`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() and mmCIF files with LoadMMCIF() (this also gives you access to the MMCifInfo class). It offers tighter control over the exact loading behaviour.

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, remote_repo='pdb', 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 repository given as remote_repo. The filename is then interpreted as the entry id as further specified for the remote_repo parameter.
remote_repo – Remote repository to fetch structure if remote is True. Must be one in [‘pdb’, ‘smtl’, ‘pdb_redo’]. In case of ‘pdb’ and ‘pdb_redo’, the entry must be given as lower case pdb id, which loads the deposited assymetric unit (e.g. ‘1ake’). In case of ‘smtl’, the entry must also specify the desired biounit (e.g. ‘1ake.1’).
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

PDBStrToEntity(pdb_string, profile=IOProfile(), process=False)¶

Load entity from a string in PDB format. By default the entity is loaded with an empty IO Profile and is not processed with the Processor, even if one is available in the IO Profile.

Parameters:

pdb_string – A PDB file as a string.
profile – The IO Profile to read the entity with. For more information on the IO Profiles available, see IO Profiles for entity importer.
process – If set to True, run the Processor contained in the IO Profile.

Return type:

EntityHandle.

To get an entity equivalent to one loaded with LoadPDB(), set the profile and process arguments as follows:

with open('protein.pdb') as pdb_fd:
    pdb_str = pdb.read()
    ent = io.PDBStrToEntity(pdb_str, ost.io.profiles['DEFAULT'], True)

class ost.io.OMF¶

Experimental data format capable of storing minimally required information of a ost.mol.EntityHandle in a heavily compressed manner (OMF - OpenStructure Minimal Format). Shares lots of ideas with the mmtf or binaryCIF formats but comes with no dependencies attached.

static FromEntity(ent)¶

Generates ost.io.OMF object starting from an ost.mol.EntityHandle. ent is is assigned as assymetric unit, no biounits are defined (i.e. GetBU() raises an error in any case`).

Parameters:: ent (ost.mol.EntityHandle) – Structural data
Returns:: The created ost.io.OMF object

static FromFile(filepath)¶

Generates ost.io.OMF object from a file stored with ToFile().

Parameters:: filepath (str) – The file
Returns:: The created ost.io.OMF object

static FromMMCIF(ent, info)¶

Generates ost.io.OMF object starting from an ost.mol.EntityHandle with an associated MMCifInfo (you get this stuff with ost.io.LoadMMCIF()). ent is assigned as assymetric unit and the biounits are fetched from info.

Parameters:

ent (ost.mol.EntityHandle) – Structural data
info (MMCifInfo) – Biounits are fetched from here

Returns:

The created ost.io.OMF object

static FromBytes(bytes_string)¶

Generates ost.io.OMF object from a bytes object created with ToBytes().

Parameters:: bytes_string (bytes) – The super heavily compressed OMF structure

ToFile(filepath)¶

Stores object to file

Parameters:: filepath (str) – The file

ToBytes()¶

Stores object to bytes string

Returns:: The bytes string

GetAU()¶

Getter for assymetric unit

Returns:: The assymetric unit as ost.mol.EntityHandle

GetAUChain(chain_name)¶

Getter for single chain in the assymetric unit

Parameters:: chain_name (str) – The name of the chain you want
Returns:: ost.mol.EntityHandle of the AU only containing the specified chain

GetBU(bu_idx)¶

Getter for Biounit

Parameters:: bu_idx (int) – The index from the biounit as it has been read from info in FromMMCIF().
Returns:: The Biounit as ost.mol.EntityHandle
Raises:: RuntimeError if bu_idx doesn’t exist

Loading Molecular Structures From Remote Repositories¶

LoadPDB() already provides access to selected structural databases in the internet when enabling the remote flag. Predefined ost.io.remote.RemoteRepository objects are available as

from ost.io import remote
repo_name = 'smtl'
repo = remote.REMOTE_REPOSITORIES.get(repo_name)

# url for entry with id 1ake.1
print(repo.URLForID('1ake.1'))

where repo_name can be one of [‘pdb’, ‘cif’, ‘pdb_redo’, ‘smtl’]. Instead of explicit access, you can directly fetch data using:

RemoteGet(id, from_repo='pdb')¶

Invokes RemoteRepository.Get() on predefined repositories (‘pdb’, ‘smtl’, ‘cif’, ‘pdb_redo’)

Parameters:: from_repo (str) – One of the predefined repositories

RemoteLoad(id, from_repo='pdb')¶

Invokes RemoteRepository.Load() on predefined repositories (‘pdb’, ‘smtl’, ‘cif’, ‘pdb_redo’)

Parameters:: from_repo (str) – One of the predefined repositories

class RemoteRepository(name, url_pattern, type, id_transform='upper')¶

A remote repository represents a structural database accessible through the internet, e.g. the PDB or SWISS-MODEL template library.

Parameters:

name (str) – Name of the repository
url_pattern (str) – URL pattern for repository. Required format is described in URLForID()
type (str) – Data format to expect at resolved URL must be in (‘pdb’, ‘cif’)
id_transform (str) – Transformation to apply to ID before resolving URL in URLForID(). Must be in (‘lower’, ‘upper’)

Get(id)¶

Resolves URL with URLForID(), dumps the content in a temporary file and returns its path.

Parameters:: id (str) – ID to resolve

Load(id)¶

Resolves URL with URLForID() and directly loads/returns the according ost.mol.EntityHandle. Loading invokes the ost.io.LoadPDB()/ost.io.LoadMMCIF() with default parameterization. If you need custom settings, you might want to consider to call Get() and do the loading manually.

Parameters:: id (str) – ID to resolve

URLForID(id)¶: Resolves URL given url_pattern and id_transform provided at object initialization. The url_pattern must contain substring ‘$ID’. Given id, the URL to the structure gets constructed by applying id_transform and inserting it at the location of ‘$ID’. e.g. ‘https://files.rcsb.org/view/$ID.pdb’ given 1ake as id and ‘upper’ as id_transform resolves to: ‘https://files.rcsb.org/view/1AKE.pdb’

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:

ent (EntityHandle or EntityView) – The entity to be saved
filename (string) – The filename
format (string) – Name of the format

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

Raises:

IOException if the restrictions of the PDB format are not satisfied (with the exception of atom numbers, see above):

Chain names with more than one character

Atom positions with coordinates outside range [-999.99, 9999.99]

Residue names longer than three characters

Atom names longer than four characters

Numeric part of ost.mol.ResNum outside range [-999, 9999]

Alternative atom indicators longer than one character

EntityToPDBStr(ent, profile=IOProfile())¶

Return entity as a string in PDB format.

Parameters:

entity – The EntityHandle or EntityView
profile – The IO Profile to read the entity with. For more information on the IO Profiles available, see IO Profiles for entity importer.

Raises:

IOException if the restrictions of the PDB format are not satisfied (see ost.io.SavePDB())

Return type:

string.

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.

Parameters:

filename (string) – The filename
format (string) – Name of the format

Return type:

SequenceHandle

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 alignments (here from CLUSTAL)
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.

Parameters:

filename (string) – The filename
format (string) – Name of the format

Return type:

SequenceList

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.

Parameters:

filename (string) – The filename
format (string) – Name of the format

Return type:

AlignmentHandle

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.

Parameters:

filename (string) – The filename
format (string) – Name of the format

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.

AlignmentFromString(data, format)¶

Load alignment from string.

The format argument is mandatory. For a list of supported formats, see Supported Sequence File Formats.

Parameters:

data (string) – The alignment
format (string) – Name of the format

Return type:

AlignmentHandle

SequenceFromString(data, format)¶

Load sequence from string.

The format argument is mandatory. For a list of supported formats, see Supported Sequence File Formats.

Parameters:

data (string) – The sequence
format (string) – Name of the format

Return type:

SequenceHandle

SequenceListFromString(data, format)¶

Load a list of sequences from string.

The format argument is mandatory. For a list of supported formats, see Supported Sequence File Formats.

Parameters:

data (string) – The list of sequences
format (string) – Name of the format

Return type:

SequenceList

SequenceProfileFromString(data, format)¶

Load sequence profile from string.

The format argument is mandatory.

Parameters:

data (string) – String containing the data you would read from a file with specified format.
format (string) – Name of the format. Can either be “hhm” or “pssm”.

Return type:

ProfileHandle

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 for multiple alignments (here in FASTA format)
io.SaveAlignment(aln, 'aln.fasta')

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

Parameters:

sequence (SequenceHandle) – The sequence
filename (string) – The filename
format (string) – Name of the format

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.

Parameters:

seq_list (SequenceList) – The sequence list
filename (string) – The filename
format (string) – Name of the format

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.

Parameters:

aln (AlignmentHandle) – The alignment
filename (string) – The filename
format (string) – Name of the format

AlignmentToString(ali, format)¶

Return alignment as a string.

The format argument is mandatory. For a list of supported formats see Supported Sequence File Formats.

Parameters:

ali (AlignmentHandle) – The alignment
format (string) – Name of the format

Return type:

string

SequenceToString(seq, format)¶

Return sequence as a string.

The format argument is mandatory. For a list of supported formats see Supported Sequence File Formats.

Parameters:

seq (SequenceHandle) – The sequence
format (string) – Name of the format

Return type:

string

SequenceListToString(seq_list, format)¶

Return sequence list as a string.

The format argument is mandatory. For a list of supported formats see Supported Sequence File Formats.

Parameters:

seq_list – The sequence list
format (string) – Name of the format

Return type:

string

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())

Stereochemical Parameters¶

In order to check the structure for some stereo-chemical and steric clashes before computing the lDDT scores it is required to pass parameter file based on Engh and Huber parameters, and on the atomic radii as defined in the Cambridge Structural Database. OpenStructure ships with default file called stereo_chemical_props.txt located in $OST_ROOT/share/openstructure directory. A function ReadStereoChemicalPropsFile() is used to read this file.

ReadStereoChemicalPropsFile(filename='', check=True)¶

Read stereochemical parameters - if not provided a local version will be used.

Parameters:

filename (str) – The path to the parameter file that will be used. If set to “”, it reads the default file shipped with OpenStructure.
check (bool) – Raise an error when any of the resulting tables are empty.

Returns:

Object containing stereochemical parameters

Return type:

StereoChemicalProps

GetStereoChemicalPropsFile()¶: Get the default path to the stereochemical paramteres file.

`io` - Input and Output of Sequences, Structures and Maps¶

Molecular Structures¶

Loading Molecular Structures¶

Loading Molecular Structures From Remote Repositories¶

Saving Molecular Structures¶

Sequences and Alignments¶

Loading sequence or alignment files¶

Saving Sequence Data¶

Density Maps¶

Loading Density Maps¶

Saving Density Maps¶

Stereochemical Parameters¶

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io - Input and Output of Sequences, Structures and Maps¶

Molecular Structures¶

Loading Molecular Structures¶

Loading Molecular Structures From Remote Repositories¶

Saving Molecular Structures¶

Sequences and Alignments¶

Loading sequence or alignment files¶

Saving Sequence Data¶

Density Maps¶

Loading Density Maps¶

Saving Density Maps¶

Stereochemical Parameters¶

`io` - Input and Output of Sequences, Structures and Maps¶