RESTful API

Table 1. RESTful API Parameters of "structure" Module

Request

Name	/rest/structure/searchdb
Description	Download chemical structures from databases
Method	POST
Header	Content-Type: text/plain
Body	x-www-form-urlencoded

Parameters

Key	Value[a]	Description
database	chemspider,pubchem, hmdb	The database from which structures are downloaded
mass	e.g. 100.5400	Exact mass (MIMW) of the compound
adduct	M+3H, M+2H+Na, M+H+2Na, M+3Na, M+2H, M+H+NH4, M+H+Na, M+H+K, M+ACN+2HM+2Na, M+2ACN+2HM+3ACN+2HM+H, M+NH4 M+Na M+CH3OH+H, M+K M+ACN+H M+2Na-H, M+IsoProp+HM+ACN+Na, M+2K+H M+DMSO+H, M+2ACN+H, M+IsoProp+Na+H2M+H, 2M+NH4 2M+Na, 2M+3H2O+2H2M+K, 2M+ACN+H 2M+ACN+Na, M-3H,M-2H, M-H2O-HM-H, M+Na-2H, M+Cl M+K-2H, M+FA-H, M+Hac-H M+Br, M+TFA-H 2M-H, 2M+FA-H, 2M+Hac-H, 3M-H	Mass adduct type
error	e.g. 0.5	Instrumental error of the mass spectrometer
errorUnit	Da, ppm, ppb	Unit of the instrumental error
fileFormat	sdf, zip	The format of the response data file
location	e.g. C:\Users\lochana\Documents|Directory in which response data files are saved

[a] Possible values or examples are shown as a comma separated list

Table 2. RESTful API Parameters of "prefilter" Module

Request

Name	/rest/prefilter/applyPreFilters
Description	Remove irrelevant chemical structures from downloaded data
Method	POST
Header	Content-Type: text/plain
Body	x-www-form-urlencoded

Parameters

Key	Value[a]	Description
inputFilePath	e.g. C:\Users\lochana\Documents\sample.sdf	File path to downloaded chemical structures file
removeHeavyIsotopes	True, False	Whether to remove heavy isotopes or not
removeStereoisomers	True, False	Whether to remove stereoisomers or not
keepCompounds	e.g. C, H, O	Keep compounds with any of user specified elements
compoundMustContain	e.g. N, O	Keep compounds if they contain all of user specified elements
eliminateOverallCharges	True, False	Whether to remove compounds with an overall charge

[a] Possible values or examples are shown as a comma separated list

Table 3. RESTful API Parameters of "filter " Module

Request

Name	/rest/filter/applyFilter
Description	Filter compounds according to qspr models
Method	POST
Header	Content-Type: text/plain
Body	x-www-form-urlencoded

Parameters

Key	Value[a]	Description
inputFilePath	e.g. C:\Users\lochana\Documents\sample.sdf	File path to structure data file
propertyFilePath	e.g. C:\Users\lochana\Documents\property.txt	File path to property file
propertyName	e.g. RI	Name of the property
experimentalValue	e.g. 258.46	Experimental value of the property
error	e.g. 0.90	Error in the measurement

[a] Possible values or examples are shown as a comma separated list

Table 4. RESTful API Parameters of "ms-match" Module

Request

Name	/rest/msmatch/runCFMID
Description	Spectral matching with CFM-ID
Method	POST
Header	Content-Type: text/plain
Body	x-www-form-urlencoded

Parameters

Key	Value[a]	Description
inputFilePath	e.g. C:\Users\lochana\Documents\sample.sdf	File path to structure data file
spectrumFilePath	e.g. C:\Users\lochana\Documents\spectrum.txt	File path to spectrum file
ppmMassTolerance	e.g. 10	Mass tolerance in ppm
absMassTolerance	e.g. 0.01	Absolute mass tolerance in Daltons
probabilityThreshold	e.g. 0.001	Probability below unlikely fragmentations are pruned
scoreType	Jaccard, DotProduct	Scoring function for comparing spectra
algorithm	cfmid	Mass spectra simulator
outputFilePath	e.g. C:\Users\lochana\chemid\sample.sdf	File path to output file

[a] Possible values or examples are shown as a comma separated list

Table 5. RESTful API Parameters of "id " Module

Request

Name	/rest/id/rank
Description	Rank candidate compounds according to a composite score
Method	POST
Header	Content-Type: text/plain
Body	x-www-form-urlencoded

Parameters

Key	Value[a]	Description
inputFilePath	e.g. C:\Users\lochana\Documents\sample.sdf	File path to structure data file
experimentalRI	e.g. 240	Experimental retention index (RI) value
experimentalECOM50	e.g. 5.6	Experimental ECOM50 value
experimentalCCS	e.g. 258.46	Experimental collision cross section (CCS) value
cfmIDScore	e.g. 0.90	CFM-ID spectral matching score
weightRI	e.g. 1.00	User specified RI weight (between 0 to 1)
weightECOM50	e.g. 0.25	User specified ECOM50 weight (between 0 to 1)
weightCCS	e.g. 0.50	User specified CCS weight (between 0 to 1)
weightCFMID	e.g. 1.00	User specified CFMID weight (between 0 to 1)
keepRI	True, False	Whether to include RI in the composite score
keepECOM50	True, False	Whether to include ECOM50 in the composite score
keepCCS	True, False	Whether to include CCS in the composite score
keepCFMID	True, False	Whether to include CFMID in the composite score

[a] Possible values or examples are shown as a comma separated list