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

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

http://cactus.nci.nih.gov/chemical/structure/aspirin/sdf

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

http://cactus.nci.nih.gov/chemical/structure/"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)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=alc

cdxml (CambridgeSoft ChemDraw XML format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cdxml

cerius (MSI Cerius II format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cerius

charmm (Chemistry at HARvard Macromolecular Mechanics file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=charmm

cif (Crystallographic Information File)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cif

cml (Chemical Markup Language)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=cml

ctx (Gasteiger Clear Text format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=ctx

gjf (Gaussian input data file)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=gjf

gromacs (GROMACS file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=gromacs

hyperchem (HyperChem file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=hyperchem

jme (Java Molecule Editor format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=jme

maestro (Schroedinger MacroModel structure file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=maestro

mol (Symyx molecule file)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mol

mol2 (Tripos Sybyl MOL2 format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sybyl2

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mol2

mrv (ChemAxon MRV format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=mrv

pdb (Protein Data Bank)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=pdb

sdf (Symyx Structure Data Format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sdf

sdf3000 (Symyx Structure Data Format 3000)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sdf3000

sln (SYBYL Line Notation)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sln

smiles (SMILES)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=smile

xyz (xyz file format)

http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=xyz

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

http://cactus.nci.nih.gov/chemical/structure/InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N/file?format=pdb
http://cactus.nci.nih.gov/chemical/structure/CC(=O)Oc1ccccc1C(O)=O/file?format=mrv
http://cactus.nci.nih.gov/chemical/structure/045DA3288E1A0233-FICuS-01-39/file?format=cml

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

  1. Hi Markus:

    Is there any way to resolve a SMILES to a 3D MOL file?

    Thanks and best regards,
    Yogesh

  7. 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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