com.chemaxon.overlap.wui.resources

Class MoleculesResource

java.lang.Object

com.chemaxon.overlap.wui.resources.MoleculesResource

@Path(value="molecules")
public final class MoleculesResource
extends Object

Represents molecule sets.

Constructor Summary

Constructors

Constructor and Description
MoleculesResource()

Method Summary

Modifier and Type	Method and Description
MoleculeInfo	findId(MolsRes set, String id, boolean smiles) Find index of an ID.
MoleculeSetsInfo	get() Create JSON list of available molecule sets.
byte[]	getCxBinFormat(MolsRes set, int index, boolean clean2d, String format) Get molecule in an arbitrary binary format.
String	getCxFormat(MolsRes set, int index, boolean clean2d, String format) Get molecule in an arbitrary text based format.
String	getId(MolsRes set, int index) Get ID of a single molecule.
MoleculeIds	getIds(MolsRes set, List<Integer> indices, String missing) Fetch IDs for multiple molecules.
MoleculeInfo	getMolInfo(MolsRes set, int index, boolean smiles, boolean props) Create description of a single molecule.
byte[]	getPng(MolsRes set, int index, int w, int h, String aromatize, String hydrogenize) Get molecule image in PNG format.
byte[]	getPngOrPlaceholder(MolsRes set, int index, int w, int h, String aromatize, String hydrogenize) Get molecule image in PNG format or a placeholder image for absent molecules.
MoleculePropRange	getPropertyOnIndexRange(MolsRes set, String propname, int start, int maxcount, String missing) Fetch property values for a range of Molecule indices.
MoleculePropRange	getPropertyOnIndexRangePOST(MolsRes set, String propname, int start, int maxcount, String missing) Fetch property values for a range of Molecule indices - POST endpoint.
MoleculeProps	getProps(MolsRes set, List<Integer> indices, List<String> props, String missing) Fetch multiple property values
Response	getSdf(MolsRes set, int index) Get molecule in SDF format.
MoleculeSetInfo	getSetInfo(String set) Create description of a molecule set.
MoleculeProp	getSingleProperty(MolsRes set, int index, String propname) Get a single property value.
SizeInfoDto	getSizeinfo(MolsRes set, SizeInfoMethod method, boolean dc) Experimental endpoint to estimate allocated size.
Response	getSmiles(MolsRes set, int index) Get molecule in Smiles format.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MoleculesResource

public MoleculesResource()

Method Detail

get

@GET
 @Produces(value="application/json")
public MoleculeSetsInfo get()

Create JSON list of available molecule sets.

Returns:

List of molecule set descriptions for each set

getSetInfo

@Path(value="{set}")
 @GET
 @Produces(value="application/json")
public MoleculeSetInfo getSetInfo(@PathParam(value="set")
                                                                                                  String set)

Create description of a molecule set.

Parameters:

set - Set name

Returns:

Metadata about the molecule set

findId

@GET
 @Path(value="{set}/find-id")
 @Produces(value="application/json")
public MoleculeInfo findId(@PathParam(value="set")
                                                                                                   MolsRes set,
                                                                                                   @QueryParam(value="id")
                                                                                                   String id,
                                                                                                   @QueryParam(value="smiles") @DefaultValue(value="true")
                                                                                                   boolean smiles)

Find index of an ID. Note that this method currently uses simple linear search; the performance is not optimal. This method return the molecule description if given ID is found. If the ID is not found then the thrown WuiNotFoundException will result in a "Not Found (404)" response status.

Parameters:

set - Set name

id - Id to find. Note that it is not possible to look up absent IDs

smiles - Lookup SMILES. If false passed no SMILES will retrieved in the response. If true is passed but the given structure SMILES is absent then the response will not fail and no SMILES will be returned.

Returns:

Description of the first matching molecule.

Throws:

WuiNotFoundException - when given set or id is not found. In case of absent SMILES the response objects MolsRes.MoleculeInfo#smiles will be null.

getProps

@POST
 @Path(value="{set}/get-multiple-props")
 @Consumes(value="application/x-www-form-urlencoded")
 @Produces(value="application/json")
public MoleculeProps getProps(@PathParam(value="set")
                                                                                                                                                                        MolsRes set,
                                                                                                                                                                        @FormParam(value="indices[]")
                                                                                                                                                                        List<Integer> indices,
                                                                                                                                                                        @FormParam(value="props[]")
                                                                                                                                                                        List<String> props,
                                                                                                                                                                        @FormParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                                        String missing)

Fetch multiple property values

Parameters:

set - Set name

indices - Indices for which the stored properties are requested

props - Properties requested. When no property specified all properties are returned

missing - Value to use for missing property values

Returns:

Index to property mapping for the requested indices

getPropertyOnIndexRange

@GET
 @Path(value="{set}/props/{propname}/get-properties-on-index-range")
 @Produces(value="application/json")
public MoleculePropRange getPropertyOnIndexRange(@PathParam(value="set")
                                                                                                                                                                MolsRes set,
                                                                                                                                                                @PathParam(value="propname")
                                                                                                                                                                String propname,
                                                                                                                                                                @QueryParam(value="start") @DefaultValue(value="0")
                                                                                                                                                                int start,
                                                                                                                                                                @QueryParam(value="maxcount") @DefaultValue(value="2147483647")
                                                                                                                                                                int maxcount,
                                                                                                                                                                @QueryParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                                String missing)

Fetch property values for a range of Molecule indices.

Parameters:

set - Set name

propname - Property name

start - Index of first structure

maxcount - Maximal structure count

missing - Value to use for missing values

Returns:

Index to ID mapping for the requested indices

getPropertyOnIndexRangePOST

@POST
 @Path(value="{set}/props/{propname}/get-properties-on-index-range")
 @Produces(value="application/json")
public MoleculePropRange getPropertyOnIndexRangePOST(@PathParam(value="set")
                                                                                                                                                                     MolsRes set,
                                                                                                                                                                     @PathParam(value="propname")
                                                                                                                                                                     String propname,
                                                                                                                                                                     @FormParam(value="start") @DefaultValue(value="0")
                                                                                                                                                                     int start,
                                                                                                                                                                     @FormParam(value="maxcount") @DefaultValue(value="2147483647")
                                                                                                                                                                     int maxcount,
                                                                                                                                                                     @FormParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                                     String missing)

Fetch property values for a range of Molecule indices - POST endpoint.

Parameters:

set - Set name

propname - Property name

start - Index of first structure

maxcount - Maximal structure count

missing - Value to use for missing values

Returns:

Index to ID mapping for the requested indices

getIds

@POST
 @Path(value="{set}/get-multiple-ids")
 @Consumes(value="application/x-www-form-urlencoded")
 @Produces(value="application/json")
public MoleculeIds getIds(@PathParam(value="set")
                                                                                                                                                                  MolsRes set,
                                                                                                                                                                  @FormParam(value="indices[]")
                                                                                                                                                                  List<Integer> indices,
                                                                                                                                                                  @FormParam(value="missing") @DefaultValue(value="????")
                                                                                                                                                                  String missing)

Fetch IDs for multiple molecules.

Parameters:

set - Set name

indices - Indices for which the stored IDs are requested

missing - Value to use for missing structures

Returns:

Index to ID mapping for the requested indices

getMolInfo

@GET
 @Path(value="{set}/{index}")
 @Produces(value="application/json")
public MoleculeInfo getMolInfo(@PathParam(value="set")
                                                                                                       MolsRes set,
                                                                                                       @PathParam(value="index")
                                                                                                       int index,
                                                                                                       @QueryParam(value="smiles") @DefaultValue(value="true")
                                                                                                       boolean smiles,
                                                                                                       @QueryParam(value="props") @DefaultValue(value="true")
                                                                                                       boolean props)

Create description of a single molecule.

Parameters:

set - Set name

index - Molecule index in the set

smiles - Lookup SMILES. If false passed no SMILES will retrieved in the response

props - Include additional properties

Returns:

Description of the selected molecule

getSingleProperty

@GET
 @Path(value="{set}/{index}/props/{propname}")
 @Produces(value="application/json")
public MoleculeProp getSingleProperty(@PathParam(value="set")
                                                                                                                               MolsRes set,
                                                                                                                               @PathParam(value="index")
                                                                                                                               int index,
                                                                                                                               @PathParam(value="propname")
                                                                                                                               String propname)

Get a single property value.

Parameters:

set - Set name

index - Molecule index in the set

propname - Name of additional property

Returns:

Value of the additional property

getId

@GET
 @Path(value="{set}/{index}/id")
 @Produces(value="text/plain")
public String getId(@PathParam(value="set")
                                                                                         MolsRes set,
                                                                                         @PathParam(value="index")
                                                                                         int index)

Get ID of a single molecule.

Parameters:

set - Set name

index - Molecule index in the set

Returns:

ID of the given molecule or String ???? when ID is absent

getSmiles

@GET
 @Path(value="{set}/{index}/smiles")
 @Produces(value="chemical/x-daylight-smiles")
public Response getSmiles(@PathParam(value="set")
                                                                                                                   MolsRes set,
                                                                                                                   @PathParam(value="index")
                                                                                                                   int index)

Get molecule in Smiles format.

Parameters:

set - Set name

index - Molecule index in the set

Returns:

Molecule in SMILES format with ID appended.

getSdf

@GET
 @Path(value="{set}/{index}/sdf")
 @Produces(value="chemical/x-mdl-sdfile")
public Response getSdf(@PathParam(value="set")
                                                                                                        MolsRes set,
                                                                                                        @PathParam(value="index")
                                                                                                        int index)
                                                                                                 throws IOException

Get molecule in SDF format.

Parameters:

set - Set name

index - Molecule index in the set

Returns:

Molecule in SDF format with ID set to SDF property "id".

Throws:

IOException - Propagated from MolExporter

getPng

@GET
 @Path(value="{set}/{index}/png")
 @Produces(value="image/png")
public byte[] getPng(@PathParam(value="set")
                                                                                          MolsRes set,
                                                                                          @PathParam(value="index")
                                                                                          int index,
                                                                                          @QueryParam(value="w") @DefaultValue(value="100")
                                                                                          int w,
                                                                                          @QueryParam(value="h") @DefaultValue(value="100")
                                                                                          int h,
                                                                                          @QueryParam(value="aromatize") @DefaultValue(value="source")
                                                                                          String aromatize,
                                                                                          @QueryParam(value="hydrogenize") @DefaultValue(value="source")
                                                                                          String hydrogenize)
                                                                                   throws IOException,
                                                                                          WuiNotFoundException

Get molecule image in PNG format. When the given molecule is absent then status 404 is set and a JSON response with details is sent.

Parameters:

set - Set name

index - Molecule index in the set

w - Image width in pixels

h - Image height in pixels

aromatize - Aromatize options, use source, aromatize or dearomatize

hydrogenize - Hydrogenize options. use source, hydrogenize or dehydrogenize

Returns:

Molecule in SDF format with ID set to SDF property "id".

Throws:

IOException - Propagated from MolExporter

WuiNotFoundException - When molecule is absent

getPngOrPlaceholder

@GET
 @Path(value="{set}/{index}/png-or-placeholder")
 @Produces(value="image/png")
public byte[] getPngOrPlaceholder(@PathParam(value="set")
                                                                                                                      MolsRes set,
                                                                                                                      @PathParam(value="index")
                                                                                                                      int index,
                                                                                                                      @QueryParam(value="w") @DefaultValue(value="100")
                                                                                                                      int w,
                                                                                                                      @QueryParam(value="h") @DefaultValue(value="100")
                                                                                                                      int h,
                                                                                                                      @QueryParam(value="aromatize") @DefaultValue(value="source")
                                                                                                                      String aromatize,
                                                                                                                      @QueryParam(value="hydrogenize") @DefaultValue(value="source")
                                                                                                                      String hydrogenize)
                                                                                                               throws IOException,
                                                                                                                      WuiNotFoundException

Get molecule image in PNG format or a placeholder image for absent molecules. When the given molecule is absent then a placeholder image is generated. Note that when the set is not found or the index is out of range still a status 404 with an error report JSON is returned.

Parameters:

set - Set name

index - Molecule index in the set

w - Image width in pixels

h - Image height in pixels

aromatize - Aromatize options, use source, aromatize or dearomatize

hydrogenize - Hydrogenize options. use source, hydrogenize or dehydrogenize

Returns:

Molecule in SDF format with ID set to SDF property "id".

Throws:

IOException - Propagated from MolExporter

WuiNotFoundException

getCxFormat

@GET
 @Path(value="{set}/{index}/cxformat")
 @Produces(value="text/plain")
public String getCxFormat(@PathParam(value="set")
                                                                                                     MolsRes set,
                                                                                                     @PathParam(value="index")
                                                                                                     int index,
                                                                                                     @QueryParam(value="clean2d") @DefaultValue(value="false")
                                                                                                     boolean clean2d,
                                                                                                     @QueryParam(value="f")
                                                                                                     String format)
                                                                                              throws IOException

Get molecule in an arbitrary text based format.

Parameters:

set - Set name

index - Molecule index in the set

clean2d - Clean2D structure

format - Format string parameter to pass to MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String)

Returns:

Export result

Throws:

IOException - Propagated from MolExporter

getCxBinFormat

@GET
 @Path(value="{set}/{index}/cxbinformat")
 @Produces(value="application/octet-stream")
public byte[] getCxBinFormat(@PathParam(value="set")
                                                                                                                         MolsRes set,
                                                                                                                         @PathParam(value="index")
                                                                                                                         int index,
                                                                                                                         @QueryParam(value="clean2d") @DefaultValue(value="false")
                                                                                                                         boolean clean2d,
                                                                                                                         @QueryParam(value="f")
                                                                                                                         String format)
                                                                                                                  throws IOException

Get molecule in an arbitrary binary format.

Parameters:

set - Set name

index - Molecule index in the set

clean2d - Clean2D structure

format - Format string parameter to pass to MolExporter.exportToBinFormat(chemaxon.struc.Molecule, java.lang.String)

Returns:

Export result

Throws:

IOException - Propagated from MolExporter

getSizeinfo

@Beta
 @GET
 @Produces(value="application/json")
 @Path(value="{set}/get-sizeinfo")
public SizeInfoDto getSizeinfo(@PathParam(value="set")
                                                                                                                   MolsRes set,
                                                                                                                   @QueryParam(value="method")
                                                                                                                   SizeInfoMethod method,
                                                                                                                   @QueryParam(value="dc") @DefaultValue(value="false")
                                                                                                                   boolean dc)

Experimental endpoint to estimate allocated size. Please note that this endpoint is under construction, use with caution: execution might fail and execution might have significant memory/cpu impact. The availability/functionality of this endpoint might change in any of the subsequent releases.

Parameters:

set - Set name

method - Size info method to use.

dc - Duplicate check on the large storages.

Returns:

Size info description