Resolve a structure identifier as SDF, CML, MRV, PDB …

We’d like to present a new feature of the Chemical Identifier Resolver: in addition to the already available SD file format representation

the service can now represent a structure (identifier) also in many different text-based structure (file) formats. The general URL format is:"identifier"/file?format="format"

The different chemical structure representations are generated by the chemoinformatic toolkit CACTVS. Although CACTVS can offer a whole lot more formats (including binary ones) we make the following (few) available here:

alc (Alchemy format)

cdxml (CambridgeSoft ChemDraw XML format)

cerius (MSI Cerius II format)

charmm (Chemistry at HARvard Macromolecular Mechanics file format)

cif (Crystallographic Information File)

cml (Chemical Markup Language)

ctx (Gasteiger Clear Text format)

gjf (Gaussian input data file)

gromacs (GROMACS file format)

hyperchem (HyperChem file format)

jme (Java Molecule Editor format)

maestro (Schroedinger MacroModel structure file format)

mol (Symyx molecule file)

mol2 (Tripos Sybyl MOL2 format)

mrv (ChemAxon MRV format)

pdb (Protein Data Bank)

sdf (Symyx Structure Data Format)

sdf3000 (Symyx Structure Data Format 3000)

sln (SYBYL Line Notation)

smiles (SMILES)

xyz (xyz file format)

All these workof course also with Standard InChIKey, SMILES or NCI/CADD Identifier as structure identifier:

7 thoughts on “Resolve a structure identifier as SDF, CML, MRV, PDB …

  1. Hi – excellent resource!

    However… I have been trying to use it to get CML and have found some issues that you might not already be aware of
    1. The response mime type is text/plain as opposed to something more suitable for CML (chemical/x-cml or even just a plain XML type)
    2. I think there should be an XML PI, i.e. or preferably also including an attribute to denote the encoding (utf8 ?)
    3. I couldn’t get it to work in Jmol. Jmol thinks it is CML but reports “no atoms found”

    Good stuff, all the same… Cheers, Adam

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