[BETA VERSION] API

The MAD API enables programmatic access to MAD in unique and advanced ways. We design a REST API that allows users to access structures and topologies of molecules parameterized with the Martini coarse-grained force field. This API allows users to download files and retrieve information from the database, making it easy to access and work with the data.
The advantages of having this API include:

- Easy access to the Martini Database's data and resources
- Flexibility and convenience in accessing and working with the data
- Ability to automate tasks and integration with other tools and systems
- Enabling third-party developers to build new applications using the data and functionality of the Martini Database.

Here is a notebook detailing an example of the use of api for pedagogical purposes( Download)

Techical part

In our case, we only prodivide the GET method to download molecule files or have forcefield information. This is the format of the route :
https://mad.ibcp.fr/api/molecule/get/[forcefield]/[molecule_name][.extention]/[version]

Parameter	Type	Default	Description
Forcefield	string	None	Which forcefield do you want (exemple : martini22, martini3001)
Molecule name	string	None	Name (Alias) of your molecule (example : POPE)
File type	string	.zip	You can ask for a specific type of file ('.itp', '.gro', '.pdb') or you can download everything in zip format, in this case adds '.zip' or nothing).
Version	string	1.0	(Optional) If your molecule has several version you can ask for a specific version.

Exemple

Forcefield information :
https://mad.ibcp.fr/api/molecule/get/martini3001
Output exemple :

        
          {
            "0": {
              "alias": "DAPA",
              "name": "di-C20:4-C22:5 PA (DAPA)",
              "citation": "Souza, P.C.T.; Alessandri, R.; Barnoud, J.; Thallmair, S.; Faustino, I.; Grünewald, F.; Patmanidis,
              I.; Abdizadeh, H.; Bruininks, B.M.H.;\nWassenaar, T.A.; Kroon, P.C.; Melcr, J.; Nieto, V.; Corradi, V.; Khan,
              H.M.; Domański, J.; Javanainen, M.; Martinez-Seara, H.;\nReuter, N.; Best, R.B.; Vattulainen, I.; Monticelli, L.;
              Periole, X.; Tieleman, D.P.; de Vries, A.H.; Marrink, S.J.; Nature Methods\n2021; 10.1038/s41592-021-01098-3",
              "category": "Lipids",
              "version": [ "1.0" ]
              },
            "1": {
              "alias": "DAPC",
              "name": "di-C20:4-C22:5 PC (DAPC)",
              "citation": "Souza, P.C.T.; Alessandri, R.; Barnoud, J.; Thallmair, S.; Faustino, I.; Grünewald, F.; Patmanidis,
              I.; Abdizadeh, H.; Bruininks, B.M.H.;\nWassenaar, T.A.; Kroon, P.C.; Melcr, J.; Nieto, V.; Corradi, V.; Khan,
              H.M.; Domański, J.; Javanainen, M.; Martinez-Seara, H.;\nReuter, N.; Best, R.B.; Vattulainen, I.; Monticelli, L.;
              Periole, X.; Tieleman, D.P.; de Vries, A.H.; Marrink, S.J.; Nature Methods\n2021; 10.1038/s41592-021-01098-3",
              "category": "Lipids",
              "version": [ "1.0" ]
              }, 
            ...
          }

Get pdb file :
https://mad.ibcp.fr/api/molecule/get/martini3001/DAPA.itp
Output exemple :

        
          ;;;;;; Martini lipid topology for di-C20:4-C22:5 PA (DAPA)
          ;
          ; Description:
          ;   A general model phosphatidic acid (PA) lipid corresponding to atomistic e.g. C20:4(5c,8c,11c,14c) di-arachidonic acid (AA), 
          ;   - C22:5(4c,7c,10c,13c,16c) docosapentaenoic acid tails.
          ; Parameterization:
          ;   This topology follows the standard Martini 3 lipid definitions for building blocks.  Further optimization in the bonded parameters are currently on development.
          ;
          ; Reference(s):
          ; Souza, P.C.T.; Alessandri, R.; Barnoud, J.; Thallmair, S.; Faustino, I.; Grünewald, F.; Patmanidis, I.; Abdizadeh, H.; Bruininks, B.M.H.; 
          ; Wassenaar, T.A.; Kroon, P.C.; Melcr, J.; Nieto, V.; Corradi, V.; Khan, H.M.; Domański, J.; Javanainen, M.; Martinez-Seara, H.; 
          ; Reuter, N.; Best, R.B.; Vattulainen, I.; Monticelli, L.; Periole, X.; Tieleman, D.P.; de Vries, A.H.; Marrink, S.J.;  Nature Methods 
          ; 2021; 10.1038/s41592-021-01098-3
          ;
          ;@INSANE alhead=O, allink=G G, altail=DDDDC DDDDC, alname=DAPA, charge=-1.0
          ;@RESNTEST DAP==DAPA if: atoms[0]==PO4
          ;@BEADS PO4 GL1 GL2 D1A D2A D3A D4A C4A D1B D2B D3B D4B C4B 
          ;@BONDS PO4-GL1 GL1-GL2 GL1-D1A D1A-D2A D2A-D3A D3A-D4A D4A-C4A GL2-D1B D1B-D2B D2B-D3B D3B-D4B D4B-C4B 
          ;
          
          ; Command line
          ;	-o martini_v3.0_DAPA.itp -alname DAPA -alhead O -allink G G -altail DDDDC DDDDC
          ;
          
          
          ; Category
          ;	lipids
          ;
          ; Name
          ;	 di-C20:4-C22:5 PA (DAPA)
          ;
          ; Alias
          ;	DAPA
          ;
          ; Force field
          ;	martini3001
          ;
          ; Version
          ;	1.0
          ;
          
          [moleculetype]
          ; molname      nrexcl
            DAPA          1
          
          [atoms]
          ; id 	type 	resnr 	residu 	atom 	cgnr 	charge
             1 	Q5 	 1 	DAPA 	PO4 	 1 	-1.0 	
             2 	SN4a	 1 	DAPA 	GL1 	 2 	0 	
             3 	N4a	 1 	DAPA 	GL2 	 3 	0 	
             4 	C4h	 1 	DAPA 	D1A 	 4 	0 	
             5 	C4h	 1 	DAPA 	D2A 	 5 	0 	
             6 	C4h	 1 	DAPA 	D3A 	 6 	0 	
             7 	C4h	 1 	DAPA 	D4A 	 7 	0 	
             8 	C1 	 1 	DAPA 	C4A 	 8 	0 	
             9 	C4h	 1 	DAPA 	D1B 	 9 	0 	
            10 	C4h	 1 	DAPA 	D2B 	10 	0 	
            11 	C4h	 1 	DAPA 	D3B 	11 	0 	
            12 	C4h	 1 	DAPA 	D4B 	12 	0 	
            13 	C1 	 1 	DAPA 	C4B 	13 	0 	
          
          [bonds]
          ;  i  j 	funct 	length 	force.c.
             1  2 	1 	0.42 	1350 	
             2  3 	1 	0.312	2500 	
             2  4 	1 	0.47 	5000 	
             4  5 	1 	0.47 	3800 	
             5  6 	1 	0.47 	3800 	
             6  7 	1 	0.47 	3800 	
             7  8 	1 	0.47 	3800 	
             3  9 	1 	0.47 	3600 	
             9 10 	1 	0.47 	3800 	
            10 11 	1 	0.47 	3800 	
            11 12 	1 	0.47 	3800 	
            12 13 	1 	0.47 	3800 	
          
          [angles]
          ;  i  j  k 	funct 	angle 	force.c.
             1  2  3 	2 	108.0 	21.5 	
             1  2  4 	2 	139.1   31.2 	
             2  4  5 	2 	100.0 	10.0 	
             4  5  6 	2 	100.0 	10.0 	
             5  6  7 	2 	100.0 	10.0 	
             6  7  8 	2 	120.0 	35.0 	
             3  9 10 	2 	100.0 	10.0 	
             9 10 11 	2 	100.0 	10.0 	
            10 11 12 	2 	100.0 	10.0 	
            11 12 13 	2 	120.0 	35.0

Get all files for a specific version :
https://mad.ibcp.fr/api/molecule/get/martini3001/TEST.zip/2.0
Open an widnows to download file.
or do wget https://mad.ibcp.fr/api/molecule/get/martini3001/TEST.zip/2.0