open3spn2 | C coarse-grained DNA forcefields

by cabb99 Python Version: 0.3.2 License: MIT

X-Ray Key Features Code Snippets Community Discussions Vulnerabilities Install Support

kandi X-RAY | open3spn2 Summary

open3spn2 is a Python library typically used in Healthcare, Pharma, Life Sciences applications. open3spn2 has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install open3spn2' or download it from GitHub, PyPI.

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

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Support

open3spn2 has a low active ecosystem.

It has 11 star(s) with 3 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 4 have been closed. On average issues are closed in 11 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of open3spn2 is 0.3.2

Quality

open3spn2 has 0 bugs and 0 code smells.

Security

open3spn2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

open3spn2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

open3spn2 is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

open3spn2 releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions are available. Examples and code snippets are not available.

It has 1450 lines of code, 85 functions and 5 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed open3spn2 and discovered the below as its top functions. This is intended to give you an instant insight into open3spn2 implemented functionality, and help decide if they suit your requirements.

Test whether the DNA from a DNA sequence
Compute the topology
Compute the geometry for a sequence
Set the positions of the simulation
Returns the force group
Return a dict containing the command class
Extract version information from setup py
Get project root directory
Create a ConfigParser instance from a root
Evaluate the force field
Removes all forces
Parse log file
Test the energy of the cell
Compute the potential energy of a trajectory
Create the versioneer config file
Install versioneer
Define interaction
Adds non - bonded exclusion to a force
Scans the setup py file and checks if it is missing
Generate a system from a pdb file
Set the positions of the experiment
Generate test energy term and system
Yield test forces
Returns the force group of the cross product
Compute the energy for a given trajectory
Validate the xyz file
Return test DNA from XYZ file

Get all kandi verified functions for this library.

open3spn2 Key Features

No Key Features are available at this moment for open3spn2.

open3spn2 Examples and Code Snippets

No Code Snippets are available at this moment for open3spn2.

Community Discussions

No Community Discussions are available at this moment for open3spn2.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install open3spn2

Installation of the open3SPN2 repository is available through anaconda. Some of the dependencies are contained in the omnia channel (openmm, pdbfixer) or in the conda-forge channel (mdtraj). It is also necessary to install X3DNA >= 2.4 and set the environment variable $X3DNA to the location of the installation folder.For protein-DNA simulations you will also need to install openAWSEM and add the openAWSEM path to the $PYTHONPATH environment variable. In linux you can set the path variables on ~/.bashrc. Note: open3SPN2 requires the installation of openMM. As of Feb 10 2020, openMM requires 3.5 <= python <= 3.7 and 7.5 <= CUDA <= 10.1.