ensembler | Automated omics-scale protein modeling and simulation setup

 by   choderalab Python Version: v1.0.6 License: GPL-2.0

kandi X-RAY | ensembler Summary

kandi X-RAY | ensembler Summary

ensembler is a Python library typically used in Simulation applications. ensembler has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Automated omics-scale protein modeling and simulation setup.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              ensembler has a low active ecosystem.
              It has 43 star(s) with 21 fork(s). There are 21 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 40 open issues and 28 have been closed. On average issues are closed in 84 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of ensembler is v1.0.6

            kandi-Quality Quality

              ensembler has 0 bugs and 0 code smells.

            kandi-Security Security

              ensembler has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              ensembler code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              ensembler is licensed under the GPL-2.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              ensembler releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              ensembler saves you 11322 person hours of effort in developing the same functionality from scratch.
              It has 22920 lines of code, 370 functions and 56 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed ensembler and discovered the below as its top functions. This is intended to give you an instant insight into ensembler implemented functionality, and help decide if they suit your requirements.
            • Generate solvate models
            • Add data to project
            • Add iteration number to metadata
            • Write metadata to file
            • Cluster models
            • Get the targets and templates
            • Return a sequence of templates resolved seq
            • Get the targets
            • Gather templates from a UniProt XML file
            • Gather template sequences from target Explorer
            • Query the UniProt XML from UniProt XML
            • Iteratively loop through template templates
            • Query target explorer
            • Write the default overrides file
            • Render the simulation
            • Construct a Trajectory object
            • Checks if the project directory is a top - level project directory
            • Create a mdtraj file
            • Build Modeller models
            • Generate implicit start models
            • Parse command line arguments
            • Align targets and templates
            • R Determine the nwaters
            • Write the python version file
            • Gather templates from given PDB sequences
            • Run molprobability validation
            Get all kandi verified functions for this library.

            ensembler Key Features

            No Key Features are available at this moment for ensembler.

            ensembler Examples and Code Snippets

            No Code Snippets are available at this moment for ensembler.

            Community Discussions

            QUESTION

            Encoding categorical columns - Label encoding vs one hot encoding for Decision trees
            Asked 2020-Jun-06 at 23:48

            The way decision trees and random forest work using splitting logic, I was under the impression that label encoding would not be a problem for these models, as we are anyway going to split the column. For eg: if we have gender as 'male', 'female' and 'other', with label encoding, it becomes 0,1,2 which is interpreted as 0<1<2. But since we are going to split the columns, I thought it didn't matter as it is the same thing whether we are going to split on 'male' or '0'. But when I tried both label and one hot encoding on the dataset, one hot encoding gave better accuracy and precision. Can you kindly share your thoughts.

            ...

            ANSWER

            Answered 2020-Jun-06 at 20:48

            You can see it as a regularization effect: your model is simpler, and so more generalizable. So you get better performances.

            Taking your example of the sex feature: [male, female, other] with label encoding become [0, 1, 2].

            Now suppose there is a particular configuration of the other features which works only for females: the tree needs two branches to select females, one which select sex bigger than zero, and the other which select sex lower than 2.

            Instead, with one-hot encoding, you only need a branch to do the selection, say sex_female bigger than zero.

            Source https://stackoverflow.com/questions/62237033

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

            Vulnerabilities

            No vulnerabilities reported

            Install ensembler

            First go to the [Modeller website](http://salilab.org/modeller/) and get a license key (registration required; free for academic non-profit institutions).

            Support

            Go to the [official online documentation](http://ensembler.readthedocs.org/). Read a preprint of the paper [on bioRxiv](http://dx.doi.org/10.1101/018036). See the example dataset from [modeling all human tyrosine kinases](http://datadryad.org/review?doi=doi:10.5061/dryad.7fg32).
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/choderalab/ensembler.git

          • CLI

            gh repo clone choderalab/ensembler

          • sshUrl

            git@github.com:choderalab/ensembler.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link