ADCP | AutoDock CrankPep for peptide and disordered protein | Genomics library

 by   ccsb-scripps C Version: Current License: No License

kandi X-RAY | ADCP Summary

kandi X-RAY | ADCP Summary

ADCP is a C library typically used in Artificial Intelligence, Genomics applications. ADCP has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

AutoDock CrankPep or ADCP is an AutoDock docking engine specialized for docking peptides. It combines technology form the protein folding filed with an efficient representation of a rigid receptor as affinity grids to fold the peptide in the context of the energy landscape created by the receptor. A Monte-Carlo search is used to fold the peptide while concurrently optimizing the interaction between the peptide and the receptor molecule, yielding docked peptides. The program can dock peptides provides as 3D structures in PDB files or from a sequence string. It has been show to successfully re-dock peptides with up to 20 amino acids in length. ADCP is developed based on CRANKITE. Podtelezhnikov,A.A. and Wild,D.L. (2008) Source Code Biol. Med., 3, 12. ADCP is available under the GNU LGPL v2.0 OpenSource license. Please visit adcp.scripps.edu for more details. There are two ways of using ADCP. The first and recommended way is to use the prepared Python wrapper runADCP.py. runADCP works directly with a zipped target file (.trg) prepared by AGFR. Please see adcp.scripps.edu/tutorial for more details.
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              ADCP has a low active ecosystem.
              It has 23 star(s) with 6 fork(s). There are 5 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 7 open issues and 0 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of ADCP is current.

            kandi-Quality Quality

              ADCP has 0 bugs and 50 code smells.

            kandi-Security Security

              ADCP has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              ADCP code analysis shows 0 unresolved vulnerabilities.
              There are 3 security hotspots that need review.

            kandi-License License

              ADCP does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              ADCP releases are not available. You will need to build from source code and install.
              It has 242 lines of code, 4 functions and 1 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

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            ADCP Key Features

            No Key Features are available at this moment for ADCP.

            ADCP Examples and Code Snippets

            No Code Snippets are available at this moment for ADCP.

            Community Discussions

            QUESTION

            Strange array from .mat file. How to access the data?
            Asked 2021-Mar-04 at 22:36

            I´m using Jupyter Lab!

            I opened a '.mat' file, using hdf5storage. This file was generated by a software which operates an instrument of data acquisition (ADCP by Rowe, for who may ask! Oceanographic stuff...)

            I can access the keys and extract the data from all keys but one... the 'Gps' contains latitude and longitude data, supposely in a two columns and many rows array... but its shape is (1x1), and when I print it I can see the data, but don´t know how to access it!

            How can I access this data?

            The file is here....

            https://drive.google.com/file/d/15JEA5y5_Zt52FpPa--Cp_wwl2TYrnlQZ/view?usp=sharing

            This is the notebook (what fits on the screen) but you can see what I mean.

            ...

            ANSWER

            Answered 2021-Mar-04 at 22:36

            Looks like this the 'old' style MATLAB mat file, which I can load with scipy.io.loadmat

            Source https://stackoverflow.com/questions/66477232

            QUESTION

            Converting a day decimal number array to unix timestamp in Python
            Asked 2021-Jan-06 at 14:48

            I have an array of numbers (e.g 279.341, 279.345, 279.348) which relate to the date and time in 2017 (its supposed to be October 6th 2017). To be able to compare this data to another dataset I need to convert that array into an array of UNIX timestamps.

            I have successfully done something similar in matlab (code below) but don't know how to translate this to Python.

            MatLab:

            ...

            ANSWER

            Answered 2021-Jan-06 at 14:48

            assuming these numbers are fractional days of the year (UTC) and the year is 2017, in Python you would do

            Source https://stackoverflow.com/questions/65596612

            QUESTION

            How can I summarize reactive data from outside a render function in a Shiny app?
            Asked 2020-Feb-06 at 16:16

            For this particular shiny example I am trying to apply a circular model and display and summarize it within the ggplot and a summary table. This is straightforward up until trying to add in reactive 'brushplot' capabilities. Each of the data points represent a date and the point of the selective graph is to be able to discard undesirable dates. As far as I've figured out, this requires the filtering and model fitting to be within a renderPlot which then leads to complications (unable to find the data/model) trying to call the filtered data and the circular model's statistical outputs outside the function and/or within another reactive function. This yields the Error: object 'k_circ.lm' not found So my questions are:

            1. How can I read the filtered data from the renderPlot function to the summarytable matrix?
            2. How could I similarly add the fitted model values and residuals from k_circ.lm?
            3. Is there a better or simpler way to arrange app to avoid this?

            Alternatative code lines are commented out for a working (if poorly formatted) summary table.

            ...

            ANSWER

            Answered 2020-Feb-06 at 03:11

            Here's a few ideas - but there are multiple approaches to handling this, and you probably want to restructure your server function a bit more after working with this further.

            First, you probably want a reactive expression that will update your model based on vals$keeprows as this changes with your clicks. Then, you can access the model results from this expression from both your plot and data table.

            Here is an example:

            Source https://stackoverflow.com/questions/60083504

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

            Vulnerabilities

            No vulnerabilities reported

            Install ADCP

            You can download it from GitHub.

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            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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