altmod | MODELLER plugin - altMOD is a MODELLER | Machine Learning library

by pymodproject Python Version: 1.0 License: MIT

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | altmod Summary

altmod is a Python library typically used in Artificial Intelligence, Machine Learning applications. altmod has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However altmod build file is not available. You can download it from GitHub.

altMOD is a MODELLER ([1] plugin for improved 3D homology model building. Right now, it allows to incorporate in the program's objective function terms for interatomic distances statistical potentials, such as DOPE [2] and DFIRE [3]. The effect of adding statistical potentials in the objective function of MODELLER is described in Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling" (Janson et al., 2019). In a benchmark with 225 single-template homology models, we found that the inclusion of DOPE in the objective function of MODELLER brings an average improvement of 1.3% and 2.0% in GDT-HA [4] and lDDT [5] and a large improvement of -29.8% in MolProbity scores [6]. The altMOD package also contains code for easily running MODELLER with user-defined parameters for homology-derived distance restraints (see the examples folder).

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Quality

Security

License

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Support

altmod has a low active ecosystem.

It has 4 star(s) with 1 fork(s). There are 2 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 1 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of altmod is 1.0

Quality

altmod has no bugs reported.

Security

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

License

altmod 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

altmod releases are available to install and integrate.

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

Implementation of HomCSR method
Analyze the optimal target template pair
Return the minimum value of the model
Returns the code for a modeller res code
Rebuilds the LODELLERS file
Get the mean and standard deviations for each template
Return a list of all template files in the PIR alignment directory
Apply a multi - gaussian
Calculate the RST field
Adjust value to absolute value
Compute the distance between two atoms
Return a modeller atom from a modeller residue
Calculate the distance between two modeller angles
Run the Adam algorithm
Optimize a structure
Cluster PDB files
Set custom hddr options
Set the target structure
Build a homCSR file

Get all kandi verified functions for this library.

altmod Key Features

No Key Features are available at this moment for altmod.

altmod Examples and Code Snippets

No Code Snippets are available at this moment for altmod.

Community Discussions

Trending Discussions on altmod

python mask netcdf data using shapefile

Traits/UI (chaco) plotting application breaks, when run in a 32-bit Anaconda environment, on 64-bit Ubuntu 16.04

QUESTION

python mask netcdf data using shapefile

Asked 2018-Jul-21 at 17:45

I am using the following packages:

...

ANSWER

Answered 2018-Jul-18 at 21:45

You should have a look at the following packages:

salem and the region of interest example
regionmask

Both may get you to what you want.

Source https://stackoverflow.com/questions/51398563

QUESTION

Traits/UI (chaco) plotting application breaks, when run in a 32-bit Anaconda environment, on 64-bit Ubuntu 16.04

Asked 2017-Feb-09 at 15:28

I have a Traits/UI (chaco) plotting application, which runs fine in the root environment of my Anaconda 64-bit installation, on 64-bit Ubuntu 16.04. However, when I try to run it from a 32-bit environment, which I created for testing, it fails.

It appears to be defaulting to the "null" graphical back-end toolkit for some reason, giving me a stack trace, which ends thusly:

File "/home/dbanas/anaconda2/envs/pybert_32/lib/python2.7/site-packages/enable/toolkit.py", line 40, in _init_toolkit format_exception_only(t, v)) ImportError: Unable to import the image backend for the null toolkit (reason: ['ImportError: libGL.so.1: cannot open shared object file: No such file or directory\n']).

So, I realized that I didn't have 32-bit Gtk+ library support installed on my system. I installed that. And, now, the application segment faults when I launch it in my 32-bit environment! Here is the stack trace, from gdb:

...

ANSWER

Answered 2017-Feb-09 at 15:28

The problem was missing 32-bit libraries, which is not surprising, since I'm running 64-bit Ubuntu. However, getting the system to tell me which libraries were missing required changing the Python GUI application from the qt4 back-end to the wx back-end, like so:

Source https://stackoverflow.com/questions/41420712

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

Vulnerabilities

No vulnerabilities reported

Install altmod

Just put the altmod directory (the one with the __init__.py file inside it) of this package in one of your sys.path directories.

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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