yank | extensible Python framework for GPU-accelerated

 by   choderalab Python Version: 0.25.2 License: MIT

kandi X-RAY | yank Summary

kandi X-RAY | yank Summary

yank is a Python library typically used in Simulation applications. yank has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub.

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
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            kandi-support Support

              yank has a highly active ecosystem.
              It has 156 star(s) with 69 fork(s). There are 24 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 229 open issues and 521 have been closed. On average issues are closed in 230 days. There are 10 open pull requests and 0 closed requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of yank is 0.25.2

            kandi-Quality Quality

              yank has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              yank is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              yank 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.
              yank saves you 15206 person hours of effort in developing the same functionality from scratch.
              It has 30353 lines of code, 664 functions and 51 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed yank and discovered the below as its top functions. This is intended to give you an instant insight into yank implemented functionality, and help decide if they suit your requirements.
            • Generate the protocol for the given experiment
            • Create the sampler for the given experiment description
            • Create a constraint for the given experiment description
            • Build an experiment
            • Run the simulation
            • Check if a phase is complete
            • Generate a mixing plot
            • Get the mixing data for each phase
            • Generates the equilibration plots
            • Get the equilibrium data
            • Determines missing parameters
            • Generate the free energy of the experiment
            • Determine missing parameters
            • Write the version py file
            • Restrict a thermodynamic state
            • Strict a given thermodynamic state
            • Randomize ligand
            • Plot a free energy trace
            • Execute the script
            • Decorator to generate a development feature
            • Generate decorator plots
            • Determine the restriction parameters
            • Return the general simulation data
            • Analyze the energy of the model
            • Create an AlchemicalPhase object
            • Call MCMCMove constructor
            Get all kandi verified functions for this library.

            yank Key Features

            No Key Features are available at this moment for yank.

            yank Examples and Code Snippets

            No Code Snippets are available at this moment for yank.

            Community Discussions

            QUESTION

            Is it possible to 're-push' yanked version gem published at rubygems.org at same version?
            Asked 2021-Jun-07 at 15:13

            This is what I am talking about. My attempt is to repush the exact same version, 0.1.12. My previous push is invalid, it broken gem what I push. I highly want to publish this version, like I already implement the sem-versioning.

            the pushing process yield:

            ...

            ANSWER

            Answered 2021-Jun-07 at 15:13

            Nope, you can not re-submit the same version number, this is made on purpose for security reasons, avoiding maintainers to upload the same version without getting noticed by the developers. So you will need to release a new version of your gem

            Source https://stackoverflow.com/questions/67865389

            QUESTION

            vim copy into clipboard with colon cmd
            Asked 2021-May-23 at 05:48

            I want to yank multiple lines with a colon command into the UNIX-clipboard without visual mode, like this: :1,4"+y or :1,$"+y

            The clipboard is active --> echo has('clipboard') returns 1

            I'm on raspberry pi and tried gvim and vim. Can anybody shed some light onto this? Thank you and kind regards!

            ...

            ANSWER

            Answered 2021-May-23 at 01:27

            This is possible with the :yank command, which can be abbreviated :y. It takes as its argument the register without the ". So, your examples could be written as so:

            Source https://stackoverflow.com/questions/67655240

            QUESTION

            Sankey D3.JS return a negative value for node size
            Asked 2021-May-14 at 10:27

            After making a graph in parallel coordinates, I'm starting now a graph in Sankey Diagram type. So I Looked at this code : https://www.d3-graph-gallery.com/graph/sankey_basic.html and litteraly yanked it to try to understand how it's made to add later some interactions, but in first time I want to use my own data (https://raw.githubusercontent.com/augustin-laurent/Visualization_Tool/master/data.json).

            But after changing the input file, I got an error that says the height of the nodes is a negative value :

            ...

            ANSWER

            Answered 2021-May-14 at 10:27

            It looks like the Sankey library probably has a bug with node positioning computation.

            The problem can be solved by reducing node padding: nodePadding = 5.

            See it's working in the snippet:

            Source https://stackoverflow.com/questions/67531498

            QUESTION

            Clipboard not shared between wsl and windows 10 neovim
            Asked 2021-Apr-29 at 18:33

            I have a problem when using the paper clip in wsl, when using neovim when pressing yy to copy a line I can only paste it in neovim, but what I would like to do is paste it without any complications in a page or a txt file in windows with notepad, that was just an example, I would also like to be able to copy from windows and paste with the letter p in neovim directly, before I could do this, with the same previous configuration file, however I had to format my windows by virus.

            Here my configuration file:

            ...

            ANSWER

            Answered 2021-Apr-29 at 18:33

            Neovim delegates clipboard access to external application. As you don't have any it cannot work. This is clearly written to you in the picture above.

            Windows clip is not supported, because it cannot read from clipboard; xclip won't work, because it needs X-server to work (isn't it obvious from its name?) and so on.

            Normally Neovim makes use of win32yank to access Windows clipboard. So try to download it and put somewhere on WSL path.

            Source https://stackoverflow.com/questions/67205353

            QUESTION

            Vim - remove a file from quickfix
            Asked 2021-Apr-23 at 08:04

            Say I have 10 lines in quickfix coming from 3 files: 1.txt, 2.txt, and 3.txt.

            ...

            ANSWER

            Answered 2021-Apr-23 at 08:04

            You can use :help c_ctrl-r_ctrl-f to insert the filename under the cursor.

            With it, your command:

            Source https://stackoverflow.com/questions/67224069

            QUESTION

            How do I handle a model dataset that has a column of IDs?
            Asked 2021-Apr-11 at 13:50

            I am trying to build a model for NFL Draft prospects probability of success. I am having trouble finding a way to print the players names with their corresponding model output. For example, currently it prints something like this "[79 22 36 72 20 48 2 68 16 36 11 68 68 16 22 17 60 62 15 17 11 68 0 84 28 22 45 48 79 84 2 37 68]", I would like the player associated with those outputs to print as well. I am working with some template code I found online for the type of model I would like to build. I will post it below.

            LINK TO DATA: https://docs.google.com/spreadsheets/d/1BQa34rfq7oC3jOO65c4xUqKTuhDGKf46pPwGmjSS3ko/edit?usp=sharing

            Column "Player" really doesn't matter during training as this data is historical drafts going back to 2004 but obviously for the final output when I ask the model to predict this years prospects I would needs the names output as well.

            ...

            ANSWER

            Answered 2021-Apr-11 at 13:50

            QUESTION

            qemu: prevent a guest from hogging CPU
            Asked 2021-Mar-23 at 15:47

            I was reading some materials about qemu internals, and here it mentions that:

            "Jumping into guest code takes away our control of execution and gives control to the guest. While a thread is running guest code it cannot simultaneously be in the event loop because the guest has (safe) control of the CPU. Typically the amount of time spent in guest code is limited because reads and writes to emulated device registers and other exceptions cause us to leave the guest and give control back to QEMU. In extreme cases a guest can spend an unbounded amount of time without giving up control and this would make QEMU unresponsive. In order to solve the problem of guest code hogging QEMU's thread of control signals are used to break out of the guest. A UNIX signal yanks control away from the current flow of execution and invokes a signal handler function. This allows QEMU to take steps to leave guest code and return to its main loop where the event loop can get a chance to process pending events."

            So it's not clear to me what generates signals (qemu's IO thread or the kernel?) and how does it help to break out of the thread executing guest code? If the kernel sends such signal to the qemu process, then I would assume that qemu intentionally injects certain instructions (binary translation) in the guest code, which result in exceptions and then signals?

            ...

            ANSWER

            Answered 2021-Mar-23 at 15:47

            No, QEMU isn't injecting anything into the guest code. Typically a (host) signal is sent by another QEMU thread like the iothread to the vCPU thread. The point of doing this is that the whole mechanism of signals is that when the host kernel sends a signal to a thread, it stops that thread doing whatever it was doing (ie running guest code) and makes it run the signal handler (which is QEMU process code) instead. None of this is related to anything the guest sees like a guest CPU exception, except in the very indirect sense that once QEMU has control again it might decide that the situation means that it should now tell the guest about something by means of delivering it an exception or interrupt (eg "IO event completed, emulated SCSI controller has sent you an interrupt").

            For KVM, receiving a signal also means that the kernel will cause the vCPU thread to return from the KVM_RUN ioctl call, and it will then re-enter the QEMU main loop.

            For TCG, I think that blog post is now a bit out of date (it is 10 years old, after all[*]) -- we don't need to send a signal to the vCPU thread to make it stop running guest code, because when we translate the guest code we include at the beginning of each block of translated code a fragment which says "if a flag is set, stop". So the iothread can stop the vCPU thread just by setting the flag.

            [*] More generally, don't trust the detail in that blog post to still be correct today. Most notably, QEMU now only supports the "iothread" model, and the "non-iothread" handling has been removed completely; and in many situations TCG can support multiple vCPU threads and need not run all vCPUs on a single host thread.

            Source https://stackoverflow.com/questions/66749278

            QUESTION

            How to copy text from one vi file to another vi file while using tmux
            Asked 2021-Feb-26 at 14:10

            I am using tmux on a Linux server, and I am in two distinct directories on both tmux panes.

            I have foo.txt open in pane 1, and bar.txt open in pane 2.

            I want to copy text from pane 1 and move it to pane 2.

            These were my steps:

            1. Be in pane 1 (control+B, 0).
            2. vi foo.txt
            3. selecting text in VISUAL MODE followed by "+y in foo.txt (get the mesage "10 lines yanked")
            4. Switching to pane 2 (control+B, 1)
            5. vi bar.txt
            6. and then hitting p when the file opened up in my terminal.

            However, that did not work. How can I pull this off? I am using a Mac (keyboard) but the server is linux.

            ...

            ANSWER

            Answered 2021-Feb-26 at 14:10

            I had been dealt with this problem and wrote down a note on this here: https://github.com/g6ai/dotfiles/wiki/tmux.conf

            Here I assume you are ssh-ing into Linux from macOS. You could found my tmux.conf in the same dotfiles repo.

            Source https://stackoverflow.com/questions/66020448

            QUESTION

            how can i print vim register value in command line mode?
            Asked 2021-Feb-12 at 14:09

            Hey i want to print javap java.lang.Object in vim terminal but not for only 'Object' class but any class that i yanked in particular register.

            let say i yanked word Integer with "kyaw in vim so i want to print output of javap java.lang.Integer.

            For that i tried this command but that's not working.

            ...

            ANSWER

            Answered 2021-Feb-12 at 11:05

            In the command-line, inserting the content of a register is done with :help c_ctrl-r. In your case:

            Source https://stackoverflow.com/questions/66157747

            QUESTION

            Yank text from VIM editor from one session to another session
            Asked 2021-Feb-10 at 12:40

            I use Putty to connect to a server and I use 2 sessions, because I want to compare 2 .sh files and I find it easier to have both files on different windows.

            I am using VIM as a text editor and want to yank a line from the file of the first session to the file of the second session.

            I am using V"+y to yank and then p to paste, but it only works if I close the file in the current session and open the other file in the same session.

            Is it even possible to yank text from one session and paste it in another?

            ...

            ANSWER

            Answered 2021-Jan-14 at 07:53
            1. You can have two windows in one single Vim "session":

            Source https://stackoverflow.com/questions/65713814

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

            Vulnerabilities

            No vulnerabilities reported

            Install yank

            See the [Quickstart instructions](http://getyank.org/latest/quickstart.html).

            Support

            Documentation, tutorials, and best practices can be found at [getyank.org](http://getyank.org).
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