sdf1 KB

Ethanol — SDfile With Data Fields (.sdf)

An SDfile wrapping the identical ethanol molfile plus five tagged data fields and the mandatory $$$$ terminator. The property block syntax — a header line, a value and a blank line — is where SDfile parsers usually diverge from molfile parsers.

Scientific data Editor testing Conversion testing

Preview — first 39 linessdf

ethanol
  NovusEx 3D  synthetic idealised geometry
Idealised geometry. Property block follows the connection table.
  9  8  0  0  0  0  0  0  0  0999 V2000
   -1.2456    0.2436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.5876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1636    0.2296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1345   -0.3861    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2734    0.8797    0.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2734    0.8797   -0.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384   -1.2270    0.8850 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0384   -1.2270   -0.8850 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9524   -0.3175    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  1  4  1  0
  1  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
M  END
> <NAME>
ethanol

> <FORMULA>
C2H6O

> <MOLECULAR_WEIGHT>
46.069

> <SMILES>
CCO

> <SOURCE>
Novus Examples synthetic fixture (idealised geometry)

$$$$

Specifications

Format: MDL SDfile
Records: 1
Data Fields: 5
Record Terminator: $$$$
Field Syntax: > <NAME> then value then a blank line
Embedded Molfile: identical to the paired .mol

Testing contract

Expected to pass

Scenario: Parse the record, extract the embedded connection table and read all five tagged data fields.
Expected result: The connection table is byte-identical to the paired molfile, the five fields parse with FORMULA equal to C2H6O, and the record terminates on $$$$ rather than at end of file.

What is a .sdf file?

SDF (Structure-Data File) is MDL's multi-record chemistry format. Each record is a molfile — a counts line, an atom block, and a bond block — followed by tagged data fields written as `> <NAME>` lines with their values, and terminated by a `$$$$` delimiter. It is how compound libraries with per-molecule properties are shipped between cheminformatics tools.

How to use this file

Use an example .sdf file to test cheminformatics readers and property extractors, verifying record splitting on the `$$$$` delimiter, that data fields are associated with the right structure, and that a malformed record does not consume the rest of the file.

How to use this file for testing

“Ethanol — SDfile With Data Fields (.sdf)” is a deterministic Novus Examples fixture for Scientific data, Editor testing, Conversion testing. Citation catalogs (BibTeX, RIS), chemistry structures (MDL Molfile, PDB), and gridded binary data (NetCDF, FITS) — for testing reference managers, molecule viewers, and scientific-data loaders.

Documented properties for this file: 1 records · MDL SDfile. Compare results against paired or grouped companions on this page when present (clean↔damaged, searchable↔scanned, or format twins) so scores stay reproducible across runs.

Download the file once, keep the path stable in CI or local scripts, and treat the spec table as the contract: dimensions, seeds, field lists, and roles are intentional. Corrupt or invalid samples are labelled as such — expect parsers to fail loudly rather than silently accept them.

Scientific fixtures are small, valid, and fully synthetic — no real organism, patient, sample, or observation. Point your parser or loader at the file and check it reads the documented records, variables, or headers; binary formats ship a readable twin or metadata listing for comparison.