OEFormat

The OEFormat namespace encodes symbolic constants representing the molecular file formats that may be read or written by OEChem TK.

See also

• File Formats section

This namespace contains the following constants:

Default

The default file format type is OEFormat.SMI.

CAN

This constant indicates Canonical SMILES file format.

CDX

This constant indicates ChemDraw CDX file format.

CIF

This constant indicates the small molecule Crystallographic Information File (CIF) format.

CSV

This constant indicates the comma separated values file format as specified by RFC 4180. The first column is canonical isomeric SMILES, the second column is the molecule title, the remaining columns are SD data as determined by the first molecule read or written to the oemolstreambase.

See also

CSV File Format

CXSMILES

This constant indicates the Chemaxon Extended SMILES format.

Enhanced stereogroup information is the only information in cxsmiles appendices currently supported. Please contact support@eyesopen.com if there are additional cxsmiles features that you would like to see supported.

The specific features supported for this format are limited to, MDL Chiral OFF and Enhanced stereochemical representation . The supported features cannot be in the presence of other unsupported features since a partial parse of the appendix information is disallowed.

See Chemaxon Extended SMILES and SMARTS for a complete specification of all possible features.

FASTA

This constant indicates FASTA protein sequence file format.

INCHI

This constant indicates IUPAC InChI file format.

INCHIKEY

This constant indicates IUPAC InChI Key file format.

ISM

This constant indicates Canonical isomeric SMILES file format. This is the same as the OEFormat.SMI file format.

MAXFORMAT

The maximum integral value any constant in the OEFormat can have.

Note

Values in this namespace are guaranteed to be contiguous.

MDL

This constant indicates MDL Mol file format.

MF

This constant indicates Molecular Formula (Hill order) format.

MMCIF

This constant indicates macromolecular Crystallographic Information File (mmCIF) file format.

MMOD

This constant indicates Macromodel file format.

MOL2

This constant indicates Tripos Sybyl mol2 file format.

MOL2H

This constant indicates Tripos Sybyl mol2 file format with explicit hydrogens.

MOPAC

This constant indicates MOPAC file format.

OEB

This constant indicates OpenEye OEBinary file format.

OEZ

This constant indicates Zstd compressed OpenEye OEBinary file format. Currently this file format only supports multi-conformer molecules derived from the OEMCMolBase class.

Note

This file format was introduced in the 2019.Apr toolkits. OpenEye applications or toolkits released before Apr/2019 will not be able to read this new file format.

See also

• Compressed Input and Output section

PDB

This constant indicates Protein Databank PDB file format.

RDF

This constant indicates MDL RDF reaction file format.

SDF

This constant indicates MDL SD file format.

SKC

This constant indicates MDL ISIS Sketch file format.

SLN

This constant indicates Tripos Sybyl Line Notation file format.

SMI

This constant indicates canonical isomeric SMILES file format. This is the same as the OEFormat.ISM file format.

UNDEFINED

This constant indicates an unrecognized or undefined file format.

USM

This constant indicates SMILES file format.

XYZ

This constant indicates XMol XYZ file format.