pymod | PyMod 3 - sequence similarity searches | Genomics library

by pymodproject Python Version: v3.0 License: LGPL-2.1

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | pymod Summary

pymod is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. pymod has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. However pymod build file is not available. You can download it from GitHub.

PyMod 3 is an open source PyMOL plugin, designed to act as an interface between PyMOL and several bioinformatics tools (for example: BLAST+, HMMER, Clustal Omega, MUSCLE, PSIPRED and MODELLER). The current PyMod release, PyMod 3, is compatible with the most recent PyMOL versions (see the Requirements section below) and has been extended with new functionalities with respect to its predecessor (PyMod 2). Starting from the amino acid sequence of a target protein, users may take advantage of PyMod 3 to carry out the three steps of the homology modeling process (that is, template searching, target-template sequence alignment and model building) in order to build a 3D atomic model of a target protein (or protein complex). Additionally, PyMod 3 may also be used outside the homology modeling context, in order to extend PyMOL with numerous types of functionalities. Sequence similarity searches, multiple sequence/structure alignment building, evolutionary conservation analyses, domain parsing and loop modeling can be performed in the PyMod 3/PyMOL environment.

Support

Quality

Security

License

Reuse

Support

pymod has a low active ecosystem.

It has 59 star(s) with 18 fork(s). There are 8 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 9 have been closed. On average issues are closed in 114 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of pymod is v3.0

Quality

pymod has 0 bugs and 0 code smells.

Security

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

pymod code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pymod is licensed under the LGPL-2.1 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

pymod releases are available to install and integrate.

pymod has no build file. You will be need to create the build yourself to build the component from source.

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

Top functions reviewed by kandi - BETA

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

Launch Modeller .
Generate an isosurface .
Generate draw specifications for this item .
Create the main menu .
Gets the state of the matrix .
Initialize the shader program .
Check if PyMod .
Perform qblast search .
Generate an Isocurve .
Move the handle to the given position .

Get all kandi verified functions for this library.

pymod Key Features

No Key Features are available at this moment for pymod.

pymod Examples and Code Snippets

No Code Snippets are available at this moment for pymod.

Community Discussions

Trending Discussions on pymod

Noob trying to get values from his EnergyMeter via Modbus RTU RS485 in python

Use modules from a repo in pandas columns

(Yet Another) 'ImportError: No module named my_module'

Cannot import C++ extension if in the package root directory

QUESTION

Noob trying to get values from his EnergyMeter via Modbus RTU RS485 in python

Asked 2021-May-14 at 13:08

fist Post as i normaly find the answers if i search long enough. But today is the day... I bought a EnergyMeter from Aliexpress with MODBUS RTU connection and im trying to read it out. I already tried a lot of stuff from all over the Internet.

This is the Datasheet of the EnergyMeter1

I tried pyModbus and minimalmodbus.

My both Scripts:

...

ANSWER

Answered 2021-May-14 at 13:08

Thanks to @Brits i got it running. I had to use read_float(0, functioncode=4, number_of_registers=2) where 0 is decimal. If i want to read 001A i had to convert from hex to dec = 26. Works very good

Source https://stackoverflow.com/questions/67528300

QUESTION

Use modules from a repo in pandas columns

Asked 2021-Mar-17 at 12:24

I'm trying to use some modules from pyModeS in columns of a pandas data frame.

The data frame in question is this one:

...

ANSWER

Answered 2021-Mar-17 at 12:24

Use custom function, unfortunately performance depends of pms module processing:

Source https://stackoverflow.com/questions/66670234

QUESTION

(Yet Another) 'ImportError: No module named my_module'

Asked 2020-Sep-16 at 17:29

Ok, I stripped the code to ultra minimal to illustrate the problem and make it reproducible

context :

Python 3.7
No VENV or funny stuff

Talk is cheap. Show you the code :

code structure :

...

ANSWER

Answered 2020-Sep-16 at 11:36

Once you have a package-like directory structure, run python with the -m option to run a module as a script:

Source https://stackoverflow.com/questions/63918893

QUESTION

Cannot import C++ extension if in the package root directory

Asked 2020-Apr-07 at 07:50

Note: Since asking this question, I discovered later on that python -m pip install -e . will install the extension to cmod with .venv/lib/python3.8/site-packages/hello-c-extension.egg-link pointing to the project in the current directory. I've also switched to a src layout in later commits and have found https://pythonwheels.com/ to be a great reference for high-quality packages that distribute wheels. However, I'm still curious to know about the behavior of setup.py subcommands.

As part of some research on manylinux, I am using a toy project to build different platform wheels for a C++ extension module.

It seems that when building and installing locally, I cannot import the C++ extension module if my current directory is the project root directory. This prevents me from running unit tests, among other things. I believe the reason for this is that . becomes the first component of sys.path, and so the pure-Python version is picked up while the compiled extension is not.

How can I fix this? Am I running the local build/install correctly?

The package structure looks like this:

...

ANSWER

Answered 2020-Apr-07 at 07:50

The cause of the problems

Is this really ... how it's supposed to work? What would be the proper way to run unit tests for the extension module in this case?

Python imports from sys.path. This means that it will search each and every directory for the import, from index 0 through to the last item in sys.path.

Note that a hacky approach to a fix would be to add the following before the import: sys.path.append(sys.path.pop(0)). This still allows local imports, but means that site-packages and the standard library are searched first.

How can I fix this? Am I running the local build/install correctly?

I'll answer the first question below.

Yes, your build/install is fine, but to fix the import problem, you'll need to tweak it slightly.

Fixing the problem

Switch to the src/cmod layout. A great link - which is pointed out by yourself in the questions comments - is here.

This approach is discussed in the comments, and since asking the question you've actually implemented this. (60093f1).

I'll now quote some of that article; it explains this better than I could.

The src directory is a better approach because:

You get import parity. The current directory is implicitly included in sys.path; but not so when installing & importing from site-packages. Users will never have the same current working directory as you do.

This constraint has beneficial implications in both testing and packaging:

You will be forced to test the installed code (e.g.: by installing in a virtualenv). This will ensure that the deployed code works (it's packaged correctly) - otherwise your tests will fail. Early. Before you can publish a broken distribution.

You will be forced to install the distribution. If you ever uploaded a distribution on PyPI with missing modules or broken dependencies it's because you didn't test the installation. Just beeing able to successfuly build the sdist doesn't guarantee it will actually install!

And pip install -e . will no longer mess stuff up.

Source https://stackoverflow.com/questions/61004746

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

Vulnerabilities

No vulnerabilities reported

Install pymod

PyMod 3 plugin file (current version 3.0.2): download from here.
Please refer to the PyMod 3 User's Guide to learn how to install PyMod 3 on your system. Long story short: PyMod 3 can be installed as any other PyMOL plugin. Download the PyMod 3 plugin file (a ZIP file named pymod3.zip, see the link above) and use the PyMOL plugin manager (Plugin -> Plugin Manager from the menu of its main window) to install it. The external tools of PyMod 3 can be obtained and configured through an easy-to-use installer dialog which can be launched by the plugin (Help -> Install PyMod Components from the main menu of the plugin). The way to configure MODELLER in PyMod may vary according to your PyMOL version (in the User's Guide we cover different scenarios).

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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