io.rst

:mod:`~ost.io` - Input and Output of Sequences, Structures and Maps

The io module deals with input and output of :class:`entities <ost.mol.EntityHandle>`, :class:`alignments <ost.seq.AlignmentHandle>`, :class:`sequences <ost.seq.SequenceHandle>`, :class:`images <ost.img.ImageHandle>`. Importers for common file formats containing molecules such as PDB, SDF and CHARMM trajectory files are available. Sequence and alignment file formats such as FASTA and CLUSTALW are supported as well, alongside various image data (e.g. png, dm3) and density map files (e.g. CCP4, MRC).

Molecular Structures

Loading Molecular Structures

The :mod:`~ost.io` modules offers several ways to load molecular structures depending on your requirements. The most general way is offered by :func:`~ost.io.LoadEntity`, which will automatically detect the file format based on the file extension.

Some of the formats have a dedicated function that allows you to tweak many parameters that affect the import. PDB files can be loaded with :func:`~ost.io.LoadPDB`. It offers a tighter control over the exact loading behaviour.

Saving Molecular Structures

Saving a complete entity or a view is a matter of calling :func:`~ost.io.SaveEntity`.

ent=io.LoadEntity('protein.pdb')
# save full entity
io.SaveEntity(ent, 'full.pdb')
# only save C-alpha atoms
io.SaveEntity(ent.Select('aname=CA and peptide=true'), 'calpha.pdb')

:func:`~ost.io.SavePDB` provides a simple way to save several entities into one file:

ent=io.LoadEntity('protein.pdb')
# Save complete entity
io.SavePDB(ent, 'full.pdb')
# Save chain A and chain B separately
io.SavePDB([ent.Select('cname=A'), ent.Select('cname=B')], 'split.pdb')

Sequences and Alignments

Loading sequence or alignment files

For a list of file formats supported by :func:`LoadSequence` see :doc:`formats`.

raises:	:exc:`~ost.io.IOUnknownFormatException` if the format string supplied is not recognized or the file format can not be detected based on the file extension :exc:`~ost.io.IOException` if the import fails due to an erroneous or inexistent file

Saving Sequence Data

Saving sequence data is performed by calling :func:`SaveSequence`. For files with non-standard extensions, the format can be set explicitly specifying the 'format' parameter.

# recognizes FASTA file by file extension
io.SaveSequence(myseq,'seq.fasta')
# for saving a SequenceList
io.SaveSequenceList(seqlist,'seqlist.fasta')
# or multiple aligned fasta files
io.SaveAlignment(aln,'algnm.aln',format="clustal")

For a list of file formats supported by :func:`SaveSequence` see :doc:`formats`.

raises:	:exc:`~ost.io.IOUnknownFormatException` if the format string supplied is not recognized or the file format can not be detected based on the file extension :exc:`~ost.io.IOException` if the import fails due to an erroneous or inexistent file