Docking Analysis in DOCK3.8

Location of new scripts/Install Instructions

You can retrieve these scripts from the "docktop" repository on github, which is public.

git clone https://github.com/docking-org/docktop.git

Python 3.8+

Conda Environment

The simplest way to source python 3.8+ is to just install via conda.

conda create -n py311 python==3.11
conda activate py311

No other packages are required!

Manual Install

On Wynton you can use the version installed @ /wynton/group/bks/soft/python-versions/python-3.8-install

If you want to install python3.8 on your own, try the following:

wget https://www.python.org/ftp/python/3.8.8/Python-3.8.8.tgz

# MY_SOFT is the directory you want to install to
tar -C $MY_SOFT -xzf Python-3.8.8.tgz
pushd $MY_SOFT/Python-3.8.8
./configure --prefix=$MY_SOFT
make && make install
popd

# add the new python 3.8 executable to your path to use
export PATH=$PATH:$MY_SOFT/python-3.8-install/bin

# optional: clean up the configuration files
# rm -r $MY_SOFT/Python-3.8.8.tgz
# rm Python-3.8.8.tgz

top_poses.py

Description

Main pose retrieval algorithm, runs on multiple processes.

Input can be a directory or a file. If input is a directory, the script will use a recursive find command to locate all test.mol2.gz* files residing in the directory structure.

If input is a file, each line in the file should map to a valid pose file, e.g:

/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0000/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0001/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0002/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0003/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0004/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0005/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0006/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0007/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0008/test.mol2.gz
/wynton/group/bks/work/yingyang/5HT-1d/04_LSD/run_dock_es1.5_ld0.3/docked_chunks/chunk0009/test.mol2.gz

Output prefix is where the top N poses will be written out when the script has finished. e.g /scratch/top_poses.mol2.gz, as well as a human-readable .scores file.

Usage

usage: top_poses.py [-h] [-n NPOSES] [-o OUTPREFIX] [-j NPROCESSES] [--id-file INPUT_ID_FILE]
                    [--verbose] [--quiet] [--log-interval LOG_INTERVAL]
                    [--find-min-size FIND_MIN_SIZE]
                    dockresults_path

Retrieve the top N poses from docking results

positional arguments:
  dockresults_path      Can be either a directory containing docking results, or a file where each
                        line points to a docking results file.

optional arguments:
  -h, --help            show this help message and exit
  -n NPOSES             How many top poses to retrieve, default of 150000
  -o OUTPREFIX          Output file prefix. Each run will produce two files, a mol2.gz containing
                        pose data, and a .scores file containing relevant score information.
                        Default is "top_poses"
  -j NPROCESSES         How many processes should be dedicated to this run, default is 2. If your
                        files are spread across multiple disks, increasing this number will
                        improve performance.
  --id-file INPUT_ID_FILE
                        Only retrieve poses matching ids specified in an external file.
  --verbose             write verbose logs to stdout
  --quiet               write minimum logs to stdout
  --log-interval LOG_INTERVAL
                        number of poses between log statements. Ignored if --quiet enabled
  --find-min-size FIND_MIN_SIZE
                        filter out test.mol2.gz* files below a minimum bytes size

Note on Parallel Processing

By default, this script allocates two extra threads (-j 2) to read in files. This ensures that the main thread can sort poses uninterrupted, while the others take care of the grunt work of reading and annotating files. Increasing the number of reader threads beyond two does not guarantee an improvement in performance, but depending on the filesystem(s) your docking poses live on, they could. For example, on Wynton it can be helpful to allocate up to 8 extra threads for reading files, due to the way the filesystem works on Wynton. On the BKS cluster, increasing the number of reader threads beyond two will have a negligible (or even negative) impact, unless your files happen to be striped across multiple servers.

Checking Logs

If everything went smoothly, your log should end with a string of text that looks like this:

received all input!
joining threads...
done processing! writing out...
299900 / 300000

You may also see a message that looks like this:

short timeout reached while retrieving pose... trying again! curr=...

This just indicates slowness in the file reading, and is common to see at the beginning of a log or when the filesystem is under high load.