| Name | LatticePy JSON |
| Version |
0.1.3
JSON |
| download |
| home_page | |
| Summary | A package for simulating molecules on a lattice. |
| upload_time | 2023-09-01 17:31:39 |
| maintainer | |
| docs_url | None |
| author | Sohit Miglani |
| requires_python | |
| license | MIT |
| keywords |
proteins
simulation
lattice
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# LatticePy
A python package for MCMC simulations of folding and phase separation in biomolecules on a lattice. LatticePy currently supports the simulation of amino acids and protein polymers on a lattice with any given number of units.
## Installation
### Stable Release
Run the following command in bash (Not on PyPi yet) :
```bash
pip3 install LatticePy
```
### Developers Release
Run the following command in bash:
```bash
pip3 install git+https://github.com/sohitmiglani/LatticePy#egg=LatticePy
```
## Tutorial
### - Import the package and initialize the lattice. You can customize the bounds of the lattice, the compactness energy, the beta (1/Temperature), and the lattice type.
```python
from LatticePy import lattice
mylattice = lattice(bound=50, E_c=1.5, beta=0, lattice_type='simple_cubic')
```
### - Add your polymer
- By a list of polarities
```python
polymer = [-1, -1, -1, 1, 1, -1, -1, 1, -1, -1, -1, -1, 1, -1, 1, 1, 1, -1, 1, -1, 1, -1, 1, 1, 1, -1, -1]
mylattice.add_polymer(polymer, n_polymers=1, placement='straight') # to add it in a straight line
mylattice.add_polymer(polymer, n_polymers=1, placement='randomly') # to add it in a random fashion which may cause knots
```
- By sequence
```python
sequence = 'MTKSHSEEVIVPEFNSSAKELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEH'
mylattice.add_protein(sequence, type='straight', n_polymers=1)
```
### - Simulate your polymers with annealing
Change the parameters as you see fit
```python
mylattice.simulate(n_mcmc=200000,
interval=1000,
record_intervals = True,
anneal=True,
beta_lower_bound=0,
beta_upper_bound=2,
beta_interval=0.05)
```
### - Visualize the energy variation over all the MCMC steps
```python
mylattice.energy_variation_graph()
```
### - Visualize in an interactive 3-D lattice
```python
mylattice.visualize()
```
You can see the interactive 3-D lattice for this run <a href="https://www.sohitmiglani.com/LatticePy_figure"
target="_blank" rel="noopener noreferrer">here.<a/>
### - Get important statistics
```python
mylattice.native_contacts
```
20
```python
mylattice.energy
```
-58.7
```python
mylattice.non_covalent_hydrophobic_contacts
```
9
Raw data
{
"_id": null,
"home_page": "",
"name": "LatticePy",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "proteins,simulation,lattice",
"author": "Sohit Miglani",
"author_email": "sohitmiglani@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/17/4d/1b6960fa72d16bd93a23de3c1e84d1eea08e7adab1e5a0c5e3762f4b5884/LatticePy-0.1.3.tar.gz",
"platform": null,
"description": "# LatticePy\nA python package for MCMC simulations of folding and phase separation in biomolecules on a lattice. LatticePy currently supports the simulation of amino acids and protein polymers on a lattice with any given number of units.\n\n## Installation\n\n### Stable Release\nRun the following command in bash (Not on PyPi yet) :\n\n```bash\npip3 install LatticePy\n```\n\n### Developers Release\nRun the following command in bash:\n\n```bash\npip3 install git+https://github.com/sohitmiglani/LatticePy#egg=LatticePy\n```\n\n## Tutorial\n\n### - Import the package and initialize the lattice. You can customize the bounds of the lattice, the compactness energy, the beta (1/Temperature), and the lattice type.\n```python\nfrom LatticePy import lattice\nmylattice = lattice(bound=50, E_c=1.5, beta=0, lattice_type='simple_cubic')\n```\n\n### - Add your polymer\n\n- By a list of polarities\n```python\npolymer = [-1, -1, -1, 1, 1, -1, -1, 1, -1, -1, -1, -1, 1, -1, 1, 1, 1, -1, 1, -1, 1, -1, 1, 1, 1, -1, -1]\nmylattice.add_polymer(polymer, n_polymers=1, placement='straight') # to add it in a straight line\nmylattice.add_polymer(polymer, n_polymers=1, placement='randomly') # to add it in a random fashion which may cause knots\n```\n\n- By sequence\n```python\nsequence = 'MTKSHSEEVIVPEFNSSAKELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEH'\nmylattice.add_protein(sequence, type='straight', n_polymers=1)\n```\n### - Simulate your polymers with annealing\n\nChange the parameters as you see fit\n```python\nmylattice.simulate(n_mcmc=200000, \n interval=1000, \n record_intervals = True, \n anneal=True, \n beta_lower_bound=0, \n beta_upper_bound=2, \n beta_interval=0.05)\n```\n\n### - Visualize the energy variation over all the MCMC steps\n\n```python\nmylattice.energy_variation_graph()\n```\n\n\n### - Visualize in an interactive 3-D lattice\n\n```python\nmylattice.visualize()\n```\n\nYou can see the interactive 3-D lattice for this run <a href=\"https://www.sohitmiglani.com/LatticePy_figure\" \n target=\"_blank\" rel=\"noopener noreferrer\">here.<a/>\n\n### - Get important statistics\n\n```python\nmylattice.native_contacts\n```\n20\n\n```python\nmylattice.energy\n```\n-58.7\n\n```python\nmylattice.non_covalent_hydrophobic_contacts\n```\n9\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "A package for simulating molecules on a lattice.",
"version": "0.1.3",
"project_urls": null,
"split_keywords": [
"proteins",
"simulation",
"lattice"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "f837f3bd6fd1d99d9eab8dda4a9586662b3f6dc63fb38b31d21f34a38d39e79c",
"md5": "f740298d1139f3c25b52c527f3347f30",
"sha256": "7ff24aecb2af5b97029065d187e3c6b488c500cba88e0606a14b14035989f514"
},
"downloads": -1,
"filename": "LatticePy-0.1.3-py3-none-any.whl",
"has_sig": false,
"md5_digest": "f740298d1139f3c25b52c527f3347f30",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 10130,
"upload_time": "2023-09-01T17:31:38",
"upload_time_iso_8601": "2023-09-01T17:31:38.167832Z",
"url": "https://files.pythonhosted.org/packages/f8/37/f3bd6fd1d99d9eab8dda4a9586662b3f6dc63fb38b31d21f34a38d39e79c/LatticePy-0.1.3-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "174d1b6960fa72d16bd93a23de3c1e84d1eea08e7adab1e5a0c5e3762f4b5884",
"md5": "b19bc01d2455ed91656334131d7a2740",
"sha256": "007257fd0522bf8a94049ddc12e14493d062bce2103c83b5d944204941ec1ec0"
},
"downloads": -1,
"filename": "LatticePy-0.1.3.tar.gz",
"has_sig": false,
"md5_digest": "b19bc01d2455ed91656334131d7a2740",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 9836,
"upload_time": "2023-09-01T17:31:39",
"upload_time_iso_8601": "2023-09-01T17:31:39.707861Z",
"url": "https://files.pythonhosted.org/packages/17/4d/1b6960fa72d16bd93a23de3c1e84d1eea08e7adab1e5a0c5e3762f4b5884/LatticePy-0.1.3.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-09-01 17:31:39",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "latticepy"
}
