FSV 1.0.9

Fragmentation-based Strain Visualisation

Fragmentation-based Strain Visualisation (FSV)

Description

Fragmentation-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 FSV-x.x.x-py3-none-any.whl

requirements

FSV:

• 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

FSV -inp input.inp

FSV -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)

Including in FSV tools:

autofragment.py autofragment auto fragmentation! input: xyz file/ or Gaussian gjf file with/without connectivity ouput: gjf file with connectivity， fraglist for M1, pymol script for visualization

atompair.py atompair pair atom between two gjfs with same connectivity info but different label order input: gjf1 gjf2 Gaussian files with connectivity ouput: new gjf2 with same atom label to gjf1

the symmetric atoms can not be separated (warning information)

pml_str.py pml_str add addtional command to the pml files such as bond id x, id x and unbond id x, id x (using ; to separate lines) in a "" not ''

write_run_pml.py write_run_pml write Pymol run pml to generate strain png files for multi-conformer case (IRC/MD).
inputs: method number eg.: M2 125

multi_mov.py multi_mov after Run Pymol pml to generate strain png files for multi-conformer case (IRC/MD). Generate electronic energy (MEP) and strain energy figure for each conformer, then combine them with stran visualization png to generate a movie
inputs: energy_xlsx type(IRC/MD) where xlsx file including pos, Energy, Strain M1/M2/M3 columns

Combine_multi_conf.py Combine_multi Similar to Combine_fig_MS.py, but for multiple conformers. inputs: conf_id1 conf_id2 ... conf_idn combine selected confs

Combine_fig_MS.py/Combine_fig_ppt.py Combine_fig_MS/Combine_fig_ppt combine multiple pngs (M1, M2, M3) into one png for publication (label a/b/c/d) or ppt (file names)

Citation