This document describes how SLiMAN can be accessed with programs.
The SLiMAN API is composed of 11 functions, that can be embeded in scripts for its use without the web interface.
Function details, parameters and sample codes are listed below.

Function Name	Parameters	Action(s)	Returned Data	Usage Conditions	Sample Code	Test
INITIALIZE	RUN : INITIALIZE	Initiate the connexion between client and SLiMAN API Also initiate the new project	TOKEN=project token TIEMOUT=Date until which you can work on this project NOTE=You can now send a request to SLIMIP	AntiSpam Timeout AntiInitSpam Timeout Previous project deleted	Perl Python2 Python3 Ruby Java
SLIMIP	RUN : SLIMIP TOKEN : project token LIST : list of input proteins (Uniprot Accession | Identifier	Short Linear Motif Interaction Prediction N*N Motif-Domain pairing predictions	INPUT_PROTEINS=list of proteins that are used for the run NOT_VALID_PROTEINS=list of proteins that are not part of the database DOUBLONS=list of proteins that are already included in the INPUT_PROTEINS EXPECTED_REQUEST_TIME=expcected computational time (sec) when SLIMIP data should be accessible using HITS query NOTE=LAUNCHED	AntiSpam Timeout Project Token match Initiated project	Perl Python2 Python3 Ruby Java
HITS	RUN : HITS TOKEN : project token FILES : FileTypes of retrieve (CSV | JSON)	Retrieve predictions generated by SLIMIP	JSON=json_file CSV=csv_file	AntiSpam Timeout Project Token match Ended SLiMIP computation	Perl Python2 Python3 Ruby Java
SLIMID	RUN : SLIMID TOKEN : project token LIST : list of hit IDs	Short Linear Motif Interacting with Domains Align Hits with closely related PDB templates	NO_TEMPLATES_HITS=list of hits without available templates (separated by comas) UNVALIDATED_HITS=list of hits not included in SLIMIP predictions (separated by comas) ALREADY_PERFORMED=list of alignments already performed (separated by comas) ALIGNMENT_QUERIED_FOR_HIT=list of hits that will be aligned (separated by comas) NOTE=LAUNCHED	AntiSpam Timeout Project Token match Valid HitID Number of templates available >0	Perl Python2 Python3 Ruby Java
ALIGNMENTS	RUN : ALIGNMENTS TOKEN : project token ID : hit ID FILES : FileType to retrieve (MOTIF | DOMAIN | JSON)	Retrieve alignments performed by SLIMID	HIT_ID=hit_id of the returned aligment MOTIF_ALIGNMENTS=Motifs MAFFT alignements DOMAIN_ALIGNEMENTS=Domains MAFFT alignements JSON=MAFFT and BLAST DOMAIN and MOTIF alignments	AntiSpam Timeout Project Token match Valid HitID Ended SLiMID alignments computation	Perl Python2 Python3 Ruby Java
SLIMIM	RUN : SLIMIM TOKEN : project token INPUTS : ID:hit ID/LIST:list of template names to use	Short Linear Motif Interaction Modeling Comparative modeling of the pointed interaction	HIT_ID=hit_id of the modeling query WRONG_TEMPLATE_NAMES=templates names that are not in the alignement file (separated by comas) TOTAL_TEMPLATES_USED=number of templates used for the modeling USED_TEMPLATES=list of used templates names (separated by comas) NOTE=LAUNCHED	AntiSpam Timeout Project Token match Valid HitID Ended SLiMID alignments computation Valid set of templates names to be used	Perl Python2 Python3 Ruby Java
MODELS	RUN : MODELS TOKEN : project token INPUTS : ID:hit ID/LIST:list of template names to use/FILES:BLAST | MAFFT	Retrieve models generated by SLIMIM	HIT_ID=hit_id of the returned models UNUSED_TEMPLATES=templates names that were not used for the modeling MODELS=>templatename1\npdb_model1_of_the_complexe	AntiSpam Timeout Project Token match Valid HitID Ended SLiMIM modeling computation Valid set of template names used to generate complexes Valid set of alignments software used of the modeling	Perl Python2 Python3 Ruby Java
TNAMES	RUN : TNAMES INPUTS : PFAM:PFamID/ELM:ELM_class_name	Retrieve templates names for a specific ELM-PFAM combination	TOTAL_TEMPLATES=number of available templates for this ELM-PFAM combination TEMPLATES_NAMES=names of all available templates for this ELM-PFAM combination (separated by comas)	AntiSpam Timeout Valid ELM-PFAM combination	Perl Python2 Python3 Ruby Java
TEMPLATES	RUN : TEMPLATES INPUTS : PFAM:PFamID/ELM:ELM_class_name/LIST:list of templates to retrieve	Retrieve PDB templates for a specific ELM-PFAM combination	WRONG_ACCESS=list of queried templates not found (separated by comas) TOTAL_TEMPLATES=number of templates returned TEMPLATE_NAMES=names of the returned templates (separated by comas) TEMPLATES=>template_name1\ntemplate1.pdb	AntiSpam Timeout Valid ELM-PFAM combination Valid set of templates names to be retrieved	Perl Python2 Python3 Ruby Java
HELP	RUN : HELP	Retrieve the SLiMAN API documentation	SLiMAN REST-API Readme Contains API rules	AntiSpam Timeout	Perl Python2 Python3 Ruby Java
DELETE	RUN : DELETE TOKEN : project token	Delete current project Remove data from SLiMAN server Stop connexion	NOTE=DELETED	AntiSpam Timeout Project Token match	Perl Python2 Python3 Ruby Java

Parameter	Value(s)	Description
RUN	string	Name of the function to be called
TOKEN	string	Your current project Token
INPUTS	InputKey:InputValue1,InputValue2	Set of InputKey:InputValues separated by / e.g : Key:Values/Key2:Value

Input Key	Input Value(s)	Description
LIST	string,string,etc...	Series of strings separated by comas
FILES	CSV | JSON | BLAST | MAFFT	Series of filetypes separated by comas
ID	integer	Index of the HitID to be pointed
PFAM	string	PFam ID to be pointed
ELM	string	ELM class name to be pointed