### Install TS2CG from Source

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Download-and-install-TS2CG

Clone the repository and install locally, optionally using a virtual environment.

```console
git clone https://github.com/weria-pezeshkian/TS2CG-v2.0
cd TS2CG-v2.0
python3 -m venv venv && source venv/bin/activate # Not required, but often convenient.
pip3 install .
```

--------------------------------

### Install TS2CG from GitHub

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Download-and-install-TS2CG

Install the latest version directly from the GitHub repository.

```console
pip3 install git+https://github.com/weria-pezeshkian/TS2CG-v2.0
```

--------------------------------

### Install TS2CG from Source

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Clone the TS2CG repository from GitHub and install it from the source code using pip.

```bash
git clone https://github.com/weria-pezeshkian/TS2CG-v2.0
cd TS2CG-v2.0
pip3 install .
```

--------------------------------

### Example system.top file for 1D Fourier-shaped POPC bilayer

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

This is an example of the topology file generated by PCG for a 1D Fourier-shaped POPC bilayer system.

```plaintext
;This file was generated by TS2CG membrane builder script i.e., PCG  
 [ system ]  
 Expect a large membrane  
 [ molecules ]  
; domain 0  
 ;  in the upper monolayer  
     POPC  585     
; domain 0  
 ;  in the lower monolayer  
     POPC  585      

```

--------------------------------

### q File Format Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example of the q file format used as input for the PLM executable.

```text
50.000     50.000     50.000
1840
0       21.4    33.8    32.7    0
1       38.1    26.1    32.3    0
2       40.9    24.2    19.9    0
...
1839    31.2   323.2    23      0
3680
0        75      776    1043    1
1       796     1821     752    1
2       995     1027     279    1
3       662    1162      56     1
4       167      38     391     1
...
```

--------------------------------

### View generated topology

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-1

Example of the system.top file generated by the PCG script.

```text
;This file was generated by TS2CG membrane builder script i.e., PCG 
 [ system ] 
 Expect a large membrane 
 [ molecules ] 
; domain 0 
 ;  in the upper monolayer 
     POPC  6256     
; domain 0 
 ;  in the lower monolayer 
     POPC  3876  
```

--------------------------------

### Run Solvation Command

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example command to execute the solvation tool with specific input, output, ion, and template files.

```console
SOL -in in.gro -o out.gro -ion 20 20 -tem water.gro
```

--------------------------------

### Run TS2CG command line

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example command to execute TS2CG with specific parameters for surface generation.

```console
TS2CG PLM -TSfile Traj1.tsi -bilayerThickness 4 -rescalefactor 3 3 3 -o output
```

--------------------------------

### Install TS2CG via PyPi

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Download-and-install-TS2CG

Install the package using pip. Note that the PyPi repository may not contain the latest development versions.

```console
pip3 install TS2CG
```

--------------------------------

### Initial System Setup with TS2CG PLM

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-3

Use this command to set up the initial simulation system before defining lipid domains. Ensure the -TSfile points to your system's topology file.

```bash
TS2CG PLM -TSfile Sphere_2.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4
```

--------------------------------

### Check CMake Version

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Download-and-install-TS2CG

Verify that CMake version 3.10 or later is installed on the system.

```console
cmake --version
```

--------------------------------

### Topology File Content

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-3

Example output of the generated system.top file showing lipid distribution across domains and monolayers.

```text
;This file was generated by TS2CG membrane builder script i.e., PCG 
 [ system ] 
 Expect a large membrane 
 [ molecules ] 
; domain 0 
 ;  in the upper monolayer 
     POPC  5834     
; domain 0 
 ;  in the lower monolayer 
     POPC  3614     
; domain 1 
 ;  in the upper monolayer 
     DOPC  259     
; domain 1 
 ;  in the lower monolayer 
     DOPC  160     
; domain 2 
 ;  in the upper monolayer 
     POPE  162     
; domain 2 
 ;  in the lower monolayer 
     POPE  100
```

--------------------------------

### GROMACS Coordinate File Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example of a .gro file format showing atom positions and velocities.

```text
TS2CG manual
    6
    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
   1.82060   1.82060   1.82060
```

--------------------------------

### Load Point Folder

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-9

Load an existing point folder to start modifying the membrane structure.

```python
point=TS2CG.core.point.Point("./point_tut4_start")
```

--------------------------------

### View Inclusion Data Format

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-8

Example of the IncData.dat file structure showing protein IDs, types, and coordinates.

```text
< Inclusion NoInc       3   >
< id typeid pointid lx ly lz  >
           0      1      5      0.499      -0.864      0.059
           1      1      22     0.481      -0.765     -0.429
           2      2      30    -0.177      -0.945      0.275
```

--------------------------------

### Get TS2CG Help

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Display help information for the main TS2CG executable and its subcommands like SOL, PLM, and PCG.

```console
TS2CG -h
```

```console
TS2CG {SOL,PLM,PCG,...} -h
```

--------------------------------

### PCG Input File Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example of an .str input file used for configuring lipids, domains, and protein inclusions.

```text
include protein.gro
[Lipids List]
;LipidName  RatioUp RatioDown   Area/Lipid
Domain 0
POPC        0.5     0.5         0.63
POPE        0.5     0.5         0.64
End
Domain 1
POPC        0.5     0.5         0.63
POPE        0.5     0.5         0.64
End
[Shape Data]
ShapeType    Flat
Box    40    40    40
Density      2     2
Thickness    3.8
WallRange    0     1    0    1
End
[Protein List]
;ProteinName    Incl.Id     Surface_Coverage    0   0   z-position
STxB            1           0.5                 0   0   -1.1
end Protein
```

--------------------------------

### Lipid Library (.LIB) File Format

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Example format for a .LIB file used by PCG, defining bead positions for different lipid types. Includes Martini map and CG information.

```text
Description Martini Map CG
Version Martini 3
;Martini 3 lipid library for TS2CG 2.0

[POPC]
; BeadID  BeadName  X-offset  Y-offset  Z-offset
1 NC3 0 0    1
2 PO4 0 0    0
3 GL1 0 0   -1
4 GL2 0 0.5 -1
5 C1A 0 0   -2
6 D2A 0 0   -3
7 C3A 0 0   -4
8 C4A 0 0   -5
9 C1B 1 0   -2
10 C2B 1 0  -3
11 C3B 1 0  -4
12 C4B 1 0  -5

[POPE]
1 NH3 0 0    1
2 PO4 0 0    0
3 GL1 0 0   -1
4 GL2 0.5 0 -1
5 C1A 0 0   -2
6 D2A 0 0   -3
7 C3A 0 0   -4
8 C4A 0 0   -5
9 C1B 1 0   -2
10 C2B 1 0  -3
11 C3B 1 0  -4
12 C4B 1 0  -5

[CDL0]
; Cardiolipin - 4 acyl chains
1 GL0     0.5   1    1
2 PO41      0   0    0
3 GL11      0   0   -1
4 GL12      0   1   -1
5 C1A1      0   0   -2
...
```

--------------------------------

### Configure TS2CG CMake Project

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/CMakeLists.txt

Sets the project requirements, C++ standard, and defines subdirectories and installation targets.

```cmake
cmake_minimum_required(VERSION 3.10)
project(TS2CG)

set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_STANDARD_REQUIRED ON)

add_subdirectory(TS2CG/cpp/Solvate)
add_subdirectory(TS2CG/cpp/Pointillism)
add_subdirectory(TS2CG/cpp/MembraneBuilder)

install(TARGETS SOL PLM PCG
        RUNTIME DESTINATION TS2CG)
```

--------------------------------

### Get All Exclusions

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/Tutorials/tut9/Tutorial9.ipynb

Retrieves all exclusion zones defined for the system. Useful for inspecting existing exclusions before making changes.

```python
point.exclusions.get_all()
```

--------------------------------

### Define lipid composition

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-1

Example content for an input.str file defining the lipid domain and area per lipid.

```text
[Lipids List]

Domain 0
POPC  1 1 0.64  
End
```

--------------------------------

### Define Domain in Sphere.tsi

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-3

Example of a line in the .tsi file with the domain ID appended to the end.

```text
45     23.4753129908     28.0982228567     26.6006234584	2
```

--------------------------------

### Define GROMACS Topology File

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

A complete example of a .top file defining a Urea molecule in water, including force field parameters, atomic definitions, and system constraints.

```GROMACS Topology
;
;       Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"
[ moleculetype ]
; name  nrexcl
Urea         3
[ atoms ]
   1  C  1  URE      C      1     0.880229  12.01000   ; amber C  type
   2  O  1  URE      O      2    -0.613359  16.00000   ; amber O  type
   3  N  1  URE     N1      3    -0.923545  14.01000   ; amber N  type
   4  H  1  URE    H11      4     0.395055   1.00800   ; amber H  type
   5  H  1  URE    H12      5     0.395055   1.00800   ; amber H  type
   6  N  1  URE     N2      6    -0.923545  14.01000   ; amber N  type
   7  H  1  URE    H21      7     0.395055   1.00800   ; amber H  type
   8  H  1  URE    H22      8     0.395055   1.00800   ; amber H  type
[ bonds ]
    1    2
    1    3
    1    6
    3    4
    3    5
    6    7
    6    8
[ dihedrals ]
;   ai    aj    ak    al funct  definition
     2     1     3     4   9
     2     1     3     5   9
     2     1     6     7   9
     2     1     6     8   9
     3     1     6     7   9
     3     1     6     8   9
     6     1     3     4   9
     6     1     3     5   9
[ dihedrals ]
     3     6     1     2   4
     1     4     3     5   4
     1     7     6     8   4
[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai   funct    fc
   1     1     1000    1000    1000 ; Restrain to a point
   2     1     1000       0    1000 ; Restrain to a line (Y-axis)
   3     1     1000       0       0 ; Restrain to a plane (Y-Z-plane)
[ dihedral_restraints ]
; ai   aj    ak    al  type  phi  dphi  fc
    3    6     1    2     1  180     0  10
    1    4     3    5     1  180     0  10
; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"
[ system ]
Urea in Water
[ molecules ]
;molecule name   nr.
Urea             1
SOL              1000
```

--------------------------------

### tsi File Format Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Example of the tsi file format, which contains DTS simulation trajectory outputs including vertices, triangles, and inclusions.

```text
version 1.1
box 50.000     50.000     50.000
vertex 1840
0       21.4    33.8    32.7    0
1       38.1    26.1    32.3    0
2       40.9    24.2    19.9    0
...
1839    31.2   323.2    23      0
triangle 3680
0        75      776    1043    1
1       796     1821     752    1
2       995     1027     279    1
3       662    1162      56     1
4       167      38     391     1
...
inclusion 3
0         1       22       0    1
1         1        5       0    1
2         2       30       0    1
```

--------------------------------

### Generated Topology File Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-2

This is an example of the topology file generated by the TS2CG PCG tool. It lists the counts of each lipid type in different domains of the system.

```text
;This file was generated by TS2CG membrane builder script i.e., PCG 
 [ system ] 
 Expect a large membrane 
 [ molecules ] 
; domain 0 
 ;  in the upper monolayer 
     POPC  3056     
     DOPC  3056     
; domain 0 
 ;  in the lower monolayer 
     POPC  1893     
     DOPC  1893     

```

--------------------------------

### Get Help for TS2CG DOP Command

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-7

This command displays the help message for the TS2CG DOP tool, showing expected input formats and available options for modifying point folders.

```bash
TS2CG DOP -h
```

--------------------------------

### TSI File Format Structure

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Example structure of a TSI (Triangulated Surface Input) file, detailing version, box dimensions, vertex coordinates, triangle connectivity, and optional inclusion/exclusion zone data.

```text
version 1.1
box 50.000     50.000     50.000
vertex 1840
0       21.4    33.8    32.7    0
1       38.1    26.1    32.3    0
2       40.9    24.2    19.9    0
...
1839    31.2   323.2    23      0
triangle 3680
0        75      776    1043    1
1       796     1821     752    1
2       995     1027     279    1
...
inclusion 3
0   1   5    0   1
1   1   22   0   1
2   2   30   0   1
exclusion 1
0   30   1
```

--------------------------------

### Display SOL help information

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Displays the help menu for the solvation executable.

```console
TS2CG SOL -h
```

--------------------------------

### Membrane Builder (PCG) from Point Folder

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Build a membrane system using a specified point folder as input. This allows for building from pre-generated point data.

```bash
TS2CG PCG -dts point -str input.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system
```

--------------------------------

### Access TS2CG Help

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Download-and-install-TS2CG

Display the main help menu or module-specific help for Pointillism, Membrane Builder, and Solvate.

```console
TS2CG --help
```

```console
TS2CG PLM -h
```

```console
TS2CG PCG -h
```

```console
TS2CG SOL -h
```

--------------------------------

### Assign Lipid Domain ID

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-5

Example of a vertex line in the .tsi file updated with a lipid domain ID.

```text
5     22.0396876425     23.6080597437     26.8858740866    1
```

--------------------------------

### Configure input.str File

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-5

Final structure of the input.str file including lipid domains and protein definitions.

```text
include P1.gro 
include P2.gro

[Lipids List]
Domain   0  
POPC     1   1   0.64
End
Domain   1  
DOPC     1   1   0.64
End
Domain   2  
POPE     1   1   0.64
End

[Protein List]
protein1     1   0.01   0   0   -2.5
```

--------------------------------

### Generate Initial Point Folder with PCG

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-7

Use the PCG command with the -WPointDir flag to create an initial point folder for the specified shape. This folder contains InnerBM.dat and OuterBM.dat.

```bash
TS2CG PCG -str input.str -function analytical_shape -defout system -WPointDir 
```

--------------------------------

### Build Bilayer Vesicle with PCG

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-8

Constructs the final system using the modified point folder.

```bash
TS2CG PCG -str input_vesicle.str -Bondlength 0.2 -LLIB "./files/Martini3.LIB" -dts ./point_vesicle_new2 -incdirtype Local -defout system_vesicle
```

--------------------------------

### Complete Workflow: Vesicle with Proteins (Bash)

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

A multi-step bash script demonstrating a full workflow from a TS file to a solvated membrane system with proteins, using TS2CG and GROMACS commands.

```bash
# Step 1: Generate point representation from TS file
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4 -o point

# Step 2: Add circular lipid domains around protein positions
TS2CG DAI -p point -r 4 -d 1 -t 1  # Domain 1 around protein type 1
TS2CG DAI -p point -r 4 -d 2 -t 2  # Domain 2 around protein type 2

# Step 3: Build membrane with proteins
# input.str content:
# include P1.gro
# include P2.gro
# [Lipids List]
# Domain 0
# POPC 1 1 0.64
# End
# Domain 1
# DOPC 1 1 0.64
# End
# Domain 2
# POPE 1 1 0.64
# End
# [Protein List]
# protein1 1 0.01 0 0 -2.5
# protein2 2 0.01 0 0 -2.5
# End Protein

TS2CG PCG -str input.str -dts point -Bondlength 0.2 -LLIB Martini3.LIB -defout system

# Step 4: Energy minimization in vacuum (GROMACS)
gmx grompp -f em.mdp -c system.gro -p system.top -o em.tpr -maxwarn 1
gmx mdrun -v -deffnm em

# Step 5: Short equilibration in vacuum
gmx grompp -f eq_vacuum.mdp -c em.gro -p system.top -o eq_v.tpr -maxwarn 1
gmx mdrun -v -deffnm eq_v

# Step 6: Solvate the system
TS2CG SOL -in eq_v.gro -tem water.gro -o solvated.gro -Rcutoff 0.32 -ion 50 50
# Add water/ion counts from info.txt to system.top

# Step 7: Production simulation (GROMACS)
gmx grompp -f prod.mdp -c solvated.gro -p system.top -o prod.tpr
gmx mdrun -v -deffnm prod
```

--------------------------------

### Initialize TS2CG Environment

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-9

Import necessary libraries and the TS2CG framework to begin membrane modifications.

```python
# We do some imports to help us with our different steps below:

import numpy as np

# And we load TS2CG to get access to the framework

import TS2CG
```

--------------------------------

### Get Inclusions by Type

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/Tutorials/tut9/Tutorial9.ipynb

Retrieves all inclusions of a specific type. Useful for filtering and processing specific protein types.

```python
point.inclusions.get_by_type(2)
```

--------------------------------

### Membrane Builder (PCG) Basic Usage

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Build a simple POPC vesicle by placing lipids onto a point representation. Requires an input string file (.str), a bond length, and a lipid library file.

```bash
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system
```

--------------------------------

### Define Lipid Ratios and Shape Parameters in .str File

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-7

This .str file defines the lipids to be used and the shape of the membrane. It's a prerequisite for generating the initial point folder.

```plaintext
;lipidnname ratio_up ratio_down  APL
POPC   1    1    0.64   ;Not necessary in this step but shouldn´t be removed.
End

[Shape Data]
ShapeType 1D_PBC_Fourier
Box    30    10    20
WallRange    0     1    0    1
Density      3     1
Thickness    4
Mode        1.5    1    0
Mode        2.5    2    0
End
```

--------------------------------

### Curvature-Based Lipid Placement Workflow (Bash)

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

A bash script demonstrating how to place lipids based on preferred membrane curvature using the DOP tool. It involves creating a point folder, defining lipid preferences, and running the DOP tool.

```bash
# Step 1: Create point folder for analytical shape
TS2CG PCG -str input_shape.str -function analytical_shape -defout system -WPointDir

# Step 2: Create domain_input.txt with lipid curvature preferences
# ; domain lipid percentage c0 density
# 0    POPC    .7    0.0    0.64
# 1    CDL0    .3   -0.5    1.2
# CDL0 with negative c0 will be placed in negatively curved regions

# Step 3: Run DOP to assign domains based on curvature
TS2CG DOP -s domain_input.txt -ni input_DOP.str -k 10

# Step 4: Build membrane with curvature-assigned domains
TS2CG PCG -dts point -str input_DOP.str -LLIB Martini3.LIB -defout system

# Higher k values increase the precision of curvature-based placement
```

--------------------------------

### Execute PCG script

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-1

Places lipids onto the generated points using the composition file and a lipid library.

```bash
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system
```

--------------------------------

### Get Protein Inclusions by Type with Python Point Class

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Filter and retrieve protein inclusions of a specific type using the `.inclusions.get_by_type(type_id)` method.

```python
# Get inclusions by protein type
type1_proteins = point.inclusions.get_by_type(1)
```

--------------------------------

### Run CG Membrane Builder

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/Tutorials/tut9/Tutorial9.ipynb

Executes the CG Membrane builder with specified parameters. Use this to generate membrane structures based on input files and settings.

```bash
!TS2CG PCG -str input.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system -dts point_tut4_start
```

--------------------------------

### Get All Inclusions

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/Tutorials/tut9/Tutorial9.ipynb

Retrieves and displays all current inclusions within the Point object. The result is a dictionary containing details like id, type_id, point_id, and orientation for each inclusion.

```python
#First, let's look at the inclusions we got.
point.inclusions.get_all()
# We see a dictionary of all the inclusions, their id, their type and their location on the point grid as the point id.
```

--------------------------------

### Generate Point Folder with PLM

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-8

Initializes a point folder from a TS file for subsequent protein placement.

```bash
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4 -o point_vesicle
```

--------------------------------

### Get All Protein Inclusions with Python Point Class

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Retrieve all protein inclusions using the `.inclusions.get_all()` method. The output includes details like `id`, `type_id`, `point_id`, and `orientation`.

```python
# Get all protein inclusions
all_inclusions = point.inclusions.get_all()
print(all_inclusions)
# Output: [{'id': 0, 'type_id': 1, 'point_id': 5, 'orientation': array([...])}, ...]
```

--------------------------------

### Complete .str File with Lipids and Proteins

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-4

The final .str file includes lipid definitions and protein definitions. This configuration is used to set up the simulation environment.

```plaintext
include  P1.gro
include  P2.gro
[Lipids List]
Domain  0  
; lipidnname ratio_up ratio_down  APL
POPC    1    1    0.64
End
[Protein List]
protein1     1     0.01     0     0     -2.5
protein2     2     0.01     0     0     -2.5
End Protein
```

--------------------------------

### Execute PCG for 1D Fourier-shaped POPC bilayer

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

Command to run PCG with a specified .str input file to generate a 1D Fourier-shaped POPC bilayer system. Outputs are system.gro and system.top.

```bash
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system -function analytical_shape    

```

--------------------------------

### Create Circular Domain with TS2CG DAI

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-3

Use the DAI module to create a circular lipid domain. Specify the points for domain creation, the desired radius (-r), and the domain ID (-d). This example creates domain 1 around points [5, 22] with a radius of 4.

```bash
TS2CG DAI -p point -r 4 -d 1 -m 5,22
```

--------------------------------

### Membrane Builder (PCG) with Wall Beads

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Generate wall beads for shape preservation when building membrane systems from analytical shapes. Specify the wall bead name with -WallBName.

```bash
TS2CG PCG -str input.str -function analytical_shape -LLIB Martini3.LIB -defout system -Wall -WallBName WL
```

--------------------------------

### Solvation with Ions

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Add ions during solvation using the `-ion` flag followed by the number of positive and negative ions. Ensure the template water file (`-tem`) is compatible.

```bash
# Add ions (20 positive and 20 negative)
TS2CG SOL -in system.gro -tem water.gro -o solvated.gro -Rcutoff 0.32 -ion 20 20
```

--------------------------------

### Membrane Builder (PCG) Generate Point Folder Only

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Generate only the point folder for a membrane system, useful for further modification with advanced Python tools like DOP, DAI, or INU. Does not build the full system.

```bash
TS2CG PCG -str input.str -function analytical_shape -defout system -WPointDir
```

--------------------------------

### Generate Vesicle Vertex Positions

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-4

Use this command to generate a .gro file containing the vertex positions of a vesicle. This is a prerequisite for identifying protein placement locations.

```bash
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 0 -rescalefactor 0.2 0.2 0.2
```

--------------------------------

### Save and Generate Structure

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-9

Save the modified point folder and execute the PCG command to generate the system structure.

```python
# Now we overwrite the point folder with our altered version.

point.save()

#Let's run PCG and look at the new inclusion.

!TS2CG PCG -str input.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system -dts point_tut4_start
```

```python
!TS2CG PCG -str input.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system -dts point_tut4_start
```

--------------------------------

### Include Protein .gro Files in .str

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-4

Include the protein .gro files at the top of your input.str file. This makes the protein structure data available for simulation.

```plaintext
include P1.gro 
include P2.gro
```

--------------------------------

### Create 1D Fourier-shaped POPC bilayer .str file

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

This .str file defines a 1D Fourier-shaped POPC bilayer, including lipid composition and shape parameters. It's used as input for the PCG command.

```plaintext
[Lipids List]
Domain      0
POPC        1   1   0.64  
End
 
[Shape Data]
ShapeType   1D_PBC_Fourier
Box         30     10     20
WallRange   0      1      0     1
Density     3      1
Thickness   3.8
Mode        1.5    1     0
Mode        2.5    2     0
End

```

--------------------------------

### TS2CG Command Line Options

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

This section details the available command-line options for the TS2CG tool, including their types, default values, and descriptions.

```APIDOC
## TS2CG Command Line Options

### Description
Command line options for the TS2CG tool.

### Parameters
#### Command Line Options
- **-rescalefactor** (rx ry rz) - Default: (1 1 1) - Rescaling factor
- **-bilayerThickness** (double) - Default: 3.8 - Bilayer thickness
- **-monolayer** (int) - Default: 0 - To generate monolayer instead (1/-1).
- **-r** (string) - Default: PLM - Function (PLM/in_out/check/add_pbc).
- **-smooth** (------) - Default: no - Might be necessary for rough surfaces.
- **-o** (string) - Default: point - Name of the output folder.
- **-resizebox** (------) - Default: no - Find a better box for the system.
- **-TSfile** (string) - Default: TS.tsi - TS file name (three file format types: *.q, *.tsi, *.dat).
- **-Mashno** (int) - Default: 1 - Number of Mosaicing, your point number grows as 4^Mashno.
- **-AlgType** (string) - Default: Type1 - Algorithm type for Mosaicing (Type1 and Type2); no difference has been reported yet.

### Notes
- The approximated area per lipid does not need to be precise, it will be modified during the later processes.
- The number of the output points is always larger or equal the number of the vertices in the input triangulated surface. With option `-Mashno` you can tune how many points you want (No_of_vertex*4^Mashno).
- There is no guarantee to get proper surface if rx, ry, rz are not equal.
- Use Mashno [1-4], unless you know what you are doing.

### Usage Example
```console
TS2CG PLM -TSfile Traj1.tsi -bilayerThickness 4 -rescalefactor 3 3 3 -o output
```
```

--------------------------------

### Generate Curved Membrane Point Folder

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-8

Generates a point folder specifically for a curved membrane structure.

```bash
TS2CG PLM -TSfile prep/Small_Curved.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4
```

--------------------------------

### Membrane Builder (PCG) Analytical Shapes

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Build membrane systems based on analytical shapes without needing a triangulated surface file. Specify the shape using the -function analytical_shape flag.

```bash
TS2CG PCG -str input.str -function analytical_shape -LLIB Martini3.LIB -defout system
```

--------------------------------

### Basic Solvation with Water

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Use `TS2CG SOL` to add coarse-grained water and ions. Specify input (`-in`), template water (`-tem`), and output (`-o`) files. `-Rcutoff` defines the cutoff radius for solvation.

```bash
# Basic solvation
TS2CG SOL -in system.gro -tem water.gro -o solvated.gro -Rcutoff 0.32
```

--------------------------------

### Define 1D Fourier Shape in .str file

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

Define a 1D periodic structure with Fourier modes in a .str file. Requires ShapeType, Box, Density, Thickness, WallRange, and Mode parameters.

```plaintext
1D Fourier Shape
[Shape Data]
ShapeType    1D_PBC_Fourier 
Box    30    10    20
Density      3     1
Thickness    3.8     
WallRange    0     1    0    1  
Mode         1.5   1    0
Mode         2.5   2    0  
End

```

--------------------------------

### Run TS2CG with custom parameters

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/blob/master/README.md

Executes the TS2CG program with specified DTS folder, input file, seed, and bond length.

```console
TS2CG PCG -dts point -str input.str -seed 39234  -Bondlength 0.15 
```

--------------------------------

### Define Flat Shape in .str file

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

Configure a flat membrane shape in a .str file. Essential parameters are ShapeType, Box, Density, Thickness, and WallRange.

```plaintext
Flat
[Shape Data]
ShapeType    Flat         
Box    40    40    40
Density      2     2
Thickness    3.8  
WallRange    0     1    0    1
End                         
 

```

--------------------------------

### PCG flags for generating wall beads

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-6

Use these flags with the PCG command to generate wall beads. This will produce Wall.itp and Wall.pdb files in addition to the standard .top and .gro files.

```bash
-Wall -WallBName WL

```

--------------------------------

### Execute TS2CG PLM and PCG Commands

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-4

Commands to generate a POPC membrane and process protein structures.

```bash
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4
```

```bash
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system
```

--------------------------------

### Create Domain Around Manual Points

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Use `TS2CG DAI` to create lipid domains. Specify domain ID (`-d`), radius (`-r`), and points using `-m`. The `-p point` flag indicates point-based assignment.

```bash
# Create domain around manually specified points
TS2CG DAI -p point -r 4 -d 1 -m 5,22
# Creates domain ID 1 with radius 4 around points 5 and 22
```

--------------------------------

### Solvation with Custom Ion Names and Seed

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Specify custom ion names using `-pname` and `-nname`, and set a random seed for reproducibility with `-seed`.

```bash
# Custom ion names and seed
TS2CG SOL -in system.gro -tem water.gro -o solvated.gro -Rcutoff 0.4 -ion 50 50 -pname NA -nname CL -seed 12345
```

--------------------------------

### Pointillism (PLM) with Increased Point Density

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Generate a point representation from a membrane triangulated surface file with increased point density. Specify an output folder for the generated points.

```bash
TS2CG PLM -TSfile membrane.tsi -bilayerThickness 3.8 -rescalefactor 3 3 3 -Mashno 2 -o output_folder
```

--------------------------------

### Pointillism (PLM) Monolayer Generation

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Generate a point representation for a single monolayer instead of a bilayer. Use the -monolayer flag with a value of 1.

```bash
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4 -monolayer 1
```

--------------------------------

### Solvate (SOL) CLI

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

The SOL executable solvates membrane systems by adding coarse-grained water and ions around the membrane structure.

```APIDOC
## SOL - Add Water and Ions

### Description
Solvates membrane systems by adding coarse-grained water and ions around the membrane structure.

### Parameters
#### Command Line Arguments
- **-in** (string) - Required - Input system file (.gro)
- **-tem** (string) - Required - Template water file (.gro)
- **-o** (string) - Required - Output file name
- **-Rcutoff** (float) - Required - Cutoff radius for solvation
- **-ion** (int, int) - Optional - Number of positive and negative ions to add
- **-pname** (string) - Optional - Custom name for positive ions
- **-nname** (string) - Optional - Custom name for negative ions
- **-seed** (int) - Optional - Random seed for reproducibility

### Request Example
TS2CG SOL -in system.gro -tem water.gro -o solvated.gro -Rcutoff 0.32 -ion 20 20
```

--------------------------------

### Run PLM operation

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-1

Executes the pointillism operation to increase vertex count and generate monolayers from a .tsi file.

```bash
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4
```

--------------------------------

### Execute PCG Tool in TS2CG

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-2

Utilize the PCG tool with a .str input file to place lipids on generated points. Requires a library file and defines output names.

```bash
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system    
```

--------------------------------

### Define Lipid Domains and Curvature Parameters

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-7

This domain_input.txt file specifies the lipids, their proportions, their preferred curvature (C0), and area per lipid. It's used by TS2CG DOP to modify the point folder.

```plaintext
; domain lipid percentage c0 density
0    POPC    .7    0.0    0.64
1    CDL0    .3   -0.5    1.2
```

--------------------------------

### Create Domain with Larger Radius for Protein Type

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Create a domain with a larger radius for a specific protein type by adjusting the `-r` value.

```bash
# Create domain around specific protein type with larger radius
TS2CG DAI -p point -r 5 -d 2 -t 2
# Creates domain ID 2 with radius 5 around all proteins of type 2
```

--------------------------------

### Run PCG with Updated Input

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-9

Execute the TS2CG PCG tool with a modified input string to incorporate new lipids into a specified domain. Ensure the input string and library file are correctly referenced.

```bash
!TS2CG PCG -str input_POPE.str -Bondlength 0.2 -LLIB Martini3.LIB -defout system -dts point_tut4_start
```

--------------------------------

### INU with Reproducible Seed

Source: https://context7.com/weria-pezeshkian/ts2cg-v2.0/llms.txt

Ensure reproducibility for `TS2CG INU` by specifying a random seed using the `--seed` flag.

```bash
# Specify random seed for reproducibility
TS2CG INU -p point -n 5 -t 1 -r 4 --seed 12345 -o point_seeded
```

--------------------------------

### Build Lipid Bilayer with Modified Point Folder using PCG

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-7

This PCG command builds the final lipid bilayer using the modified point folder and .str file generated by TS2CG DOP. It produces system.top and system.gro files.

```bash
TS2CG PCG -dts point -str input_DOP.str -LLIB ./files/Martini3.LIB -defout system
```

--------------------------------

### Place Proteins in Curved Region with TS2CG INU

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-8

Use the INU command to place a specified number of proteins of a certain type into a region with negative curvature. Adjust parameters like 'k' to control amplification and leaflet placement.

```bash
TS2CG INU -p point_SmallCurved -n 10 -t 1 -r 5 -c -0.5 -k 100 -o point_SmallCurved_new
```

--------------------------------

### Define Protein and Lipid Domains for Simulation

Source: https://github.com/weria-pezeshkian/ts2cg-v2.0/wiki/Tutorial-5

This configuration defines protein and lipid domains for simulation, with proteins positioned at specified vertices and surrounded by their designated lipid domains. Ensure correct formatting for simulation input.

```plaintext
protein2     2   0.01   0   0   -2.5
End Protein
```