Package chemaxon.sss
Interface SearchConstants
-
- All Known Implementing Classes:
MolSearch
,MolSearchOptions
,Search
,SearchOptions
,StandardizedMolSearch
@PublicAPI public interface SearchConstants
Constants for structure searching
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-
Field Summary
Fields Modifier and Type Field Description static int
ABS_STEREO_ALWAYS_ON
Option for absolute stereo matching.static int
ABS_STEREO_CHIRAL_FLAG
Option for absolute stereo matching.static int
ABS_STEREO_TABLE_OPTION
Option for absolute stereo matching.static int
ATTACHED_DATA_MATCH_EXACT
Option value constant for exact match of attached data.static int
ATTACHED_DATA_MATCH_GENERAL
Option value constant for general match of attached data.static int
ATTACHED_DATA_MATCH_IGNORE
Option value constant for ignoring attached data.static int
ATTACHMENT_ATOM
Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.static int
ATTACHMENT_LABEL
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" forR1
, "2" forR2
, ...static int
ATTACHMENT_MAP
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setAtomMap(int)
.static int
ATTACHMENT_NONE
Constant for attachment point representation in ligands: none (no attachment point data).static int
ATTACHMENT_POINT
Constant for attachment point representation in ligands: R-group attachment.static int
ATTACHMENT_RLABEL
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setExtraLabel(java.lang.String)
.static int
CHARGE_MATCHING_DEFAULT
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).static int
CHARGE_MATCHING_EXACT
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).static int
CHARGE_MATCHING_IGNORE
Option value constant for ignore charge searching (charge information is ignored during searching).static float
DEFAULT_DISSIMILARITY_THRESHOLD
Default threshold value for similarity search.static int
DEFAULT_SEARCHTYPE
Default search type equals SUBSTRUCTURE.static String
DISSIMILARITY_PROPERTY_NAME
Name of the mrv/sdf property which stores the dissimilarity values.static int
DUPLICATE
Duplicate search (formerly called perfect).static int
FULL
Full structure search.static int
FULL_FRAGMENT
Full fragment search (formerly called exact fragment).static int
HCOUNT_MATCHING_AUTO
Default option for H count matching (setHCountMatching).static int
HCOUNT_MATCHING_EQUAL
Option for H count matching.static int
HCOUNT_MATCHING_GREATER_OR_EQUAL
Option for H count matching.static int
HIT_EXCLUDEDQ
Hit constant denoting excluded query atom.static int
HIT_LP
Hit constant denoting isolated lone-pair match.static int
HIT_MULTICENTER
Hit constant denoting multicenter atoms in query.static int
HIT_NON_R
Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.static int
HIT_ORDERING_NONE
Option value constant.static int
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
Option value constant.static int
HIT_R
Hit constant denoting R-node matches in case of R-group search.static int
HIT_R_EMPTY_MATCH
Hit constant denoting R-node empty match.static int
HIT_UNMAPABLE
Hit constant denoting unmapable atoms in query (e.g.static int
IMPLICIT_H_MATCHING_DEFAULT
Option value constant for default mode.static int
IMPLICIT_H_MATCHING_DISABLED
Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen.static int
IMPLICIT_H_MATCHING_ENABLED
Option value constant for indicate matching between implicit and explicit hydrogens.static int
IMPLICIT_H_MATCHING_IGNORE
Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching.static int
ISOTOPE_MATCHING_DEFAULT
Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).static int
ISOTOPE_MATCHING_EXACT
Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).static int
ISOTOPE_MATCHING_IGNORE
Option value constant for ignore isotope searching (isotope information is ignored during searching).static int
MARKUSH_HIT_INNER
Option value constant for returning hit indices of the inner, compiled representation of a Markush target.static int
MARKUSH_HIT_ORIGINAL
Option value constant for returning hit indices of the original Markush target.static int
MATCH_COUNT_BETWEEN
static int
MATCH_COUNT_RELATION
static int
NO_ABAS
Substructure search that applies only screening.static int
NO_SCREEN
Substructure search that applies only atom-by-atom search.static int
POSITION_ON_0TH_HEAVY_ATOM
Hit constant denoting hit position of a non-heavy atom (e.g.static int
RADICAL_MATCHING_DEFAULT
Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).static int
RADICAL_MATCHING_EXACT
Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).static int
RADICAL_MATCHING_IGNORE
Option value constant for ignore radical searching (radical information is ignored during searching).static String[]
SEARCH_MODE_NAMES
Deprecated.As of JChem 5.12, replaced bySEARCH_TYPE_NAMES
.static String[]
SEARCH_TYPE_NAMES
The names of the search types.static int
SIMILARITY
Similarity search.static int
STEREO_DIASTEREOMER
The diastereomers targets of a given query structure are also matched.static int
STEREO_ENANTIOMER
The enantiomer targets of a given query structure are also matched.static int
STEREO_EXACT
Equality is needed in stereochemistry.static int
STEREO_IGNORE
Stereo information is not considered during searching.static int
STEREO_MODEL_COMPREHENSIVE
Option value constant to use comprehensive stereo model, which combines the advantages of local and global stereo models.static int
STEREO_MODEL_DEFAULT
For markush search in all cases and for non-markush duplicate search in query tablesSTEREO_MODEL_LOCAL
, for non-markush duplicate search (with the exception of query tables)STEREO_MODEL_GLOBAL
.static int
STEREO_MODEL_GLOBAL
Option value constant to use global stereo information (global parity, global double bond stereo configuration, etc).static int
STEREO_MODEL_LOCAL
Option value constant to use local stereo information only (local parity, local double bond stereo configuration, etc).static int
STEREO_SPECIFIC
Stereo information is considered during searching.static int
SUBSTRUCTURE
Substructure search that applies both screening and atom-by-atom search.static int
SUPERSTRUCTURE
Superstructure search (Value=6)static int
TAUTOMER_SEARCH_DEFAULT
Option value constant for indicating that tautomer duplicate search option is not explicitly set.static int
TAUTOMER_SEARCH_OFF
Option value constant for switching tautomer searching off.static int
TAUTOMER_SEARCH_ON
Option value constant for switching tautomer searching on.static int
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.static int
UNDEF_R_MATCHING_ALL
Option value constant.static int
UNDEF_R_MATCHING_GROUP
Option value constant.static int
UNDEF_R_MATCHING_GROUP_H
Option value constant.static int
UNDEF_R_MATCHING_GROUP_H_EMPTY
Option value constant.static int
UNDEF_R_MATCHING_UNDEF_R
Option value constant.static int
VAGUE_BOND_DEFAULT
Option value constant for vague bond level HALF.static int
VAGUE_BOND_LEVEL_HALF
Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1.static int
VAGUE_BOND_LEVEL1
Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries.static int
VAGUE_BOND_LEVEL2
Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search.static int
VAGUE_BOND_LEVEL3
Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search.static int
VAGUE_BOND_LEVEL4
Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search.static int
VAGUE_BOND_OFF
Option value constant to disable vague bond matching.
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Field Detail
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DEFAULT_SEARCHTYPE
static final int DEFAULT_SEARCHTYPE
Default search type equals SUBSTRUCTURE.- See Also:
SUBSTRUCTURE
, Constant Field Values
-
NO_SCREEN
static final int NO_SCREEN
Substructure search that applies only atom-by-atom search. (Value=0)- See Also:
- Constant Field Values
-
NO_ABAS
static final int NO_ABAS
Substructure search that applies only screening. (Value=1)- See Also:
- Constant Field Values
-
SUBSTRUCTURE
static final int SUBSTRUCTURE
Substructure search that applies both screening and atom-by-atom search. (Value=2)
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SIMILARITY
static final int SIMILARITY
Similarity search. (Value=3)
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FULL
static final int FULL
Full structure search. (Prior to version 5.2 called EXACT.) Query and target must have the same heavy atom (non-H) network for matching. All other properties are otherwise evaluated the same way as substructure search. Please note that this search type is not suitable for equality check. For that, please use DUPLICATE search type. (Value=4)- Since:
- JChem 5.2
- See Also:
DUPLICATE
,SUBSTRUCTURE
, JChem chemical database concepts, Constant Field Values
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DUPLICATE
static final int DUPLICATE
Duplicate search (formerly called perfect). Used for deciding absolute equality of molecular features (eg duplicate check before database insert). Equality is always subject to standardization in the database. Query features are not evaluated. (Value=5) For this search mode there is no search per minute license limitation in JChemBase, these searches are not counted.- Since:
- JChem 5.2
- See Also:
- JChem chemical database concepts, Constant Field Values
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SUPERSTRUCTURE
static final int SUPERSTRUCTURE
Superstructure search (Value=6)- Since:
- JChem 3.0
- See Also:
- JChem chemical database concepts, Constant Field Values
-
FULL_FRAGMENT
static final int FULL_FRAGMENT
Full fragment search (formerly called exact fragment). Query must be FULL matching to a target fragment. (Value=7)- Since:
- JChem 5.2
- See Also:
FULL
, JChem chemical database concepts, Constant Field Values
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STEREO_SPECIFIC
static final int STEREO_SPECIFIC
Stereo information is considered during searching.- See Also:
- Constant Field Values
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STEREO_IGNORE
static final int STEREO_IGNORE
Stereo information is not considered during searching.- See Also:
- Constant Field Values
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STEREO_EXACT
static final int STEREO_EXACT
Equality is needed in stereochemistry. ("All stereo info is exactly the same.") It mainly has an effect when the query has no stereo information: it only matches non-stereo target. Similarly, a query with a wiggly tetrahedral center will only match wiggly tetrahedral center, and not specific R and S configurations. If STEREO_SPECIFIC is set, non-stereo query matches both nonstereo and stereo target.- See Also:
- Constant Field Values
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STEREO_DIASTEREOMER
static final int STEREO_DIASTEREOMER
The diastereomers targets of a given query structure are also matched. This means that it is only required that if a query atom has stereo information, the target atom should have as well but the two configurations are treated the same.- See Also:
- Constant Field Values
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STEREO_ENANTIOMER
static final int STEREO_ENANTIOMER
The enantiomer targets of a given query structure are also matched.- See Also:
- Constant Field Values
-
SEARCH_TYPE_NAMES
static final String[] SEARCH_TYPE_NAMES
The names of the search types.- Since:
- JChem 5.12
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SEARCH_MODE_NAMES
@Deprecated static final String[] SEARCH_MODE_NAMES
Deprecated.As of JChem 5.12, replaced bySEARCH_TYPE_NAMES
.The names of the search types.- Since:
- JChem 3.0
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DEFAULT_DISSIMILARITY_THRESHOLD
static final float DEFAULT_DISSIMILARITY_THRESHOLD
Default threshold value for similarity search. (Value=0.3)- See Also:
- Constant Field Values
-
DISSIMILARITY_PROPERTY_NAME
static final String DISSIMILARITY_PROPERTY_NAME
Name of the mrv/sdf property which stores the dissimilarity values.- See Also:
- Constant Field Values
-
HCOUNT_MATCHING_AUTO
static final int HCOUNT_MATCHING_AUTO
Default option for H count matching (setHCountMatching). The search tries to find out from the source of the query structure which H count matching option to use. (HCOUNT_MATCHING_EQUAL for smiles and smarts, and HCOUNT_MATCHING_GREATER_OR_EQUAL for mdl molfiles.)
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HCOUNT_MATCHING_EQUAL
static final int HCOUNT_MATCHING_EQUAL
Option for H count matching. Means that a query atom with H count should only match a target atom with hydrogens (implicit or explicit) equal to the H count. This is the Daylight(smiles, smarts) behaviour.- See Also:
- Constant Field Values
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HCOUNT_MATCHING_GREATER_OR_EQUAL
static final int HCOUNT_MATCHING_GREATER_OR_EQUAL
Option for H count matching. Means that a query atom with H count should only match a target atom with hydrogens (implicit or explicit) equal to or greater than the H count. One exception is H count = 0, which means no Hydrogens extra to those explicitly drawn. This is the MDL(sd, molfile) behaviour.- See Also:
- Constant Field Values
-
ABS_STEREO_TABLE_OPTION
static final int ABS_STEREO_TABLE_OPTION
Option for absolute stereo matching. Gets setting from property table.- See Also:
- Constant Field Values
-
ABS_STEREO_CHIRAL_FLAG
static final int ABS_STEREO_CHIRAL_FLAG
Option for absolute stereo matching. Chiral flag in molecule determines absolute configuration.- See Also:
- Constant Field Values
-
ABS_STEREO_ALWAYS_ON
static final int ABS_STEREO_ALWAYS_ON
Option for absolute stereo matching. Always treats chiral centers as abslute configuration.- See Also:
- Constant Field Values
-
MARKUSH_HIT_ORIGINAL
static final int MARKUSH_HIT_ORIGINAL
Option value constant for returning hit indices of the original Markush target. (Default.) For RgMolecule targets, the indices correspond to the graph union.- Since:
- JChem 3.2
- See Also:
MARKUSH_HIT_INNER
, Constant Field Values
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MARKUSH_HIT_INNER
static final int MARKUSH_HIT_INNER
Option value constant for returning hit indices of the inner, compiled representation of a Markush target.- Since:
- JChem 3.2
- See Also:
MARKUSH_HIT_ORIGINAL
, Constant Field Values
-
TAUTOMER_SEARCH_OFF
static final int TAUTOMER_SEARCH_OFF
Option value constant for switching tautomer searching off.- Since:
- JChem 5.4
- See Also:
TAUTOMER_SEARCH_ON
,TAUTOMER_SEARCH_DEFAULT
, Constant Field Values
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TAUTOMER_SEARCH_ON
static final int TAUTOMER_SEARCH_ON
Option value constant for switching tautomer searching on.- Since:
- JChem 5.4
- See Also:
TAUTOMER_SEARCH_OFF
,TAUTOMER_SEARCH_DEFAULT
,TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
, Constant Field Values
-
TAUTOMER_SEARCH_DEFAULT
static final int TAUTOMER_SEARCH_DEFAULT
Option value constant for indicating that tautomer duplicate search option is not explicitly set. Default bahavior isTAUTOMER_SEARCH_OFF
except in case of duplicate search in a database table created with "Duplicate search uses tautomers" option.- Since:
- JChem 5.4
- See Also:
TAUTOMER_SEARCH_OFF
,TAUTOMER_SEARCH_ON
,TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
, Constant Field Values
-
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
static final int TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
Option value constant for switching tautomer searching on without considering stereochemistry in tautomer regions.- Since:
- JChem 5.4
- See Also:
TAUTOMER_SEARCH_OFF
,TAUTOMER_SEARCH_DEFAULT
,TAUTOMER_SEARCH_ON
, Constant Field Values
-
ISOTOPE_MATCHING_DEFAULT
static final int ISOTOPE_MATCHING_DEFAULT
Option value constant for default isotope searching (isotope query matches only isotope target, nonisotope query matches all).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
ISOTOPE_MATCHING_EXACT
static final int ISOTOPE_MATCHING_EXACT
Option value constant for exact isotope searching (isotope query matches only isotope target, nonisotope query only matches nonisotope).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
ISOTOPE_MATCHING_IGNORE
static final int ISOTOPE_MATCHING_IGNORE
Option value constant for ignore isotope searching (isotope information is ignored during searching).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
CHARGE_MATCHING_DEFAULT
static final int CHARGE_MATCHING_DEFAULT
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
CHARGE_MATCHING_EXACT
static final int CHARGE_MATCHING_EXACT
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
CHARGE_MATCHING_IGNORE
static final int CHARGE_MATCHING_IGNORE
Option value constant for ignore charge searching (charge information is ignored during searching). As of JChem 5.3, this option forces IMPLICIT_H_MATCHING_IGNORE in case of duplicate search.- Since:
- JChem 3.2
- See Also:
IMPLICIT_H_MATCHING_IGNORE
, Constant Field Values
-
RADICAL_MATCHING_DEFAULT
static final int RADICAL_MATCHING_DEFAULT
Option value constant for default radical searching (radical query matches only radical target, nonradical query matches all).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
RADICAL_MATCHING_EXACT
static final int RADICAL_MATCHING_EXACT
Option value constant for exact radical searching (radical query matches only radical target, nonradical query only matches nonradical).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
RADICAL_MATCHING_IGNORE
static final int RADICAL_MATCHING_IGNORE
Option value constant for ignore radical searching (radical information is ignored during searching).- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
VAGUE_BOND_OFF
static final int VAGUE_BOND_OFF
Option value constant to disable vague bond matching.- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
VAGUE_BOND_LEVEL1
static final int VAGUE_BOND_LEVEL1
Until 5.3 it was an option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries. From 5.3 extends to 1-atom ligands of aromatic rings and 1 long connections between aromatic rings also (default from 5.3 to 15.9.14).- Since:
- JChem 3.2
- See Also:
VAGUE_BOND_LEVEL_HALF
, Constant Field Values
-
VAGUE_BOND_LEVEL_HALF
static final int VAGUE_BOND_LEVEL_HALF
Option value constant to handle some ambiguous aromaticity, 5-membered Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1 S1C=CC=C1. This is the default value before 5.3 and after 15.9.14.- Since:
- JChem 5.3
- See Also:
VAGUE_BOND_LEVEL1
, Constant Field Values
-
VAGUE_BOND_DEFAULT
static final int VAGUE_BOND_DEFAULT
Option value constant for vague bond level HALF.- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
VAGUE_BOND_LEVEL2
static final int VAGUE_BOND_LEVEL2
Option value constant to vague handling of aromaticity; In the query all single ring bonds are replaced by "single or aromatic" and all double ring bonds are replaced by "double or aromatic" prior to search. (Caution: Not very efficient during fingerprint screening!)- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
VAGUE_BOND_LEVEL3
static final int VAGUE_BOND_LEVEL3
Option value constant to vague handling of aromaticity; In the query all single bonds are replaced by "single or aromatic" and all double bonds are replaced by "double or aromatic" prior to search. (Caution: very inefficient during fingerprint screening!)- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
VAGUE_BOND_LEVEL4
static final int VAGUE_BOND_LEVEL4
Option value constant to vaguely handle bond types; All bond types are ignored (all bonds are replaced by "any" bonds prior to search. (Caution: very inefficient during fingerprint screening!)- Since:
- JChem 3.2
- See Also:
- Constant Field Values
-
STEREO_MODEL_DEFAULT
static final int STEREO_MODEL_DEFAULT
For markush search in all cases and for non-markush duplicate search in query tablesSTEREO_MODEL_LOCAL
, for non-markush duplicate search (with the exception of query tables)STEREO_MODEL_GLOBAL
. Otherwise it isSTEREO_MODEL_COMPREHENSIVE
.- Since:
- JChem 3.2.3
- See Also:
STEREO_MODEL_LOCAL
, Constant Field Values
-
STEREO_MODEL_LOCAL
static final int STEREO_MODEL_LOCAL
Option value constant to use local stereo information only (local parity, local double bond stereo configuration, etc). This is useful for substructure search. When a symmetric atom/bond in the query is specified, this method only matches target atoms/bonds with specified stereochemistry. (For example, query C[[email protected]](C)(C)C does not match CC(C)(C)C.)- Since:
- JChem 3.2.3
- See Also:
- Constant Field Values
-
STEREO_MODEL_COMPREHENSIVE
static final int STEREO_MODEL_COMPREHENSIVE
Option value constant to use comprehensive stereo model, which combines the advantages of local and global stereo models. This setting is suitable for all search types. In principle, it is similar to the local stereo model, except when the target is symmetrical. In the symmetrical target case the matching is accepted, regardless of stereo information. For example, substructure query C[[email protected]](C)(C)C matches both CC(C)(C)C , C[[email protected]@](C)(C)C and CCC[[email protected]@](C)(CC)C(C)C.- Since:
- JChem 3.2.3
- See Also:
- Constant Field Values
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STEREO_MODEL_GLOBAL
static final int STEREO_MODEL_GLOBAL
Option value constant to use global stereo information (global parity, global double bond stereo configuration, etc). This value is suitable for duplicate, full and full fragment searches, as in these cases the full stereospecific environment is always available for both the query and target structures. (Therefore a symmetrical atom/bond with stereo configuration may match to an unspecified strereo atom/bond. For example, C[[email protected]](C)(C)C matches CC(C)(C)C.)- Since:
- JChem 3.2.3
- See Also:
- Constant Field Values
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IMPLICIT_H_MATCHING_DEFAULT
static final int IMPLICIT_H_MATCHING_DEFAULT
Option value constant for default mode. Its value is IMPLICIT_H_MATCHING_ENABLED in almost every cases. There is only one exception: in case of duplicate search against a query table in a database the default value is IMPLICIT_H_MATCHING_DISABLED.- Since:
- JChem 5.0
- See Also:
IMPLICIT_H_MATCHING_ENABLED
,IMPLICIT_H_MATCHING_DISABLED
,IMPLICIT_H_MATCHING_IGNORE
, Constant Field Values
-
IMPLICIT_H_MATCHING_ENABLED
static final int IMPLICIT_H_MATCHING_ENABLED
Option value constant for indicate matching between implicit and explicit hydrogens. In case of duplicate search the sum of implicit and explicit hydrogens of the query atom and the sum on the matched target atom must equal.- Since:
- JChem 5.0
- See Also:
IMPLICIT_H_MATCHING_DEFAULT
,IMPLICIT_H_MATCHING_DISABLED
,IMPLICIT_H_MATCHING_IGNORE
, Constant Field Values
-
IMPLICIT_H_MATCHING_DISABLED
static final int IMPLICIT_H_MATCHING_DISABLED
Option value constant for indicate matching of an explicit hydrogen only to another explicit hydrogen. The number of implicit hydrogens (of the matching atoms) are not checked.- Since:
- JChem 5.0
- See Also:
IMPLICIT_H_MATCHING_DEFAULT
,IMPLICIT_H_MATCHING_ENABLED
,IMPLICIT_H_MATCHING_IGNORE
, Constant Field Values
-
IMPLICIT_H_MATCHING_IGNORE
static final int IMPLICIT_H_MATCHING_IGNORE
Option value constant to indicate that hydrogens, either explicit or implicit, are ignored during searching. Hydrogens having special properties (radical, charge, isotope or more/less than one bond) are still considered.
Option CHARGE_MATCHING_IGNORE forces IMPLICIT_H_MATCHING_IGNORE in case of duplicate search. In case of duplicate search against a query table in a database IMPLICIT_H_MATCHING_IGNORE is switched to IMPLICIT_H_MATCHING_DISABLED. Hydrogens receive the excluded atom hit indexHIT_EXCLUDEDQ
in this case.- Since:
- JChem 5.3
- See Also:
CHARGE_MATCHING_IGNORE
,IMPLICIT_H_MATCHING_DEFAULT
,IMPLICIT_H_MATCHING_ENABLED
,IMPLICIT_H_MATCHING_DISABLED
, Constant Field Values
-
UNDEF_R_MATCHING_ALL
static final int UNDEF_R_MATCHING_ALL
Option value constant. Undefined R-atom in query matches any atom in target.- Since:
- JChem 5.1
- See Also:
UNDEF_R_MATCHING_UNDEF_R
,UNDEF_R_MATCHING_GROUP
,UNDEF_R_MATCHING_GROUP_H
,UNDEF_R_MATCHING_GROUP_H_EMPTY
, Constant Field Values
-
UNDEF_R_MATCHING_UNDEF_R
static final int UNDEF_R_MATCHING_UNDEF_R
Option value constant. Undefined R-atom in query matches only an undefined R-atom in target.- Since:
- JChem 5.1
- See Also:
UNDEF_R_MATCHING_ALL
,UNDEF_R_MATCHING_GROUP
,UNDEF_R_MATCHING_GROUP_H
,UNDEF_R_MATCHING_GROUP_H_EMPTY
, Constant Field Values
-
UNDEF_R_MATCHING_GROUP
static final int UNDEF_R_MATCHING_GROUP
Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, including at least one heavy atom.- Since:
- JChem 5.2
- See Also:
UNDEF_R_MATCHING_ALL
,UNDEF_R_MATCHING_UNDEF_R
,UNDEF_R_MATCHING_GROUP_H
,UNDEF_R_MATCHING_GROUP_H_EMPTY
, Constant Field Values
-
UNDEF_R_MATCHING_GROUP_H
static final int UNDEF_R_MATCHING_GROUP_H
Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom.- Since:
- JChem 5.3
- See Also:
UNDEF_R_MATCHING_ALL
,UNDEF_R_MATCHING_UNDEF_R
,UNDEF_R_MATCHING_GROUP
,UNDEF_R_MATCHING_GROUP_H_EMPTY
, Constant Field Values
-
UNDEF_R_MATCHING_GROUP_H_EMPTY
static final int UNDEF_R_MATCHING_GROUP_H_EMPTY
Option value constant. Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom or the empty set.- Since:
- JChem 5.3
- See Also:
UNDEF_R_MATCHING_ALL
,UNDEF_R_MATCHING_UNDEF_R
,UNDEF_R_MATCHING_GROUP
,UNDEF_R_MATCHING_GROUP_H
, Constant Field Values
-
HIT_ORDERING_NONE
static final int HIT_ORDERING_NONE
Option value constant. Hit ordering type: no ordering.- Since:
- JChem 5.4
- See Also:
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
, Constant Field Values
-
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
static final int HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
Option value constant. Hit ordering type for undefined R-atom matching. If this option is set then R-atom heavy group matches are given precedence in order of R-group ID.- Since:
- JChem 5.4
- See Also:
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
, Constant Field Values
-
POSITION_ON_0TH_HEAVY_ATOM
static final int POSITION_ON_0TH_HEAVY_ATOM
Hit constant denoting hit position of a non-heavy atom (e.g. implicit H, lone pair, ...) on the atom by index 0.- Since:
- JChem 5.11.4
- See Also:
- Constant Field Values
-
HIT_R
static final int HIT_R
Hit constant denoting R-node matches in case of R-group search.- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_MULTICENTER
static final int HIT_MULTICENTER
Hit constant denoting multicenter atoms in query.- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_UNMAPABLE
static final int HIT_UNMAPABLE
Hit constant denoting unmapable atoms in query (e.g. star atoms in polymerization).- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_LP
static final int HIT_LP
Hit constant denoting isolated lone-pair match.- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_R_EMPTY_MATCH
static final int HIT_R_EMPTY_MATCH
Hit constant denoting R-node empty match.- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_NON_R
static final int HIT_NON_R
Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
HIT_EXCLUDEDQ
static final int HIT_EXCLUDEDQ
Hit constant denoting excluded query atom.- Excluded query atoms
- Hydrogens receive this constant in case of ignoring hydrogens.
- Since:
- JChem 5.3
- See Also:
- Constant Field Values
-
ATTACHMENT_NONE
static final int ATTACHMENT_NONE
Constant for attachment point representation in ligands: none (no attachment point data).- See Also:
- Constant Field Values
-
ATTACHMENT_POINT
static final int ATTACHMENT_POINT
Constant for attachment point representation in ligands: R-group attachment.- See Also:
- Constant Field Values
-
ATTACHMENT_MAP
static final int ATTACHMENT_MAP
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setAtomMap(int)
. Maps with R-group ID:1
forR1
,2
forR2
, ...- See Also:
- Constant Field Values
-
ATTACHMENT_LABEL
static final int ATTACHMENT_LABEL
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" forR1
, "2" forR2
, ...- See Also:
- Constant Field Values
-
ATTACHMENT_RLABEL
static final int ATTACHMENT_RLABEL
Constant for attachment point representation in ligands: sets attachment points byMolAtom.setExtraLabel(java.lang.String)
. Labels with full R-atom name: "R1" forR1
, "R2" forR2
, ...- See Also:
- Constant Field Values
-
ATTACHMENT_ATOM
static final int ATTACHMENT_ATOM
Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.- See Also:
- Constant Field Values
-
MATCH_COUNT_BETWEEN
static final int MATCH_COUNT_BETWEEN
- See Also:
- Constant Field Values
-
MATCH_COUNT_RELATION
static final int MATCH_COUNT_RELATION
- See Also:
- Constant Field Values
-
ATTACHED_DATA_MATCH_IGNORE
static final int ATTACHED_DATA_MATCH_IGNORE
Option value constant for ignoring attached data.- Since:
- JChem 5.2
- See Also:
ATTACHED_DATA_MATCH_GENERAL
,ATTACHED_DATA_MATCH_EXACT
, Constant Field Values
-
ATTACHED_DATA_MATCH_GENERAL
static final int ATTACHED_DATA_MATCH_GENERAL
Option value constant for general match of attached data.- Since:
- JChem 5.2
- See Also:
ATTACHED_DATA_MATCH_IGNORE
,ATTACHED_DATA_MATCH_EXACT
, Constant Field Values
-
ATTACHED_DATA_MATCH_EXACT
static final int ATTACHED_DATA_MATCH_EXACT
Option value constant for exact match of attached data.- Since:
- JChem 5.2
- See Also:
ATTACHED_DATA_MATCH_IGNORE
,ATTACHED_DATA_MATCH_GENERAL
, Constant Field Values
-
-