@PublicAPI public interface SearchConstants
Modifier and Type | Field and Description |
---|---|
static int |
ABS_STEREO_ALWAYS_ON
Option for absolute stereo matching.
|
static int |
ABS_STEREO_CHIRAL_FLAG
Option for absolute stereo matching.
|
static int |
ABS_STEREO_TABLE_OPTION
Option for absolute stereo matching.
|
static int |
ATTACHED_DATA_MATCH_EXACT
Option value constant for exact match of attached data.
|
static int |
ATTACHED_DATA_MATCH_GENERAL
Option value constant for general match of attached data.
|
static int |
ATTACHED_DATA_MATCH_IGNORE
Option value constant for ignoring attached data.
|
static int |
ATTACHMENT_ATOM
Constant for attachment point representation in ligands:
sets attachment points by attaching an any-atom.
|
static int |
ATTACHMENT_LABEL
Constant for attachment point representation in ligands:
sets attachment points by
MolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" for R1 , "2" for R2 , ... |
static int |
ATTACHMENT_MAP
Constant for attachment point representation in ligands:
sets attachment points by
MolAtom.setAtomMap(int) . |
static int |
ATTACHMENT_NONE
Constant for attachment point representation in ligands:
none (no attachment point data).
|
static int |
ATTACHMENT_POINT
Constant for attachment point representation in ligands:
R-group attachment.
|
static int |
ATTACHMENT_RLABEL
Constant for attachment point representation in ligands:
sets attachment points by
MolAtom.setExtraLabel(java.lang.String) . |
static int |
CHARGE_MATCHING_DEFAULT
Option value constant for default charge searching (charged query
matches only charged target, noncharged query matches all).
|
static int |
CHARGE_MATCHING_EXACT
Option value constant for exact charge searching (charged query
matches only charged target, noncharged query only matches noncharged).
|
static int |
CHARGE_MATCHING_IGNORE
Option value constant for ignore charge searching (charge information
is ignored during searching).
|
static float |
DEFAULT_DISSIMILARITY_THRESHOLD
Default threshold value for similarity search.
|
static int |
DEFAULT_SEARCHTYPE
Default search type equals SUBSTRUCTURE.
|
static java.lang.String |
DISSIMILARITY_PROPERTY_NAME
Name of the mrv/sdf property which stores the dissimilarity values.
|
static int |
DUPLICATE
Duplicate search (formerly called perfect).
|
static int |
FULL
Full structure search.
|
static int |
FULL_FRAGMENT
Full fragment search (formerly called exact fragment).
|
static int |
HCOUNT_MATCHING_AUTO
Default option for H count matching (setHCountMatching).
|
static int |
HCOUNT_MATCHING_EQUAL
Option for H count matching.
|
static int |
HCOUNT_MATCHING_GREATER_OR_EQUAL
Option for H count matching.
|
static int |
HIT_EXCLUDEDQ
Hit constant denoting excluded query atom.
|
static int |
HIT_LP
Hit constant denoting isolated lone-pair match.
|
static int |
HIT_MULTICENTER
Hit constant denoting multicenter atoms in query.
|
static int |
HIT_NON_R
Dummy hit constant used temporarily in BackTrack for denoting a non-R-node match.
|
static int |
HIT_ORDERING_NONE
Option value constant.
|
static int |
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
Option value constant.
|
static int |
HIT_R
Hit constant denoting R-node matches in case of R-group search.
|
static int |
HIT_R_EMPTY_MATCH
Hit constant denoting R-node empty match.
|
static int |
HIT_UNMAPABLE
Hit constant denoting unmapable atoms in query (e.g.
|
static int |
IMPLICIT_H_MATCHING_DEFAULT
Option value constant for default mode.
|
static int |
IMPLICIT_H_MATCHING_DISABLED
Option value constant for indicate matching of an explicit
hydrogen only to another explicit hydrogen.
|
static int |
IMPLICIT_H_MATCHING_ENABLED
Option value constant for indicate matching between implicit and
explicit hydrogens.
|
static int |
IMPLICIT_H_MATCHING_IGNORE
Option value constant to indicate that hydrogens, either explicit
or implicit, are ignored during searching.
|
static int |
ISOTOPE_MATCHING_DEFAULT
Option value constant for default isotope searching (isotope query
matches only isotope target, nonisotope query matches all).
|
static int |
ISOTOPE_MATCHING_EXACT
Option value constant for exact isotope searching (isotope query
matches only isotope target, nonisotope query only matches nonisotope).
|
static int |
ISOTOPE_MATCHING_IGNORE
Option value constant for ignore isotope searching (isotope information
is ignored during searching).
|
static int |
MARKUSH_HIT_INNER
Option value constant for returning hit indices of the inner, compiled
representation of a Markush target.
|
static int |
MARKUSH_HIT_ORIGINAL
Option value constant for returning hit indices of the original Markush
target.
|
static int |
MATCH_COUNT_BETWEEN |
static int |
MATCH_COUNT_RELATION |
static int |
NO_ABAS
Substructure search that applies only
screening.
|
static int |
NO_SCREEN
Substructure search that applies only
atom-by-atom search.
|
static int |
POSITION_ON_0TH_HEAVY_ATOM
Hit constant denoting hit position of a non-heavy atom (e.g.
|
static int |
RADICAL_MATCHING_DEFAULT
Option value constant for default radical searching (radical query
matches only radical target, nonradical query matches all).
|
static int |
RADICAL_MATCHING_EXACT
Option value constant for exact radical searching (radical query matches
only radical target, nonradical query only matches nonradical).
|
static int |
RADICAL_MATCHING_IGNORE
Option value constant for ignore radical searching (radical information
is ignored during searching).
|
static java.lang.String[] |
SEARCH_MODE_NAMES
Deprecated.
As of JChem 5.12, replaced by
SEARCH_TYPE_NAMES . |
static java.lang.String[] |
SEARCH_TYPE_NAMES
The names of the search types.
|
static int |
SIMILARITY
Similarity search.
|
static int |
STEREO_DIASTEREOMER
The diastereomers targets
of a given query structure are also matched.
|
static int |
STEREO_ENANTIOMER
The enantiomer targets
of a given query structure are also matched.
|
static int |
STEREO_EXACT
Equality is needed in stereochemistry.
|
static int |
STEREO_IGNORE
Stereo information is not considered during searching.
|
static int |
STEREO_MODEL_COMPREHENSIVE
Option value constant to use comprehensive stereo model, which combines
the advantages of local and global stereo models.
|
static int |
STEREO_MODEL_DEFAULT
For markush search in all cases and for non-markush duplicate search in query tables
STEREO_MODEL_LOCAL ,
for non-markush duplicate search (with the exception of query tables) STEREO_MODEL_GLOBAL . |
static int |
STEREO_MODEL_GLOBAL
Option value constant to use global stereo information (global
parity, global double bond stereo configuration, etc).
|
static int |
STEREO_MODEL_LOCAL
Option value constant to use local stereo information only (local parity,
local double bond stereo configuration, etc).
|
static int |
STEREO_SPECIFIC
Stereo information is considered during searching.
|
static int |
SUBSTRUCTURE
Substructure search that applies both
screening and atom-by-atom search.
|
static int |
SUPERSTRUCTURE
Superstructure search (Value=6)
|
static int |
TAUTOMER_SEARCH_DEFAULT
Option value constant for indicating that
tautomer duplicate search option is not explicitly set.
|
static int |
TAUTOMER_SEARCH_OFF
Option value constant for switching tautomer searching off.
|
static int |
TAUTOMER_SEARCH_ON
Option value constant for switching tautomer searching on.
|
static int |
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
Option value constant for switching tautomer searching on without considering stereochemistry
in tautomer regions.
|
static int |
UNDEF_R_MATCHING_ALL
Option value constant.
|
static int |
UNDEF_R_MATCHING_GROUP
Option value constant.
|
static int |
UNDEF_R_MATCHING_GROUP_H
Option value constant.
|
static int |
UNDEF_R_MATCHING_GROUP_H_EMPTY
Option value constant.
|
static int |
UNDEF_R_MATCHING_UNDEF_R
Option value constant.
|
static int |
VAGUE_BOND_DEFAULT
Option value constant for vague bond level HALF.
|
static int |
VAGUE_BOND_LEVEL_HALF
Option value constant to handle some ambiguous aromaticity, 5-membered
Kekule representation queries, like *1C=CC=C1 [C,N,O]1C=CC=C1 C1C=CC=C1
S1C=CC=C1.
|
static int |
VAGUE_BOND_LEVEL1
Until 5.3 it was an option value constant to handle some ambiguous
aromaticity, 5-membered Kekule representation queries.
|
static int |
VAGUE_BOND_LEVEL2
Option value constant to vague handling of aromaticity; In the query all
single ring bonds are replaced by "single or aromatic" and all double
ring bonds are replaced by "double or aromatic" prior to search.
|
static int |
VAGUE_BOND_LEVEL3
Option value constant to vague handling of aromaticity; In the query all
single bonds are replaced by "single or aromatic" and all double bonds
are replaced by "double or aromatic" prior to search.
|
static int |
VAGUE_BOND_LEVEL4
Option value constant to vaguely handle bond types; All
bond types are ignored (all bonds are replaced by "any" bonds prior to
search.
|
static int |
VAGUE_BOND_OFF
Option value constant to disable vague bond matching.
|
static final int DEFAULT_SEARCHTYPE
SUBSTRUCTURE
,
Constant Field Valuesstatic final int NO_SCREEN
static final int NO_ABAS
static final int SUBSTRUCTURE
static final int SIMILARITY
static final int FULL
DUPLICATE
,
SUBSTRUCTURE
,
JChem chemical database concepts,
Constant Field Valuesstatic final int DUPLICATE
static final int SUPERSTRUCTURE
static final int FULL_FRAGMENT
FULL
,
JChem chemical database concepts,
Constant Field Valuesstatic final int STEREO_SPECIFIC
static final int STEREO_IGNORE
static final int STEREO_EXACT
static final int STEREO_DIASTEREOMER
static final int STEREO_ENANTIOMER
static final java.lang.String[] SEARCH_TYPE_NAMES
@Deprecated static final java.lang.String[] SEARCH_MODE_NAMES
SEARCH_TYPE_NAMES
.static final float DEFAULT_DISSIMILARITY_THRESHOLD
static final java.lang.String DISSIMILARITY_PROPERTY_NAME
static final int HCOUNT_MATCHING_AUTO
static final int HCOUNT_MATCHING_EQUAL
static final int HCOUNT_MATCHING_GREATER_OR_EQUAL
static final int ABS_STEREO_TABLE_OPTION
static final int ABS_STEREO_CHIRAL_FLAG
static final int ABS_STEREO_ALWAYS_ON
static final int MARKUSH_HIT_ORIGINAL
MARKUSH_HIT_INNER
,
Constant Field Valuesstatic final int MARKUSH_HIT_INNER
MARKUSH_HIT_ORIGINAL
,
Constant Field Valuesstatic final int TAUTOMER_SEARCH_OFF
TAUTOMER_SEARCH_ON
,
TAUTOMER_SEARCH_DEFAULT
,
Constant Field Valuesstatic final int TAUTOMER_SEARCH_ON
TAUTOMER_SEARCH_OFF
,
TAUTOMER_SEARCH_DEFAULT
,
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
,
Constant Field Valuesstatic final int TAUTOMER_SEARCH_DEFAULT
TAUTOMER_SEARCH_OFF
except in case of duplicate search in a database table created with
"Duplicate search uses tautomers" option.TAUTOMER_SEARCH_OFF
,
TAUTOMER_SEARCH_ON
,
TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
,
Constant Field Valuesstatic final int TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO
TAUTOMER_SEARCH_OFF
,
TAUTOMER_SEARCH_DEFAULT
,
TAUTOMER_SEARCH_ON
,
Constant Field Valuesstatic final int ISOTOPE_MATCHING_DEFAULT
static final int ISOTOPE_MATCHING_EXACT
static final int ISOTOPE_MATCHING_IGNORE
static final int CHARGE_MATCHING_DEFAULT
static final int CHARGE_MATCHING_EXACT
static final int CHARGE_MATCHING_IGNORE
IMPLICIT_H_MATCHING_IGNORE
,
Constant Field Valuesstatic final int RADICAL_MATCHING_DEFAULT
static final int RADICAL_MATCHING_EXACT
static final int RADICAL_MATCHING_IGNORE
static final int VAGUE_BOND_OFF
static final int VAGUE_BOND_LEVEL1
VAGUE_BOND_LEVEL_HALF
,
Constant Field Valuesstatic final int VAGUE_BOND_LEVEL_HALF
VAGUE_BOND_LEVEL1
,
Constant Field Valuesstatic final int VAGUE_BOND_DEFAULT
static final int VAGUE_BOND_LEVEL2
static final int VAGUE_BOND_LEVEL3
static final int VAGUE_BOND_LEVEL4
static final int STEREO_MODEL_DEFAULT
STEREO_MODEL_LOCAL
,
for non-markush duplicate search (with the exception of query tables) STEREO_MODEL_GLOBAL
.
Otherwise it is STEREO_MODEL_COMPREHENSIVE
.STEREO_MODEL_LOCAL
,
Constant Field Valuesstatic final int STEREO_MODEL_LOCAL
static final int STEREO_MODEL_COMPREHENSIVE
static final int STEREO_MODEL_GLOBAL
static final int IMPLICIT_H_MATCHING_DEFAULT
IMPLICIT_H_MATCHING_ENABLED
,
IMPLICIT_H_MATCHING_DISABLED
,
IMPLICIT_H_MATCHING_IGNORE
,
Constant Field Valuesstatic final int IMPLICIT_H_MATCHING_ENABLED
IMPLICIT_H_MATCHING_DEFAULT
,
IMPLICIT_H_MATCHING_DISABLED
,
IMPLICIT_H_MATCHING_IGNORE
,
Constant Field Valuesstatic final int IMPLICIT_H_MATCHING_DISABLED
IMPLICIT_H_MATCHING_DEFAULT
,
IMPLICIT_H_MATCHING_ENABLED
,
IMPLICIT_H_MATCHING_IGNORE
,
Constant Field Valuesstatic final int IMPLICIT_H_MATCHING_IGNORE
HIT_EXCLUDEDQ
in this case.CHARGE_MATCHING_IGNORE
,
IMPLICIT_H_MATCHING_DEFAULT
,
IMPLICIT_H_MATCHING_ENABLED
,
IMPLICIT_H_MATCHING_DISABLED
,
Constant Field Valuesstatic final int UNDEF_R_MATCHING_ALL
UNDEF_R_MATCHING_UNDEF_R
,
UNDEF_R_MATCHING_GROUP
,
UNDEF_R_MATCHING_GROUP_H
,
UNDEF_R_MATCHING_GROUP_H_EMPTY
,
Constant Field Valuesstatic final int UNDEF_R_MATCHING_UNDEF_R
UNDEF_R_MATCHING_ALL
,
UNDEF_R_MATCHING_GROUP
,
UNDEF_R_MATCHING_GROUP_H
,
UNDEF_R_MATCHING_GROUP_H_EMPTY
,
Constant Field Valuesstatic final int UNDEF_R_MATCHING_GROUP
UNDEF_R_MATCHING_ALL
,
UNDEF_R_MATCHING_UNDEF_R
,
UNDEF_R_MATCHING_GROUP_H
,
UNDEF_R_MATCHING_GROUP_H_EMPTY
,
Constant Field Valuesstatic final int UNDEF_R_MATCHING_GROUP_H
UNDEF_R_MATCHING_ALL
,
UNDEF_R_MATCHING_UNDEF_R
,
UNDEF_R_MATCHING_GROUP
,
UNDEF_R_MATCHING_GROUP_H_EMPTY
,
Constant Field Valuesstatic final int UNDEF_R_MATCHING_GROUP_H_EMPTY
UNDEF_R_MATCHING_ALL
,
UNDEF_R_MATCHING_UNDEF_R
,
UNDEF_R_MATCHING_GROUP
,
UNDEF_R_MATCHING_GROUP_H
,
Constant Field Valuesstatic final int HIT_ORDERING_NONE
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
,
Constant Field Valuesstatic final int HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
HIT_ORDERING_UNDEF_R_MATCHING_GROUP_FIRST
,
Constant Field Valuesstatic final int POSITION_ON_0TH_HEAVY_ATOM
static final int HIT_R
static final int HIT_MULTICENTER
static final int HIT_UNMAPABLE
static final int HIT_LP
static final int HIT_R_EMPTY_MATCH
static final int HIT_NON_R
static final int HIT_EXCLUDEDQ
static final int ATTACHMENT_NONE
static final int ATTACHMENT_POINT
static final int ATTACHMENT_MAP
MolAtom.setAtomMap(int)
.
Maps with R-group ID: 1
for R1
, 2
for R2
, ...static final int ATTACHMENT_LABEL
MolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" for R1
, "2" for R2
, ...static final int ATTACHMENT_RLABEL
MolAtom.setExtraLabel(java.lang.String)
.
Labels with full R-atom name: "R1" for R1
, "R2" for R2
, ...static final int ATTACHMENT_ATOM
static final int MATCH_COUNT_BETWEEN
static final int MATCH_COUNT_RELATION
static final int ATTACHED_DATA_MATCH_IGNORE
ATTACHED_DATA_MATCH_GENERAL
,
ATTACHED_DATA_MATCH_EXACT
,
Constant Field Valuesstatic final int ATTACHED_DATA_MATCH_GENERAL
ATTACHED_DATA_MATCH_IGNORE
,
ATTACHED_DATA_MATCH_EXACT
,
Constant Field Valuesstatic final int ATTACHED_DATA_MATCH_EXACT
ATTACHED_DATA_MATCH_IGNORE
,
ATTACHED_DATA_MATCH_GENERAL
,
Constant Field Values