Conversion Between Various Formats: structconvert
This utility converts between files in Maestro, MDL SD, PDB, Sybyl Mol2, SMILES, CIF, and CSV formats. The entire contents of the file are converted by default, but you can specify a subset of structures.Only the first structure is written when writing to PDB format. The syntax is as follows:
structconvert [options] [-i[format]] inputfile [-o[format]] outputfile
where format can be one of the following:
mae
|
Maestro format |
cif
|
CIF format |
sd
|
V2000 SD file format |
pdb
|
PDB format |
mol2
|
Sybyl (.mol2) format |
smi
|
SMILES format |
csv
|
CSV file with SMILES for structure |
If the -i and -o format options are omitted, the file extensions are used to determine the format, which can include conversion between compressed and uncompressed versions of the same file format. For details of the syntax and options, see structconvert Command Help.
The format conversions have the following limitations:
- PDB and SMILES format cannot be interconverted.
- Only the first structure is written when writing to PDB format.
- SMILES cannot be directly converted to Maestro format.
For conversion to and from PDB format, structconvert supports all the options that are supported by pdbconvert.