Bash Script Writer for IDPConformerGenerator v0.6.X


Philosophy and Usage:

The web-tool "IDPConfGen Scriptor" hopes to bridge the gap between users whom are not comfortable with command-line-interface (CLI) only programs. To maintain the speeds and flexibility that CLI programs present while making things more user friendly, IDPConfGen Scriptor presents all of the functionalities that IDPConformerGenerator presents in a GUI format for ease of use. Please refer to the documentation for further usage details. For any questions or concerns about the Web-Scriptor, please raise an issue on the public repository.

To get started, please select a subclient below, then fill in the required parameters. After you are satisfied, please click "Load Preview" to see the code and "Download" when satisfied.

NOTE: clicking the dropdown menu will reset the form and preview.

Select Subclient *

idpconfgen build \

Build from a database of torsion angles and secondary structure information.

Path to database *

Protein sequence or path to FASTA file *

Amino Acid Substitutions

Number of conformers

Secondary structure filters:

Note: the default samples only for loops.

Regex for duser

Path to CSSS file

Sidechain, Physical, and Energy Options

Sidechain options

Backbone Energy Threshold (kJ)

Sidechain Energy Threshold (kJ)

Path to save energy log

Forcefield Parameters

Bond Geometry Database Path

MC-SCE related parameters:

Mode

Number of trials

Batch size

Temperature (K)

Technical Specifications

Number of CPU Cores

Random seed

Path to custom fragment size probabilities

Path to output folder

idpconfgen pdbdl \

Downloads structures from the RCSB databank for PDB formatted files of individual chains.

The PDB ID list can be given in the format of a file listing the PDBIDs or as a list of arguments passed to the script call.

The following PDBID formats are allowed:
- XXXX
- XXXXY
- XXXX_Y

Where, XXXX is the PDB ID code and Y the chain identifier. Y can have more then one character, for example, XXXXAB, will select chain 'AB' of PDB ID XXXX (for mmCIF cases); digits are also allowed. If no chainID is provided, saves each chain of the PDB file separately.

Detailed procedures:
* PDBs/mmCIFs are saved parsed in PDB format.
* Known solvent and ligands are removed
* Considers only altLoc 'A' or ' '.
* Considers only elements composing aminoacids
* selects only the first model for multi MODEL structures
* renumbers atoms for saved chains
* passes through pdb-tools `pdb_delinsert` filter.

Accepts TAR files as output destination.

DO NOT forget check "update destination folder" to perform the actual download. Otherwise a simple comparison between source and destination is performed.

Path to PDBID list *

Path to destination folder where PDB files are stored

Chunks to process in RAM

Number of CPU Cores

idpconfgen fetch \

Downloads structures from RCSB Databank provided a list of PDB identifiers. The PDB ID list can be given in the format of a file listing the PDBIDs or as a list of arguments passed to the script call.

Structure files are saved to the local destination in its raw format, that is, without any filtering or parsing.

The following PDBID formats are allowed:
- XXXX

Where, XXXX is the PDB ID code.

By default, PDB structure files are prioritized. If you prefer to prioritize mmCIF files, check the box for `--mmcif`.

Path to PDBID list *

Path to destination folder where PDB files are stored

Chunks to process in RAM

Number of CPU Cores

idpconfgen merge \

Collates and re-numbers conformers within subfolders of a given folder.

For example, if there are 5 subfolders filled with 100 conformers each, copy and re-number them to make 500 conformers in the working dir. or destination dir.

Path to directory containing subfolders of conformers to merge *

Path to destination folder to collate structures

Prefix for file names

idpconfgen sscalc \

Extracts secondary structure information from PDBs.

Uses an external third party software (DSSP). Client has been upgraded to DSSP-PPII according to:
Mansiaux Y, Joseph AP, Gelly J-C, de Brevern AG (2011) Assignment of PolyProline II conformation and analysis od sequence-structure relationship. PLoS One 6(3): e18401. doi:10.1371/journal.pone.0018401

Path to PDB files on the disk. TAR file acceptable *

Path to the DSSP executable

Output path for annotated secondary structure .JSON

Destination path for split PDB storage

Minimum size accepted for fragment/segment

Chunks to process in RAM

Number of CPU Cores

idpconfgen dssppii \

Adds polyproline type-2 helix assignment to DSSP.

Mainly an extension if running DSSP v2-v3.

Path to PDB file to operate on *

Path to the DSSP executable

Path to output file

Number of CPU Cores

idpconfgen ssext \

Extract secondary structure protein segments from PDBs.

Requires a *.JSON file as generated by `idpconfgen sscalc`.

Path to PDB files on the disk. TAR file acceptable *

Path to the *.JSON file generated by `sscalc` *

Destination folder where PDB files will be stored

Secondary structure type to extract

List of atom names to save

Minimum size accepted for fragment/segment

Number of CPU Cores

idpconfgen torsions \

Extracts backbone torsion angles (in radians by default) from PDBs.

PROTOCOL:
1. Reads backbone coordinates (N, CA, C) from PDB/mmCIF files.
2. Calculates torsion angles from the backbone.
3. Saves results to a JSON dictionary where keys are the input file names and the value is a dictionary containing three lists: 'OMEGA', 'PHI', and 'PSI'.
4. If `source` JSON file is given, updates that file with the new information. Preexisting keys are deleted.

For each PDB/mmCIF analyzed, fails if:
1. The number of N, CA, and C atoms differ.
2. There are unexpected inconsistencies in the PDB/mmCIF files.
3. Any of the consecutive atoms are more than 2.1A apart.

Path to PDB files on the disk. TAR file acceptable *

Updates a source file with new output

Note: for extended plotting options, please refer to the CLI.

Output file path

Number of CPU Cores

idpconfgen torsionsJ \

Calculates J-torsion angles from PDB/mmCIF files.

Calculate torsion angles between the HN-CaHA atoms, where H is the first atom and HA the last atom and angles are given by the right-hand rule where the thumb points from N to CA. If the resulting angle exceeds 180 degrees, the corresponding value in negative angles is given instead.

The calculated angles will be stored in a JSON file in the folder where the CLI was executed, named 'torsionsJ_HN-CaHA.json', and with one entry per structure. Structures are allowed to have unsorted atoms as long as residues are ordered.

If input structures lack protons at the N-terminal, the flag `--no_hn_term` should be given. In this case, the first calculated torsion angle corresponds to the second residue. In the case there are N-terminal nitrogen has protons, the dihedral angle between these and the `HA` atom for the first residue will also be calculated. It is up to the user to decide whether or not this first angle has physical meaning. In the resulting torsion angle lists, NaN values will be placed at proline sites. Different values can be given with the option --proline_value.

Path to PDB files on the disk. TAR file acceptable *

Proline value

Note: enabling "No H/H1 N-term" considers N-terminal to have `H` or `H1` labels.

HN Labels

Decimals size

Number of CPU Cores

idpconfgen bgeo \

Create a database of covalent bond geometries for the backbone.

Given a PDB file:
1) reads each of its trimers, and for the middle residue:
2) Calculates phi/psi and rounds them to the closest 10 degree bin
3) assigns the planar angles found for that residue to the trimer/torsion key.
4) updates that information in dictionary (library)

You can provide a folder with several PDB/mmCIF files.

Path to a folder of PDB files on the disk *

idpconfgen fastaext \

Extracts FASTA information from PDBs.

Path to PDB files on the disk. TAR file acceptable *

Path to the output file

Number of CPU Cores

idpconfgen validate \

Conformer validator.

NOTE: THIS CLIENT IS CURRENTLY UNDER CONSTRUCTION

Path to PDB files on the disk. TAR file acceptable *

Atoms to consider

Elements to consider

VDW Radii Set

Residues apart

Bond tolerance

Validations

Number of CPU Cores

idpconfgen csssconv \

Ability to parse probabilistic secondary-structure predictions based on user preference.

The output will be printed to the terminal window. To save the output to a file use the `>` command. Note that output MUST have the extension .JSON.

Path to CheSPI probs8 file to operate on

Path to delta2D output file to operate on

Path to output CSSS.JSON file

idpconfgen makecsss \

Generates a CSSS.JSON file based on user specifications for secondary structure sampling on a per residue basis.

Has the ability to edit previously generated CSSS files as well with `--file-csss`. The output will be printed to the terminal window. To save the output to a file use the `>` or `--output` command. Note that output MUST have the extension .JSON.

Path to existing CSSS file

Custom secondary structure probabilities

Path to output .JSON file

Preview:

#!/bin/bash

idpconfgen -h \

To run this function, either download and `bash` the script in your terminal or copy-and-paste the preview into your terminal.
You **MUST** have the `idpconfgen` environment activated while running these functions.

NOTE: Because you will be downloading an executable bash script, your browser may warn you about file safety. If you are not comfortable, feel free to "Load Preview" and copy the contents of the preview window into a `.sh` file.