Table of Contents¶

Introduction¶

Flowchart describing the ELASPIC pipeline.

ELASPIC can be run using two different pipelines: the Local pipeline and the Database pipeline.

Database pipeline¶

The database pipeline allows mutations to be performed on a proteome-wide scale, without having to specify a structural template for each protein. This pipeline requires a local copy of ELASPIC domain definitions and templates, as well as a local copy of the BLAST and PDB databases.

The general overview of the database pipleine is presented in the figure to the right. A user runs the ELASPIC pipeline specifying the Uniprot ID of the protein being mutated, and one or more mutations affecting that protein. At each decision node, the pipeline queries the database to check whether or not the required information has been previously calculated. If the required data has not been calculated, the pipeline calculates it on the fly and stores the results in the database for later retrieval. The pipeline proceeds until homology models of all domains in the protein, and all domain-domain interactions involving the protein, have been calculated, and the $\Delta \Delta G$ has been predicted for every specified mutation.

Local pipeline¶

The local pipeline works without downloading and installing a local copy of the ELASPIC and PDB databases, but requires a PDB structure or template to be provided for every protein. Pipeline output is saves as JSON files inside the working directory, rather than being uploaded to the database as in the case of the database pipeline. The general overview of the local pipleine is presented in the figure to the right.

The local pipeline still requires a local copy of the Blast nr database.

Installation Guide¶

In order to use the ELASPIC Local pipeline of your computer:

Install Python and ELASPIC (Installing Python and ELASPIC).
Download the BLAST database and preferrably also the PDB database to a local folder (Downloading external datasets).

In order to use the ELASPIC Database pipeline, in addition to the steps above:

Create a local database and modify the configuration file to match your system and database setting (Updating the configuration file).
Download Profs domain definitions for your organism of interest, and upload the data to a local database (Importing precalculated data).

Installing Python and ELASPIC¶

Download and install the Anaconda Python Distribution (Python 3) for Linux.

Add bioconda, salilab, and ostrokach channels to your ~/.condarc file:

conda config --add channels ostrokach
conda config --add channels salilab
conda config --add channels bioconda

Obtain a Modeller license, and export the license as KEY_MODELLER in your ~/.bashrc file:
```
# ~/.bashrc
export KEY_MODELLER=XXXXXXX
```
Install ELASPIC and all its dependencies into a new conda environment:
```
conda create -n elaspic elaspic
```
Activate the new environment and use elaspic:
```
source activate elaspic
elaspic --help
```

Downloading external datasets¶

Blast¶

Download and extract the nr and pdbaa databases from ftp://ftp.ncbi.nlm.nih.gov/blast/db/, and change the blast_db_dir variable in your configuration file to point to the directory containing the uncompressed files.

PDB¶

Download the contents of the ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/ folder, and change the pdb_dir variable in your configuration file to point to the directory containing the downloaded data.

Updating the configuration file¶

Edit the ELASPIC configuration file ./config/config_file.ini to match your system:

Settings in the [SEQUENCE] section should be modified to match the location of your local BLAST and PDB databases.
Settings in the [DATABASE] section should be modified to match the local MySQL, PostgreSQL, or SQLite database.
Settings in the [DEFAULT] and [MODEL] may be left unchanged, since the default values are good enough in most cases.

Configuration options¶

[DEFAULT]¶

global_temp_dir: Location for storing temporary files. It will be used only if the TMPDIR environmental variable is not set. Default = ‘/tmp/’.
temp_dir string: A folder in the global_temp_dir that will contain all the files that are relevant to ELASPIC. Inside this folder, every job will create its own unique subfolder. Default = ‘elaspic/’.
debug: Whether or not to show detailed debugging information. If True, the logging level will be set to logging.DEBUG. If False, the logging level will be set to logging.INFO. Default = True.
look_for_interactions: Whether or not to compute models of protein-protein interactions. Default = True.
remake_provean_supset: Whether or not to remake the Provean supporting set if one or more sequences cannot be found in the BLAST database. Default = False.
n_cores: Number of cores to use by programs that support multithreading. Default = 1.
web_server: Whether or not the ELASPIC pipeline is being run as part of a webserver. Default = False.
provean_temp_dir: Location to store provean temporary files if working on any note other than beagle or banting. For internal use only. Default = ‘’.
copy_data: Whether or not to copy calculated data back to the archive. Set to ‘False’ if you are planning to copy the data yourself (e.g. from inside a PBS or SGE script). Default = True.

[SEQUENCE]¶

blast_db_dir: Location of the blast nr and pdbaa databases.
blast_db_dir_fallback: Place to look for blast nr and pdbaa databases if blast_db_dir does not exist.
matrix_type: Substitution matrix for calculating the mutation conservation score. Default = ‘blosum80’.
gap_start: Penalty for starting a gap when calculating the mutation conservation score. Default = -16.
gap_extend: Penalty for extending a gap when calculating the mutation conservation score. Default = -4.

[MODEL]¶

modeller_runs

Number of models that MODELLER should make before choosing the best one. Not implemented! Default = 1.

foldx_water

-CRYSTAL: use water molecules in the crystal structure to bridge two protein atoms.
-PREDICT: predict water molecules that make 2 or more hydrogen bonds to the protein.
-COMPARE: compare predicted water bridges with bridges observed in the crystal structure.
-IGNORE: don’t predict water molecules. Default.

Source: http://foldx.crg.es/manual3.jsp.

foldx_num_of_runs

Number of times that FoldX should evaluate a given mutation. Default = 1.

[DATABASE]¶

db_type

The database that you are using. Supported databases are MySQL, PostgreSQL, and SQLite.

sqlite_db_dir

Location of the SQLite database. Required only if db_type is SQLite.

db_schema

The name of the schema that holds all elaspic data.

db_schema_uniprot

The name of the database schema that holds uniprot sequences. Defaults to db_schema.

db_database

The name of the database that contains db_schema and db_schema_uniprot. Required only if db_type is PostgreSQL. Defaults to db_schema.

db_username

The username for the database. Required only if db_type is MySQL or PostgreSQL.

db_password

The password for the database. Required only if db_type is MySQL or PostgreSQL.

db_url

The IP address of the database. Required only if db_type is MySQL or PostgreSQL.

db_port

The listening port of the database. Required only if db_type is MySQL or PostgreSQL.

db_socket

Path to the socket file, if it is not in the default location. Used only if db_url is localhost. For example: /usr/local/mysql5/mysqld.sock for MySQL and /var/lib/postgresql for PostgreSQL.

schema_version

Database schema to use for storing and retreiving data. Default = ‘elaspic’.

archive_type

extracted: all archive files are contained in an extracted directory tree.
7zip: archive is made of three compressed 7zip files (provean/provean.7z, uniprot_domain/uniprot_domain.7z, uniprot_domain_pair/uniprot_domain_pair.7z), provided on the elaspic downloads page.

archive_dir

Location for storing and retrieving precalculated data.

pdb_dir

Location of all pdb structures, equivalent to the “data/data/structures/divided/pdb/” folder in the PDB ftp site. Optional.

Environmental variables¶

PATH¶: A colon-separated list of paths where ELASPIC should look for required programs, such as BLAST, T-coffee, Modeller, and cd-hit.

TMPDIR¶: Location to store all temporary files and folders.

Importing precalculated data¶

ELASPIC downloads page¶

The ELASPIC downloads page contains all precalculated data that is required to run the ELASPIC pipeline on a local machine.

The *.tsv.gz files correspond to different tables of the ELASPIC database:

The domain.tar.gz file in the root folder contains Profs domain definitions for files in the PDB, and corresponds to the domain table.
The domain_contact.tar.gz file in the root folder contains a list of interactions between those domains, and corresponds to the domain_contact table.
All other tables are split into separate folders according to the organism of origin. The files are named using the {table_name}.tsv.gz convention, where table_name is the name of the table in the database.

The *.7z files contain precalculated data:

The provean, uniprot_domain, and uniprot_domain_pair subfolders contain precalculated provean supporting sets, and homology models of protein domains and domain-domain interactions, respectively.

Precalculated mutations:

The Homo_sapiens folder contains an additional subfolder precalculated_mutations, which contains $\Delta \Delta G$ scores for mutations in various datasets.

Note

The configure_test.sh and run_test.sh scripts in the ./scripts folder contain examples of how to download and set up a local copy of the database.

Downloading data¶

In order to run up ELASPIC on a local computer, you need to download precalculated data for your organism of interest. If your goal is to only test the pipeline, you can download a test dataset from the folder current_release/Homo_sapiens_test.

To download all precalculated data for a given organism, use the wget command:

# Download external files
wget -P "${TEST_DIR}/elaspic.kimlab.org" \
    http://elaspic.kimlab.org/static/download/current_release/domain.tsv.gz
wget -P "${TEST_DIR}/elaspic.kimlab.org" \
    http://elaspic.kimlab.org/static/download/current_release/domain_contact.tsv.gz
wget -P "${TEST_DIR}" \
    -r --no-parent --reject "index.html*" --cut-dirs=4  \
    http://elaspic.kimlab.org/static/download/current_release/Homo_sapiens_test/

You need to extract the provean supporting sets and domain homology models into a folder specified by the archive_dir variable in your configuration_file:

mkdir archive  # Set 'archive_dir' variable in the config file to this folder

7z x "${TEST_DIR}/elaspic.kimlab.org/provean/provean.7z" -o"archive"
7z x "${TEST_DIR}/elaspic.kimlab.org/uniprot_domain/uniprot_domain.7z" -o"archive"
7z x "${TEST_DIR}/elaspic.kimlab.org/uniprot_domain_pair/uniprot_domain_pair.7z" -o"archive"

Importing data into a database¶

You also need to create a local SQL database and fill it with precalculated data.

Modify the database variables in the ELASPIC configuration file to match your local MySQL, PostgreSQL, or SQLite database, and use the elaspic database CLI to create a new database and fill it with precalculated data.

First, you need to create an empty database:

elaspic database -c {your_configuration_file}.ini create

Next, you need to load all precalculated data for the organism in question to your database:

elaspic database -c {your_configuration_file}.ini load_data

To delete the database that you just created, run:

elaspic database -c {your_configuration_file}.ini delete

Command Line Interface¶

After following instructions in the Installation Guide, you should be able to run ELASPIC from the command line using the elaspic command:

$ elaspic --help
usage: elaspic [-h] {run,database,train} ...

optional arguments:
  -h, --help            show this help message and exit

command:
  {run,database,train}
    run                 Run ELASPIC.
    database            Perform maintenance tasks on the ELASPIC database.
    train               Train the ELASPIC classifiers.

Type --help to see the options available for each subcommand:

elaspic run --help
elaspic database --help
elaspic database load_data --help
etc...

elaspic run¶

Run the ELASPIC pipeline.

If you wish to mutate an existing PDB, you should specify the name of the PDB file to be mutated, and the mutation(s):

elaspic run \
    --structure_file {structure_file} \
    --mutations {mutations}

If you wish to first create a homology model of a protein, you should provide a fasta file containing the sequence of the protein to be modelled, a PDB file containing the structural template, and the mutation(s):

elaspic run \
    --sequence_file {sequence_file} \
    --structure_file {structure_file} \
    --mutations {mutations}

If you wish to perform mutagenesis on a proteome-wide scale, you need to download protein domain definitions from the elaspic downloads page, and optionally a local copy of the PDB database. After saving your database information to a configuration file, you can run specify the uniprot id and mutation(s):

elaspic run \
  --config_file {config_file} \
  --uniprot_id {uniprot_id} \
  --mutations {mutations}

elaspic train¶

Train the machine learning predictor for the ELASPIC pipeline.

This is automatically done at install time, and you do not need to do this again unless you update your scikit-learn version.

elaspic database¶

Perform maintenance tasks on the ELASPIC database.

You must provide a configuration file containing the details of your database installation for any of these commands to work. For more information about configuration files, see Updating the configuration file.

elaspic database create¶

Create a new database schema.

elaspic database load_data¶

Load data to the database.

elaspic database delete¶

Delete the database schema.

Benchmarks¶

Work in progres...

Statistics¶

Work in progres...

Database¶

Database schema¶

Download: pdf png mwb

Database tables¶

domain¶

Profs domain definitions for all proteins in the PDB.

Columns:

cath_id: Unique id identifying each domain in the PDB. Constructed by concatenating the pdb_id, pdb_chain, and an index specifying the order of the domain in the chain.
pdb_id: The PDB id in which the domain is found.
pdb_chain: The PDB chain in which the domain is found.
pdb_domain_def: Domain definitions of the domain, in PDB RESNUM coordinates.
pdb_pdbfam_name: The Profs name of the domain.
pdb_pdbfam_idx: An integer specifying the number of times a domain with domain name pdb_pdbfam_name has occurred in this chain up to this point. It is used to make every (pdb_id, pdb_chain, pdb_pdbfam_name, pdb_pdbfam_idx) tuple unique.
domain_errors: List of errors that occurred when annotating this domain, or when using this domain to make structural homology models.

domain_contact¶

Interactions between Profs domains in the PDB. Only interactions that were predicted to be biologically relevant by NOXclass are included in this table.

Columns:

domain_contact_id: A unique integer identifying each domain pair.
cath_id_1: Unique id identifying the first interacting domain in the domain table.
cath_id_2: Unique id identifying the second interacting domain in the domain table.
min_interchain_distance: The closest that any residue in domain one comes to any residue in domain two.
contact_volume: The volume covered by contacting residues.
contact_surface_area: The surface area of the contacting regions of the first and second domains.
atom_count_1: The number of atoms in the first domain.
atom_count_2: The number of atoms in the second domain.
number_of_contact_residues_1: The number of residues in the first domain that come within 5 Å of the second domain.
number_of_contact_residues_2: The number of residues in the second domain that come withing 5 Å of the first domain.
contact_residues_1: A list of all residues in the first domain that come within 5 Å of the second domain. The residue number corresponds to the position of the residue in the domain.
contact_residues_2: A list of all residues in the second domain that come within 5 Å of the first domain. The residue number corresponds to the position of the residue in the domain.
crystal_packing: The probability that the interaction is a crystallization artifacts, as defined by NOXclass.
domain_contact_errors: List of errors that occurred when annotating this domain pair, or when using this domain as a template for making structural homology models.

uniprot_sequence¶

Protein sequences from the Uniprot KB, obtained by parsing uniprot_sprot_fasta.gz, uniprot_trembl_fasta.gz, and homo_sapiens_variation.txt files from the Uniprot ftp site.

Columns:

db

The database to which the protein sequence belongs. Possible values are sp for SwissProt and tr for TrEMBL.

uniprot_id

The uniprot id of the protein.

uniprot_name

The uniprot name of the protein.

protein_name

The protein name.

organism_name

Name of the organism in which this protein is found.

gene_name

Name of the gene that codes for this protein sequence.

protein_existence

Evidence for the existence of the protein:

Experimental evidence at protein level
Experimental evidence at transcript level
Protein inferred from homology
Protein predicted
Protein uncertain

sequence_version

Version of the protein amino acid sequence.

uniprot_sequence

Amino acid sequence of the protein.

provean¶

Description of the Provean supporting set calculated for a protein sequence. The construction of a supporting set is the most lengthy step in running Provean. Therefore, the supporting set is precalculated and stored for every protein sequence.

Columns:

uniprot_id: The uniprot id of the protein.
provean_supset_filename: The filename of the Provean supporting set. The supporting set contains the ids and sequences of all proteins in the NCBI nr database that are used by Provean to construct a multiple sequence alignment for the given protein.
provean_supset_length: The number of sequences in Provean supporting set.
provean_errors: List of errors that occurred while the Provean supporting set was being calculated.
provean_date_modified: Date and time that this row was last modified.

uniprot_domain¶

Pfam domain definitions for proteins in the uniprot_sequence table. This table was obtained by downloading Pfam domain definitions for all known proteins from the SIMAP website, and mapping the protein sequence to uniprot using the MD5 hash of each sequence.

Columns:

uniprot_domain_id: Unique id identifying each domain.
uniprot_id: The uniprot id of the protein containing the domain.
pdbfam_name: The Profs name of the domain. In most cases this will be equivalent to the Pfam name of the domain.
pdbfam_idx: The index of the Profs domain. pdbfam_idx ranges from 1 to the number of domains with the name pdbfam_name in the given protein. The (pdbfam_name, pdbfam_idx) tuple uniquely identifies each domain.
pfam_clan: The Pfam clan to which this Profs domain belongs.
alignment_def: Alignment domain definitions of the Profs domain. This field is obtained by removing gaps in the alignment_subdefs column.
pfam_names: Pfam names of all Pfam domains that were combined to create the given Profs domain.
alignment_subdefs: Comma-separated list of domain definitions for all Pfam domains that were merged to create the given Profs domain.
path_to_data: Location for storing homology models, mutation results, and all other data that are relevant to this domain. This path is prefixed by archive_dir.

uniprot_domain_template¶

Structural templates for domains in the uniprot_domain table. Lists PDB crystal structures that will be used for making homology models.

Columns:

uniprot_domain_id: An integer which uniquely identifies each uniprot domain in the uniprot_domain table.
template_errors: List of errors that occurred during the process for finding the template.
cath_id: The unique id identifying the structural template of the domain.
domain_start: The Uniprot position of the first amino acid of the Profs domain.
domain_end: The Uniprot position of the last amino acid of the Profs domain.
domain_def: Profs domain definitions for domains with structural templates. Domain definitions in this column are different from domain definitions in the alignment_def column of the uniprot_domain table in that they have been expanded to match domain boundaries of the Profs structural template, identified by the cath_id.
alignment_identity: Percent identity of the domain to its structural template.
alignment_coverage: Percent coverage of the domain to its structural template.
alignment_score: A score obtained by combining alignment_identity ($SeqId$) and alignment_coverage ($Cov$) using the following equation, as described by Mosca et al.:

(1)\[Score = 0.95 \cdot \frac{SeqId}{100} \cdot \frac{Cov}{100} + 0.05 \cdot \frac{Cov}{100}\]
t_date_modified: The date and time when this row was last modified.

uniprot_domain_model¶

Homology models for templates in the uniprot_domain_template table.

Columns:

uniprot_domain_id

An integer which uniquely identifies each uniprot domain in the uniprot_domain table.

model_errors

List of errors that occurred when making the homology model.

alignment_filename

The name of the alignment that was given to Modeller when making the homology model.

model_filename

The name of the homology model that was produced by Modeller.

chain

The chain that contains the domain in question in the homology (this is now set to ‘A’ in all models).

norm_dope

Normalized DOPE score of the model (lower is better).

sasa_score

Comma-separated list of the percent solvent-accessible surface area for each residue.

m_date_modified

The date and time when this row was last modified.

model_domain_def

Domain definitions for the region of the domain that is covered by the structural template.

In most cases, this field is identical to the domain_def field in the uniprot_domain_template table. However, it sometimes happens that the best Profs structural template only covers a fraction of the Pfam domain. In that case, the alignment_def column in the uniprot_domain table, and the domain_def column in the uniprot_domain_template table, will contain the original Pfam domain definitions, and the model_domain_def column will contain domain definitions for only the region that is covered by the structural template.

uniprot_domain_mutation¶

Characterization of mutations introduced into structures in the uniprot_domain_model table.

Columns:

uniprot_id

Uniprot ID of the protein that was mutated.

uniprot_domain_id

Unique id which identifies the Profs domain that was mutated in the uniprot_domain table.

mutation

Mutation that was introduced into the protein, in Uniprot coordinates.

mutation_errors

List of errors that occured while evaluating the mutation.

model_filename_wt

The name of the file which contains the homology model of the domain after the model was relaxed with FoldX but before the mutation was introduced.

model_filename_mut

The name of the file which contains the homology model of the domain after the model was relaxed with FoldX and after the mutation was introduced.

chain_modeller

The chain which contains the domain that was mutated in the model_filename_wt and the model_filename_mut structures.

mutation_modeller

The mutation that was introduced into the protein, in PDB RESNUM coordinates. This identifies the mutated residue in the model_filename_wt and the model_filename_mut structures.

stability_energy_wt

Comma-separated list of scores returned by FoldX for the wildtype protein. The comma-separated list can be converted into a DataFrame with each column clearly labelled using the elaspic.predictor.format_mutation_features(). The FoldX energy terms are:

dg

backbone_hbond

sidechain_hbond

van_der_waals

electrostatics

solvation_polar

solvation_hydrophobic

van_der_waals_clashes

entropy_sidechain

entropy_mainchain

sloop_entropy

mloop_entropy

cis_bond

torsional_clash

backbone_clash

helix_dipole

water_bridge

disulfide

electrostatic_kon

partial_covalent_bonds

energy_ionisation

entropy_complex

number_of_residues

stability_energy_mut

Comma-separated list of scores returned by FoldX for the mutant protein. FoldX energy terms are the same as in stability_energy_wt, but for the mutated amino acid rather than the wildtype.

physchem_wt

Physicochemical properties describing the interaction of the wildtype residue with residues on the opposite chain. The terms are:

number of atoms in interacting residues that have the same charge.

number of atoms in interacting residues that have an opposite charge.

number of hydrogen bonds (very rough calculation).

number of carbons in interacting residues within 4 A of the mutated residue (rough measure of the van der Waals force).

physchem_wt_ownchain

Physicochemical properties describing the interaction of the wildtype residue with residues on the same chain. The terms are the same as in physchem_wt.

physchem_mut

Physicochemical properties describing the interaction of the mutant residue with residues on the opposite chain. The terms are the same as in physchem_wt.

physchem_mut_ownchain

Physicochemical properties describing the interaction of the mutant residue with residues on the same chain. The terms are the same as in physchem_wt.

matrix_score

Score assigned to the wt -> mut transition by the BLOSUM substitution matrix.

secondary_structure_wt

Secondary structure of the wildtype residue predicted by stride.

solvent_accessibility_wt

Percent solvent accessible surface area of the wildtype residue, predicted by msms.

secondary_structure_mut

Secondary structure of the mutated residue predicted by stride.

solvent_accessibility_mut

Percent solvent accessible surface area of the mutated residue, predicted by msms.

provean_score

Score produced by Provean for this mutation.

ddg

Change in the Gibbs free energy of folding that our classifier predicts for this mutation.

mut_date_modified

Date and time that this row was last modified.

uniprot_domain_pair¶

Potentially-interacting pairs of domains for proteins that are known to interact, according to Hippie, IRefIndex, and Rolland et al. 2014.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
uniprot_domain_id_1: Unique id of the first domain.
uniprot_domain_id_2: Unique id of the second domain.
rigids: Phased out.
domain_contact_ids: List of unique ids identifying all domain-domain pairs in the PDB, where one domain belongs to the protein containing uniprot_domain_id_1 and the other domain belongs to the protein containing uniprot_domain_id_2. This was used as crystallographic evidence that the two proteins interact.
path_to_data: Location for storing homology models, mutation results, and all other data that is relevant to this domain pair. This path is prefixed by archive_dir.

uniprot_domain_pair_template¶

Structural templates for pairs of domains in the uniprot_domain_pair table.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
domain_contact_id: Unique id of the domain pair in the domain_contact table that was used as a template for the modelled domain pair.
cath_id_1: Unique id of the structural template for the first domain.
cath_id_2: Unique id of the structural template for the second domain.
identical_1: Fraction of residues in the Blast alignment of the first domain to its template that are identical.
conserved_1: Fraction of residues in the Blast alignment of the first domain to its template that are conserved.
coverage_1: Fraction of the first domain that is covered by the blast alignment.
score_1: Score obtained by multiplying identical_1 by coverage_1.
identical_if_1: Fraction of interface residues [1] that are identical in the Blast alignment of the first domain.
conserved_if_1: Fraction of interface residues [1] that are conserved in the Blast alignment of the first domain.
coverage_if_1: Fraction of interface residues [1] that are covered by the Blast alignment of the first domain.
score_if_1: Score obtained by combining identical_if_1 and coverage_if_1 using (2).
identical_2: Fraction of residues in the Blast alignment of the second domain to its template that are identical.
conserved_2: Fraction of residues in the Blast alignment of the second domain to its template that are conserved.
coverage_2: Fraction of the second domain that is covered by the blast alignment.
score_2: Score obtained by multiplying identical_2 by coverage_2.
identical_if_2: Fraction of interface residues [1] that are identical in the Blast alignment of the second domain.
conserved_if_2: Fraction of interface residues [1] that are conserved in the Blast alignment of the second domain.
coverage_if_2: Fraction of interface residues [1] that are covered by the Blast alignment of the second domain.
score_if_2: Score obtained by combining identical_if_2 and coverage_if_2 using (2).
score_total: The product of score_1 and score_2.
score_if_total: The product of score_if_1 and score_if_2.
score_overall: The product of score_total and score_if_total. This is the score that was used to select the best Profs domain pair to be used as a template.
t_date_modified: The date and time when this row was last updated.
template_errors: List of errors that occured while looking for the structural template.

[1]	(1, 2, 3, 4, 5, 6) Interface residues are defined as residues that are within 5 Å of the partner domain.

uniprot_domain_pair_model¶

Structural models of interactions between pairs of domains in the uniprot_domain_pair table.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
model_errors: List of errors that occured while making the homology model.
alignment_filename_1: Name of the file containing the alignment of the first domain with its structural template.
alignment_filename_2: Name of the file containing the alignment of the second domain with its structural template.
model_filename: Name of the file containing the homology model of the domain-domain interaction created by Modeller.
chain_1: Chain containing the first domain in the model specified by model_filename.
chain_2: Chain containing the second domain in the model specified by model_filename.
norm_dope: The normalized DOPE score of the model.
interface_area_hydrophobic: Hydrophobic surface area of the interface, calculated using POPS.
interface_area_hydrophilic: Hydrophilic surface area of the interface, calculated using POPS.
interface_area_total: Total surface area of the interface, calculated using POPS.
interface_dg: Gibbs free energy of binding for this domain-domain interaction, predicted using FoldX. Not implemented yet!
interacting_aa_1: List of amino acid positions in the first domain that are within 5 Å of the second domain. Positions are specified using uniprot coordinates.
interacting_aa_2: List of amino acids in the second domain that are within 5 Å of the first domain. Position are specified using uniprot coordinates.
m_date_modified: Date and time that this row was last modified.
model_domain_def_1: Domain boundaries of the first domain that are covered by the Profs structural template.
model_domain_def_2: Domain boundaries of the second domain that are covered by the Profs structural template.

uniprot_domain_pair_mutation¶

Characterization of interface mutations introduced into structures in the uniprot_domain_pair_model table.

Columns:

uniprot_id: Uniprot ID of the protein that is being mutated.
uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
mutation: Mutation for which the $\Delta \Delta G$ score is being predicted, specified in Uniprot coordinates.
mutation_errors: List of errors obtained when evaluating the impact of the mutation.
model_filename_wt: Filename of the homology model relaxed by FoldX but containing the wildtype residue.
model_filename_mut: Filename of the homology model relaxed by FoldX and containing the mutated residue.
chain_modeller: Chain containing the domain that was mutated, in homology models specified by model_filename_wt and model_filename_mut.
mutation_modeller: Mutation for which the $\Delta \Delta G$ score is being predicted, specified in PDB RESNUM coordinates.
analyse_complex_energy_wt: Comma-separated list of FoldX scores describing the effect of the wildtype residue on the stability of the protein domain.
stability_energy_wt: Comma-separated list of FoldX scores describing the effect of the wildtype residue on protein-protein interaction interface.
analyse_complex_energy_mut: Comma-separated list of FoldX scores describing the effect of the mutated residue on the stability of the protein domain.
stability_energy_mut: Comma-separated list of FoldX scores describing the effect of the mutated residue on protein-protein interaction interface.
physchem_wt: Comma-separated list of physicochemical properties describing the interaction between the wildtype residue and other residues on the opposite chain.
physchem_wt_ownchain: Comma-separated list of physicochemical properties describing the interaction between the wildtype residue and other residues on the same chain.
physchem_mut: Comma-separated list of physicochemical properties describing the interaction between the mutated residue and other residues on the opposite chain.
physchem_mut_ownchain: Comma-separated list of physicochemical properties describing the interaction between the mutated residue and other residues on the same chain.
matrix_score: Score assigned to the wt -> mut transition by the BLOSUM substitution matrix.
secondary_structure_wt: Secondary structure of the wildtype residue, predicted by stride.
solvent_accessibility_wt: Percent solvent accessible surface area of the wildtype residue, predicted by msms.
secondary_structure_mut: Secondary structure of the mutated residue, predicted by stride.
solvent_accessibility_mut: Percent solvent accessible surface area of the mutated residue, predicted by msms.
contact_distance_wt: Shortest distance between the wildtype residue and a residue on the opposite chain.
contact_distance_mut: Shortest distance between the mutated reside and a residue on the opposite chain.
provean_score: Provean score for this mutation.
ddg: Predicted change in Gibbs free energy of binding caused by this mutation.
mut_date_modified: Date and time when this row was last modified.

Modules¶

elaspic package¶

Submodules¶

elaspic.call_foldx module¶

elaspic.call_modeller module¶

elaspic.call_tcoffee module¶

Alignes sequences using t_coffee in expresso mode.

TCoffee.align(GAPOPEN=-0.0, GAPEXTEND=-0.0)[source]¶

Calls t_coffee (make sure BLAST is installed locally!).

Parameters:

alignment_fasta_file (string) – A file containing the fasta sequences to be aligned
alignment_template_file (string) – A file containing the structural templates for the fasta sequences described above
GAPOPEN (int or str) – See t_coffee manual
GAPEXTEND (int or str) – See t_coffee manual
Returns –
-------- –
alignment_output_file (str) – Name of file which contains the alignment in fasta format.

elaspic.conf module¶

A singleton class that keeps track of ELASPIC configuration settings.

Configs.clear()[source]¶

Configs.copy()[source]¶

Configs.get(key, fallback=None)[source]¶

Configs.items()[source]¶

Configs.keys()[source]¶

Configs.update(**kwargs)[source]¶

Configs.values()[source]¶

Singleton.instance = None¶

elaspic.conf.get_temp_dir(global_temp_dir='/tmp', elaspic_foldername='')[source]¶: If a TMPDIR is given as an environment variable, the tmp directory is created relative to that. This is useful when running on banting (the cluster in the ccbr) and also on Scinet. Make sure that it points to ‘/dev/shm/’ on Scinet.

elaspic.conf.read_configuration_file(config_file, unique_temp_dir=None)[source]¶

elaspic.conf.read_database_configs(configParser)[source]¶: [DATABASE]

elaspic.conf.read_model_configs(configParser)[source]¶: [MODEL]

elaspic.conf.read_sequence_configs(configParser)[source]¶: [SEQUENCE]

elaspic.database_pipeline module¶

elaspic.elaspic_database module¶

MyDatabase.add_domain(d)[source]¶

MyDatabase.add_domain_errors(t, error_string)[source]¶

MyDatabase.add_uniprot_sequence(uniprot_sequence)[source]¶: Add new sequences to the database. :param uniprot_sequence: UniprotSequence object :rtype: None

MyDatabase.configure_session()[source]¶

Configure the Session class to use the current engine.

autocommit and autoflush are enabled for the sqlite database in order to improve performance.

MyDatabase.copy_table_to_db(table_name, table_folder)[source]¶: Copy data from a .tsv file to a table in the database.

MyDatabase.create_database_tables(clear_schema=False, keep_uniprot_sequence=True)[source]¶

Create a new database in the schema specified by the schema_version global variable. If clear_schema == True, remove all the tables in the schema first.

Warning

Using this function with an existing database can lead to loss of data. Make sure that you know what you are doing!

Parameters:	clear_schema (bool) – Whether or not to delete all tables in the database schema before creating new tables. keep_uniprot_sequence (bool) – Whether or not to keep the uniprot_sequence table. Only relevant if clear_schema is True.

MyDatabase.delete_database_tables(drop_schema=False, keep_uniprot_sequence=True)[source]¶

Parameters:	drop_schema (bool) – Whether or not to drop the schema after dropping the tables. keep_uniprot_sequence (bool) – Wheter or not to keep the table (and schema) containing uniprot sequences.

MyDatabase.get_alignment(model, path_to_data)[source]¶

MyDatabase.get_domain(pfam_names, subdomains=False)[source]¶: Returns pdbfam-based definitions of all pfam domains in the pdb.

MyDatabase.get_domain_contact(pfam_names_1, pfam_names_2, subdomains=False)[source]¶: Returns domain-domain interaction information from pdbfam. Note that the produced dataframe may not have the same order as the keys.

MyDatabase.get_engine(echo=False)[source]¶: Get an SQLAlchemy engine that can be used to connect to the database.

MyDatabase.get_rows_by_ids(row_object, row_object_identifiers, row_object_identifier_values)[source]¶: Get the rows from the table row_object identified by keys row_object_identifiers with values row_object_identifier_values

MyDatabase.get_uniprot_domain(uniprot_id, copy_data=False)[source]¶

MyDatabase.get_uniprot_domain_pair(uniprot_id, copy_data=False, uniprot_domain_pair_ids=[])[source]¶

MyDatabase.get_uniprot_mutation(d, mutation, uniprot_id=None, copy_data=False)[source]¶

MyDatabase.get_uniprot_sequence(uniprot_id, check_external=True)[source]¶

Parameters:	uniprot_id (str) – Uniprot ID of the protein check_external (bool) – Whether or not to look online if the protein sequence is not found in the local database.
Returns:	Contains the sequence of the specified uniprot
Return type:	SeqRecord

MyDatabase.load_db_from_archive()[source]¶: TODO: In the future I should move back to using json...

MyDatabase.merge_model(d, files_dict={})[source]¶: Adds MODELLER models to the database.

MyDatabase.merge_mutation(mut, path_to_data=False)[source]¶

MyDatabase.merge_provean(provean, provean_supset_file, path_to_data)[source]¶: Adds provean score to the database.

MyDatabase.merge_row(row_instance)[source]¶: Adds a list of rows (row_instances) to the database.

MyDatabase.mysql_command_template = "load data local infile '{table_folder}/{table_name}.tsv' into table {table_db_schema}.{table_name} fields terminated by '\\t' escaped by '\\\\\\\\' lines terminated by '\\n'; "¶

MyDatabase.mysql_load_table_template = 'mysql --local-infile --host={db_url} --user={db_username} --password={db_password} {table_db_schema} -e "{sql_command}" '¶

MyDatabase.psql_command_template = "\\\\copy {table_db_schema}.{table_name} from '{table_folder}/{table_name}.tsv' with csv delimiter E'\\t' null '\\N' escape '\\\\'; "¶

MyDatabase.psql_load_table_template = 'PGPASSWORD={db_password} psql -h {db_url} -p {db_port} -U {db_username} -d {db_database} -c "{sql_command}" '¶

MyDatabase.remove_model(d)[source]¶

Remove a model from the database.

Do this if you realized that the model you built is incorrect or that some of the data is missing.

Raises:	`errors.ModelHasMutationsError` – The model you are trying to delete has precalculated mutations, so it can’t be that bad. Delete those mutations and try again.

MyDatabase.session_scope()[source]¶: Provide a transactional scope around a series of operations. Enables the following construct: with self.session_scope() as session:.

MyDatabase.sqlite_table_filename = '{table_folder}/{table_name}.tsv'¶

elaspic.elaspic_database.check_exception(exc, valid_exc)[source]¶

elaspic.elaspic_database.decorate_all_methods(decorator)[source]¶: Decorate all methods of a class with decorator.

elaspic.elaspic_database.enable_sqlite_foreign_key_checks(engine)[source]¶

elaspic.elaspic_database.get_uniprot_base_path(d)[source]¶: The uniprot id is cut into several chunks to create folders that will hold a manageable number of pdbs.

elaspic.elaspic_database.get_uniprot_domain_path(d)[source]¶: Return the path to individual domains or domain pairs.

elaspic.elaspic_database.pickle_dump(obj, filename)[source]¶

elaspic.elaspic_database.retry_archive(fn)[source]¶: Decorator to keep probing the database untill you succeed.

elaspic.elaspic_database.retry_database(fn)[source]¶: Decorator to keep probing the database untill you succeed.

elaspic.elaspic_database.scinet_cleanup(folder, destination, name=None)[source]¶: zip and copy the results from the ramdisk to /scratch

elaspic.elaspic_database_tables module¶

Created on Thu Jun 11 16:52:31 2015

@author: ostrokach

Profs domain definitions for all proteins in the PDB.

Columns:

cath_id: Unique id identifying each domain in the PDB. Constructed by concatenating the pdb_id, pdb_chain, and an index specifying the order of the domain in the chain.
pdb_id: The PDB id in which the domain is found.
pdb_chain: The PDB chain in which the domain is found.
pdb_domain_def: Domain definitions of the domain, in PDB RESNUM coordinates.
pdb_pdbfam_name: The Profs name of the domain.
pdb_pdbfam_idx: An integer specifying the number of times a domain with domain name pdb_pdbfam_name has occurred in this chain up to this point. It is used to make every (pdb_id, pdb_chain, pdb_pdbfam_name, pdb_pdbfam_idx) tuple unique.
domain_errors: List of errors that occurred when annotating this domain, or when using this domain to make structural homology models.

Domain.cath_id¶

Domain.domain_errors¶

Domain.pdb_chain¶

Domain.pdb_domain_def¶

Domain.pdb_id¶

Domain.pdb_pdbfam_idx¶

Domain.pdb_pdbfam_name¶

Interactions between Profs domains in the PDB. Only interactions that were predicted to be biologically relevant by NOXclass are included in this table.

Columns:

domain_contact_id: A unique integer identifying each domain pair.
cath_id_1: Unique id identifying the first interacting domain in the domain table.
cath_id_2: Unique id identifying the second interacting domain in the domain table.
min_interchain_distance: The closest that any residue in domain one comes to any residue in domain two.
contact_volume: The volume covered by contacting residues.
contact_surface_area: The surface area of the contacting regions of the first and second domains.
atom_count_1: The number of atoms in the first domain.
atom_count_2: The number of atoms in the second domain.
number_of_contact_residues_1: The number of residues in the first domain that come within 5 Å of the second domain.
number_of_contact_residues_2: The number of residues in the second domain that come withing 5 Å of the first domain.
contact_residues_1: A list of all residues in the first domain that come within 5 Å of the second domain. The residue number corresponds to the position of the residue in the domain.
contact_residues_2: A list of all residues in the second domain that come within 5 Å of the first domain. The residue number corresponds to the position of the residue in the domain.
crystal_packing: The probability that the interaction is a crystallization artifacts, as defined by NOXclass.
domain_contact_errors: List of errors that occurred when annotating this domain pair, or when using this domain as a template for making structural homology models.

DomainContact.atom_count_1¶

DomainContact.atom_count_2¶

DomainContact.cath_id_1¶

DomainContact.cath_id_2¶

DomainContact.contact_residues_1¶

DomainContact.contact_residues_2¶

DomainContact.contact_surface_area¶

DomainContact.contact_volume¶

DomainContact.crystal_packing¶

DomainContact.domain_1¶

DomainContact.domain_2¶

DomainContact.domain_contact_errors¶

DomainContact.domain_contact_id¶

DomainContact.min_interchain_distance¶

DomainContact.number_of_contact_residues_1¶

DomainContact.number_of_contact_residues_2¶

Description of the Provean supporting set calculated for a protein sequence. The construction of a supporting set is the most lengthy step in running Provean. Therefore, the supporting set is precalculated and stored for every protein sequence.

Columns:

uniprot_id: The uniprot id of the protein.
provean_supset_filename: The filename of the Provean supporting set. The supporting set contains the ids and sequences of all proteins in the NCBI nr database that are used by Provean to construct a multiple sequence alignment for the given protein.
provean_supset_length: The number of sequences in Provean supporting set.
provean_errors: List of errors that occurred while the Provean supporting set was being calculated.
provean_date_modified: Date and time that this row was last modified.

Provean.provean_date_modified¶

Provean.provean_errors¶

Provean.provean_supset_filename¶

Provean.provean_supset_length¶

Provean.uniprot_id¶

Provean.uniprot_sequence¶

Pfam domain definitions for proteins in the uniprot_sequence table. This table was obtained by downloading Pfam domain definitions for all known proteins from the SIMAP website, and mapping the protein sequence to uniprot using the MD5 hash of each sequence.

Columns:

uniprot_domain_id: Unique id identifying each domain.
uniprot_id: The uniprot id of the protein containing the domain.
pdbfam_name: The Profs name of the domain. In most cases this will be equivalent to the Pfam name of the domain.
pdbfam_idx: The index of the Profs domain. pdbfam_idx ranges from 1 to the number of domains with the name pdbfam_name in the given protein. The (pdbfam_name, pdbfam_idx) tuple uniquely identifies each domain.
pfam_clan: The Pfam clan to which this Profs domain belongs.
alignment_def: Alignment domain definitions of the Profs domain. This field is obtained by removing gaps in the alignment_subdefs column.
pfam_names: Pfam names of all Pfam domains that were combined to create the given Profs domain.
alignment_subdefs: Comma-separated list of domain definitions for all Pfam domains that were merged to create the given Profs domain.
path_to_data: Location for storing homology models, mutation results, and all other data that are relevant to this domain. This path is prefixed by archive_dir.

UniprotDomain.IS_TRAINING_SCHEMA = False¶

UniprotDomain.alignment_def¶

UniprotDomain.alignment_subdefs¶

UniprotDomain.path_to_data¶

UniprotDomain.pdbfam_idx¶

UniprotDomain.pdbfam_name¶

UniprotDomain.pfam_clan¶

UniprotDomain.pfam_names¶

UniprotDomain.uniprot_domain_id¶

UniprotDomain.uniprot_id¶

UniprotDomain.uniprot_sequence¶

Homology models for templates in the uniprot_domain_template table.

Columns:

uniprot_domain_id

An integer which uniquely identifies each uniprot domain in the uniprot_domain table.

model_errors

List of errors that occurred when making the homology model.

alignment_filename

The name of the alignment that was given to Modeller when making the homology model.

model_filename

The name of the homology model that was produced by Modeller.

chain

The chain that contains the domain in question in the homology (this is now set to ‘A’ in all models).

norm_dope

Normalized DOPE score of the model (lower is better).

sasa_score

Comma-separated list of the percent solvent-accessible surface area for each residue.

m_date_modified

The date and time when this row was last modified.

model_domain_def

Domain definitions for the region of the domain that is covered by the structural template.

In most cases, this field is identical to the domain_def field in the uniprot_domain_template table. However, it sometimes happens that the best Profs structural template only covers a fraction of the Pfam domain. In that case, the alignment_def column in the uniprot_domain table, and the domain_def column in the uniprot_domain_template table, will contain the original Pfam domain definitions, and the model_domain_def column will contain domain definitions for only the region that is covered by the structural template.

UniprotDomainModel.alignment_filename¶

UniprotDomainModel.chain¶

UniprotDomainModel.m_date_modified¶

UniprotDomainModel.model_domain_def¶

UniprotDomainModel.model_errors¶

UniprotDomainModel.model_filename¶

UniprotDomainModel.norm_dope¶

UniprotDomainModel.sasa_score¶

UniprotDomainModel.template¶

UniprotDomainModel.uniprot_domain_id¶

Characterization of mutations introduced into structures in the uniprot_domain_model table.

Columns:

uniprot_id

Uniprot ID of the protein that was mutated.

uniprot_domain_id

Unique id which identifies the Profs domain that was mutated in the uniprot_domain table.

mutation

Mutation that was introduced into the protein, in Uniprot coordinates.

mutation_errors

List of errors that occured while evaluating the mutation.

model_filename_wt

The name of the file which contains the homology model of the domain after the model was relaxed with FoldX but before the mutation was introduced.

model_filename_mut

The name of the file which contains the homology model of the domain after the model was relaxed with FoldX and after the mutation was introduced.

chain_modeller

The chain which contains the domain that was mutated in the model_filename_wt and the model_filename_mut structures.

mutation_modeller

The mutation that was introduced into the protein, in PDB RESNUM coordinates. This identifies the mutated residue in the model_filename_wt and the model_filename_mut structures.

stability_energy_wt

Comma-separated list of scores returned by FoldX for the wildtype protein. The comma-separated list can be converted into a DataFrame with each column clearly labelled using the elaspic.predictor.format_mutation_features(). The FoldX energy terms are:

dg

backbone_hbond

sidechain_hbond

van_der_waals

electrostatics

solvation_polar

solvation_hydrophobic

van_der_waals_clashes

entropy_sidechain

entropy_mainchain

sloop_entropy

mloop_entropy

cis_bond

torsional_clash

backbone_clash

helix_dipole

water_bridge

disulfide

electrostatic_kon

partial_covalent_bonds

energy_ionisation

entropy_complex

number_of_residues

stability_energy_mut

Comma-separated list of scores returned by FoldX for the mutant protein. FoldX energy terms are the same as in stability_energy_wt, but for the mutated amino acid rather than the wildtype.

physchem_wt

Physicochemical properties describing the interaction of the wildtype residue with residues on the opposite chain. The terms are:

number of atoms in interacting residues that have the same charge.

number of atoms in interacting residues that have an opposite charge.

number of hydrogen bonds (very rough calculation).

number of carbons in interacting residues within 4 A of the mutated residue (rough measure of the van der Waals force).

physchem_wt_ownchain

Physicochemical properties describing the interaction of the wildtype residue with residues on the same chain. The terms are the same as in physchem_wt.

physchem_mut

Physicochemical properties describing the interaction of the mutant residue with residues on the opposite chain. The terms are the same as in physchem_wt.

physchem_mut_ownchain

Physicochemical properties describing the interaction of the mutant residue with residues on the same chain. The terms are the same as in physchem_wt.

matrix_score

Score assigned to the wt -> mut transition by the BLOSUM substitution matrix.

secondary_structure_wt

Secondary structure of the wildtype residue predicted by stride.

solvent_accessibility_wt

Percent solvent accessible surface area of the wildtype residue, predicted by msms.

secondary_structure_mut

Secondary structure of the mutated residue predicted by stride.

solvent_accessibility_mut

Percent solvent accessible surface area of the mutated residue, predicted by msms.

provean_score

Score produced by Provean for this mutation.

ddg

Change in the Gibbs free energy of folding that our classifier predicts for this mutation.

mut_date_modified

Date and time that this row was last modified.

UniprotDomainMutation.chain_modeller¶

UniprotDomainMutation.ddg¶

UniprotDomainMutation.matrix_score¶

UniprotDomainMutation.model¶

UniprotDomainMutation.model_filename_mut¶

UniprotDomainMutation.model_filename_wt¶

UniprotDomainMutation.mut_date_modified¶

UniprotDomainMutation.mutation¶

UniprotDomainMutation.mutation_errors¶

UniprotDomainMutation.mutation_modeller¶

UniprotDomainMutation.physchem_mut¶

UniprotDomainMutation.physchem_mut_ownchain¶

UniprotDomainMutation.physchem_wt¶

UniprotDomainMutation.physchem_wt_ownchain¶

UniprotDomainMutation.provean_score¶

UniprotDomainMutation.secondary_structure_mut¶

UniprotDomainMutation.secondary_structure_wt¶

UniprotDomainMutation.solvent_accessibility_mut¶

UniprotDomainMutation.solvent_accessibility_wt¶

UniprotDomainMutation.stability_energy_mut¶

UniprotDomainMutation.stability_energy_wt¶

UniprotDomainMutation.uniprot_domain_id¶

UniprotDomainMutation.uniprot_id¶

Potentially-interacting pairs of domains for proteins that are known to interact, according to Hippie, IRefIndex, and Rolland et al. 2014.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
uniprot_domain_id_1: Unique id of the first domain.
uniprot_domain_id_2: Unique id of the second domain.
rigids: Phased out.
domain_contact_ids: List of unique ids identifying all domain-domain pairs in the PDB, where one domain belongs to the protein containing uniprot_domain_id_1 and the other domain belongs to the protein containing uniprot_domain_id_2. This was used as crystallographic evidence that the two proteins interact.
path_to_data: Location for storing homology models, mutation results, and all other data that is relevant to this domain pair. This path is prefixed by archive_dir.

UniprotDomainPair.domain_contact_ids¶

UniprotDomainPair.path_to_data¶

UniprotDomainPair.rigids¶

UniprotDomainPair.uniprot_domain_1¶

UniprotDomainPair.uniprot_domain_2¶

UniprotDomainPair.uniprot_domain_id_1¶

UniprotDomainPair.uniprot_domain_id_2¶

UniprotDomainPair.uniprot_domain_pair_id¶

UniprotDomainPair.uniprot_id_1¶

UniprotDomainPair.uniprot_id_2¶

Structural models of interactions between pairs of domains in the uniprot_domain_pair table.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
model_errors: List of errors that occured while making the homology model.
alignment_filename_1: Name of the file containing the alignment of the first domain with its structural template.
alignment_filename_2: Name of the file containing the alignment of the second domain with its structural template.
model_filename: Name of the file containing the homology model of the domain-domain interaction created by Modeller.
chain_1: Chain containing the first domain in the model specified by model_filename.
chain_2: Chain containing the second domain in the model specified by model_filename.
norm_dope: The normalized DOPE score of the model.
interface_area_hydrophobic: Hydrophobic surface area of the interface, calculated using POPS.
interface_area_hydrophilic: Hydrophilic surface area of the interface, calculated using POPS.
interface_area_total: Total surface area of the interface, calculated using POPS.
interface_dg: Gibbs free energy of binding for this domain-domain interaction, predicted using FoldX. Not implemented yet!
interacting_aa_1: List of amino acid positions in the first domain that are within 5 Å of the second domain. Positions are specified using uniprot coordinates.
interacting_aa_2: List of amino acids in the second domain that are within 5 Å of the first domain. Position are specified using uniprot coordinates.
m_date_modified: Date and time that this row was last modified.
model_domain_def_1: Domain boundaries of the first domain that are covered by the Profs structural template.
model_domain_def_2: Domain boundaries of the second domain that are covered by the Profs structural template.

UniprotDomainPairModel.alignment_filename_1¶

UniprotDomainPairModel.alignment_filename_2¶

UniprotDomainPairModel.chain_1¶

UniprotDomainPairModel.chain_2¶

UniprotDomainPairModel.interacting_aa_1¶

UniprotDomainPairModel.interacting_aa_2¶

UniprotDomainPairModel.interface_area_hydrophilic¶

UniprotDomainPairModel.interface_area_hydrophobic¶

UniprotDomainPairModel.interface_area_total¶

UniprotDomainPairModel.interface_dg¶

UniprotDomainPairModel.m_date_modified¶

UniprotDomainPairModel.model_domain_def_1¶

UniprotDomainPairModel.model_domain_def_2¶

UniprotDomainPairModel.model_errors¶

UniprotDomainPairModel.model_filename¶

UniprotDomainPairModel.norm_dope¶

UniprotDomainPairModel.template¶

UniprotDomainPairModel.uniprot_domain_pair_id¶

Characterization of interface mutations introduced into structures in the uniprot_domain_pair_model table.

Columns:

uniprot_id: Uniprot ID of the protein that is being mutated.
uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
mutation: Mutation for which the $\Delta \Delta G$ score is being predicted, specified in Uniprot coordinates.
mutation_errors: List of errors obtained when evaluating the impact of the mutation.
model_filename_wt: Filename of the homology model relaxed by FoldX but containing the wildtype residue.
model_filename_mut: Filename of the homology model relaxed by FoldX and containing the mutated residue.
chain_modeller: Chain containing the domain that was mutated, in homology models specified by model_filename_wt and model_filename_mut.
mutation_modeller: Mutation for which the $\Delta \Delta G$ score is being predicted, specified in PDB RESNUM coordinates.
analyse_complex_energy_wt: Comma-separated list of FoldX scores describing the effect of the wildtype residue on the stability of the protein domain.
stability_energy_wt: Comma-separated list of FoldX scores describing the effect of the wildtype residue on protein-protein interaction interface.
analyse_complex_energy_mut: Comma-separated list of FoldX scores describing the effect of the mutated residue on the stability of the protein domain.
stability_energy_mut: Comma-separated list of FoldX scores describing the effect of the mutated residue on protein-protein interaction interface.
physchem_wt: Comma-separated list of physicochemical properties describing the interaction between the wildtype residue and other residues on the opposite chain.
physchem_wt_ownchain: Comma-separated list of physicochemical properties describing the interaction between the wildtype residue and other residues on the same chain.
physchem_mut: Comma-separated list of physicochemical properties describing the interaction between the mutated residue and other residues on the opposite chain.
physchem_mut_ownchain: Comma-separated list of physicochemical properties describing the interaction between the mutated residue and other residues on the same chain.
matrix_score: Score assigned to the wt -> mut transition by the BLOSUM substitution matrix.
secondary_structure_wt: Secondary structure of the wildtype residue, predicted by stride.
solvent_accessibility_wt: Percent solvent accessible surface area of the wildtype residue, predicted by msms.
secondary_structure_mut: Secondary structure of the mutated residue, predicted by stride.
solvent_accessibility_mut: Percent solvent accessible surface area of the mutated residue, predicted by msms.
contact_distance_wt: Shortest distance between the wildtype residue and a residue on the opposite chain.
contact_distance_mut: Shortest distance between the mutated reside and a residue on the opposite chain.
provean_score: Provean score for this mutation.
ddg: Predicted change in Gibbs free energy of binding caused by this mutation.
mut_date_modified: Date and time when this row was last modified.

UniprotDomainPairMutation.analyse_complex_energy_mut¶

UniprotDomainPairMutation.analyse_complex_energy_wt¶

UniprotDomainPairMutation.chain_modeller¶

UniprotDomainPairMutation.contact_distance_mut¶

UniprotDomainPairMutation.contact_distance_wt¶

UniprotDomainPairMutation.ddg¶

UniprotDomainPairMutation.matrix_score¶

UniprotDomainPairMutation.model¶

UniprotDomainPairMutation.model_filename_mut¶

UniprotDomainPairMutation.model_filename_wt¶

UniprotDomainPairMutation.mut_date_modified¶

UniprotDomainPairMutation.mutation¶

UniprotDomainPairMutation.mutation_errors¶

UniprotDomainPairMutation.mutation_modeller¶

UniprotDomainPairMutation.physchem_mut¶

UniprotDomainPairMutation.physchem_mut_ownchain¶

UniprotDomainPairMutation.physchem_wt¶

UniprotDomainPairMutation.physchem_wt_ownchain¶

UniprotDomainPairMutation.provean_score¶

UniprotDomainPairMutation.secondary_structure_mut¶

UniprotDomainPairMutation.secondary_structure_wt¶

UniprotDomainPairMutation.solvent_accessibility_mut¶

UniprotDomainPairMutation.solvent_accessibility_wt¶

UniprotDomainPairMutation.stability_energy_mut¶

UniprotDomainPairMutation.stability_energy_wt¶

UniprotDomainPairMutation.uniprot_domain_pair_id¶

UniprotDomainPairMutation.uniprot_id¶

Structural templates for pairs of domains in the uniprot_domain_pair table.

Columns:

uniprot_domain_pair_id: Unique id identifying each domain-domain interaction.
domain_contact_id: Unique id of the domain pair in the domain_contact table that was used as a template for the modelled domain pair.
cath_id_1: Unique id of the structural template for the first domain.
cath_id_2: Unique id of the structural template for the second domain.
identical_1: Fraction of residues in the Blast alignment of the first domain to its template that are identical.
conserved_1: Fraction of residues in the Blast alignment of the first domain to its template that are conserved.
coverage_1: Fraction of the first domain that is covered by the blast alignment.
score_1: Score obtained by multiplying identical_1 by coverage_1.
identical_if_1: Fraction of interface residues [1] that are identical in the Blast alignment of the first domain.
conserved_if_1: Fraction of interface residues [1] that are conserved in the Blast alignment of the first domain.
coverage_if_1: Fraction of interface residues [1] that are covered by the Blast alignment of the first domain.
score_if_1: Score obtained by combining identical_if_1 and coverage_if_1 using (2).
identical_2: Fraction of residues in the Blast alignment of the second domain to its template that are identical.
conserved_2: Fraction of residues in the Blast alignment of the second domain to its template that are conserved.
coverage_2: Fraction of the second domain that is covered by the blast alignment.
score_2: Score obtained by multiplying identical_2 by coverage_2.
identical_if_2: Fraction of interface residues [1] that are identical in the Blast alignment of the second domain.
conserved_if_2: Fraction of interface residues [1] that are conserved in the Blast alignment of the second domain.
coverage_if_2: Fraction of interface residues [1] that are covered by the Blast alignment of the second domain.
score_if_2: Score obtained by combining identical_if_2 and coverage_if_2 using (2).
score_total: The product of score_1 and score_2.
score_if_total: The product of score_if_1 and score_if_2.
score_overall: The product of score_total and score_if_total. This is the score that was used to select the best Profs domain pair to be used as a template.
t_date_modified: The date and time when this row was last updated.
template_errors: List of errors that occured while looking for the structural template.

[1]	(1, 2, 3, 4, 5, 6) Interface residues are defined as residues that are within 5 Å of the partner domain.

UniprotDomainPairTemplate.cath_id_1¶

UniprotDomainPairTemplate.cath_id_2¶

UniprotDomainPairTemplate.conserved_1¶

UniprotDomainPairTemplate.conserved_2¶

UniprotDomainPairTemplate.conserved_if_1¶

UniprotDomainPairTemplate.conserved_if_2¶

UniprotDomainPairTemplate.coverage_1¶

UniprotDomainPairTemplate.coverage_2¶

UniprotDomainPairTemplate.coverage_if_1¶

UniprotDomainPairTemplate.coverage_if_2¶

UniprotDomainPairTemplate.domain_1¶

UniprotDomainPairTemplate.domain_2¶

UniprotDomainPairTemplate.domain_contact¶

UniprotDomainPairTemplate.domain_contact_id¶

UniprotDomainPairTemplate.domain_pair¶

UniprotDomainPairTemplate.identical_1¶

UniprotDomainPairTemplate.identical_2¶

UniprotDomainPairTemplate.identical_if_1¶

UniprotDomainPairTemplate.identical_if_2¶

UniprotDomainPairTemplate.score_1¶

UniprotDomainPairTemplate.score_2¶

UniprotDomainPairTemplate.score_if_1¶

UniprotDomainPairTemplate.score_if_2¶

UniprotDomainPairTemplate.score_if_total¶

UniprotDomainPairTemplate.score_overall¶

UniprotDomainPairTemplate.score_total¶

UniprotDomainPairTemplate.t_date_modified¶

UniprotDomainPairTemplate.template_errors¶

UniprotDomainPairTemplate.uniprot_domain_pair_id¶

Structural templates for domains in the uniprot_domain table. Lists PDB crystal structures that will be used for making homology models.

Columns:

uniprot_domain_id: An integer which uniquely identifies each uniprot domain in the uniprot_domain table.
template_errors: List of errors that occurred during the process for finding the template.
cath_id: The unique id identifying the structural template of the domain.
domain_start: The Uniprot position of the first amino acid of the Profs domain.
domain_end: The Uniprot position of the last amino acid of the Profs domain.
domain_def: Profs domain definitions for domains with structural templates. Domain definitions in this column are different from domain definitions in the alignment_def column of the uniprot_domain table in that they have been expanded to match domain boundaries of the Profs structural template, identified by the cath_id.
alignment_identity: Percent identity of the domain to its structural template.
alignment_coverage: Percent coverage of the domain to its structural template.
alignment_score: A score obtained by combining alignment_identity ($SeqId$) and alignment_coverage ($Cov$) using the following equation, as described by Mosca et al.:

(2)\[Score = 0.95 \cdot \frac{SeqId}{100} \cdot \frac{Cov}{100} + 0.05 \cdot \frac{Cov}{100}\]
t_date_modified: The date and time when this row was last modified.

UniprotDomainTemplate.alignment_coverage¶

UniprotDomainTemplate.alignment_identity¶

UniprotDomainTemplate.alignment_score¶

UniprotDomainTemplate.cath_id¶

UniprotDomainTemplate.domain¶

UniprotDomainTemplate.domain_def¶

UniprotDomainTemplate.domain_end¶

UniprotDomainTemplate.domain_start¶

UniprotDomainTemplate.t_date_modified¶

UniprotDomainTemplate.template_errors¶

UniprotDomainTemplate.uniprot_domain¶

UniprotDomainTemplate.uniprot_domain_id¶

Protein sequences from the Uniprot KB, obtained by parsing uniprot_sprot_fasta.gz, uniprot_trembl_fasta.gz, and homo_sapiens_variation.txt files from the Uniprot ftp site.

Columns:

db

The database to which the protein sequence belongs. Possible values are sp for SwissProt and tr for TrEMBL.

uniprot_id

The uniprot id of the protein.

uniprot_name

The uniprot name of the protein.

protein_name

The protein name.

organism_name

Name of the organism in which this protein is found.

gene_name

Name of the gene that codes for this protein sequence.

protein_existence

Evidence for the existence of the protein:

Experimental evidence at protein level
Experimental evidence at transcript level
Protein inferred from homology
Protein predicted
Protein uncertain

sequence_version

Version of the protein amino acid sequence.

uniprot_sequence

Amino acid sequence of the protein.

UniprotSequence.db¶

UniprotSequence.gene_name¶

UniprotSequence.organism_name¶

UniprotSequence.protein_existence¶

UniprotSequence.protein_name¶

UniprotSequence.sequence_version¶

UniprotSequence.uniprot_id¶

UniprotSequence.uniprot_name¶

UniprotSequence.uniprot_sequence¶

elaspic.elaspic_database_tables.get_db_specific_param(key)[source]¶

elaspic.elaspic_database_tables.get_table_args(table_name, index_columns=[], db_specific_params=[])[source]¶: Returns a tuple of additional table arguments.

elaspic.elaspic_model module¶

elaspic.elaspic_predictor module¶

Created on Wed Sep 30 16:54:21 2015

@author: strokach

Predictor.feature_name_conversion = {'seq_id_avg': 'alignment_identity', 'normDOPE': 'norm_dope'}¶

Predictor.score(df, core_or_interface)[source]¶

Parameters:	df (DataFrame) – One or more rows with all data required to predict $Delta Delta G$ score. Like something that you would get when you join the appropriate rows in the database.
Returns:	df – Same as the input dataframe, except with one additional column: ddg.
Return type:	Dataframe

elaspic.elaspic_predictor.convert_features_to_differences(df, keep_mut=False)[source]¶: Creates a new set of features (ending in _change) that describe the difference between values of the wildtype (features ending in _wt) and mutant (features ending in _mut) features. If keep_mut is False, removes all mutant features (features ending in _mut).

elaspic.elaspic_predictor.format_mutation_features(feature_df, core_or_interface)[source]¶

Converts columns containing comma-separated lists of FoldX features and physicochemical features into a DataFrame where each feature has its own column.

Parameters:	feature_df (DataFrame) – A pandas DataFrame containing a subset of rows from the uniprot_domain_mutation or the uniprot_domain_pair_mutation tables. core_or_interface (int or str) – If 0 or ‘core’, the feature_df DataFrame contains columns from the uniprot_domain_mutation table. If 1 or ‘interface, the feature_df DataFrame contains columns from the uniprot_domain_pair_mutation table.
Returns:	Contains the same data as feature_df, but with columns containing comma-separated lists of features converted to columns containing a single feature each.
Return type:	DataFrame

elaspic.elaspic_sequence module¶

Class for calculating sequence level features.

Sequence.mutate(mutation)[source]¶

Sequence.provean_supset_exists¶

Sequence.provean_supset_file¶

Sequence.result¶

Sequence.score_pairwise(seq1, seq2, matrix=None, gap_s=None, gap_e=None)[source]¶: Get the BLOSUM (or what ever matrix is given) score.

elaspic.elaspic_sequence.convert_basestring_to_seqrecord(sequence, sequence_id='id')[source]¶

elaspic.elaspic_sequence.download_uniport_sequence(uniprot_id, output_dir)[source]¶

elaspic.errors module¶

exception elaspic.errors.AlignmentNotFoundError(save_path, alignment_filename)[source]¶: Bases: Exception

exception elaspic.errors.Archive7zipError(result, error_message, return_code)[source]¶: Bases: Exception

exception elaspic.errors.Archive7zipFileNotFoundError(result, error_message, return_code)[source]¶: Bases: elaspic.errors.Archive7zipError

exception elaspic.errors.ChainsNotInteractingError[source]¶: Bases: Exception

exception elaspic.errors.DataError[source]¶: Bases: Exception

exception elaspic.errors.FoldXAAMismatchError[source]¶: Bases: Exception

exception elaspic.errors.FoldxError[source]¶: Bases: Exception

exception elaspic.errors.InterfaceMismatchError[source]¶: Bases: Exception

exception elaspic.errors.LowIdentity[source]¶: Bases: Exception

exception elaspic.errors.MSMSError[source]¶: Bases: Exception

exception elaspic.errors.ModelHasMutationsError[source]¶

Bases: Exception

Don’t delete a model that has precalculated mutations!

exception elaspic.errors.ModellerError[source]¶: Bases: Exception

exception elaspic.errors.MutationMismatchError[source]¶: Bases: Exception

exception elaspic.errors.MutationOutsideDomainError[source]¶: Bases: Exception

exception elaspic.errors.MutationOutsideInterfaceError[source]¶: Bases: Exception

exception elaspic.errors.NoModelFoundError[source]¶: Bases: Exception

exception elaspic.errors.NoSequenceFound[source]¶: Bases: Exception

exception elaspic.errors.NoTemplatesFoundError[source]¶: Bases: Exception

exception elaspic.errors.PDBChainError[source]¶: Bases: Exception

exception elaspic.errors.PDBDomainDefsError[source]¶

Bases: Exception

PDB domain definitions not found in the pdb file

exception elaspic.errors.PDBEmptySequenceError[source]¶

Bases: Exception

One of the sequences is missing from the alignment. The most likely cause is that the alignment domain definitions were incorrect.

exception elaspic.errors.PDBError[source]¶: Bases: Exception

exception elaspic.errors.PDBNotFoundError[source]¶: Bases: Exception

exception elaspic.errors.PopsError(message, pdb, chains)[source]¶: Bases: Exception

exception elaspic.errors.ProteinDefinitionError[source]¶: Bases: Exception

exception elaspic.errors.ProveanError[source]¶: Bases: Exception

exception elaspic.errors.ProveanResourceError(message, child_process_group_id)[source]¶: Bases: Exception

exception elaspic.errors.ResourceError[source]¶: Bases: Exception

exception elaspic.errors.TcoffeeBlastError(result, error, alignInFile, system_command)[source]¶: Bases: Exception

exception elaspic.errors.TcoffeeError(result, error, alignInFile, system_command)[source]¶: Bases: Exception

exception elaspic.errors.TcoffeePDBidError(result, error, alignInFile, system_command)[source]¶: Bases: Exception

exception elaspic.errors.TemplateCoreError[source]¶: Bases: Exception

exception elaspic.errors.TemplateInterfaceError[source]¶: Bases: Exception

exception elaspic.errors.WrongConfigKeyError[source]¶: Bases: Exception

elaspic.helper module¶

A class for collecting all the print statements from modeller in order to redirect them to the logger later on

WritableObject.write(string)[source]¶

color.BLUE = '\x1b[94m'¶

color.BOLD = '\x1b[1m'¶

color.CYAN = '\x1b[96m'¶

color.DARKCYAN = '\x1b[36m'¶

color.END = '\x1b[0m'¶

color.FAIL = '\x1b[91m'¶

color.GREEN = '\x1b[92m'¶

color.HEADER = '\x1b[95m'¶

color.OKBLUE = '\x1b[94m'¶

color.OKGREEN = '\x1b[92m'¶

color.PURPLE = '\x1b[95m'¶

color.RED = '\x1b[91m'¶

color.UNDERLINE = '\x1b[4m'¶

color.WARNING = '\x1b[93m'¶

color.YELLOW = '\x1b[93m'¶

elaspic.helper.decode_aa_list(interface_aa)[source]¶

elaspic.helper.decode_domain_def(domains, merge=True, return_string=False)[source]¶: Unlike split_domain(), this function returns a tuple of tuples of strings, preserving letter numbering (e.g. 10B)

elaspic.helper.decode_text_as_list(list_string)[source]¶: Uses the database convention to decode a string, describing domain boundaries of multiple domains, as a list of lists.

elaspic.helper.encode_domain(domains, merged=True)[source]¶

elaspic.helper.encode_list_as_text(list_of_lists)[source]¶: Uses the database convention to encode a list of lists, describing domain boundaries of multiple domains, as a string.

elaspic.helper.get_echo(system_constant)[source]¶

elaspic.helper.get_hostname()[source]¶

elaspic.helper.get_lock(name)[source]¶

elaspic.helper.get_logger(do_debug=True, logger_filename=None)[source]¶

elaspic.helper.get_path_to_current_file()[source]¶: Find the location of the file that is being executed

elaspic.helper.get_username()[source]¶

elaspic.helper.get_which(bin_name)[source]¶

elaspic.helper.kill_child_process(child_process)[source]¶

elaspic.helper.lock(fn)[source]¶: Allow only a single instance of function fn, and save results to a lock file.

elaspic.helper.log_print_statements(logger)[source]¶: Channel print statements to the debug logger

elaspic.helper.make_tarfile(output_filename, source_dir)[source]¶

elaspic.helper.open_exclusively(filename, mode='a')[source]¶

elaspic.helper.print_heartbeets()[source]¶

elaspic.helper.row2dict(row)[source]¶

elaspic.helper.run_subprocess(system_command, **popen_argvars)[source]¶

elaspic.helper.run_subprocess_locally(working_path, system_command, **popen_argvars)[source]¶

elaspic.helper.slugify(filename_string)[source]¶

elaspic.helper.subprocess_check_output(system_command, **popen_argvars)[source]¶

elaspic.helper.subprocess_check_output_locally(working_path, system_command, **popen_argvars)[source]¶

elaspic.helper.subprocess_communicate(child_process)[source]¶

elaspic.helper.switch_paths(working_path)[source]¶

elaspic.helper.underline(print_string)[source]¶

elaspic.local_pipeline module¶

elaspic.machine_learning module¶

elaspic.machine_learning.cross_validate_predictor(data, features, clf_options, output_filename=None)[source]¶

elaspic.machine_learning.get_final_predictor(data, features, options)[source]¶: Train a predictor using the entire dataset.

elaspic.machine_learning.write_row_to_file(results, output_filename)[source]¶: TODO: Add a datetime column to each written row.

elaspic.pipeline module¶

Foo.run()[source]¶

elaspic.pipeline.execute_and_remember(f)[source]¶: Some basic memoizer.

elaspic.pipeline.lock(fn)[source]¶: Allow only a single instance of function fn, and save results to a lock file.

elaspic.structure_analysis module¶

Runs the program pops to calculate the interface size of the complexes This is done by calculating the surface of the complex and the seperated parts. The interface is then given by the substracting.

AnalyzeStructure.get_dssp()[source]¶: Not used because crashes on server.

AnalyzeStructure.get_interchain_distances(pdb_chain=None, pdb_mutation=None, cutoff=None)[source]¶

AnalyzeStructure.get_interface_area(chain_ids)[source]¶

AnalyzeStructure.get_physi_chem(chain_id, mutation)[source]¶

Return the atomic contact vector, that is, counting how many interactions between charged, polar or “carbon” residues there are. The “carbon” interactions give you information about the Van der Waals packing of the residues. Comparing the wildtype vs. the mutant values is used in the machine learning algorithm.

‘mutation’ is of the form: ‘A16’ where A is the chain identifier and 16 the residue number (in pdb numbering) of the mutation chainIDs is a list of strings with the chain identifiers to be used if more than two chains are given, the chains not containing the mutation are considered as “opposing” chain

AnalyzeStructure.get_sasa(program_to_use='pops')[source]¶: Get Solvent Accessible Surface Area scores.

Note

deprecated

Use python:fn:get_seasa instead.

AnalyzeStructure.get_seasa()[source]¶

AnalyzeStructure.get_secondary_structure()[source]¶

AnalyzeStructure.get_stride()[source]¶

AnalyzeStructure.get_structure_file(chains, ext='.pdb')[source]¶

AnalyzeStructure.working_dir = None¶: Folder with all the binaries (i.e. ./analyze_structure)

elaspic.structure_tools module¶

MMCIFParserMod.get_structure(structure_id, gzip_fh)[source]¶: Altered get_structure method which accepts gzip file handles as input.

Only accept the specified chains when saving.

SelectChains.accept_residue(residue)[source]¶

elaspic.structure_tools.pdb_id¶: ___

elaspic.structure_tools.domain_boundaries¶

list of lists of lists

Elements in the outer list correspond to domains in each chain of the pdb. Elements of the inner list contain the start and end of each fragment of each domain. For example, if there is only one chain with pdb domain boundaries 1-10:20-45, this would correspond to domain_boundaries [[[1,10],[20,45]]].

StructureParser.extract()[source]¶: Extract the wanted chains out of the PDB file. Removes water atoms and selects the domain regions (i.e. selects only those parts of the domain that are within the domain boundaries specified).

StructureParser.get_chain_seqres_sequence(chain_id, *args, **varargs)[source]¶: Call get_chain_seqres_sequence using chain with id chain_id

StructureParser.get_chain_sequence_and_numbering(chain_id, *args, **varargs)[source]¶: Call get_chain_sequence_and_numbering using chain with id chain_id

StructureParser.save_sequences(output_dir='')[source]¶

StructureParser.save_structure(output_dir='', remove_disordered=False)[source]¶

elaspic.structure_tools.calculate_distance(atom_1, atom_2, cutoff=None)[source]¶

Calculate the distance between two points in 3D space.

Parameters:	cutoff (float, optional) – The maximum distance allowable between two points.

elaspic.structure_tools.chain_is_hetatm(chain)[source]¶: Return True if the chain is made up entirely of HETATMs.

elaspic.structure_tools.convert_aa(aa, quiet=False)[source]¶: Convert amino acids from three letter code to one letter code or vice versa

Note

Deprecated!

Use ''.join(AAA_DICT[aaa] for aaa in aa) and ''.join(A_DICT[a] for a in aa).

elaspic.structure_tools.convert_position_to_resid(chain, positions, domain_def_tuple=None)[source]¶: Convert mutation_domain to mutation_modeller. In mutation_modeller, the first amino acid in a chain may start with something other than 1.

elaspic.structure_tools.convert_resnum_alphanumeric_to_numeric(resnum)[source]¶: Convert residue numbering that has letters (i.e. 1A, 1B, 1C...) to residue numbering without letters (i.e. 1, 2, 3...).

Note

Deprecated!

Use get_chain_sequence_and_numbering().

elaspic.structure_tools.download_pdb_file(pdb_id, output_dir)[source]¶: Move PDB structure to the local working directory.

elaspic.structure_tools.euclidean_distance(a, b)[source]¶: Calculate the Euclidean distance between two lists or tuples of arbitrary length.

elaspic.structure_tools.get_aa_residues(chain)[source]¶

elaspic.structure_tools.get_chain_seqres_sequence(chain, aa_only=False)[source]¶

Get the amino acid sequence for the construct coding for the given chain.

Extracts a sequence from a PDB file. Usefull when interested in the sequence that was used for crystallization and not the ATOM sequence.

Parameters:	aa_only (bool) – If aa_only is set to False, selenomethionines will be included in the sequence. See: http://biopython.org/DIST/docs/api/Bio.PDB.Polypeptide-module.html.

elaspic.structure_tools.get_chain_sequence_and_numbering(chain, domain_def_tuple=None, include_hetatms=False)[source]¶

Get the amino acid sequence and a list of residue ids for the given chain.

Parameters:	chain (Bio.PDB.Chain.Chain) – The chain for which to get the amino acid sequence and numbering.

elaspic.structure_tools.get_interacting_residues(model, r_cutoff=5, skip_hetatm_chains=True)[source]¶

Returns all interactions between residues on different chains in model.

Returns:	A dictionary of interactions between chains i (0..n-1) and j (i+1..n). Keys are (chain_idx, chain_id, residue_idx, residue_resnum, residue_amino_acid) tuples. (e.g. (0, ‘A’, 0, ‘0’, ‘M’), (0, 1, ‘2’, ‘K’), ...) Values are a list of tuples having the same format as the keys.
Return type:	dict

You can reverse the order of keys and values like this:

complement = dict()
for key, values in get_interacting_chains(model):
    for value in values:
        complement.setdefault(value, set()).add(key)

You can get a list of all interacting chains using this command:

{(key[0], value[0])
 for (key, values) in get_interacting_chains(model).items()
 for value in values}

elaspic.structure_tools.get_interactions(model, chain_id, r_cutoff=6)[source]¶

elaspic.structure_tools.get_interactions_between_chains(model, chain_id_1, chain_id_2, r_cutoff=6)[source]¶

Calculate interactions between residues in pdb_chain_1 and pdb_chain_2. An interaction is defines as a pair of residues where at least one pair of atom is closer than r_cutoff. The default value for r_cutoff is 5 Angstroms.

Deprecated since version 1.0: Use python:fn:get_interacting_residues instead. It gives you both the residue index and the resnum.

Returns:	Keys are (residue_number, residue_amino_acid) tuples (e.g. (‘0’, ‘M’), (‘1’, ‘Q’), ...). Values are lists of (residue_number, residue_amino_acid) tuples. (e.g. [(‘0’, ‘M’), (‘1’, ‘Q’), ...]).
Return type:	OrderedDict

elaspic.structure_tools.get_interactions_between_chains_slow(model, pdb_chain_1, pdb_chain_2, r_cutoff=5)[source]¶: Calculate interactions between residues in pdb_chain_1 and pdb_chain_2. An interaction is defines as a pair of residues where at least one pair of atom is closer than r_cutoff. The default value for r_cutoff is 5 Angstroms.

Deprecated since version 1.0: Use get_interacting_residues() instead. It gives you both the residue index and the resnum.

elaspic.structure_tools.get_pdb[source]¶

Parse a pdb file with biopythons PDBParser() and return the structure.

Parameters:	pdb_code (str) – Four letter code of the PDB file pdb_path (str) – Biopython pdb structure temp_dir (str, optional, default=’/tmp/’) – Path to the folder for storing temporary files pdb_type (‘ent’/’pdb’/’cif’, optional, default=’ent’) – The extension of the pdb to use
Raises:	`PDBNotFoundError` – If the pdb file could not be retrieved from the local (and remote) databases

elaspic.structure_tools.get_pdb_file(pdb_id, pdb_database_dir, pdb_type='ent')[source]¶: Get PDB file from a local mirror of the PDB database.

elaspic.structure_tools.get_pdb_id(pdb_file)[source]¶

elaspic.structure_tools.get_pdb_parser(pdb_type, temp_dir='/tmp')[source]¶: Get PDB parser that can work with structures of the specified type.

elaspic.structure_tools.get_pdb_structure(pdb_file, pdb_id=None)[source]¶: Set QUIET to False to output warnings like incomplete chains etc.

elaspic.structure_tools.get_structure_sequences(file_or_structure, seqres_sequence=False)[source]¶: Convenience function returining a dictionary of sequences for a given file or a Biopython Structure, Model or Chain.

elaspic.structure_tools.suppress_logger(fn)[source]¶

Module contents¶

Indices and tables¶

Module Index