DockingReport

Overview

DockingReport is a utility program that creates a PDF report for one or more molecules docked by FRED or HYBRID. The PDF report lists includes a 2D depiction of each molecule, a breakdown of the score by atom, a breakdown of the score components by atom, a comparison of the molecule’s score compared to the other docked molecules, SD data tagged to the molecule and other general molecule properties (e.g., molecular weight). DockingReport also includes a ‘Residue Fingerprint’ which highlights which residues in the receptor site the ligand is interacting with (greyed out residues are residues in the site that other ligands interact with, but the current ligand does not).

../_images/docking_report.png
Example dock report

Example Commands

Creating a report for named molecules

Creates a report for 2 molecules blockbuster1 and blockbuster2 that were docked by FRED.

Input files

  • fred_docked.oeb.gz

    Molecules docked by FRED including two molecules named blockbuster1 and blockbuster2 respectively.

  • receptor.oeb.gz

    The receptor file the molecules in docked.oeb.gz were docked to.

Command line

prompt> docking_report -docked_poses fred_docked.oeb.gz \
                    -receptor receptor.oeb.gz \
                    -names blockbuster1 blockbuster2

Output files

  • docking_report.pdf

    PDF dock report for blockbuster1 and blockbuster2.

Creating a report for molecules identified by SMILES

Creates a report for molecules, docked by HYBRID, that have the same canonical smiles as molecules in a specified file.

Input files

  • hybrid_docked.oeb.gz

    Molecules docked by HYBRID.

  • receptor1.oeb.gz and receptor2.oeb.gz

    The receptor files HYBRID used to dock the molecules in docked.oeb.gz.

  • interesting_molecules.sdf

    Set molecules to create reports for. The molecules in this file will be converted into canonical SMILES, and a report will be generated for each molecule in docked.oeb.gz that has the same canonical SMILES as any one of the molecules in interesting_molecules.sdf

Command line

prompt> docking_report -docked_poses hybrid_docked.oeb.gz \
                    -receptor receptor1.oeb.gz receptor2.oeb.gz \
                    -smiles_file interesting_molecules.sdf

Output files

  • docking_report.pdf

    PDF dock report for all molecules in docked.oeb.gz that have the same canonical SMILES as one of the molecules in interesting_molecules.sdf.

Command Line Help

A description of the command line interface can be obtained by executing DockingReport with the --help option.

> docking_report --help

will generate the following output:

Help functions:
  docking_report --help simple      : Get a list of simple parameters
  docking_report --help all         : Get a complete list of parameters
  docking_report --help defaults    : List the defaults for all parameters
  docking_report --help <parameter> : Get detailed help on a parameter
  docking_report --help html        : Create an html help file for this program
  docking_report --help versions    : List the toolkits and versions used in the application

Required Parameters

Input

-docked_poses <filename>

A file with poses that were docked by either FRED or HYBRID.

[ Aliases = -poses ]

-receptor <filename> [<filename> ...]

Receptor file the poses passed to -docked_poses were docked too. If the poses were docked with hybrid HYBRID using multiple receptor structures then the same set of receptor structures should be passed to this flag.

[ Aliases = -rec ]

Optional Parameters

Input Options

-names <molecule name> [<molecule name> ...] [No Default]

This option identifies one or more molecules passed to the -docked_poses option by name. Molecules specified with this flag will have a report generated for them.

Note

Either this flag or -smiles_file must be specified.

[ Aliases = -title ]

-smiles_file <filename> [No Default]

This option identified molecules passed to the -docked_poses option by canonical SMILES. Molecules identified with this flag will have a report generated for them.

Note

Either this flag or -names must be specified.

[ Aliases = -smiles ]

-sd_tags <Tag> [<Tag> ...] [No Default]

This flag specifies a specific set of SD tagged data to include in the dock report. If this flag is not specified all the SD data will be include in the dock report.

Note

The dock report has a limited amount of space for SD data and can only include 10 pieces of SD data for each docked molecule (additional SD data will not appear in this report).

[ Aliases = -sdtags ]

Output Options

-report_file <filename> [Default: docking_report.pdf]

Name of the docked report file to generate.

The file must be a PDF file (i.e., have a .pdf extension).

[ Aliases = -report ]