PyRESP GEN PROGRAM version 1.0

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This program is developed for automatically generating the input file for program PyRESP (a python version) or pol_resp (fortran version)

Author info: Qiang Zhu PostDoc AT UC Irvine Qiang's Blog

Architecture

• constant.py : definition of constant variables
• pyresp_gen.py : main program for pyresp gen
• prepin.py : function of dumping 1st stage and 2nd stage input file
• zmatrix.py : function for getting information from esp data, building distance matrix, finding equivalent atoms and bonds, and dump esp data to xyz for visualization.a
• pyresp_gen_env.yml : a environment library file
• examples : a bundle of examples for test

How to intall

Dependencies

This program runs with python 3. To run this program, make sure the following dependencies are installed:

• numpy: A Python library supporting for large, multi-dimensional arrays and matrices.
• scipy: A Python library used for scientific computing and technical computing.

You can manually install the aformationed library one by one. However, for your convenience, a environment file named pyresp_gen_env.yml was provided. A corresponding environment could be created using following command:

conda env create -f pyresp_gen_env.yml

How to use

Step 1:

Downloading the source code and put them to your desired location \your\path;

Step 2:

Installing the required libraries and activate them. If you are utilizing the anaconda, you can easily install the libraries with the environment file pyresp_gen_env.yml we supplied. Then, just activate the environment you created with the following command:

conda activate your_env_name

Step 3:

Setting the environment path:

• For Mac User: Editing the ~/.zshrc and adding the following line:

export PATH=/your/path/to/pyresp_gen:$PATH

• For Linux User: Editing the ~/.bashrc file and adding the same line

Executing the pyresp_gen command line

usage:
pyresp_gen.py [-h] --espdat ESPDAT [--Istage ISTAGE] [--IIstage IISTAGE] [--ptype PTYPE] [--dtype DTYPE] [--nmol NMOL] [--charge CHARGE] \
			  [--QWT1 QWT1] [--QWT2 QWT2] [--PWT1 PWT1] [--PWT2 PWT2] [--EXC12 EXC12] [--EXC13 EXC13] [--DEPTH DEPTH] [--verbose VERBOSE]

For help just type pyresp_gen.py -h which will show the explanation of each arguments. Here, we explained them in detail.

• -h or --help : show help message and exit

• -i or --espdat : input file of esp data

• -f1 or --Istage : name for the 1st stage input file, if you not specified, default name pyrespgen.1st will be applied

• -f2 or --IIstage : name for the 2nd stage input file, if you not specified, default name pyrespgen.2nd will be applied

• -p or --ptype : polarization type, in this version, only support chg: additive model ind: RESP-ind model perm: RESP-perm model <- default

• -d or --dtype : Damping function type, in this version supproted types are listed below: (1) applequist (2) tinker (3) exponential (4) linear (5) pgm <- default

• -nmol or --nmol : Number of conformations. In this version could only handle one conformation

• -q or --charge : Total charge of this structure or conformer

• -qwt1 or --QWT1 : Charge restraint in the 1st stage: default is set to be 0.0005

• -qwt2 or --QWT2 : Charge restraint in the 2nd stage: defalt is set to be 0.001

• -pwt1 or --PWT1 : Permanent dipoles restraint in the 1st stage

• -pwt2 or --PWT2 : Permanent dipoles restraint in the 2nd stage

• -exc12 or --EXC12 : including (0) or excluding (1) 1-2 interactions

• -exc13 or --EXC13 : including (0) or excluding (1) 1-3 interactions

• -depth or --DEPTH : Maximum depth for searching equivalance atoms

• -v or --verbose : Print verbose info.