Translate from GlycoCT to CSDB

GlycoCT is a carbohydrate structure description language developed within EurocarbDB and Glycome-DB project. To translate structure from GlycoCT please use API at the following address: http://csdb.glycoscience.ru/database/core/convert_api.php. The GlycoCT encoded structure should be passed as POST or GET parameter named 'glycoct'. If you use GET, the GlycoCT code should be URL-encoded in one line. The output contains: CSDB encoded structure (line 1), molecule type (line2), error messages if present (lines 3+), blank line and a copy of input Glyco-CT code, for example:

POST or GET input (example):
glycoct=
"RES
1r:r1
REP
REP1:3o(6+1)2n=-1--1
RES
2s:phosphate
3b:a-dman-HEX-1:5
4s:n-acetyl
5s:acetyl
LIN
1:2n(1+1)3o
2:3d(2+1)4n
3:3o(3|4+1)5n"

glycan_only=
"on" (off by default)
=> Web-service output:
<HTTP headers>

CSDB Linear: -6)[Ac(1-?),Ac(1-2)]aDManpN(1-P-
Molecule type: CHEM
Errors: fuzzy outgoing linkage position was replaced with a wildcard for linkage 3

Input:
<copy of the processed glycoct input parameter (multiline)>

Test web-service using GET: http://csdb.glycoscience.ru/database/core/convert_api.php?glycoct=...

Below you can try this translation online:

Ignore non-carbohydrate moieties

Translate from CSDB


(blankspaces not allowed)

Destination format:  

Automated web-service (web API)

To translate structure from CSDB in automated manner please use API at the following address: http://csdb.glycoscience.ru/database/core/convert_api.php. The structure in CSDB Linear language should be passed as POST or GET parameter named 'csdb'. If you use GET, the CSDB code should be URL-encoded.

The destination format should be specified in 'format' parameter and can be: smiles | wurcs | glycam | mol | pdb | pdbg.

The output contains: the destination format name, the service response (line 1), error messages if present (lines 2+), blank line, a copy of input CSDB code.

Example 1. Test it using GET: http://csdb.glycoscience.ru/database/core/convert_api.php?csdb=aDGlcp(1-2)aLRhap&format=glycam
POST or GET input (example):
csdb=aDGlcp(1-2)aLRhap

format=glycam
=> Web-service output:
<HTTP headers>

GLYCAM: a-D-Glcp-(1-2)-a-L-Rhap-OH
Errors: none

Input: aDGlcp(1-2)aLRhap
 
Example 2. Test it using GET: http://csdb.glycoscience.ru/database/core/convert_api.php?csdb=?DGlc?&format=mol
POST or GET input (example):
csdb=?DGlc?

format=mol
=> Web-service output:
<HTTP headers>

MOL: 

STRUCTURE 0 (?DGlcp), variant 0 SMILES O[6CH2][5C@H]1O[1C@@H](O)[2C@H](O)[3C@@H](O)[4C@@H]1O : MOL=http://csdb.glycoscience.ru/jsmol/mols/<hash data>.mol
STRUCTURE 0 (?DGlcp), variant 1 SMILES O[6CH2][5C@H]1O[1C@H](O)[2C@H](O)[3C@@H](O)[4C@@H]1O : MOL=http://csdb.glycoscience.ru/jsmol/mols/<hash data>.mol
STRUCTURE 1 (?DGlcf), variant 0 SMILES O[6CH2][5C@@H](O)[4C@H]1O[1C@H](O)[2C@H](O)[3C@H]1O : MOL=http://csdb.glycoscience.ru/jsmol/mols/<hash data>.mol
STRUCTURE 1 (?DGlcf), variant 1 SMILES O[6CH2][5C@@H](O)[4C@H]1O[1C@@H](O)[2C@H](O)[3C@H]1O : MOL=http://csdb.glycoscience.ru/jsmol/mols/<hash data>.mol
STRUCTURE 2 (xDGlca), SMILES O=[1CH][2C@H](O)[3C@@H](O)[4C@H](O)[5C@H](O)[6CH2]O : MOL=http://csdb.glycoscience.ru/jsmol/mols/<hash data>.mol

Errors: none

Input: ?DGlc?
 
Example 3. Test it using GET: http://csdb.glycoscience.ru/database/core/convert_api.php?csdb=aDGlcp(1-2)bDFruf&format=pdbg
POST or GET input (example):
csdb=aDGlcp(1-2)bDFruf

format=pdbg
=> Web-service output:
<HTTP headers>

PDB: 

STRUCTURE 0 (aDGlcp(1-2)bDFruf), SMILES O[1CH2][2C@@]1(O[101C@H]2O[105C@H]([106CH2]O)[104C@@H](O)[103C@H](O)[102C@H]2O)O[5C@H]([6CH2]O)[4C@@H](O)[3C@@H]1O :
PDB=http://csdb.glycoscience.ru/jsmol/mol2pdb.py?mode=glycam&file=<hash data> <PDB>actual PDB data for aDGlcp</PDB> Errors: none Input: ?DGlcp

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