Fragmentation-based Strain Visualisation
Project description
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:
-
- atomic/fragments resolution based on fragmentations
-
- bond and angle resolution based on internal coordinates (bond & angle)
-
- 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
- Gaussian03/09/16
xTB:
- xtb-python
ANI:
- torchvision
- torch
- torchani
- 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
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)
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
Plot_Ene.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
Citation
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