biotraj
=======

Loading and saving raw data in trajectory formats.

This package is small excerpt from https://github.com/mdtraj/mdtraj containing only the
functionality to read and write trajectory files.
It is not intended to be used as a separate package, but is a dependency for
https://github.com/biotite-dev/biotite.
It is not integrated into the Biotite package directly due to an incompatible license.

Currently supported formats:

- *XTC*
- *TRR*
- *NetCDF*
- *DCD*


Basic trajectory file format functionality for Biotite; forked from MDTraj. 

Meet the Socket Team at BlackHat and DEF CON in Las Vegas, Aug 4-6

biotraj

Basic trajectory file format functionality for Biotite; forked from MDTraj

padix-key

(Experimental) An ambiguous license classifier was found.

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Ambiguous License Classifier

Source files are encoded using a non-standard text encoding.

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Bad text encoding

Package version is not a valid semantic version (semver).

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Bad semver

Package has dependencies with an invalid semantic version. This could be a sign of beta, low quality, or unmaintained dependencies.

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Bad dependency semver

Source files contain bidirectional unicode control characters. This could indicate a Trojan source supply chain attack. See: trojansource.codes for more information.

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Bidirectional unicode control characters

This package has multiple bin scripts with the same name. This can cause non-deterministic behavior when installing or could be a sign of a supply chain attack.

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Bin script confusion

This Chrome extension includes a content script '{scriptFile}' that runs on websites matching '{matches}'.

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Chrome Extension Content Script

This Chrome extension requests access to '{host}'.

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Chrome Extension Host Permission

This Chrome extension uses the '{permission}' permission.

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Chrome Extension Permission

This Chrome extension requests broad access to websites with the pattern '{host}'.

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Chrome Extension Wildcard Host Permission

Semantic versions published out of chronological order.

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Chronological version anomaly

Project maintainer's SSH key has been compromised.

What is a compromised SSH key?

Compromised SSH key

(Experimental) Copyleft license information was found.

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Copyleft License

Contains a Critical Common Vulnerability and Exposure (CVE).

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Title

Critical CVE

Contains a high severity Common Vulnerability and Exposure (CVE).

What is a CVE?

High CVE

Uses debug, reflection and dynamic code execution features.

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Debug access

The maintainer of the package marked it as deprecated. This could indicate that a single version should not be used, or that the package is no longer maintained and any new vulnerabilities will not be fixed.

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Deprecated

(Experimental) Contains a known deprecated SPDX license exception.

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Deprecated SPDX exception

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Deprecated license

Package name is similar to other popular packages and may not be the package you want.

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Possible typosquat attack

Dynamic require can indicate the package is performing dangerous or unsafe dynamic code execution.

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Dynamic require

Package does not contain any code. It may be removed, is name squatting, or the result of a faulty package publish.

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Empty package

Package accesses environment variables, which may be a sign of credential stuffing or data theft.

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Environment variable access

(Experimental) Something was found which is explicitly marked as unlicensed.

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Package optionally loads a dependency which is not specified within any of the package.json dependency fields. It may inadvertently be importing dependencies specified by other packages.

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Name

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File dependency

Accesses the file system, and could potentially read sensitive data.

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Filesystem access

Package has a dependency with a floating version range. This can cause issues if the dependency publishes a new major version.

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Wildcard dependency

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Git dependency

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GitHub dependency

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AI-detected potential code anomaly

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AI-detected possible typosquat

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AI-detected potential malware

AI has determined that this package may contain potential security issues or vulnerabilities.

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AI-detected potential security risk

Contains native code (e.g., compiled binaries or shared libraries). Including native code can obscure malicious behavior.

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Native code

Contains high entropy strings. This could be a sign of encrypted data, leaked secrets or obfuscated code.

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High entropy strings

Contains unicode homoglyphs which can be used in supply chain confusion attacks.

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Unicode homoglyphs

Contains a dependency which resolves to a remote HTTP URL which could be used to inject untrusted code and reduce overall package reliability.

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HTTP dependency

Install scripts are run when the package is installed. The majority of malware in npm is hidden in install scripts.

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Install scripts

Package has an invalid manifest file and can cause installation problems if you try to use it.

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Invalid manifest file

Source files contain invisible characters. This could indicate source obfuscation or a supply chain attack.

What are invisible characters?

Invisible chars

(Experimental) Package license has recently changed.

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License change

(Experimental) Contains an SPDX license exception.

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License exception

This package is not allowed per your license policy. Review the package's license to ensure compliance.

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License Policy Violation

Contains long string literals, which may be a sign of obfuscated or packed code.

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Long strings

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

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Major refactor

This package is identified as malware. It has been flagged either by Socket's AI scanner and confirmed by our threat research team, or is listed as malicious in security databases and other sources.

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Known malware

This package has inconsistent metadata. This could be malicious or caused by an error when publishing the package.

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Manifest confusion

Contains a medium severity Common Vulnerability and Exposure (CVE).

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Medium CVE

Contains a low severity Common Vulnerability and Exposure (CVE).

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Low CVE

This package contains minified code. This may be harmless in some cases where minified code is included in packaged libraries, however packages on npm should not minify code.

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Minified code

(Experimental) A package's licensing information has fine-grained problems.

Misc. License Issues

The package was published by an npm account that no longer exists.

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Non-existent author

A required dependency is not declared in package.json and may prevent the package from working.

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Missing dependency

(Experimental) Package does not have a license and consumption legal status is unknown.

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Missing license

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Missing package tarball

(Experimental) Package contains multiple licenses.

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Mixed license

(Experimental) Package contains a modified version of an SPDX license exception. Please read carefully before using this code.

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Modified license exception

(Experimental) Package contains a modified version of an SPDX license. Please read carefully before using this code.

What is a modified license?

Modified license

What is network access?

Network access

A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

What is new author?

New author

Package does not specify a list of contributors or an author in package.json.

Why is contributor and author data important?

No contributors or author data

Package does not have a linked bug tracker in package.json.

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No bug tracker

(Experimental) License information could not be found.

No License Found

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biotraj

biotraj

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