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io - Input and Output of Sequences, Structures and Maps

The io module deals with the input and output of entities, alignments, sequences, images. 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 as various image data (e.g. png, dm3) and density map files (e.g. CCP4, MRC).

Molecular Structures

Loading Molecular Structures

The io modules offer several ways to load molecular structures depending on your requirements. The most general way is offered by LoadEntity(), which will automatically detect the file format based on the file extension.

LoadEntity(filename, format='auto')

Load entity from disk. If format is set to ‘auto’, the function guesses the filetype based on the extension of the file e.g. files ending in ‘.pdb’, ‘.ent’, ‘.ent.gz’ and ‘.pdb.gz’ will automatically be loaded as PDB files. For files without or exotic extensions, the format can be set explicitly as the second parameter.

# Recognizes SDF file by file extension
ent = io.LoadEntity('file.sdf')

# In this case, there is no file extensions, so you have to say it's a
# SDF file explicitly
ent = io.LoadEntity('file', 'sdf')

For a list of file formats supported by LoadEntity(), see Supported Structure File Formats.

Raises:

IOUnknownFormatException if the format string supplied is not recognized or the file format can not be detected based on the file extension.

IOException if the import fails due to an erroneous or inexistent file.

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 LoadPDB(). It offers tighter control over the exact loading behaviour.

IO Profiles for entity importer

LoadPDB(filename, restrict_chains='', no_hetatms=None, fault_tolerant=None, load_multi=False, quack_mode=None, join_spread_atom_records=None, calpha_only=None, profile='DEFAULT', remote=False, dialect=None, seqres=False, bond_feasibility_check=None)

Load PDB file from disk and return one or more entities. Several options allow to customize the exact behaviour of the PDB import. For more information on these options, see IO Profiles for entity importer.

Residues are flagged as ligand if they are mentioned in a HET record.

Parameters:
  • restrict_chains – If not an empty string, only chains listed in the string will be imported.
  • fault_tolerant – Enable/disable fault-tolerant import. If set, overrides the value of IOProfile.fault_tolerant.
  • no_hetatms – If set to True, HETATM records will be ignored. Overrides the value of IOProfile.no_hetatms
  • load_multi – If set to True, a list of entities will be returned instead of only the first. This is useful when dealing with multi-PDB files.
  • join_spread_atom_records – If set, overrides the value of IOProfile.join_spread_atom_records.
  • remote – If set to True, the method tries to load the pdb from the remote pdb repository www.pdb.org. The filename is then interpreted as the pdb id.
  • dialect (str) – Specifies the particular dialect to use. If set, overrides the value of IOProfile.dialect
  • seqres – Whether to read SEQRES records. If set to True, the loaded entity and seqres entry will be returned as a tuple.
Return type:

EntityHandle or a list thereof if load_multi is True.

Raises:

IOException if the import fails due to an erroneous or inexistent file

Saving Molecular Structures

Saving a complete entity or a view is a matter of calling 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')

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')
SaveEntity(ent, filename, format='auto')

Save entity to disk. If format is set to ‘auto’, the function guesses the filetype based on the file extension, otherwise the supplied format is checked against the available export plugins.

Parameters:
Raises:

IOUnknownFormatException if the format string supplied is not recognized or the file format can not be detected based on the file extension.

SavePDB(models, filename, dialect=None, pqr=False, profile='DEFAULT')

Save entity or list of entities to disk. If a list of entities is supplied the PDB file will be saved as a multi PDB file. Each of the entities is wrapped into a MODEL/ENDMDL pair.

If the atom number exceeds 99999, ‘*‘ is used.

Parameters:
  • models – The entity or list of entities (handles or views) to be saved
  • filename (string) – The filename

Sequences and Alignments

Loading sequence or alignment files

LoadSequence(filename, format='auto')

Load sequence data from disk. If format is set to ‘auto’, the function guesses the filetype based on the extension of the file. Files ending in ‘.fasta’, ‘.aln’ will automatically be loaded.

For files with non-standard extensions, the format can be set explicitly specifying the format parameter.

# recognizes FASTA file by file extension
myseq = io.LoadSequence('seq.fasta')
# for obtaining a SequenceList
seqlist = io.LoadSequenceList('seqs.fasta')
# or for multiple aligned fasta files use
aln = io.LoadAlignment('algnm.aln',format="clustal")

For a list of file formats supported by LoadSequence() see Supported Sequence File Formats.

Raises:

IOUnknownFormatException if the format string supplied is not recognized or the file format can not be detected based on the file extension.

IOException if the import fails due to an erroneous or inexistent file.

LoadSequenceList(filename, format='auto')

For a description of how to use LoadSequenceList() please refer to LoadSequence(). For a list of file formats supported by LoadSequenceList() see Supported Sequence File Formats.

LoadAlignment(filename, format='auto')

For a description of how to use LoadAlignment() please refer to LoadSequence(). For a list of file formats supported by LoadAlignment() see Supported Sequence File Formats.

LoadSequenceProfile(filename, format='auto')

Load sequence profile data from disk. If format is set to ‘auto’, the function guesses the filetype based on the extension of the file. Files ending in ‘.hhm’ (output of HHblits) and ‘.pssm’ (ASCII Table (PSSM) output of PSI-BLAST as generated with blastpgp and flag -Q) will automatically be loaded.

For files with non-standard extensions, the format can be set explicitly specifying the format parameter.

# recognizes hhm file by file extension
myprof = io.LoadSequenceProfile('myhmm.hhm')
# recognizes pssm file by file extension
myprof = io.LoadSequenceProfile('myprof.pssm')

# to override format
myprof = io.LoadSequenceProfile('myfile', format='hhm')
myprof = io.LoadSequenceProfile('myfile', format='pssm')

For a list of file formats supported by LoadSequenceProfile() see Supported Sequence Profile File Formats.

Return type:

ProfileHandle

Raises:

IOUnknownFormatException if the format string supplied is not recognized or the file format can not be detected based on the file extension.

IOException if the import fails due to an erroneous or inexistent file.

Saving Sequence Data

SaveSequence(sequence, filename, format='auto')

Saving sequence data is performed by calling 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 SaveSequence() see Supported Sequence File Formats.

Raises:

IOUnknownFormatException if the format string supplied is not recognized or the file format can not be detected based on the file extension.

IOException if the import fails due to an erroneous or inexistent file.

SaveSequenceList(seq_list, filename, format='auto')

For a desription of how to use SaveSequenceList() please refer to SaveSequence(). For a list of file formats supported by SaveSequenceList() see Supported Sequence File Formats.

SaveAlignment(aln, filename, format='auto')

For a desription of how to use SaveAlignment() please refer to SaveSequence().

For a list of file formats supported by SaveAlignment() see Supported Sequence File Formats.

Density Maps

Loading Density Maps

LoadImage(filename)

Load density map from disk with the extension being guessed by the function.

Parameters:filename (string) – The filename
LoadImage(filename, format)

Load density map from disk. If no format is given, the function guesses the filetype based on the extension of the file. If the extension is unknown or not present the filetype will be guessed based on the content of the file if possible.

Parameters:
  • filename (string) – The filename
  • format – The file format
Raises:

IOUnknownFormatException if the format supplied is not recognized or the file format can not be detected based on the file extension and content.

IOException if the import fails due to an erroneous or inexistent file.

# recognizes mrc file by file extension
ent = io.LoadImage('file.mrc')

# it is always possible to explicitly set the image format
# DAT file explicitly
ent = io.LoadImage('file', Dat())

For a list of file formats supported by LoadImage(), see Supported Image File Formats.

Saving Density Maps

SaveImage(image, filename)

Save density map to disk with the function guessing the filetype based on the file extension.

SaveImage(image, filename, format)

Save density map to disk. If no format is set, the function guesses the filetype based on the file extension.

Parameters:
  • image (IMageHandle) – The density map to be saved
  • filename (string) – The filename
  • format – The file format
Raises:

IOUnknownFormatException if the file format can not be detected based on the file extension

For a list of file formats supported by SaveImage(), see Supported Image File Formats.

# load density map
image = io.LoadImage('density_map.ccp4')
# save density map
io.SaveImage(image, 'new_map.map', CCP4())

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