DOCKING_REPORT

Overview

DOCKING_REPORT 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). DOCKING_REPORT 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

Input Preparation

The input to the DOCKING_REPORT program are the output structures docked by either FRED or HYBRID and the receptor file(s) used to dock them.

Parameter List

Input

-docked_poses : Poses docked by FRED or HYBRID

-receptor : Receptor file(s) the -docked_poses were docked into.

Report Options

-names : Name of one or more molecules in -docked_poses to write a report for.

-smiles_file : File identifying one or more molecules in -docked_poses to create a report for.

-sd_tags : SD Tagged data to include in the report for each molecule.

Output

-report_file : PDF report file to create.

Note

Values in parenthesis are defaults.

Parameters Details

Input

-docked_poses <filename> [No Default: Required Parameter]

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

[ Aliases = -poses ]

-receptor <filename> [<filename> ...] [No Default: Required Parameter]

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 ]

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

-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 ]

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.