Search options
A few selected search options are described below.Tautomer search
This search option can instruct the search engine to look for all tautomer forms the query, as generated by the Marvin plugin Tautomers. (For alternative solutions to handle tautomers, see JChem Database Concepts.)
In case of duplicate search type, the tautomer
duplicate filtering approach is used.
Remark: duplicate search in a table created with "Duplicate search uses tautomers"
option results in a tautomer duplicate search
except when "Tautomer search" option is explicitly switched off.
The following restrictions apply in tautomer search mode:
- The query must not have any query features, and
- The query must have all implicit hydrogens set for proper perception of the possible tautomers.
- Double bond stereo settings may be invalid in some tautomeric forms when they refer to a tautomeric region. This kind of stereo information is ignored during tautomer search, but stereo information independent of tautomerizable groups are checked by default.
- All tetrahedral stereo centers are protected during tautomer search.
- This search option is best suited to full or full fragment search, as the tautomers of the query are generated for a whole molecule and not for a substructure.
Table 1. Tautomer search examples
| Query | Target | |||
| Tautomer searching off | Tautomer searching on | |||
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Tautomer duplicate filtering
When this search option is set the search is performed using the generic tautomer form of the query and target. The option is effective only in case of duplicate search. Furthermore, for jchem table or index search operations, "tdf:y" option has to be set for the jchem index or the underlying JChem table. The underlying method is described in detail in the JChem Database Concepts section.Restrictions: like in the case of tautomer search.
Explicit Hydrogens
From JChem version 5.1.3 explicit plain or isotope hydrogens in tautomerizable groups are treated as relocatable. The explicit Hydrogen constraint is enforced at the same time in the migrated location.Vague bond search
These search options allow to choose between several levels of strictness in matching bond types, especially regarding aromaticity. The higher the level is, the more tolerant the bond matching becomes. Vague bond options are only used when exactBondMatching is off. Otherwise (e.g. for DUPLICATE search type), vague bond level 0(off) is used.
To fully exploit vague bond functionality, it is best to use search objects
that do aromatization inside the search object:
JChemSearch and
StandardizedMolSearch.
Table 2. summarizes the vague bond levels, and the following sections describes them in detail.
Table 2.
| Vague bond level | Description |
| Level 0 (off) | Does not perform vague bond matching. |
| Level 1 (default) | Handling of 5-membered rings with ambiguous
aromaticity,
1-atom-long aromatic ring ligands and bridging bonds between two aromatic rings. |
| Level 2 | All query ring bonds, 1-atom-long
aromatic ring ligands and bridging bonds between two aromatic rings become ″or aromatic″ |
| Level 3 | All query bonds (ring and chain) become ″or aromatic″ |
| Level 4 | Ignore all bond types |
Methods used in vague bond search
5-membered rings with ambiguous aromaticity
Handles some commonly occurring 5-membered query ring patterns formulated in Kekule format that have ambiguous aromaticity. This way it can return hits "visually expected by chemists", although strict bond matching would not return these. A few such ambiguous ring substructures are depicted below, with their corresponding aromatic and nonaromatic superstructures.
Table 3.
| Ambiguous substructure | Aromatic example | Nonaromatic example |
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This method (used by default from JChem 3.2) ensures the expected matching of all queries where these substructures appear. On the other hand, when these rings are not not handled, query would match only the aromatic or the aliphatic targets, depending on the ambiguous query ring. (See examples.)
For efficiency reasons, above 5 such 5-membered ring patterns in the query, these ambiguous ring patterns work the same way as all ring bonds described in level 2 below.
Table 4. shows the difference between handling and not handling ambiguous rings.
Table 4.
| Query | Target | |||||
| Not handled | Handled | |||||
| ambiguous aromatic rings | ||||||
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1-atom-long aromatic ring ligands
Used by default from JChem 5.3. Those single or 'single or double' bonds that are connected to an aromatic ring are allowed to match to an aromatic bond, except if
- there is another ligand on the same ring atom, or
- the bond continues in a longer (more than 1 bond long) chain
Remark: when the bond is connected to an ambiguous 5-membered ring, it can match to an aromatic bond only if the ring is evaluated to aromatic.
Table 5.
| Query | Target | ||||
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Bridging bonds between two aromatic rings
Used by default from JChem 5.3. Single bonds connecting two aromatic rings are allowed to match to an aromatic bond. See also the remark about ambiguous rings at the previous method.
Table 6.
| Query | Target | |||
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Generalizing bond matching
Generalizes bond matching so that a bond can also match aromatic, or can totally ignore query bond types.
Vague bond search levels
Level 0 (vague bond matching off)
This corresponds to the behaviour before JChem 3.2.This method must be used if you would like to make distinction between different resonant structures, and you are passing molecules in Kekule(unaromatized) format into the search object. (MolSearch class only).
Level 1 (default)
Applied methods:
- 5-membered rings with ambiguous aromaticity
- 1-atom-long aromatic ring ligands
- Bridging bonds between two aromatic rings
Higher levels (vague bond levels 2-4)
The higher level vague bond options are convenience options. Their effect can be achieved also by using appropriate query bond types in the query. These options should be used during database searching carefully, because they make fingerprint screening inefficient.
They have the following effect on the query bond types:
- Level 2 Generalizes all ring bond types to also match aromatic.
- Also applies '1-atom-long aromatic ring ligands' and
- 'Bridging bonds between two aromatic rings' methods
- (since all ring bonds can match aromatic, all rings are considered aromatic)
- Level 3 Generalizes all bond types to also match aromatic.
- Level 4 Ignores all bond types.
Table 7. describes what bond type transformations are performed on the query before the search:
Table 7.
| Original bond type in query | Vague bond level | ||
| 2 (Ring bonds + special ligands
and bridging bonds) |
3 (All bonds) | 4 (All bonds) | |
 (S) |
 (S/A) |
(S/A) |
 (A) |
 (D) |
 (D/A) |
(D/A) |
(A) |
 (T) |
(A) |
(A) |
(A) |
 (Ar) |
(Ar) |
(Ar) |
(A) |
 (S/D) |
(A) |
(A) |
(A) |
| (S/A) |
(S/A) |
(S/A) |
(A) |
| (D/A) |
(D/A) |
(D/A) |
(A) |
| (A) |
(A) |
(A) |
(A) |
Abbreviations in Table 7.: S - single; D - double; T - triple; Ar - aromatic; S/D - single or double; S/A - single or aromatic; D/A - double or aromatic; A - any.
Table 8.
| Query | Target | |||||||
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| Vague bond level | Vague bond level | |||||||
| 0(off) | 2 | 3 | 4 | 0(off) | 2 | 3 | 4 | |
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Checking sp-hybridization state
The sp-hybridization option specifies if the sp-hybridization state of the atoms should be considered.Calculation of the sp-hybridization state
The following states are considered:- sp - line configuration (e.g. C in CO2)
- sp2 - planar configuration (e.g. C atoms in benzene)
- sp3 - tetrahedral configuration (e.g. C in methane)
This calculated sp-hybridization state reflects the spatial configuration of the C, N and O atoms rather than the sp-hybridization of the orbitals. It doesn't cover all the mixed orbitals of Si, S and P etc. atoms.
The rules for defining the sp-hybridization state of an atom can be seen on Table 9.
Table 9. Calculation rules
| Hybrdization state | Conditions (OR relation) |
| unknown |
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| sp3 |
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If checking is required, in some cases we obtain less hits than without sp-hybridization checking, because the formerly matching atoms have different sp-hybridization state.
Examples for searching with sp-hybridization checking
Table 10.
| Query | Target | |||
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| Sp-hybridization checking | ||||
| ON | OFF | ON | OFF | |
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Sp-hybridization checking may be used together with vague-bond level 4. In this case all bonds in the query match all kinds of target bonds. Using these two options molecules having atoms with the same sp-hybridization state are retrieved regardless of their bond type.
Table 11. Results with vague-bond level 4, ignoring all bond types.
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| Sp-hybridization checking | ||||||
| ON | OFF | ON | OFF | ON | OFF | |
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Examples for searching with different implicit H matching modes
For these examples the search type is set to duplicate.
Table 12. Results with different implicit H matching modes, duplicate search.
| Query | Target | Implicit H matching | |||
| Enabled | Disabled | Ignore | Ignore and Isotope matching switched off |
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Table 13. Charge matching mode ignore forces implicit H maching mode ignore in case of duplicate search.
| Query | Target |
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| Charge matching | |
| Ignore | |
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Summary of search options
In this section, all search options are summarized and their usage is shown in different search interfaces.
Detailed description of all search options are available from the JChem Search Option Guide.Usage of options
- MolSearch API:
Options are set through a
MolSearchOptions object:
MolSearch ms; // ... MolSearchOptions mso = ms.getSearchOptions(); mso.setImplicitHMatching(IMPLICIT_H_MATCHING_ENABLED) // Setting search options // ... - JChemSearch API:
Options are set through a
JChemSearchOptions object:
JChemSearch searcher = new JChemSearch(); // ... JChemSearchOptions searchOptions = new JChemSearchOptions(); searchOptions.setReturnsNonHits(true) // Setting search options // ... searcher.setSearchOptions(searchOptions);Remark: getSearchOptions() and setSearchOptions(...) methods are available in both MolSearch and JChemSearch objects. - Cartridge jc_compare operator: given as third parameter ('options')
- jcsearch command-line tool: command-line parameters starting with - or --.
| Feature name | Option specification in | |||
| MolSearch | JChemSearch | JChem Cartridge | jcsearch | |
| Absolute stereo (ignore chiral flag) | setQueryAbsoluteStereo(true/false), setTargetAbsoluteStereo(true/false) |
setAbsoluteStereo(ABS_STEREO_TABLE_OPTION / ABS_STEREO_CHIRAL_FLAG / ABS_STEREO_ALWAYS_ON ) |
absoluteStereo:t/c/a | --queryAbsoluteStereo:y/n, --targetAbsoluteStereo:y/n, --DBAbsoluteStereo:T/C/A |
| Attached data matching behaviour | setAttachedDataMatch (ATTACHED_DATA_MATCH_IGNORE / ATTACHED_DATA_MATCH_GENERAL / ATTACHED_DATA_MATCH_EXACT) | attachedDataMatch:i/g/e | --attachedDataMatch:i/g/e | |
| Attached data prefixes to check | setAttachedDataPrefixes (comma separated values of prefixes) | attachedDataPrefixes:comma separated values of prefixes | --attachedDataPrefixes: comma separated values of prefixes | |
| Charge matching mode | setChargeMatching( CHARGE_MATCHING_DEFAULT / CHARGE_MATCHING_EXACT / CHARGE_MATCHING_IGNORE) | exactChargeMatchingOption:d/e/i | --charge:d/e/i | |
| Chemical Terms filter expression | setFilter(chemical-terms-expression) | setChemTermsFilter(chemical-terms-expression) | ctFilter:chemical-terms-expression | -e "expression" / file name or --expression "expression" / file name |
| Copolymer matching | setCopolymerMatching( true/false ) | copolymerMatching::y/n | --copolymerMatching:y/n | |
| Dissimilarity metrics (only in DB search) | setDissimilarityMetrics( "tanimoto" / "tversky" / "dice" / "euclidean" / "normalized_euclidean" / "substructure" / "superstructure" | dissimilarityMetric | - | |
| Distinct first atom matching: enable/disable | setDistinctFirstAtomMatching(false/true) | - | - | --distinctFirstAtomMatching:n/y |
| Double bond stereo: no check / marked / all double bonds | setDoubleBondStereoMatchingMode( DBS_NONE / DBS_MARKED / DBS_ALL) | doubleBondStereo:N/M/A | --doubleBondStereo:N/M/A | |
| Enumeration of all query-target mappings | findAll() or findFirst() and consecutive
findNext() calls |
- | - | --allHits |
| Exact bond matching | setExactBondMatching(true/false) | - | - | |
| Exact special atom matching | setExactSpecialAtomMatching(String) | exactSpecialAtomMatching: comma separated identifiers of special atoms | --exactSpecialAtomMatching: comma separated identifiers of special atoms | |
| Exact stereo matching | setExactStereoMatching(true/false) | exactStereoMatching:y/n | --exactStereoSearch:y/n | |
| Exact query atom matching | setExactQueryAtomMatching(true/false) | exactQueryAtomMatching:y/n | --exactQueryAtomMatching:y/n | |
| Homology narrow translation | setHomologyNarrowTranslation( chemaxon.sss.search.options.HomologyTranslationOption ) | homologyNarrowTranslation:n/a/m | --homologyNarrowTranslation:n/a/m | |
| Homology broad translation | setHomologyBroadTranslation( chemaxon.sss.search.options.HomologyTranslationOption ) | homologyBroadTranslation:n/a/m | --homologyBroadTranslation:n/a/m | |
| Hydrogen count query property interpretation | setHCountMatching( HCOUNT_MATCHING_AUTO / HCOUNT_MATCHING_EQUAL / HCOUNT_MATCHING_GREATER_OR_EQUAL ) | HCountMatching:G/E/A | --HCountMatching:G/E/A | |
| Ignore allene stereo | setIgnoreAlleneStereo( true/false) | - | --ignoreAlleneStereo:y/n | |
| Ignore axial stereo | setIgnoreAxialStereo( true/false) | - | --ignoreAxialStereo:y/n | |
| Ignore Chemical Terms evaluation errors | setIgnoreCTExceptions( true/false ) | ignoreCTExceptions:y/n | --ignoreCTExceptions:y/n | |
| Ignore double bond stereo | setIgnoreDoubleBondStereo( true/false) | - | --ignoreDoubleBondStereo:y/n | |
| Ignore mixture brackets | setMixSgroupMatching( MIX_SGROUP_MATCHING_ON, MIX_SGROUP_MATCHING_OFF ) | ignoreMixtureBrackets:y/n | --mix:d/i | |
| Ignore polymer brackets | setPolymerMatching( true/false ) | polymer:d/i | --polymer:d/i | |
| Ignore syn-anti stereo | setIgnoreSynAntiStereo( true/false) | - | --ignoreSynAntiStereo:y/n | |
| Ignore tetrahedral stereo | setIgnoreTetrahedralStereo( true/false) | - | --ignoreTetrahedralStereo:y/n | |
| Implicit H matching mode | setImplicitHMatching(
IMPLICIT_H_MATCHING_DEFAULT / IMPLICIT_H_MATCHING_ENABLED / IMPLICIT_H_MATCHING_DISABLED / IMPLICIT_H_MATCHING_IGNORE) |
implicitHMatching:d/y/n/i | --implicitHMatching:d/y/n/i | |
| Inverse hit list | - | setReturnsNonHits(true/false) | jc_compare(...) = 0 | -n |
| Isotope matching mode | setIsotopeMatching(
ISOTOPE_MATCHING_DEFAULT / ISOTOPE_MATCHING_EXACT / ISOTOPE_MATCHING_IGNORE) |
isotope:d/e/i | --isotope:d/e/i | |
| Markush search enable/disable | setMarkushEnabled(false/true) | (cannot be set, depends on database table type) | - | --markush:n/y |
| Maximum internal search steps | setTimeoutLimit(int) | - | - | - |
| Maximum number of hits | - | setMaxResultCount(int) | maxHitCount:int | --maxResults:int |
| Maximum search time | - | setMaxTime(long) | maxTime:int | - |
| Multiple queries (in "and" relation) | - | - | - | --and |
| Multiple queries (in "or" relation) | - | - | concatenated queries | --or |
| Optimize query atom order(for performance) | setKeepQueryOrder(false/true) | - | --keepQueryOrder | |
| Optimize queries containing special query features (atom lists, bond lists, ...) | - | setOptimizeQueries(false/true) | - | --optimizeQueries:y/n |
| Order sensitive hits | setOrderSensitiveSearch(true/false) | - | - | --orderSensitive |
| Ordering of results | - | setOrder(
NO_ORDERING / ORDERING_BY_ID / ORDERING_BY_ID_OR_SIMILARITY ) |
- | - |
| Polymer end group matching | setEndgroupMatching( true/false ) | endGroupMatching:y/n | --endGroupMatching:y/n | |
| Polymer phase-shift | setPhaseShiftedMatching( true/false ) | phaseShift:y/n | --phaseShift:y/n | |
| Pre-assignment of query and target atoms | addMatch(int, int)
addMatch(int[], int[], int) |
- | - | - |
| Radical matching mode | setRadicalMatching( RADICAL_MATCHING_DEFAULT / RADICAL_MATCHING_EXACT / RADICAL_MATCHING_IGNORE) | radical:d/e/i | --radical:d/e/i | |
| Reaction search handling of unpaired maps | setReactionUnpairedMapMatching( REACTION_UNPAIRED_MAP_MATCHES_ALL / REACTION_UNPAIRED_MATCHES_UNPAIRED_ONLY) | - | --reactionUnpairedMap: all/unpairedOnly |
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| Result table | - | setResultTable(String) | - | - |
| Search type (substructure, full, full fragment, duplicate, superstructure, etc.) | setSearchType(SUBSTRUCTURE / SUPERSTRUCTURE / FULL / FULL_FRAGMENT / DUPLICATE ) | t:s/f/ff/d/t/r | -t:s/f/ff/d/i/u/c | |
| (dis)Similarity threshold for similarity search | - | setDissimilarityThreshold(float) | simThreshold:float | -t:i:float |
| Sp-hybridization state checking | setCheckSpHyb(true/false) | checkSpHyb:Y/N | --checkSpHyb:y/n | |
| Standardization configuration | setStandardizer(standardizer, boolean, boolean) | (it can be set as a table property) |
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-S / --standardize "file name" / "action string" |
| Stereo on/off | setStereoSearch(true/false) | stereoSearch:Y/N | --stereoSearch:y/n | |
| Stereo search type | setStereoSearchType (STEREO_SPECIFIC / STEREO_IGNORE / STEREO_EXACT / STEREO_DIASTEREOMER / STEREO_ENANTIOMER) | stereoSearchType:s/i/e/d/a | --stereoSearchType:s/i/e/d/a | |
| Stereo model | setStereoModel( STEREO_MODEL_LOCAL / STEREO_MODEL_COMPREHENSIVE / STEREO_MODEL_GLOBAL ) | - | --stereoModel:l/g/c | |
| SQL SELECT statement for pre-filtering | - | setFilterQuery(String) | filterQuery:select-statement | - |
| Tautomer search | setTautomerSearch( TAUTOMER_SEARCH_DEFAULT / TAUTOMER_SEARCH_ON / TAUTOMER_SEARCH_OFF ) | tautomerSearch:d/y/n | --tautomerSearch:d/y/n | |
| Tautomer duplicate filtering | setTautomerDuplicateFiltering( true/false ) | tdf:y/n | --tdf | |
| Transform monomer representations | setMonomerTransform( true/false ) | transformMonomer::y/n | --transformMonomer:y/n | |
| Undefined R-atom matching mode | setUndefinedRAtom( UNDEF_R_MATCHING_GROUP / UNDEF_R_MATCHING_GROUP_H / UNDEF_R_MATCHING_GROUP_H_EMPTY / UNDEF_R_MATCHING_ALL / UNDEF_R_MATCHING_UNDEF_R ) | undefinedRAtom:g/gh/ghe/a/u | --undefinedRAtom:g/gh/ghe/a/u | |
| Hit ordering type | setHitOrdering( HIT_ORDERING_NONE / HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST ) | - | --hitOrdering:n/g | |
| Vague bond search levels | setVagueBondLevel( VAGUE_BOND_OFF / VAGUE_BOND_LEVEL1 / VAGUE_BOND_LEVEL2 / VAGUE_BOND_LEVEL3 / VAGUE_BOND_LEVEL4 ) | vagueBond:n/1/2/3/4 | --vagueBond:n/1/2/3/4 | |
| Valence matching mode | setValenceMatching( VALENCE_MATCHING_ON / VALENCE_MATCHING_IGNORE ) | - | --valence:d/i | |
chemaxon.sss.SearchConstants)
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