View ProDy on Snyk Open Source Advisor

Package Health Score

64 / 100

security
No known security issues
popularity
Small
maintenance
Inactive
community
Active

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Popularity

Small

GitHub Stars: 434
Forks: 157
Contributors: 50

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package ProDy, we found that it has been starred 434 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Aug 13, 2023
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

MIT

Security Policy

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Maintenance

Inactive

Commit Frequency

Open Issues: 64
Open PR: 29
Last Release: 1 year ago
Last Commit: 6 days ago

Further analysis of the maintenance status of ProDy based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Inactive.

An important project maintenance signal to consider for ProDy is that it hasn't seen any new versions released to PyPI in the past 12 months, and could be considered as a discontinued project, or that which receives low attention from its maintainers.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 50
Funding: No

With more than 10 contributors for the ProDy repository, this is possibly a sign for a growing and inviting community.

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Package

Python Versions Compatibility: ==2.*, ==3.*

Age: 13 years
Latest Release: 1 year ago
Dependencies: 5 Direct
Versions: 64
Maintainers: 1
Wheels: Windows

Not sure how to use ProDy?

To help you get started, we've collected the most common ways that ProDy is being used within popular public projects.

corredD / ePMV / demo / testPrody.py View on Github

anm.buildHessian(p38ca)
anm.calcModes()

#traverseMode() function generates conformations along a single normal mode. 
#Conformations are generated in both directions along the given mode. 
#rmsd argument is used to set the RMSD distance to the farthest conformation.
#Let’s generate 10 conformations along ANM mode 1:
trajectory = prody.traverseMode(anm[0], p38ca, n_steps=5, rmsd=2.0)
coords=trajectory.getCoordsets()
#conformation...

#dumb->read in epmv or read on the fly?
p38traj = p38ca.copy()
p38traj.delCoordset(0)
p38traj.addCoordset( trajectory )
prody.writePDB('p38_mode1_trajectory.pdb', p38traj)
def computeNormalMode(userfilenamein="",userfilenameout="NMA.pdb", usermode=0,userrmsd=0.8, usernbconf=5, conf="allatom", usercutoff=15.0, usergamma=1.0) : 
	mystruct = prody.parsePDB(userfilenamein, model=1)
	mystruct_ca = mystruct.select('protein and name CA')

	anm = prody.ANM(userfilenamein+str(usermode))
	anm.buildHessian(mystruct_ca, gamma=usergamma, cutoff=usercutoff)
	anm.calcModes()
	
	bb_anm, bb_atoms = extrapolateModel(anm, mystruct_ca, mystruct.select(conf))
	ensemble = sampleModes(bb_anm[usermode], bb_atoms, n_confs=usernbconf, rmsd=userrmsd)
	nmastruct = mystruct.copy( bb_atoms )
	nmastruct.addCoordset(ensemble)
			
	writePDB(userfilenameout, nmastruct)

View more ways to use ProDy

ProDy dependencies

biopython numpy pyparsing scipy setuptools

FAQs

What is ProDy?

A Python Package for Protein Dynamics Analysis. Visit Snyk Advisor to see a full health score report for ProDy, including popularity, security, maintenance & community analysis.

Is ProDy popular?

The python package ProDy receives a total of 6,430 weekly downloads. As such, ProDy popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is ProDy well maintained?

We found indications that ProDy is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is ProDy safe to use?

The python package ProDy was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 21 November-2024, at 20:18 (UTC).

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ProDy

A Python Package for Protein Dynamics Analysis For more information about how to use this package see README

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SYNOPSIS

GETTING PRODY

DOCUMENTATION

SOURCE CODE

LICENSE

ProDy dependencies

FAQs

What is ProDy?

Is ProDy popular?

Is ProDy well maintained?

Is ProDy safe to use?

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Fix identified vulnerabilities

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Package Health Score

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Commit Frequency

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Not sure how to use ProDy?

SYNOPSIS

GETTING PRODY

DOCUMENTATION

SOURCE CODE

LICENSE

ProDy dependencies

FAQs

What is ProDy?

Is ProDy popular?

Is ProDy well maintained?

Is ProDy safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

Fix identified vulnerabilities

Monitor for new issues