CICC Web Service Usage

From Chemical Informatics and Cyberinfrastructure Collaboratory

Contents 1 BCIClusterService (for Digital Chemistry) 1.1 makebitsGenerate 1.2 divkmGenerate 1.3 smile2dkm 1.4 optclusGenerate 1.5 rnnclusGenerate 1.6 smile2ClusterPartitioned 2 InChIGoogle 2.1 Search 3 InChIServer 3.1 generate 3.2 getBasic 3.3 insert2CML 3.4 generateMasterEntry 4 OBServer 4.1 transform 5 CMLRSSServer 5.1 generate 6 ToxTreeServer 6.1 ToxHazardBrief 6.2 ToxHazardVerbose 7 OSCAR3URLServer 7.1 oscar3Lite 7.2 oscar3Full 7.3 oscar3SAF 7.4 oscar3SAF2URL 7.5 oscar3URL2SAF2URL 7.6 oscar3URLParseInto2URL

BCIClusterService (for Digital Chemistry)

makebitsGenerate

Generate fingerprints from a SMILES structure.

Input

in0 (SMIstring): A String of a SMILES structure

In1 (text): the format of ouput string: bci or tdt

Output

Fingerprint string

divkmGenerate

Cluster fingerprints with Divkmeans.

Input

in0 (SCNstring): A string of a fingerprint string

Output

A string of a clustered hierarchy with Divkmeans

smile2dkm

Generate a clustered hierarchy from a SMILES structure.

Input

in0 (SMIstring): A String of a SMILES structure

Output

A string of a clustered hierarchy with Divkmeans

optclusGenerate

Generate the best levels in a hierarchy with Kelley scoring method.

Input

in0 (DKMstring): A string of a clustered hierarchy with Divkmeans

in1 (SCNstring): A string of a fingerprint string

Output

A best partition cluster level.

rnnclusGenerate

Extract individual cluster partitions from a cluster hierarchy. (optclus included)

Input

in0 (DKMstring): A string of a clustered hierarchy with Divkmeans

in1 (SCNstring): A string of a fingerprint string

Output

A string of individual cluster partitions

smile2ClusterPartitioned

Generate a new SMILES structure with an extra cluster column that is an individual cluster partition.

Input

in0 (SMIstring): A String of a SMILES structure

Output

A string of a new SMILES structure with an extra cluster column

InChIGoogle

Search

Input

in0 (inchibasic): Search query

in1 (type): "normal" or "lucky" (or anything but normal)

Output

A search result in the HTML format.

InChIServer

generate

Generate InChI.

Input

in0 (inchiVersion): "1.12Beta", "0.932Beta", or "1" (Only 1 is supported.)

in1 (inputFormat): "mol" (Mol file), "sdf" (SDF file), or "cml" (CML file).

But "cml" file does not work fine under Linux command line InChI software (cInChI-1), and it has been neutralized now.

in2 (inputData): Input Data String (This string converts to a temporary file in the server.)

in3 (Options): Options should have a prefix “-”, and multiple options require spaces as a delimiter.

SNon - Exclude stereo (Default: Include Absolute stereo)

SRel - Relative stereo

SRac - Racemic stereo

SUCF - Use Chiral Flag: On means Absolute stereo, Off - Relative

SUU - Include omitted unknown/undefined stereo

NEWPS - Narrow end of wedge points to stereocenter (default: both)

RecMet - Include reconnected metals results

FixedH - Mobile H Perception Off (Default: On)

AuxNone - Omit auxiliary information (default: Include)

NoADP - Disable Aggressive Deprotonation (for testing only)

Compress - Compressed output

DoNotAddH - Don't add H according to usual valences: all H are explicit

Wnumber - Set time-out per structure in seconds; W0 means unlimited SDF:DataHeader Read from the input SDfile the ID under this DataHeader

CML - Input in CML format (default for input file .CML extension)

NoLabels - Omit structure number, DataHeader and ID from InChI output

Tabbed - Separate structure number, InChI, and AuxIndo with tabs

OutputSDF - Convert InChI created with default aux. info to SDfile

STDIO - Use standard input/output streams

WarnOnEmptyStructure - Warn and produce empty InChI for empty structure

Output

Output String (Input file name, InChI data, and Auxiliary Information)

getBasic

Get an InChI basic.

Input

in0 (inchiVersion): Version of InChI

in1 (InChI): InChI string

Output

InChI basic

insert2CML

Insert an InChI string to a CML molecule.

Input

in0 (inchi): InChI string

in1 (cml): molecule in CML format

Output

CML molecule with InChI

generateMasterEntry

Generate a master entry for a molecule which will be recorded in the InChI index database.

Input

in0 (inchi): InChI string for a molecule

in1 (locBase): Location base of the molecule

in2 (locId): Local ID of the molecule

Output

CML molecule with InChI

OBServer

transform

Transform a chemical format to another format using Open Babel (Current stable version 1.0.0 is used.)

Input

in0 (inputFormat): An input chemical format (e.g. inchi, cml, mol, sdf, and etc.)

in1 (inputData): A data string of a chemical structure in the input format

in2 (outputFormat): An output chemical format

in3 (options): Options for the Open Babel

Output

Converted chemical structure string

CMLRSSServer

generate

Generate CMLRSS feed from CML data.

Input

in0 (mol): Molecule(s) in CML format

in1 (title): Title of the CMLRSS feed

in2 (description): Description of the CMLRSS feed

in3 (link): Link of the CMLRSS feed

in4 (source): Source of the CMLRSS feed

Output

Converted CMLRSS feed of the CML data

ToxTreeServer

ToxHazardBrief

Estimates toxic hazard in brief by applying a decision tree approach.

Input

in0 (smiles): A String of a SMILES format structure

Output

A string of toxic hazard in Low, Intermediate, or High.

ToxHazardVerbose

Estimate toxic hazard with verbose explanation by applying a decision tree approach.

Input

in0 (smiles): A string of a SMILES format structure

Output

A string of toxic hazard with the verbose explanation of a decision tree trace applying Cramer rules

OSCAR3URLServer

oscar3Lite

Invoke OSCAR3 with the Lite option that provides named entities like chemicals.

Input

in0 (text): A string of any text including chemical resources

in1 (text): the format of in0 (xml, txt,html,etc.)

Output

A string of markup data in the XML format

oscar3Full

Invoke OSCAR3 with the Full option that provides markup experimental data as well as named entities like chemicals.

Input

in0 (text): A string of any text including chemical resources

in1 (text): the format of in0 (xml, txt, html,etc.)

Output

A string of markup data in the XML format

oscar3SAF

Invoke OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words

Input

in0 (text): A string of any text including chemical resources

in1 (text): the format of in0 (xml, txt,html,etc.)

Output

A string of markup data in the XML format

oscar3SAF2URL

Invoke OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words. And the result is denoted in an URL format that is accessible through the Internet.

Input

in0 (text): A string of any text including chemical resources

Output

A string of the URL---the location of the result file. The file has a string of markup data in the XML format

oscar3URL2SAF2URL

Invoke OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words. Both the input and the result is denoted in an URL format that is accessible through the Internet.

Input

in0 (text): A string of a URL that indicates a file of any text including chemical resources

Output

A string of the URL---the location of the result file. The file has a string of markup data in the XML format

oscar3URLParseInto2URL

Invoke OSCAR3 with the ParseInto option that enables the multiple resource processing and looks for references to markup chemical words. Both the input and the result is denoted in an URL format that is accessible through the Internet.

Input

in0 (text): A string of URL's that indicate files of any text including chemical resources

Output

A string of the URL's---the location of the result files. Those files have strings of markup data in the XML format