Maud | Enzyme models that take into account kinetics | 3D Animation library

 by   biosustain Python Version: v0.4.0.2 License: GPL-3.0

kandi X-RAY | Maud Summary

kandi X-RAY | Maud Summary

Maud is a Python library typically used in User Interface, 3D Animation applications. Maud 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 install using 'pip install Maud' or download it from GitHub, PyPI.

Enzyme models that take into account kinetics, allostery and thermodynamics
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            kandi-support Support

              Maud has a low active ecosystem.
              It has 19 star(s) with 2 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 27 open issues and 141 have been closed. On average issues are closed in 378 days. There are 3 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of Maud is v0.4.0.2

            kandi-Quality Quality

              Maud has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              Maud is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              Maud releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              It has 4788 lines of code, 165 functions and 29 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Maud and discovered the below as its top functions. This is intended to give you an instant insight into Maud implemented functionality, and help decide if they suit your requirements.
            • Calculate StanInput for a given model
            • Encode a list of wrapped elements
            • Unpack prior1d
            • Unpack a priors_2d
            • Run the predict command
            • Runs the prediction on the given data_path
            • Load a Maud input file
            • Predict from Maudy
            • Returns a prior set for a user - defined variable set
            • Convert a Pandas Series to a Pandas DataFrame
            • Load one - dimensional prior
            • Load a 2d prior from a variable
            • Load Maud input file
            • Parse ensembles
            • Parse the raw config
            • Create a KineticModel from a dict
            • Calculate Stan variable set
            • Returns the kcat coords of a given kinetic model
            • Get DC coordinates
            • Get the coordinates of a kinetic model
            • Run a variational simulation
            • Load InferenceData from command line
            • Sample sample
            • Compute the standard deviation for each component of the composition
            • Load inferenceData
            • Get a list of csv files
            Get all kandi verified functions for this library.

            Maud Key Features

            No Key Features are available at this moment for Maud.

            Maud Examples and Code Snippets

            No Code Snippets are available at this moment for Maud.

            Community Discussions

            QUESTION

            CSS file is not read properly using actix-web and maud
            Asked 2022-Feb-11 at 21:35

            CSS is not working via link rel attributes of maud with actix-web. Where I've made mistake(s)?

            I think that position where I wrote link rel attributes is correct.

            main.rs

            ...

            ANSWER

            Answered 2022-Feb-11 at 21:35

            Looking at the documentation of actix_files::Files:

            The first argument (mount_path) is the root URL at which the static files are served.

            The second argument (serve_from) is the location on disk at which files are loaded.

            You are using /static as first argument, so your files will be under http://0.0.0.0:80/static, all right.

            But as second argument you set . that is the root of the project. This means that you are publishing the whole source of your project! For example, at http://0.0.0.0:80/static/src/main.rs (http://0.0.0.0:80/static/ is the mount point, ./src/main.rs is the local file) you will download the source of your binary, and you do not want that.

            To fix your problem write instead:

            Source https://stackoverflow.com/questions/71086498

            QUESTION

            Trying to build a data frame from an existing one with means of selected column and rows
            Asked 2021-Jun-10 at 10:40

            saving community, I have a data frame with a HUGE amount of data. I would show you but the site is not letting me so I'll do my best to describe it. I have columns like this :

            Participant Task Language f0st

            Under participant I have names (18 different names but duplicated), under task I have 3 different ones (reading, narration, conversation), under language there's 2 options (FR, ENG) and under f0st I have all the numeric values of f0 (the voice fundamental frequency) in semitones, that were extracted from recordings every 1ms (hence the huge amount of data).

            So from these "raw" values, I want to build another data frame with a single mean value for each participant in each condition. So instead of hundred thousands of rows I end up with 18 rows corresponding to the number of participants. For example to build the column in the new data frame with the mean f0st for each participant, in the reading task, in FR, how do I code this?

            I hope this is clear enough! Thanks a bunch for your help :)

            @maarvd : this is the input

            ...

            ANSWER

            Answered 2021-Jun-10 at 10:40

            For your problem you could use

            Source https://stackoverflow.com/questions/67916984

            QUESTION

            Can I do a binary search on an array of objects?
            Asked 2021-Mar-26 at 16:26

            I am currently learning how to use searching and sorting algorithms and I am running into issues with a binary search on an array of objects of customers' data. The array of customers is sorted by first and last name.

            The goal is to find a customer's email and return the index.

            The data looks like:

            ...

            ANSWER

            Answered 2021-Mar-26 at 16:16

            You should be able to binary search the customer array, provided that it's ordered by customer email.

            Change the code up a bit to compare the email instead of the entire object, accessing the email property of the object.

            Source https://stackoverflow.com/questions/66820529

            QUESTION

            Why does my onscroll function stop before the element is fully scrolled?
            Asked 2021-Feb-05 at 03:48

            I wrote a function to slide a div into the viewport horizontally in the middle of a vertically scrolling page and it mostly works. It slips when you scroll through the page quickly, though, and doesn't always finish scrolling in, horizontally. If you're scrolling fast, it sometimes stops short of the left-most edge of the browser and I'm at a bit of a loss to explain why that is.

            Any takers? Codepen here: https://codepen.io/ThatWerewolfTho/pen/xxRZERv

            HTML

            ...

            ANSWER

            Answered 2021-Feb-05 at 03:48

            When the scroll goes over 100% the if fails and doesn't move it all the way. Add an else if to catch it when the percentageScrolled is >= 100

            Source https://stackoverflow.com/questions/66057139

            QUESTION

            Adding Multiple rows to a Postgres database
            Asked 2020-Oct-09 at 04:53

            EDIT: added more of the code to better understand what I'm trying to do

            I'm using Flask, pandas, and flask-SQLAchemy. currently, I'm using pandas to upload an excel file and display that in an editable html table to confirm all the data and edit anything before posting all the data. where I'm having an issue is taking all those rows of data and adding them to my Postgres database as new entries. I can only get it to post the first row. any help would be apprenticed.

            Heres the HTML used to display the editable HTML table as a form:

            ...

            ANSWER

            Answered 2020-Oct-09 at 04:53

            figured it out, required some more pandas!

            Source https://stackoverflow.com/questions/64201174

            QUESTION

            Recording using sox in c/c++
            Asked 2020-Sep-15 at 13:23

            I am trying to record sound using microphone and sox library in C/C++.

            ...

            ANSWER

            Answered 2020-Sep-15 at 13:23

            As the last parameter to sox_open_read function for microphone input, one of the audio devices drivers should be passed. In my case, it is 'alsa'.
            Example:

            Source https://stackoverflow.com/questions/63825858

            QUESTION

            MDO Architectures in OpenMDAO
            Asked 2020-Feb-28 at 20:12

            I am new to OpenMDAO and MDO in general. I enjoy using OpenMDAO and would like to know more about it. Currently I am reading about MDO architectures. What is the MDO architecture when I run a problem 'normally' in Openmdao. Would I be correct if I assume it is monolithic AAO (since it calculates the total derivative and solves the problem from there) ? I ask this because I read about the MAUD architecture (described in this paper) which confused me. Can this be considered as one of the classification of MDO architectures (since it does provide a mathematical and algorithmic framework) or is it just a pure computational architecture ?

            Finally would it make sense compare different MDO architectures (like MDF,CO,ATC,..) by implementing it in OpenMDAO for a large scale design problem ? I understand that OpenMDAO is focused on monolithic architecture. So would it be a fair to compare a monolithic with a distributed architecture in OpenMDAO ? Also does the MDO architecture bench marking results (in this paper) from OpenMDAO V1 still apply for the current version OpenMDAO V2 (i.e after the incorporation of ideas from MAUD architecture) ?

            Thank you.

            ...

            ANSWER

            Answered 2020-Feb-28 at 20:12

            You asked three questions. Im going to answer them separately (and rephrase them a bit):

            1) What kind of MDO architecture are you using when you solve a problem (the normal way) in OpenMDAO ?

            If you take a look at the Martins and Lamb paper on architectures you see they divide them up into monolithic and distributed classes. When you use OpenMDAO, you are almost always applying some form of a monolithic optimization architecture. In practice many people end up applying something that looks a lot like MDF because they have solvers in their models, but I've also commonly seen MDF/IDF hybrids, SAND, and even AAO aspects to problems.

            Broadly Id say that the flexibility of the OpenMDAO allow you to re-factor your model such that any particular equality constraint could either be handled by a solver (MDF like), by a compatibility constraint (IDF like), or directly as an equality constraint by the optimizer (SAND like) means that users have the flexibility to construct hybrid forms of various monolithic architectures.

            It is possible to implement distributed architectures with OpenMDAO, by using nested instances of the OpenMDAO Problem class for the sub-problems within a top level model. This isn't trivial, but it is possible. This approach often has one major challenge: The top level optimization problem will require derivatives across the sub-problems, which is something that OpenMDAO actually can't provide (because it requires computing post-optimality sensitivities which is non-trivial and outside the scope of MAUD)

            2) What is the relationship of MAUD to MDO Architectures?

            These two concepts are separate things that have relevant to each other but are in no way the same thing.

            • MAUD is a specific way of computing derivatives across an arbitrary super-function that is made up of a bunch of sub-functions strung together.
            • An MDO architecture a is a transformation of fundamental optimization problem formulation, into a specific form that is solvable (see this paper by Pate et al. for details on what I mean by "fundamental optimization problem formulation"). Whatever form you transform the problem into, it will require derivatives of the objective/constraint functions which can be computed however you want (possibly using MAUD/OpenMDAO, or possibly not).

            3) Is the prior benchmarking of architectures done in OpenMDAO still valid?

            In my opinion, the benchmarking done in the OpenMDAO based paper you cited, which is backed up by this other paper from Tedford and Martins that did not use OpenMDAO at all, but I think is also relevant. I don't personally expect the answers to change significantly if you attempted new problems. These two papers seem to agree that monolithic architectures (AAO, SAND, MDF, IDF) are the best performing, and most consistent over all.

            There are some cases where the distributed architectures perform well, and a group from Europe has had some good success with them for specific problems. Check out this paper from Gazaix et al. as an example.

            So if you are really interested in architectures, I would suggest that you might find a way to generate specific classes of problems that do well under different architectures and then to provide such a classification in a paper. If successful, this could be a good resource for future researchers/practitioners who need to decide which architecture to use. However, my opinion is that in the vast majority of cases monolithic architectures are going to perform the best. I suspect you'll have trouble getting distributed architectures to perform well in a broad set of cases. The Gazaix paper proves it's certainly possible to get useful results from a distributed MDO architecture, but it doesn't prove that it would be faster than an equivalent monolithic formulation.

            Source https://stackoverflow.com/questions/60432477

            QUESTION

            Extraction de donnees
            Asked 2020-Feb-27 at 09:45

            Bonjour ! Mes excuses si la question a déjà été posée, je n'ai pas trouvé de réponse.

            Je travaille sur R.

            Alors voilà, j'ai un tableau d'entrée (data_entree) qui contient des milliers de lignes et 22 colonnes. (Je ne peux pas vous coller une image d'un bout du tableau, je ne sais pas pourquoi.)

            J'ai aussi une liste mots clefs (exemple - ma liste contient en vrai 42 mots ) :

            ...

            ANSWER

            Answered 2020-Feb-27 at 09:45

            Bonjour Maud,

            Je suis désolé, je ne sais que lire le Francais un petit peu, mais je n'ecrit pas bien. Pourtant, je pense que je peux t'aider.

            Essaye ça:

            Source https://stackoverflow.com/questions/60419551

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

            Vulnerabilities

            No vulnerabilities reported

            Install Maud

            You can install using 'pip install Maud' or download it from GitHub, PyPI.
            You can use Maud like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            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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