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