The Protein Class

The Protein Class

Introduction

This section will give an overview of the methods that can be executed for the Protein class, which is a basic representation of a protein by a collection of amino acid sequences and 3D structures.

Features

  • Load, parse, and store the same (ie. from different database sources) or similar (ie. from different strains) protein sequences as SeqProp objects in the sequences attribute
  • Load, parse, and store multiple experimental or predicted protein structures as StructProp objects in the structures attribute
  • Set a single representative_sequence and representative_structure
  • Calculate, store, and access pairwise sequence alignments to the representative sequence or structure
  • Provide summaries of alignments and mutations seen
  • Map between residue numbers of sequences and structures

API

Protein

class ssbio.core.protein.Protein(ident, description=None, root_dir=None, pdb_file_type='mmtf')[source]

Store information about a protein, which represents the monomeric translated unit of a gene.

The main utilities of this class are to:

  • Load, parse, and store the same (ie. from different database sources) or similar (ie. from different strains) protein sequences as SeqProp objects in the sequences attribute
  • Load, parse, and store multiple experimental or predicted protein structures as StructProp objects in the structures attribute
  • Set a single representative_sequence and representative_structure
  • Calculate, store, and access pairwise sequence alignments to the representative sequence or structure
  • Provide summaries of alignments and mutations seen
  • Map between residue numbers of sequences and structures
Parameters:
  • ident (str) – Unique identifier for this protein
  • description (str) – Optional description for this protein
  • root_dir (str) – Path to where the folder named by this protein’s ID will be created. Default is current working directory.
  • pdb_file_type (str) – pdb, pdb.gz, mmcif, cif, cif.gz, xml.gz, mmtf, mmtf.gz - choose a file type for files downloaded from the PDB

Todo

  • Implement structural alignment objects with FATCAT
add_features_to_nglview(view, seqprop=None, structprop=None, chain_id=None, use_representatives=False)[source]

Add select features from the selected SeqProp object to an NGLWidget view object.

Currently parsing for:

  • Single residue features (ie. metal binding sites)
  • Disulfide bonds
Parameters:
  • view (NGLWidget) – NGLWidget view object
  • seqprop (SeqProp) – SeqProp object
  • structprop (StructProp) – StructProp object
  • chain_id (str) – ID of the structure’s chain to get annotation from
  • use_representatives (bool) – If the representative sequence/structure/chain IDs should be used
add_fingerprint_to_nglview(view, fingerprint, seqprop=None, structprop=None, chain_id=None, use_representatives=False, color='red', opacity_range=(0.8, 1), scale_range=(1, 5))[source]

Add representations to an NGLWidget view object for residues that are mutated in the sequence_alignments attribute.

Parameters:
  • view (NGLWidget) – NGLWidget view object
  • fingerprint (dict) – Single mutation group from the sequence_mutation_summary function
  • seqprop (SeqProp) – SeqProp object
  • structprop (StructProp) – StructProp object
  • chain_id (str) – ID of the structure’s chain to get annotation from
  • use_representatives (bool) – If the representative sequence/structure/chain IDs should be used
  • color (str) – Color of the mutations (overridden if unique_colors=True)
  • opacity_range (tuple) – Min/max opacity values (mutations that show up more will be opaque)
  • scale_range (tuple) – Min/max size values (mutations that show up more will be bigger)
add_mutations_to_nglview(view, alignment_type='seqalign', alignment_ids=None, seqprop=None, structprop=None, chain_id=None, use_representatives=False, grouped=False, color='red', unique_colors=True, opacity_range=(0.8, 1), scale_range=(1, 5))[source]

Add representations to an NGLWidget view object for residues that are mutated in the sequence_alignments attribute.

Parameters:
  • view (NGLWidget) – NGLWidget view object
  • alignment_type (str) – Specified alignment type contained in the annotation field of an alignment object, seqalign or structalign are the current types.
  • alignment_ids (str, list) – Specified alignment ID or IDs to use
  • seqprop (SeqProp) – SeqProp object
  • structprop (StructProp) – StructProp object
  • chain_id (str) – ID of the structure’s chain to get annotation from
  • use_representatives (bool) – If the representative sequence/structure/chain IDs should be used
  • grouped (bool) – If groups of mutations should be colored and sized together
  • color (str) – Color of the mutations (overridden if unique_colors=True)
  • unique_colors (bool) – If each mutation/mutation group should be colored uniquely
  • opacity_range (tuple) – Min/max opacity values (mutations that show up more will be opaque)
  • scale_range (tuple) – Min/max size values (mutations that show up more will be bigger)
align_seqprop_to_structprop(seqprop, structprop, chains=None, outdir=None, engine='needle', parse=True, force_rerun=False, **kwargs)[source]

Run and store alignments of a SeqProp to chains in the mapped_chains attribute of a StructProp.

Alignments are stored in the sequence_alignments attribute, with the IDs formatted as <SeqProp_ID>_<StructProp_ID>-<Chain_ID>. Although it is more intuitive to align to individual ChainProps, StructProps should be loaded as little as possible to reduce run times so the alignment is done to the entire structure.

Parameters:
  • seqprop (SeqProp) – SeqProp object with a loaded sequence
  • structprop (StructProp) – StructProp object with a loaded structure
  • chains (str, list) – Chain ID or IDs to map to. If not specified, mapped_chains attribute is inspected for chains. If no chains there, all chains will be aligned to.
  • outdir (str) – Directory to output sequence alignment files (only if running with needle)
  • engine (str) – biopython or needle - which pairwise alignment program to use. needle is the standard EMBOSS tool to run pairwise alignments. biopython is Biopython’s implementation of needle. Results can differ!
  • parse (bool) – Store locations of mutations, insertions, and deletions in the alignment object (as an annotation)
  • force_rerun (bool) – If alignments should be rerun
  • **kwargs – Other alignment options

Todo

  • Document **kwargs for alignment options
blast_representative_sequence_to_pdb(seq_ident_cutoff=0, evalue=0.0001, display_link=False, outdir=None, force_rerun=False)[source]

BLAST the representative protein sequence to the PDB. Saves a raw BLAST result file (XML file).

Parameters:
  • seq_ident_cutoff (float, optional) – Cutoff results based on percent coverage (in decimal form)
  • evalue (float, optional) – Cutoff for the E-value - filters for significant hits. 0.001 is liberal, 0.0001 is stringent (default).
  • display_link (bool, optional) – Set to True if links to the HTML results should be displayed
  • outdir (str) – Path to output directory of downloaded XML files, must be set if protein directory was not initialized
  • force_rerun (bool, optional) – If existing BLAST results should not be used, set to True. Default is False.
Returns:

List of new PDBProp objects added to the structures attribute

Return type:

list

df_homology_models

DataFrame – Get a dataframe of I-TASSER homology model results

df_pdb_blast

DataFrame – Get a dataframe of PDB BLAST results

df_pdb_metadata

DataFrame – Get a dataframe of PDB metadata (PDBs have to be downloaded first)

df_pdb_ranking

DataFrame – Get a dataframe of UniProt -> best structure in PDB results

filter_sequences(seq_type)[source]

Return a DictList of only specified types in the sequences attribute.

Parameters:seq_type (SeqProp) – Object type
Returns:A filtered DictList of specified object type only
Return type:DictList
find_disulfide_bridges(representative_only=True)[source]

Run Biopython’s disulfide bridge finder and store found bridges.

Annotations are stored in the protein structure’s chain sequence at: <chain_prop>.seq_record.annotations['SSBOND-biopython']

Parameters:representative_only (bool) – If analysis should only be run on the representative structure
find_representative_chain(seqprop, structprop, chains_to_check=None, seq_ident_cutoff=0.5, allow_missing_on_termini=0.2, allow_mutants=True, allow_deletions=False, allow_insertions=False, allow_unresolved=True)[source]

Set and return the representative chain based on sequence quality checks to a reference sequence.

Parameters:
  • seqprop (SeqProp) – SeqProp object to compare to chain sequences
  • structprop (StructProp) – StructProp object with chains to compare to in the mapped_chains attribute. If there are none present, chains_to_check can be specified, otherwise all chains are checked.
  • chains_to_check (str, list) – Chain ID or IDs to check for sequence coverage quality
  • seq_ident_cutoff (float) – Percent sequence identity cutoff, in decimal form
  • allow_missing_on_termini (float) – Percentage of the total length of the reference sequence which will be ignored when checking for modifications. Example: if 0.1, and reference sequence is 100 AA, then only residues 5 to 95 will be checked for modifications.
  • allow_mutants (bool) – If mutations should be allowed or checked for
  • allow_deletions (bool) – If deletions should be allowed or checked for
  • allow_insertions (bool) – If insertions should be allowed or checked for
  • allow_unresolved (bool) – If unresolved residues should be allowed or checked for
Returns:

the best chain ID, if any

Return type:

str

get_dssp_annotations(representative_only=True, force_rerun=False)[source]

Run DSSP on structures and store calculations.

Annotations are stored in the protein structure’s chain sequence at: <chain_prop>.seq_record.letter_annotations['*-dssp']

Parameters:
  • representative_only (bool) – If analysis should only be run on the representative structure
  • force_rerun (bool) – If calculations should be rerun even if an output file exists

Todo

  • Some errors arise from storing annotations for nonstandard amino acids, need to run DSSP separately for those
get_experimental_structures()[source]

DictList: Return a DictList of all experimental structures in self.structures

get_freesasa_annotations(include_hetatms=False, representative_only=True, force_rerun=False)[source]

Run freesasa on structures and store calculations.

Annotations are stored in the protein structure’s chain sequence at: <chain_prop>.seq_record.letter_annotations['*-freesasa']

Parameters:
  • include_hetatms (bool) – If HETATMs should be included in calculations. Defaults to False.
  • representative_only (bool) – If analysis should only be run on the representative structure
  • force_rerun (bool) – If calculations should be rerun even if an output file exists
get_homology_models()[source]

DictList: Return a DictList of all homology models in self.structures

get_msms_annotations(representative_only=True, force_rerun=False)[source]

Run MSMS on structures and store calculations.

Annotations are stored in the protein structure’s chain sequence at: <chain_prop>.seq_record.letter_annotations['*-msms']

Parameters:
  • representative_only (bool) – If analysis should only be run on the representative structure
  • force_rerun (bool) – If calculations should be rerun even if an output file exists
get_residue_annotations(seq_resnum, seqprop=None, structprop=None, chain_id=None, use_representatives=False)[source]

Get all residue-level annotations stored in the SeqProp letter_annotations field for a given residue number.

Uses the representative sequence, structure, and chain ID stored by default. If other properties from other structures are desired, input the proper IDs. An alignment for the given sequence to the structure must be present in the sequence_alignments list.

Parameters:
  • seq_resnum (int) – Residue number in the sequence
  • seqprop (SeqProp) – SeqProp object
  • structprop (StructProp) – StructProp object
  • chain_id (str) – ID of the structure’s chain to get annotation from
  • use_representatives (bool) – If the representative sequence/structure/chain IDs should be used
Returns:

All available letter_annotations for this residue number

Return type:

dict

get_sequence_properties(representative_only=True)[source]

Run Biopython ProteinAnalysis and EMBOSS pepstats to summarize basic statistics of the protein sequences. Results are stored in the protein’s respective SeqProp objects at .annotations

Parameters:representative_only (bool) – If analysis should only be run on the representative sequence
load_itasser_folder(ident, itasser_folder, organize=False, outdir=None, organize_name=None, set_as_representative=False, representative_chain='X', force_rerun=False)[source]

Load the results folder from an I-TASSER run (local, not from the website) and copy relevant files over to the protein structures directory.

Parameters:
  • ident (str) – I-TASSER ID
  • itasser_folder (str) – Path to results folder
  • organize (bool) – If select files from modeling should be copied to the Protein directory
  • outdir (str) – Path to directory where files will be copied and organized to
  • organize_name (str) – Basename of files to rename results to. If not provided, will use id attribute.
  • set_as_representative – If this structure should be set as the representative structure
  • representative_chain (str) – If set_as_representative is True, provide the representative chain ID
  • force_rerun (bool) – If the PDB should be reloaded if it is already in the list of structures
Returns:

The object that is now contained in the structures attribute

Return type:

ITASSERProp

load_kegg(kegg_id, kegg_organism_code=None, kegg_seq_file=None, kegg_metadata_file=None, set_as_representative=False, download=False, outdir=None, force_rerun=False)[source]

Load a KEGG ID, sequence, and metadata files into the sequences attribute.

Parameters:
  • kegg_id (str) – KEGG ID
  • kegg_organism_code (str) – KEGG organism code to prepend to the kegg_id if not part of it already. Example: eco:b1244, eco is the organism code
  • kegg_seq_file (str) – Path to KEGG FASTA file
  • kegg_metadata_file (str) – Path to KEGG metadata file (raw KEGG format)
  • set_as_representative (bool) – If this KEGG ID should be set as the representative sequence
  • download (bool) – If the KEGG sequence and metadata files should be downloaded if not provided
  • outdir (str) – Where the sequence and metadata files should be downloaded to
  • force_rerun (bool) – If ID should be reloaded and files redownloaded
Returns:

object contained in the sequences attribute

Return type:

KEGGProp

load_manual_sequence(seq, ident=None, write_fasta_file=False, outdir=None, set_as_representative=False, force_rewrite=False)[source]

Load a manual sequence given as a string and optionally set it as the representative sequence. Also store it in the sequences attribute.

Parameters:
  • seq (str, Seq, SeqRecord) – Sequence string, Biopython Seq or SeqRecord object
  • ident (str) – Optional identifier for the sequence, required if seq is a string. Also will override existing IDs in Seq or SeqRecord objects if set.
  • write_fasta_file (bool) – If this sequence should be written out to a FASTA file
  • outdir (str) – Path to output directory
  • set_as_representative (bool) – If this sequence should be set as the representative one
  • force_rewrite (bool) – If the FASTA file should be overwritten if it already exists
Returns:

Sequence that was loaded into the sequences attribute

Return type:

SeqProp

load_manual_sequence_file(ident, seq_file, copy_file=False, outdir=None, set_as_representative=False)[source]

Load a manual sequence, given as a FASTA file and optionally set it as the representative sequence. Also store it in the sequences attribute.

Parameters:
  • ident (str) – Sequence ID
  • seq_file (str) – Path to sequence FASTA file
  • copy_file (bool) – If the FASTA file should be copied to the protein’s sequences folder or the outdir, if protein folder has not been set
  • outdir (str) – Path to output directory
  • set_as_representative (bool) – If this sequence should be set as the representative one
Returns:

Sequence that was loaded into the sequences attribute

Return type:

SeqProp

load_pdb(pdb_id, mapped_chains=None, pdb_file=None, file_type=None, is_experimental=True, set_as_representative=False, representative_chain=None, force_rerun=False)[source]

Load a structure ID and optional structure file into the structures attribute.

Parameters:
  • pdb_id (str) – PDB ID
  • mapped_chains (str, list) – Chain ID or list of IDs which you are interested in
  • pdb_file (str) – Path to PDB file
  • file_type (str) – Type of PDB file
  • is_experimental (bool) – If this structure file is experimental
  • set_as_representative (bool) – If this structure should be set as the representative structure
  • representative_chain (str) – If set_as_representative is True, provide the representative chain ID
  • force_rerun (bool) – If the PDB should be reloaded if it is already in the list of structures
Returns:

The object that is now contained in the structures attribute

Return type:

PDBProp

load_uniprot(uniprot_id, uniprot_seq_file=None, uniprot_xml_file=None, download=False, outdir=None, set_as_representative=False, force_rerun=False)[source]

Load a UniProt ID and associated sequence/metadata files into the sequences attribute.

Sequence and metadata files can be provided, or alternatively downloaded with the download flag set to True. Metadata files will be downloaded as XML files.

Parameters:
  • uniprot_id (str) – UniProt ID/ACC
  • uniprot_seq_file (str) – Path to FASTA file
  • uniprot_xml_file (str) – Path to UniProt XML file
  • download (bool) – If sequence and metadata files should be downloaded
  • outdir (str) – Output directory for sequence and metadata files
  • set_as_representative (bool) – If this sequence should be set as the representative one
  • force_rerun (bool) – If files should be redownloaded and metadata reloaded
Returns:

Sequence that was loaded into the sequences attribute

Return type:

UniProtProp

map_seqprop_resnums_to_structprop_resnums(resnums, seqprop=None, structprop=None, chain_id=None, use_representatives=False)[source]

Map a residue number in any SeqProp to the structure’s residue number for a specified chain.

Parameters:
  • resnums (int, list) – Residue numbers in the sequence
  • seqprop (SeqProp) – SeqProp object
  • structprop (StructProp) – StructProp object
  • chain_id (str) – Chain ID to map to
  • use_representatives (bool) – If the representative sequence and structure should be used. If True, seqprop, structprop, and chain_id do not need to be defined.
Returns:

Mapping of sequence residue numbers to structure residue numbers

Return type:

dict

map_structprop_resnums_to_seqprop_resnums(resnums, structprop=None, chain_id=None, seqprop=None, use_representatives=False)[source]

Map a residue number in any StructProp + chain ID to any SeqProp’s residue number.

Parameters:
  • resnums (int, list) – Residue numbers in the structure
  • structprop (StructProp) – StructProp object
  • chain_id (str) – Chain ID to map from
  • seqprop (SeqProp) – SeqProp object
  • use_representatives (bool) – If the representative sequence and structure should be used. If True, seqprop, structprop, and chain_id do not need to be defined.
Returns:

Mapping of structure residue numbers to sequence residue numbers

Return type:

dict

map_uniprot_to_pdb(seq_ident_cutoff=0.0, outdir=None, force_rerun=False)[source]

Map the representative sequence’s UniProt ID to PDB IDs using the PDBe “Best Structures” API. Will save a JSON file of the results to the protein sequences folder.

The “Best structures” API is available at https://www.ebi.ac.uk/pdbe/api/doc/sifts.html The list of PDB structures mapping to a UniProt accession sorted by coverage of the protein and, if the same, resolution.

Parameters:
  • seq_ident_cutoff (float) – Sequence identity cutoff in decimal form
  • outdir (str) – Output directory to cache JSON results of search
  • force_rerun (bool) – Force re-downloading of JSON results if they already exist
Returns:

A rank-ordered list of PDBProp objects that map to the UniProt ID

Return type:

list

num_sequences

int – Return the total number of sequences

num_structures

int – Return the total number of structures

num_structures_experimental

int – Return the total number of experimental structures

num_structures_homology

int – Return the total number of homology models

pairwise_align_sequences_to_representative(gapopen=10, gapextend=0.5, outdir=None, engine='needle', parse=True, force_rerun=False)[source]

Pairwise all sequences in the sequences attribute to the representative sequence. Stores the alignments in the sequence_alignments DictList attribute.

Parameters:
  • gapopen (int) – Only for engine='needle' - Gap open penalty is the score taken away when a gap is created
  • gapextend (float) – Only for engine='needle' - Gap extension penalty is added to the standard gap penalty for each base or residue in the gap
  • outdir (str) – Only for engine='needle' - Path to output directory. Default is the protein sequence directory.
  • engine (str) – biopython or needle - which pairwise alignment program to use. needle is the standard EMBOSS tool to run pairwise alignments. biopython is Biopython’s implementation of needle. Results can differ!
  • parse (bool) – Store locations of mutations, insertions, and deletions in the alignment object (as an annotation)
  • force_rerun (bool) – Only for engine='needle' - Default False, set to True if you want to rerun the alignment if outfile exists.
pdb_downloader_and_metadata(outdir=None, pdb_file_type=None, force_rerun=False)[source]

Download ALL mapped experimental structures to the protein structures directory.

Parameters:
  • outdir (str) – Path to output directory, if protein structures directory not set or other output directory is desired
  • pdb_file_type (str) – Type of PDB file to download, if not already set or other format is desired
  • force_rerun (bool) – If files should be re-downloaded if they already exist
Returns:

List of PDB IDs that were downloaded

Return type:

list

Todo

  • Parse mmtf or PDB file for header information, rather than always getting the cif file for header info
pdb_file_type = None

strpdb, pdb.gz, mmcif, cif, cif.gz, xml.gz, mmtf, mmtf.gz - choose a file type for files downloaded from the PDB

prep_itasser_modeling(itasser_installation, itlib_folder, runtype, create_in_dir=None, execute_from_dir=None, print_exec=False, **kwargs)[source]

Prepare to run I-TASSER homology modeling for the representative sequence.

Parameters:
  • itasser_installation (str) – Path to I-TASSER folder, i.e. ~/software/I-TASSER4.4
  • itlib_folder (str) – Path to ITLIB folder, i.e. ~/software/ITLIB
  • runtype – How you will be running I-TASSER - local, slurm, or torque
  • create_in_dir (str) – Local directory where folders will be created
  • execute_from_dir (str) – Optional path to execution directory - use this if you are copying the homology models to another location such as a supercomputer for running
  • all_genes (bool) – If all genes should be prepped, or only those without any mapped structures
  • print_exec (bool) – If the execution statement should be printed to run modelling

Todo

  • Document kwargs - extra options for I-TASSER, SLURM or Torque execution
  • Allow modeling of any sequence in sequences attribute, select by ID or provide SeqProp?
protein_dir

str – Protein folder

protein_statistics

Get a dictionary of basic statistics describing this protein

representative_chain = None

str – Chain ID in the representative structure which best represents a sequence

representative_chain_seq_coverage = None

float – Percent identity of sequence coverage for the representative chain

representative_sequence = None

SeqProp – Sequence set to represent this protein

representative_structure = None

StructProp – Structure set to represent this protein, usually in monomeric form

root_dir

str – Path to where the folder named by this protein’s ID will be created. Default is current working directory.

sequence_alignments = None

DictList – Pairwise or multiple sequence alignments stored as Bio.Align.MultipleSeqAlignment objects

sequence_dir

str – Directory where sequence related files are stored

sequence_mutation_summary(alignment_ids=None, alignment_type=None)[source]

Summarize all mutations found in the sequence_alignments attribute.

Returns 2 dictionaries, single_counter and fingerprint_counter.

single_counter:

Dictionary of {point mutation: list of genes/strains} Example:

{
    ('A', 24, 'V'): ['Strain1', 'Strain2', 'Strain4'],
    ('R', 33, 'T'): ['Strain2']
}

Here, we report which genes/strains have the single point mutation.

fingerprint_counter:

Dictionary of {mutation group: list of genes/strains} Example:

{
    (('A', 24, 'V'), ('R', 33, 'T')): ['Strain2'],
    (('A', 24, 'V')): ['Strain1', 'Strain4']
}

Here, we report which genes/strains have the specific combinations (or “fingerprints”) of point mutations

Parameters:
  • alignment_ids (str, list) – Specified alignment ID or IDs to use
  • alignment_type (str) – Specified alignment type contained in the annotation field of an alignment object, seqalign or structalign are the current types.
Returns:

single_counter, fingerprint_counter

Return type:

dict, dict

sequences = None

DictList – Stored protein sequences which are related to this protein

set_representative_sequence(force_rerun=False)[source]

Automatically consolidate loaded sequences (manual, UniProt, or KEGG) and set a single representative sequence.

Manually set representative sequences override all existing mappings. UniProt mappings override KEGG mappings except when KEGG mappings have PDBs associated with them and UniProt doesn’t.

Parameters:force_rerun (bool) – Set to True to recheck stored sequences
Returns:Which sequence was set as representative
Return type:SeqProp
set_representative_structure(seq_outdir=None, struct_outdir=None, pdb_file_type=None, engine='needle', always_use_homology=False, rez_cutoff=0.0, seq_ident_cutoff=0.5, allow_missing_on_termini=0.2, allow_mutants=True, allow_deletions=False, allow_insertions=False, allow_unresolved=True, clean=True, keep_chemicals=None, force_rerun=False)[source]

Set a representative structure from a structure in the structures attribute.

Each gene can have a combination of the following, which will be analyzed to set a representative structure.
  • Homology model(s)
  • Ranked PDBs
  • BLASTed PDBs

If the always_use_homology flag is true, homology models are always set as representative when they exist. If there are multiple homology models, we rank by the percent sequence coverage.

Parameters:
  • seq_outdir (str) – Path to output directory of sequence alignment files, must be set if Protein directory was not created initially
  • struct_outdir (str) – Path to output directory of structure files, must be set if Protein directory was not created initially
  • pdb_file_type (str) – pdb, pdb.gz, mmcif, cif, cif.gz, xml.gz, mmtf, mmtf.gz - choose a file type for files downloaded from the PDB
  • engine (str) – biopython or needle - which pairwise alignment program to use. needle is the standard EMBOSS tool to run pairwise alignments. biopython is Biopython’s implementation of needle. Results can differ!
  • always_use_homology (bool) – If homology models should always be set as the representative structure
  • rez_cutoff (float) – Resolution cutoff, in Angstroms (only if experimental structure)
  • seq_ident_cutoff (float) – Percent sequence identity cutoff, in decimal form
  • allow_missing_on_termini (float) – Percentage of the total length of the reference sequence which will be ignored when checking for modifications. Example: if 0.1, and reference sequence is 100 AA, then only residues 5 to 95 will be checked for modifications.
  • allow_mutants (bool) – If mutations should be allowed or checked for
  • allow_deletions (bool) – If deletions should be allowed or checked for
  • allow_insertions (bool) – If insertions should be allowed or checked for
  • allow_unresolved (bool) – If unresolved residues should be allowed or checked for
  • clean (bool) – If structure should be cleaned
  • keep_chemicals (str, list) – Keep specified chemical names if structure is to be cleaned
  • force_rerun (bool) – If sequence to structure alignment should be rerun
Returns:

Representative structure from the list of structures. This is a not a map to the original structure, it is copied and optionally cleaned from the original one.

Return type:

StructProp

structure_alignments = None

DictList – Pairwise or multiple structure alignments - currently a placeholder

structure_dir

str – Directory where structure related files are stored

structures = None

DictList – Stored protein structures which are related to this protein

Further reading

For examples in which tools from the Protein class have been used for analysis, please see the following:

[1]Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, et al. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016;113: E8344–E8353. doi:10.1073/pnas.1613446113
[2]Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016;12: e1005039. doi:10.1371/journal.pcbi.1005039