معرفی شرکت ها
cvpack-0.3.0
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Useful Collective Variables for OpenMM
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cvpack-0.3.0 |
| نام | cvpack |
| نسخه کتابخانه | 0.3.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | Charlles Abreu <craabreu@gmail.com> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cvpack/ |
| مجوز | MIT |
Collective Variable Package
===========================
[//]: # (Badges)
[](https://github.com/RedesignScience/cvpack/actions?query=workflow%3ALinux)
[](https://github.com/RedesignScience/cvpack/actions?query=workflow%3AMacOS)
[](https://github.com/RedesignScience/cvpack/actions?query=workflow%3AWindows)
[](https://github.com/RedesignScience/cvpack/actions?query=workflow%3ALinter)
[](https://codecov.io/gh/RedesignScience/cvpack/branch/main)
[](https://readthedocs.org/projects/cvpack)
### Overview
Collective variables (CVs) are functions of the coordinates of a molecular system and provide a
means to project its conformational state onto a lower-dimensional space. By stimulating the
dynamics of a judiciously chosen set of CVs, one can obtain an enhanced sampling of the
configurational space, including regions that are otherwise difficult to access. CVPack is a Python
package that provides pre-defined CVs for the powerful molecular dynamics engine
[OpenMM](https://openmm.org). All these CVs are subclasses of OpenMM's [Force] class. As such, they
can be directly added to a [CustomCVForce] object or used to define a [BiasVariable] object for
[Metadynamics], for example.
The CVs currently implemented in CVPack are:
* [Angle](https://cvpack-for-openmm.readthedocs.io/en/latest/api/Angle.html):
The angle formed by three atoms.
* [Atomic Function](https://cvpack-for-openmm.readthedocs.io/en/latest/api/AtomicFunction.html):
A user-defined function of the coordinates of a group of atoms.
* [Centroid Function](https://cvpack-for-openmm.readthedocs.io/en/latest/api/CentroidFunction.html)
A user-defined function of the centroids of groups of atoms.
* [Distance](https://cvpack-for-openmm.readthedocs.io/en/latest/api/Distance.html):
The distance between two atoms.
* [Helix angle content](https://cvpack-for-openmm.readthedocs.io/en/latest/api/HelixAngleContent.html):
The alpha-helix angle content of a sequence of residues.
* [Helix H-bond content](https://cvpack-for-openmm.readthedocs.io/en/latest/api/HelixHBondContent.html):
The alpha-helix hydrogen-bond content of a sequence of residues.
* [Helix RMSD content](https://cvpack-for-openmm.readthedocs.io/en/latest/api/HelixRMSDContent.html):
The alpha-helix RMSD content of a sequence of residues
* [Helix torsion content](https://cvpack-for-openmm.readthedocs.io/en/latest/api/HelixTorsionContent.html):
The alpha-helix Ramachandran content of a sequence of residues.
* [Number of contacts](https://cvpack-for-openmm.readthedocs.io/en/latest/api/NumberOfContacts.html):
The number of contacts between two groups of atoms.
* [Radius of gyration](https://cvpack-for-openmm.readthedocs.io/en/latest/api/RadiusOfGyration.html):
The radius of gyration of a group of atoms.
* [RMSD](https://cvpack-for-openmm.readthedocs.io/en/latest/api/RMSD.html):
The RMSD of a group of atoms with respect to a reference structure.
* [Torsion](https://cvpack-for-openmm.readthedocs.io/en/latest/api/Torsion.html):
The torsion angle formed by four atoms.
* [Torsion similarity](https://cvpack-for-openmm.readthedocs.io/en/latest/api/TorsionSimilarity.html):
The degree of similarity between pairs of torsion angles.
### Installation
CVPack is available on [PyPI](https://pypi.org/project/cvpack/). To install it, simply run:
```bash
pip install cvpack
```
### Documentation
The documentation for CVPack is available at [Read the Docs](https://cvpack.readthedocs.io/en/stable).
### Copyright
Copyright (c) 2023, [Redesign Science](https://www.redesignscience.com)
#### Acknowledgements
Project based on the [CMS Cookiecutter] version 1.1.
[BiasVariable]: https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
[CMS Cookiecutter]: https://github.com/molssi/cookiecutter-cms
[CustomCVForce]: https://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
[Force]: https://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
[Metadynamics]: https://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
نیازمندی
| مقدار | نام |
|---|---|
| - | numpy |
| - | openmm |
| - | importlib-resources |
| >=6.1.2 | pytest |
| - | pytest-runner |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl cvpack-0.3.0:
pip install cvpack-0.3.0.whl
نصب پکیج tar.gz cvpack-0.3.0:
pip install cvpack-0.3.0.tar.gz