schrodinger.application.msv.seqio module¶

class schrodinger.application.msv.seqio.BaseProteinAlignmentReader¶

Bases: object

Base class for reading protein sequence alignments from files.

classmethod read(file_name)¶

Returns alignment read from file in Clustal *.aln format preserving order of sequences.

Parameters:	file_name (str) – Source file name. file_name – Source file name.
Raises:	IOError – If output file cannot be read.
Return type:	`ProteinAlignment`
Returns:	An alignment
Note:	The alignment can be empty if no sequence was present in the input file.

class schrodinger.application.msv.seqio.BaseProteinAlignmentWriter¶

Bases: object

Class for writing protein alignments to files.

classmethod write(aln, file_name)¶

Writes aln to a file.

Parameters:	aln (`BaseAlignment`) – Alignment to be written to a file. file_name (str) – Destination file name.

class schrodinger.application.msv.seqio.ClustalAlignmentReader¶

Bases: schrodinger.application.msv.seqio.BaseProteinAlignmentReader

Class for reading Clustal *.aln files.

classmethod read(file_name)¶

Returns alignment read from file in Clustal *.aln format preserving order of sequences.

Raises:	IOError – If the input file cannot be read.
Return type:	`ProteinAlignment`
Returns:	Read alignment. The alignment can be empty if no sequence was present in the input file.

class schrodinger.application.msv.seqio.ClustalAlignmentWriter¶

Bases: schrodinger.application.msv.seqio.BaseProteinAlignmentWriter

Class for writing Clustal *.aln files.

The format is described here: http://web.mit.edu/meme_v4.9.0/doc/clustalw-format.html

classmethod write(aln, file_name, use_unique_names=True)¶

Writes aln to a Clustal alignment file.

Raises:	IOError – If output file cannot be written.
Parameters:	aln (`BaseAlignment`) – Alignment to be written to a file. file_name (str) – Destination file name. use_unique_names (bool) – If True, write unique name for each sequence.

class schrodinger.application.msv.seqio.FastaAlignmentReader¶

Bases: object

classmethod read(file_name)¶

Loads a sequence file in FASTA format, creates sequences and appends them to alignment. Splits sequence name from the FASTA header.

Parameters:	file_name (str) – name of input FASTA file
Return type:	`ProteinAlignment`
Returns:	Read alignment.

classmethod readFromStringList(strings)¶

Return an alignment object created from an iterable of sequence strings

Parameters:	strings (Iterable of strings) – Sequences as iterable of strings (1D codes)

classmethod readFromText(lines, AlnClass=<class 'schrodinger.protein.alignment.ProteinAlignment'>)¶

Read sequences from FASTA-formatted text, creates sequences and appends them to alignment. Splits sequence name from the FASTA header.

Parameters:	lines (list of str) – list of strings representing FASTA file
Return type:	`ProteinAlignment`
Returns:	The alignment

class schrodinger.application.msv.seqio.FastaAlignmentWriter¶

Bases: schrodinger.application.msv.seqio.BaseProteinAlignmentWriter

Class for writing FASTA .fasta files.

Format is described here: U{Fasta format wikipedia<https://en.wikipedia.org/wiki/FASTA_format>}

HEADER_END = ''¶

HEADER_START = '>'¶

classmethod toString(aln, use_unique_names=True, maxl=50)¶

classmethod toStringAndNames(aln, use_unique_names=True, maxl=50, export_annotations=False, sim_ref_seq=None)¶

Converts aln to FASTA string

Parameters:	aln (`ProteinAlignment`) – Structured sequences use_unique_names (bool) – If True, write unique name for each sequence. maxl (int) – Maximum length of a line export_annotations (bool) – Whether annotations should be exported along with sequence information. If True, annotations listed in `EXPORT_ANNOTATIONS` will be exported. sim_ref_seq (`sequence.Sequence` or None) – Reference sequence to calculate similarities for the sequences to be exported. If None, similarity will not be exported.
Returns:	FASTA string
Return type:	string

classmethod toStringList(aln)¶

Convert ProteinAlignment object to list of sequence strings

Parameters:	aln (`ProteinAlignment`) – Alignment data
Return type:	list of str
Returns:	A list of sequence strings representing the alignment

classmethod write(aln, file_name, use_unique_names=True, maxl=50, export_annotations=False, sim_ref_seq=None)¶

Write aln to FASTA file

Raises:	IOError – If output file cannot be written.
Parameters:	aln (`ProteinAlignment`) – Structured sequences use_unique_names (bool) – If True, write unique name for each sequence. maxl (int) – Maximum length of a line file_name (str) – Destination file name. export_annotations (bool) – Whether annotations should be exported along with sequence information. If True, annotations listed in `EXPORT_ANNOTATIONS` will be exported. sim_ref_seq (`sequence.Sequence` or None) – Reference sequence to calculate similarities for the sequences to be exported. If None, similarity will not be exported.
Returns:	output names of each sequence
Return type:	list of str

exception schrodinger.application.msv.seqio.GetSequencesException¶

Bases: exceptions.IOError

Custom Exception for problems retrieving sequences.

class schrodinger.application.msv.seqio.MMSequenceConverter¶

Bases: object

Converts sequence between mmseq and MSV sequence formats.

Note:	This is supposed to be used with ‘with’ context manager.

classmethod readSequences(file_name, file_format=0)¶

Reads all sequences from file specified by file_name.

Parameters:	file_name (str) – Name of input file. file_format (int) – Format of the input file. By default, the format is MMSEQIO_ANY meaning file type is automatically recognized.
Return type:	List of `schrodinger.protein.sequence.ProteinSequence`.
Returns:	List of protein sequences read from the file.
Raises:	GetSequencesException – If the file could not be read.

classmethod writeSequences(sequences, file_name, file_format=1)¶

Writes sequences to a file specified by file_name.

Raises:	mmcheck.MmException – If the file could not be open for writing.
Parameters:	seqences – List of sequences to be written to file. file_name (str) – Name of input file. file_format (int) – Format of the input file. By default, the format is MMSEQIO_NATIVE.

class schrodinger.application.msv.seqio.PdbParts(pdbcode, pdbchain)¶

Bases: tuple

pdbchain¶: Alias for field number 1

pdbcode¶: Alias for field number 0

class schrodinger.application.msv.seqio.SeqDownloader¶

Bases: object

ENTREZ_FORMAT_STR = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&rettype=fasta&id=%s'¶

UNIPROT_FORMAT_STR = 'http://www.uniprot.org/uniprot/%s.fasta'¶

classmethod downloadEntrezSeq(sequence_id)¶

Download a sequence from Entrez database.

Parameters:	sequence_id (str) – Sequence ID in Entrez format.
Returns:	Full path to downloaded fasta file
Return type:	str

classmethod downloadPDB(pdb_id, pdb_dir=None, remote_ok=False)¶

Parse PDB ID string and download PDB file.

Parameters:	pdb_id (str) – PDB ID with optional chain (e.g. 4hhb, 4hhbA, 4hhb:A) pdb_dir (str) – directory to check for existing files and destination to download new files remote_ok (bool) – whether it’s okay to make a remote query.
Returns:	Full path to downloaded PDB path
Type:	str
Raises:	GetSequencesException – if pdb file can’t be downloaded

classmethod downloadUniprotSeq(sequence_id)¶

Download a sequence from Uniprot database.

Parameters:	sequence_id (str) – Sequence ID in Uniprot format.
Returns:	Full path to downloaded fasta file
Return type:	str

class schrodinger.application.msv.seqio.StructureConverter(ct, eid=None)¶

Bases: object

Reads a structure and converts it to a list of sequences

classmethod convert(ct, eid=None)¶

Convert the provided structure into a list of sequences.

Parameters:	ct (schrodinger.structure.Structure) – A structure to convert to sequences. eid (str) – The entry id to assign to the created sequences. If not given, the entry id from the structure will be used.
Returns:	A list of sequences, one per chain.
Return type:	list[sequence.Sequence]

classmethod convertStructResidue(struct_res, make_res)¶

Convert a structure._Residue into a residue.SequenceElement.

Parameters:	struct_res (structure._Residue or residue.SequenceElement) – A structure residue to convert. If this is a `residue.SequenceElement` object, it will be returned unchanged. make_res (callable) – A method to convert a string into a `residue.SequenceElement`
Returns:	A newly created residue
Return type:	residue.SequenceElement

static get_b_factor(struct_res)¶

Takes a _Residue object and returns its temperature/b factor. :param struct_res: The residue to extract the b factor from :type struct_res: schrodinger.structure._Residue or None

Returns:	The b factor of a residue
Return type:	float or None

makeSequences()¶

Note that disulfide bonds might be between chains, so need to be calculated at the ct level

Returns:	A list of sequences, one per chain.
Return type:	list[sequence.Sequence]

class schrodinger.application.msv.seqio.TextAlignmentWriter¶

Bases: schrodinger.application.msv.seqio.FastaAlignmentWriter

Class for writing alignments in text format

HEADER_END = '. '¶

HEADER_START = ''¶

schrodinger.application.msv.seqio.maestro_get_pdb(maestro_pdb_id, pdb_dir=None, remote_ok=False)¶

Download a PDB file. If specified, the chain will be split out into a separate file.

Parameters:	maestro_pdb_id (str) – 4-letter PDB code or code:chain (e.g. 4hhb or 4hhb:A) pdb_dir (str) – directory to check for existing files and destination to download new files remote_ok (bool) – whether it’s okay to make a remote query.
Returns:	downloaded PDB path
Return type:	str
Raises:	GetSequencesException – if pdb file can’t be downloaded

schrodinger.application.msv.seqio.make_maestro_pdb_id(pdb_id)¶

Convert a PDB ID to “:”-separated PDB code and PDB chain (e.g. 4hhb if chain is blank or 4hhb:A)

Parameters:	pdb_id (str) – PDB ID with optional chain, e.g. 4hhb, 4hhbA, 4hhb:A, 4hhb_A
Returns:	PDB ID with “:” between PDB code and PDB chain
Return type:	str

schrodinger.application.msv.seqio.parse_fasta_header(header, permissive=True)¶

Parse a FASTA header into a (pdb code, pdb chain) Named tuple.

Parameters:	header (str) – The header for a single entry in a FASTA file (including leading comment character) permissive (bool) – Whether to use permissive parsing. See `parse_pdb_id` for documentation.
Returns:	Named tuple of (pdbcode, pdbchain)
Type:	`PdbParts` (str, str)

schrodinger.application.msv.seqio.parse_pdb_id(pdb_id, permissive=False)¶

Parse a PDB ID into a (pdb code, pdb chain) Named tuple.

Parameters:	pdb_id (str) – PDB ID with optional chain, e.g. 4hhb, 4hhbA, 4hhb:A, 4hhb_A permissive (bool) – Whether to use permissive parsing. In strict mode, PDB ID must be 4 characters starting with a digit and single-letter chain is optional. In permissive mode, PDB ID can contain any non-whitespace characters but chain separator and single-letter chain are required.
Returns:	Named tuple of (pdbcode, pdbchain)
Type:	PdbParts (str, str)
Raises:	GetSequencesException – if pdb_id can’t be parsed

schrodinger.application.msv.seqio.to_biopython(seq)¶

Converts a sequence to a BioPython sequence

Parameters:	seq (`schrodinger.protein.sequence.ProteinSequence`) – A sequence to convert to a BioPython sequence
Return type:	`BioPython.SeqRecord`
Returns:	The sequence converted to a BioPython SeqRecord

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