutputRadicalsAsWildCardAtoms()
public void setOutputRadicalsAsWildCardAtoms(boolean outputRadicalsAsWildCardAtoms)
outputRadicalsAsWildCardAtoms
- public boolean isDetailedFailureAnalysis()
public void setDetailedFailureAnalysis(boolean detailedFailureAnalysis)
public boolean allowInterpretationOfAcidsWithoutTheWordAcid()
public void setInterpretAcidsWithoutTheWordAcid(boolean interpretAcidsWithoutTheWordAcid)
interpretAcidsWithoutTheWordAcid
- public boolean warnRatherThanFailOnUninterpretableStereochemistry()
public void setWarnRatherThanFailOnUninterpretableStereochemistry(boolean warnRatherThanFailOnUninterpretableStereochemistry)
warnRatherThanFailOnUninterpretableStereochemistry
- public static NameToStructureConfig getDefaultConfigInstance()
public NameToStructureConfig clone()
clone
in class java.lang.Object