Structure translation

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=...

fuzzy attachment sites (multiple parents of undefined graphs) are not supported
if there are combined repeat and non-repeat parts within one structure, only repeating unit is translated
nested repeating units are not supported
unconnected entitities are not supported (the structure should produce a single moiety)
if there are multiple repeats, only the first one is translated
fuzzy linkages separated with | are replaced with ?
alternative substructures (ALT section) are not supported

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.

If charged groups should be ionized, please use the 'ionize=1' parameter (makes sense for atom-level output formats only).

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.

GLYCAM, WURCS: service response is a translated structure.
SMILES: service response is one or more translated structures. Multiple structures can occur if there are uncertainties in the input structure.
MOL: service response is a URL of one or more cached MOL-files. Multiple files can occur if there are uncertainties in the input structure. Supplementary data, such as SMILES and CSDB Linear code are provided for each structural variant (see example below). MOL data contain atom to residue/position mapping in the 3rd line.
PDB: the same as MOL, but another URL to a PDB-file is given for every variant of structure, and PDB data are appended to output between <PDB> and </PDB> tags. PDB feed has atom to residue mapping utilizing ligand codes from RSCB Protein Data Bank. The residues that have no matching ligand in PDB and residues with uncertainties will have incremental names.
PDBG: the same as PDB, but atom to residue mapping uses residue/substitution codes from GLYCAM. The residues unsupported by GLYCAM and residues with uncertainties will have incremental names.

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 sucrose</PDB>

Errors: none

Input: aDGlcp(1-2)bDFruf

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