chemaxon.sss
Interface SearchConstants

All Known Implementing Classes:
HitDisplayTool, JChemSearch, JChemSearchOptions, MatchCountOptions, MolSearch, MolSearchOptions, RGroupDecomposition, Search, SearchOptions, StandardizedMolSearch

public interface SearchConstants

Constants for structure searching

Author:
Ferenc Csizmadia, Szabolcs Csepregi

Field Summary
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 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 float DEFAULT_SIMILARITY_THRESHOLD
          Deprecated. use DEFAULT_DISSIMILARITY_THRESHOLD instead
static int DISSIMILARITY
          Deprecated. use SIMILARITY instead
static int DUPLICATE
          Duplicate search (formerly called perfect).
static int EXACT
          Deprecated. use FULL
static int EXACT_FRAGMENT
          Deprecated. use FULL_FRAGMENT
static int EXACT_FRAGMENT_OFF
          Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
static int EXACT_FRAGMENT_ON
          Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
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_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. star atoms in polymerization).
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 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 KEEP_QUERY_ORDER
          Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
static int MARKUSH_AROM_FINAL_CHECK
          Option value constant to consider Markush aromatization information (ambiguous aromatic rings) during Markush search and check the hit afterwards (default).
static int MARKUSH_AROM_NO_FINAL_CHECK
          Option value constant to consider Markush aromatization information during Markush search but do not check the hit afterwards.
static int MARKUSH_AROM_OFF
          Option value constant to not consider Markush aromatization information.
static int MARKUSH_DISABLED
          Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
static int MARKUSH_ENABLED
          Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
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 MIX_SGROUP_MATCHING_OFF
          Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
static int MIX_SGROUP_MATCHING_ON
          Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
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 OPTION_CHARGE_MATCHING
          Deprecated. since 5.0
Use SearchOptions.setChargeMatching(int) instead.
static int OPTION_EXACT_FRAGMENT
          Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
static int OPTION_ISOTOPE_MATCHING
          Deprecated. since 5.0
Use SearchOptions.setIsotopeMatching(int) instead.
static int OPTION_KEEP_QUERY_ORDER
          Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
static int OPTION_MARKUSH_AROM
          Deprecated. since 5.0
Use MolSearchOptions.setMarkushArom(int) instead.
static int OPTION_MARKUSH_ENABLED
          Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
static int OPTION_MARKUSH_HIT
          Deprecated. since 5.0
Use MolSearchOptions.setHitIndexType(int)
static int OPTION_MIX_SGROUP_MATCHING
          Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
static int OPTION_RADICAL_MATCHING
          Deprecated. since 5.0
Use SearchOptions.setRadicalMatching(int) instead.
static int OPTION_STEREO_MODEL
          Deprecated. since 5.0
Use SearchOptions.setStereoModel(int) instead.
static int OPTION_TAUTOMER_SEARCH
          Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
static int OPTION_VAGUE_BOND
          Deprecated. since 5.0
static int OPTION_VALENCE_MATCHING
          Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
static int PERFECT
          Deprecated. use DUPLICATE
static int R_NODE_PLACEHOLDER
          Deprecated. as of JChem 5.3, use HIT_R instead.
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 int REARRANGE_QUERY
          Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
static java.lang.String[] SEARCH_MODE_NAMES
          The names of the search modes.
static int SEARCH_OPTIONS_LENGTH
          Number of search options stored in Search.options[] Has package visibility!
static int SIMILARITY
          Similarity search.
static int STEREO_DIASTEREOMER
          The diastereomers 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 considerd 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 substructure search or query tables this is STEREO_MODEL_LOCAL.
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_OFF
          Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
static int TAUTOMER_SEARCH_ON
          Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
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 the default vague bond level (level 1).
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.
static int VALENCE_MATCHING_IGNORE
          Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
static int VALENCE_MATCHING_ON
          Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
 

Field Detail

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)

See Also:
JChem chemical database concepts, Constant Field Values

DISSIMILARITY

static final int DISSIMILARITY
Deprecated. use SIMILARITY instead
Dissimilarity search. (Value=3)

See Also:
JChem chemical database concepts, Constant Field Values

SIMILARITY

static final int SIMILARITY
Similarity search. (Value=3)

See Also:
JChem chemical database concepts, Constant Field Values

EXACT

static final int EXACT
Deprecated. use FULL
Former name of 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)

See Also:
JChem chemical database concepts, Constant Field Values

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

PERFECT

static final int PERFECT
Deprecated. use DUPLICATE
Former name of 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.

See Also:
JChem chemical database concepts, Constant Field Values

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

SUPERSTRUCTURE

static final int SUPERSTRUCTURE
Superstructure search (Value=6)

Since:
JChem 3.0
See Also:
JChem chemical database concepts, Constant Field Values

EXACT_FRAGMENT

static final int EXACT_FRAGMENT
Deprecated. use FULL_FRAGMENT
Former name of Full fragment search (formerly called exact fragment). Query must be FULL matching to a target fragment. (Value=7)

Since:
JChem 3.1.2
See Also:
FULL, 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

STEREO_SPECIFIC

static final int STEREO_SPECIFIC
Stereo information is considered during searching.

See Also:
Constant Field Values

STEREO_IGNORE

static final int STEREO_IGNORE
Stereo information is not considerd during searching.

See Also:
Constant Field Values

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

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

SEARCH_MODE_NAMES

static final java.lang.String[] SEARCH_MODE_NAMES
The names of the search modes.

Since:
JChem 3.0

DEFAULT_SIMILARITY_THRESHOLD

static final float DEFAULT_SIMILARITY_THRESHOLD
Deprecated. use DEFAULT_DISSIMILARITY_THRESHOLD instead
Default threshold value for similarity search. (Value=0.7)

See Also:
Constant Field Values

DEFAULT_DISSIMILARITY_THRESHOLD

static final float DEFAULT_DISSIMILARITY_THRESHOLD
Default threshold value for similarity search. (Value=0.3)

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.)

See Also:
HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, Constant Field Values

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

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

SEARCH_OPTIONS_LENGTH

static final int SEARCH_OPTIONS_LENGTH
Number of search options stored in Search.options[] Has package visibility!

See Also:
Constant Field Values

OPTION_KEEP_QUERY_ORDER

static final int OPTION_KEEP_QUERY_ORDER
Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
Option constant for search methods to suppress query atom rearrangement. Default is REARRANGE_QUERY.

See Also:
Search.setOption(int, int), REARRANGE_QUERY, KEEP_QUERY_ORDER, Constant Field Values

REARRANGE_QUERY

static final int REARRANGE_QUERY
Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
Option value constant for OPTION_KEEP_QUERY_ORDER for query atom rearrangement. Instructs search to rearrange query atoms for better search performance. (Default.)

See Also:
Search.setOption(int, int), OPTION_KEEP_QUERY_ORDER, KEEP_QUERY_ORDER, Constant Field Values

KEEP_QUERY_ORDER

static final int KEEP_QUERY_ORDER
Deprecated. since 5.0
Use SearchOptions.setKeepQueryOrder(boolean) instead.
Option value constant for OPTION_KEEP_QUERY_ORDER for suppressing query atom rearrangement. Instructs search not to rearrange query atoms.

See Also:
Search.setOption(int, int), OPTION_KEEP_QUERY_ORDER, KEEP_QUERY_ORDER, Constant Field Values

OPTION_EXACT_FRAGMENT

static final int OPTION_EXACT_FRAGMENT
Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
Option constant for search classes to express that the query should only match to full fragments of the target. (No heavy atoms outside the match and each query fragment corresponds to a target fragment.)

Since:
JChem 3.1.2
See Also:
Search.setOption(int, int), FULL_FRAGMENT, FULL, Constant Field Values

EXACT_FRAGMENT_OFF

static final int EXACT_FRAGMENT_OFF
Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
Option value constant for suppressing full(formerly exact) fragment search.

Since:
JChem 3.1.2
See Also:
OPTION_EXACT_FRAGMENT, Constant Field Values

EXACT_FRAGMENT_ON

static final int EXACT_FRAGMENT_ON
Deprecated. since 5.0
Use SearchOptions.setFullFragment(boolean) instead.
Option value constant for full(formerly exact) fragment search.

Since:
JChem 3.1.2
See Also:
OPTION_EXACT_FRAGMENT, Constant Field Values

OPTION_MARKUSH_HIT

static final int OPTION_MARKUSH_HIT
Deprecated. since 5.0
Use MolSearchOptions.setHitIndexType(int)
Option constant for search classes to set the hit index model of Markush targets. By default, findFirst(), findNext() and findAll() methods return indexes for the original Markush diagram (MARKUSH_HIT_ORIGINAL). It can also be set to return indices for the inner, compiled representation (MARKUSH_HIT_INNER).

Since:
JChem 3.2
See Also:
Search.setOption(int, int), MARKUSH_HIT_ORIGINAL, MARKUSH_HIT_INNER, 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

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

OPTION_TAUTOMER_SEARCH

static final int OPTION_TAUTOMER_SEARCH
Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
Option constant for tautomer search. It should be set to the constants below. By default, it is switched off.

Since:
JChem 3.2
See Also:
TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, Search.setOption(int, int), Constant Field Values

TAUTOMER_SEARCH_OFF

static final int TAUTOMER_SEARCH_OFF
Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
Option value constant for switching tautomer searching off. This is the default tautomer search option.

Since:
JChem 3.2
See Also:
OPTION_TAUTOMER_SEARCH, Constant Field Values

TAUTOMER_SEARCH_ON

static final int TAUTOMER_SEARCH_ON
Deprecated. since 5.0
Use SearchOptions.setTautomerSearch(boolean) instead.
Option value constant for switching tautomer searching on.

Since:
JChem 3.2
See Also:
OPTION_TAUTOMER_SEARCH, Constant Field Values

OPTION_ISOTOPE_MATCHING

static final int OPTION_ISOTOPE_MATCHING
Deprecated. since 5.0
Use SearchOptions.setIsotopeMatching(int) instead.
Option constant for isotope search. It should be set to the constants below. By default, it is ISOTOPE_MATCHING_DEFAULT.

Since:
JChem 3.2
See Also:
ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, Search.setOption(int, int), 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:
OPTION_ISOTOPE_MATCHING, 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:
OPTION_ISOTOPE_MATCHING, 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:
OPTION_ISOTOPE_MATCHING, Constant Field Values

OPTION_CHARGE_MATCHING

static final int OPTION_CHARGE_MATCHING
Deprecated. since 5.0
Use SearchOptions.setChargeMatching(int) instead.
Option constant for charge search. It should be set to the constants below. By default, it is CHARGE_MATCHING_DEFAULT.

Since:
JChem 3.2
See Also:
CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, Search.setOption(int, int), 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:
OPTION_CHARGE_MATCHING, 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:
OPTION_CHARGE_MATCHING, 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).

Since:
JChem 3.2
See Also:
OPTION_CHARGE_MATCHING, Constant Field Values

OPTION_VALENCE_MATCHING

static final int OPTION_VALENCE_MATCHING
Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
Option constant for valence search. It should be set to the constants below. By default, it is VALENCE_MATCHING_ON.

Since:
JChem 3.2
See Also:
VALENCE_MATCHING_ON, VALENCE_MATCHING_IGNORE, Search.setOption(int, int), Constant Field Values

VALENCE_MATCHING_ON

static final int VALENCE_MATCHING_ON
Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
Option value constant for default valence searching (Valence is checked).

Since:
JChem 3.2
See Also:
OPTION_VALENCE_MATCHING, Constant Field Values

VALENCE_MATCHING_IGNORE

static final int VALENCE_MATCHING_IGNORE
Deprecated. since 5.0
Use SearchOptions.setValenceMatching(boolean) instead.
Option value constant for ignore valence searching (valence information is ignored during searching).

Since:
JChem 3.2
See Also:
OPTION_VALENCE_MATCHING, Constant Field Values

OPTION_RADICAL_MATCHING

static final int OPTION_RADICAL_MATCHING
Deprecated. since 5.0
Use SearchOptions.setRadicalMatching(int) instead.
Option constant for radical search. It should be set to the constants below. By default, it is RADICAL_MATCHING_DEFAULT.

Since:
JChem 3.2
See Also:
RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, Search.setOption(int, int), 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:
OPTION_RADICAL_MATCHING, 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:
OPTION_RADICAL_MATCHING, 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:
OPTION_RADICAL_MATCHING, Constant Field Values

OPTION_MARKUSH_ENABLED

static final int OPTION_MARKUSH_ENABLED
Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
Option constant for enabling/disabling markush search. It should be set to the constants below. By default, it is MARKUSH_DISABLED.

Since:
JChem 3.2
See Also:
MARKUSH_ENABLED, MARKUSH_DISABLED, Search.setOption(int, int), Constant Field Values

MARKUSH_ENABLED

static final int MARKUSH_ENABLED
Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
Option value constant to enable Markush searching (targets with Markush features are treated as Markush libraries).

Since:
JChem 3.2
See Also:
OPTION_MARKUSH_ENABLED, Constant Field Values

MARKUSH_DISABLED

static final int MARKUSH_DISABLED
Deprecated. since 5.0
Use MolSearchOptions.setMarkushEnabled(boolean) instead.
Option value constant to disable Markush targets (targets with Markush features are treated as strange molecules :-) or queries, but NOT as Markush libraries). This is the default setting.

Since:
JChem 3.2
See Also:
OPTION_MARKUSH_ENABLED, Constant Field Values

OPTION_VAGUE_BOND

static final int OPTION_VAGUE_BOND
Deprecated. since 5.0
Option constant for more loose handling of bond types. It should be set to the constants below. By default, it is VAGUE_BOND_LEVEL1.

Since:
JChem 3.2
Use SearchOptions.setVagueBondLevel(int) instead.
See Also:
VAGUE_BOND_OFF, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_DEFAULT, Search.setOption(int, int), 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:
OPTION_VAGUE_BOND, 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, the previous default was renamed to 5).

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. It was default behavior before 5.3

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 the default vague bond level (level 1).

Since:
JChem 3.2
See Also:
OPTION_VAGUE_BOND, 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:
OPTION_VAGUE_BOND, 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:
OPTION_VAGUE_BOND, 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:
OPTION_VAGUE_BOND, Constant Field Values

OPTION_MARKUSH_AROM

static final int OPTION_MARKUSH_AROM
Deprecated. since 5.0
Use MolSearchOptions.setMarkushArom(int) instead.
Option constant for handling Markush aromatization information (ambiguous aromatic rings) during Markush search. By default, it is MARKUSH_AROM_FINAL_CHECK.

Since:
JChem 3.2
See Also:
MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, Search.setOption(int, int), Constant Field Values

MARKUSH_AROM_FINAL_CHECK

static final int MARKUSH_AROM_FINAL_CHECK
Option value constant to consider Markush aromatization information (ambiguous aromatic rings) during Markush search and check the hit afterwards (default).

Since:
JChem 3.2
See Also:
OPTION_MARKUSH_AROM, Constant Field Values

MARKUSH_AROM_NO_FINAL_CHECK

static final int MARKUSH_AROM_NO_FINAL_CHECK
Option value constant to consider Markush aromatization information during Markush search but do not check the hit afterwards.

Since:
JChem 3.2
See Also:
OPTION_MARKUSH_AROM, Constant Field Values

MARKUSH_AROM_OFF

static final int MARKUSH_AROM_OFF
Option value constant to not consider Markush aromatization information.

Since:
JChem 3.2
See Also:
OPTION_MARKUSH_AROM, Constant Field Values

OPTION_MIX_SGROUP_MATCHING

static final int OPTION_MIX_SGROUP_MATCHING
Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
Option constant for handling COM, MIX and FOR sgroups during matching. By default, it is on.

Since:
JChem 3.2
See Also:
MIX_SGROUP_MATCHING_ON, MIX_SGROUP_MATCHING_OFF, Search.setOption(int, int), Constant Field Values

MIX_SGROUP_MATCHING_ON

static final int MIX_SGROUP_MATCHING_ON
Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
Option value constant to consider COM, MIX and FOR sgroups during matching. (default).

Since:
JChem 3.2
See Also:
OPTION_MIX_SGROUP_MATCHING, Constant Field Values

MIX_SGROUP_MATCHING_OFF

static final int MIX_SGROUP_MATCHING_OFF
Deprecated. since 5.0
Use SearchOptions.setMixSgroupMatching(boolean) instead.
Option value constant to ignore COM, MIX and FOR sgroups during matching.

Since:
JChem 3.2
See Also:
OPTION_MIX_SGROUP_MATCHING, Constant Field Values

OPTION_STEREO_MODEL

static final int OPTION_STEREO_MODEL
Deprecated. since 5.0
Use SearchOptions.setStereoModel(int) instead.
Option constant for the used stereo model. Default is STEREO_MODEL_LOCAL, but it may change in the future.

Since:
JChem 3.2.3
See Also:
STEREO_MODEL_LOCAL, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_GLOBAL, Search.setOption(int, int), Constant Field Values

STEREO_MODEL_DEFAULT

static final int STEREO_MODEL_DEFAULT
For substructure search or query tables this is STEREO_MODEL_LOCAL. Otherwise it is STEREO_MODEL_GLOBAL.

Since:
JChem 3.2.3
See Also:
OPTION_STEREO_MODEL, 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[C@](C)(C)C does not match CC(C)(C)C.)

Since:
JChem 3.2.3
See Also:
OPTION_STEREO_MODEL, 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[C@](C)(C)C matches both CC(C)(C)C , C[C@@](C)(C)C and CCC[C@@](C)(CC)C(C)C.

Since:
JChem 3.2.3
See Also:
OPTION_STEREO_MODEL, Constant Field Values

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[C@](C)(C)C matches CC(C)(C)C.)

Since:
JChem 3.2.3
See Also:
OPTION_STEREO_MODEL, Constant Field Values

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, 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.

Since:
JChem 5.0
See Also:
IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, 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.

Since:
JChem 5.0
See Also:
IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_ENABLED, 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_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.

Since:
JChem 5.3
See Also:
Constant Field Values

R_NODE_PLACEHOLDER

static final int R_NODE_PLACEHOLDER
Deprecated. as of JChem 5.3, use HIT_R instead.
Hit constant denoting R-node matches in case of R-group search.

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