OBSV 1.0.4

ONIOM-based Strain Visualisation

ONIOM-based Strain Visualisation (OBSV)

Description

ONIOM-based Strain Visualisation Strain energy visualization of one/multiple conformers relative to the reference structure(eg: global minima). Subsystem extracted based on ONIOM methods(link atoms and scale factors). The subsystem can be defined using three methods:

• 1. atomic/fragments resolution based on fragmentations
• 2. bond and angle resolution based on internal coordinates (bond & angle)
• 3. combination of 1 & 2

Installation

conda env create -f environment.yml

pip install OBSV-x.x.x-py3-none-any.whl

requirements

OBSV:

• python=3.9
• numpy
• pandas
• openbabel
• openpyxl

Gaussian:

• Gaussian03/09/16

xTB:

• xtb-python

ANI:

• torchvision
• torch
• torchani

MLatom:

• matplotlib
• tensorboard
• torchvision
• torch
• torchani
• MLatom (3.0.0))
• scipy
• pyh5md
• statsmodels

quantum chemical calculation packages: Gaussian: Gaussian03,09,16 xTB: xTB-python ANI: torchani Mlatom: AIQM1

Usage

OBSV -inp input.inp

OBSV -h The -inp input.inp are recommended

example of inp file showed in example directory

calculator available: ['g03', 'g09', 'g16','gfn1-xtb', 'gfn2-xtb','ani-1x', 'ani-2x', 'ani-1ccx', 'aiqm1'] inp file example:

ref = ref.gjf
conf = conf.gjf
method = int
cpu = int
pal = int
calculator = g16 
scale = e/10.0 (optional)

#fraglist (optional: only method = 1/3 required)
1-2,4-6
3

#coordination (optional: only method = 3 available)
3-5

#include (optional: only method = 2/3 and extra bond/angles (no connection ) are needed)
1 2
1 2 3 

#exclude (optional: only method = 2/3 and extra bond/angles are not need)
4 7 
4 7 9

#charge (optional: only if atomic charge not zero required)
5 1

#spin (optional: only if atomic charge not zero required)
3 1

preparations

ref: ref.gjf-reference stucture in Gaussian file, containing method lines, cartesian coordinates and connectivity

• the connectivity (bond order) values should be 1.0, 2.0, 3.0!
• 1.5 is forbidden, it should be modified before computations!

conf: conf.gjf/.xyz conformer structure, and multiple structure in one xyz file is acceptable

method: 1 for framentation method, 2 for bond/angle method, 3 1+2

cpu: number of cpu for subsystem computation

pal: number of paralle subsystem computations (available for Gaussian, xTB)

calculator: calculator (Gaussian, xTB, ANI, AIQM1) for subsystem computation

scale: log scale factor for pymol visualization

fraglist: method =1/3, define the fragmentation list

coordination: method =3, define the coordination center (similar to fraglist)

include: method =2/3, additional bond/angle for non-connected atoms

exclude: method =2/3, exclude the bond/angle

charge: define the atomic charge if not 0

spin: define the atomic spin if not 0 (using integer: spin * 2)

Citation