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Python library for HostDesigner by Benjamin P. Hay
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README.md

HostDesigner

A Program for the de Novo Structure-Based Design of Molecular Receptors with Binding Sites that Complement Metal Ion Guests *

Table of contents

Installation

HostDesigner Installation

HostDesigner V3.0 source code can be downloaded here. The source code is also provided in this repository. Detailed installation instructions are provided with the source code under 00_Documentation folder. Below a summarized version of the instructions are provided.

Compiling the code

HostDesigner is provided as Fortran source code. The code can be compiled using gfortran. The downloaded directory 01_Source contains the files needed to create the HostDesigner executable. Assuming that that both gfortran and make executables are available in the user’s path, simply open a terminal window, enter the 01_Source directory, and run make. This should produce the executable named hd3.0 in less than a minute.

cd HD_3.0/01_Source
make

Configuring the environment

HostDesigner is a command line executable and, once the system is properly configured, the user should be able to invoke it from any directory. After hd3.0 has been successfully compiled, there are two additional things that must be done for this to happen.

First, the executable must be placed in a location that is in the user’s path.

Second, the executable must be provided the location of two required data files – CONSTANTS and LIBRARY.

For a bash user with username hay the steps are as follows:

  1. Put the executable hd3.0 in a directory that is part of the user’s default path
  2. Add the following lines to .bashrc file:
export PATH=“PATH:/Users/hay/bin”
export HD_DIR=“/Users/hay/bin/hd_dir”

After completing the above steps, the configuration should be tested by opening a new terminal window and issuing a couple simple commands. Issuing the command:

which hd3.0

Should return the response:

path_to_the_executable/hd3.0

To verify that the environmental variable has been properly set, issue the command:

echo $HD_DIR

Python Interface Installation

HostDesigner python interface allows the user to create and run HostDesigner simulations with python scripts. Moreover, resulting structures can be visualized with Jupyter notebooks.

To install the interface clone the repository, enter the repository and run setup as:

git clone https://github.com/kbsezginel/HostDesigner.git
cd HostDesigner
python setup.py install

HostDesigner Python libray has following dependencies:

  • pyyaml (for saving and reading yaml files)
  • tabulate (tabulating results)
  • nglview (visualizing molecules)

The dependencies are installed with the setup file and they can be also installed separately by:

pip install -r requirements.txt

Running test cases

Directory 03_Examples in the download package contains eight test cases that can be run to verify that HostDesigner has been correctly compiled and that the system has been correctly configured. Each test case consists of a control file, input fragment(s), and a prior summary file obtained when the test was last run.

To run any of the test cases, open a terminal window, enter one of the subdirectories containing the input files (named case#), type hd3.0 on the command line, and hit return. The code should execute and begin printing information to the screen. All the test cases should complete within a couple of minutes and produce several output files. To verify expected performance, compare the output file with the .summ extension to the provided file named prior.summ, which is output obtained when the authors previously ran the example. The timings will be machine specific, but the number of links read, the number of links used, the total number of structures examined, and the number of structures stored should be identical.

Usage

A quick introduction for using HostDesigner is given here. More information on the algorithm can be found in manual.

The test cases can be run with the Python library using jupyter notebooks provided in the repository.

Running simulations

HostDesigner simulations can be run using python library with:

HostDesigner runs require following files in the run directory:

  • control: control run parameters
  • hosta: host structure a
  • hostb: host structure b

The host structures are in special HostDesigner format and more information can be found in manual. If host structures are identical optionally a single file can be used by explicitly stating name of the structure in control file. By default default names are hosta, hostb, and out. The file names for a control file can be set by:

from hostdesigner.control import sample

control = dict(sample)
control['hosta'] = host_a_file
control['hostb'] = host_b_file
control['out'] = output_file_name

LINKER

from hostdesigner.run import hd_run
from hostdesigner.control import sample

# Initializing control file for a LINKER run
control = dict(sample)
control['run_type'] = 'LINK'

hd_run('simulation/dir', control=control, verbose=2)

OVERLAY

from hostdesigner.run import hd_run
from hostdesigner.control import sample

# Initializing control file for a LINKER run
control = dict(sample)
control['run_type'] = 'OVER'

hd_run('simulation/dir', control=control, verbose=2)

Drive

from hostdesigner.run import hd_run
from hostdesigner.control import sample

# Initializing control file for a LINKER run
control = dict(sample)
control['run_type'] = 'LINK'
control['drivea'] = True
control['driveb'] = True
control['testdrive'] = True

hd_run('simulation/dir', control=control, verbose=1)

Archiving results

The simulation output files can be archived by recording the run environment. All input and output files would be stored in a tar file with the run directory name and a time stamp.

hd_run('simulation/dir', control=control, verbose=1, archive=True)

Reading results

HostDesigner results are stored in .hdo format which can be read using Hdo object.

from hostdesigner.hdo import Hdo

hdo_path = 'path/to/results.hdo'
hdo = Hdo(hdo_path)
hdo.tabulate(structures=5)
Energy Linker N_atoms RMSD Structure
4.243 2-ethylbutene 71 0.009 0
3.378 cis-3,5-dimethylcyclopentene 74 0.085 1
1.24 3-methyl-1,4-pentadiene 65 0.149 2
1.24 1,3,5-trimethylbenzene 80 0.16 3
1.24 1,3-dimethylbenzene 71 0.166 4

HostDesigner outputs two separate .hdo files where one is sorted according to RMSD and the other one is sorted according to energy. These can be read separately or alternatively results can also be sorted according to number of atoms, RMSD, and energy of the structures using the sort method.

hdo1_sorted = hdo1.sort(var='energy', structures=5)
Energy Linker N_atoms RMSD Structure
1.24 3-methyl-1,4-pentadiene 65 0.149 2
1.24 1,3,5-trimethylbenzene 80 0.16 3
1.24 1,3-dimethylbenzene 71 0.166 4
1.981 trans-2-butene 53 0.547 11
2.232 cis-3-hexene 71 0.323 6

Terms of Use

Copyright © 2015 Benjamin Hay

Supramolecular Design Institute

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

HostDesigner is provided by the authors “as is” and any express or implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the authors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use; data or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.

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