foyer | A package for atom-typing as well as applying
kandi X-RAY | foyer Summary
kandi X-RAY | foyer Summary
Foyer is an open-source Python tool for defining and applying force field atom-typing rules in a format that is both human- and machine-readable. It parametrizes chemical topologies, generating, syntactically correct input files for various simulation engines. Foyer provides a framework for force field dissemination, helping to eliminate ambiguity in atom-typing and improving reproducibility (for more information, see our paper or its corresponding pre-print).
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Create a new system
- Iterate over the atoms
- Apply the system to a structure
- Create a new system from a topology
- Create a structure from a structure
- Import a module
- Patch adjust for adjustments
- Applies the typology mapping to the given structure
- Validate SMARTS string
- Raise ValidationError
- Construct a TopologyGraph from an OpenFF Topology
- Adds a bond between two atoms
- Validates the class type and type attribute of the force field
- Imports a module
- Construct a TopologyGraph from a GMSO
- Extract periodic torsion parameters from atoms
- Extract RBTorsion force parameters
- Extract the harmonic angle parameters for the given atoms
- Registers an atom type
- Generates a topology graph from a structure
- Extracts the coordination parameters for two atoms
- Create a topology from a Residue
- Validate overrides
- Return non - bond force parameters for a given atom type
- Extract RBTors for a set of atoms
- Extracts periodic torsion parameters for the specified atoms
- Generate a topology from a non - empty structure
- Returns the scale of the force field
foyer Key Features
foyer Examples and Code Snippets
Lines of Code : 16License : Permissive (MIT)
Copyfrom foyer import Forcefield
import parmed as pmd
untyped_ethane = pmd.load_file('ethane.mol2', structure=True)
oplsaa = Forcefield(forcefield_files='oplsaa.xml')
ethane = oplsaa.apply(untyped_ethane)
# Save to any format supported by ParmEd
ethane $ docker pull mosdef/foyer:latest
$ docker run -it --name foyer -p 8888:8888 mosdef/foyer:latest\
/opt/conda/envs/foyer-docker/bin/jupyter notebook --ip="*"
$ docker run -it --name foyer mosdef/foyer:latest
Community Discussions
Trending Discussions on foyer
QUESTION
I found a problem which I cannot solve on my own and when I did my research - answers are not unanimous.
Consider the following python code:
...ANSWER
Answered 2021-May-19 at 17:04You're correct and the ones who told you it was a syntax error, it isn't. It is exactly the "mismatched data type" since the keys on the variable "rooms" are integers, but the user input or the variable "room" is specifically not an integer or a number. In other words, the user input returns a string and the "rooms" variable keys are integers which create a mismatched data type when matched together by an if statement and can probably cause confusion. To prevent this, make sure to see if both values that you're gonna be comparing are the same data types.
QUESTION
Is there a way in Python3 to slow the text that is inside a function? I have created a text-based game that uses almost exclusively functions for each section of the game, but want the text within to be typed out. For example:
...ANSWER
Answered 2021-Jan-11 at 15:11You were close, but you should look up some tutorials on how iterators work with Python. print doesn't return a value and your room_1 definition also doesn't return anything so your code was not entering the for loop.
I would recommend making a function that will print slowly.
QUESTION
Context
I have a list containing dictionnaries. I want to "flatten" (JSON without nested values) all the dictionnaries of the list. To do this, I wrote a function, flatten_json, that works as expected.
Each output of the function is appended to a new list that will be processed later on.
Code
...ANSWER
Answered 2021-Jan-06 at 12:50flattened_dict={} is your problem. Parameter defaults are evaluated only once, so when you don't pass in a dict the same one gets reused.
You'll want (sorry for brevity and formatting, on mobile)
QUESTION
I created a component with several div elements.
By adding a ?goto= parameter to the url I want to scroll the the relevant element. I now solved that with const itemsRef = useRef([]);.
My main concern now is if that's the right and performance efficient approach with itemsRef.current[element.id] = el. element.id will be unique for each element.
I also found packages such as: https://github.com/Macil/react-multi-ref
But I don't see the disadvantage of my approach yet.
Here you can find my current solution in action: https://codesandbox.io/s/scrolltoref-w5i7m?file=/src/Element.js
...ANSWER
Answered 2020-Jun-26 at 13:02useRef is basically the same as doing useState({ current: });
Given your use case, what you have done is sufficient however I would change use ref to initialise with an object since that is what you are actually using as oppose to an array:
QUESTION
I am trying to understand the usage of useMemo. Since the object doesn't change, I thought I can improve performance by adding useMemo.
However as soon I add it here, I am being asked to add findFloorPosition. Once I did that my linter asks me to add useCallback to the findFloorPosition function.
Can you give me some advice what's the right way to implement useMemo here?
ANSWER
Answered 2020-Jun-25 at 12:39Notice that you should memoize a value only if the dependency array values (the value of goto) not frequently change.
The warning occurs because the linter (eslint) only evaluates the semantics, it doesn't know that findFloorPosition is just a helper function.
So basically you need to inline the helper function like:
QUESTION
I am getting the following error when my pod is deployed and then it tries to pull the image.
...ANSWER
Answered 2020-Jun-08 at 18:52To pull an Image from a Private Registry click here
Basically you need to create a secret using docker credential. For example, using command line
QUESTION
Well, I've read the function reference for step_num2factor and didn't figured it out how to use it properly, honestly.
...ANSWER
Answered 2020-May-04 at 00:03I don't think that step_num2factor() is the best fit for this variable. Take a look at the help again, and notice that you need to give a transform argument that can be used to modify the numeric values prior to determining the levels. This would work OK if this data was all multiples of 10, but you have some values like 75 and 85, so I don't think you want that. This recipe step works best for numeric/integer-ish variables that you can more easily transform to a set of integers with a simple function.
Instead, I think you should think about step_mutate() and a simple coercion to a factor type:
QUESTION
I have a model below call "TitleModels" which i use to add my data I get from my Api. Unfortunately i am unable to set the data in RatingModels. What is the best way to set data to a model using an array? Unfortunately i get the error "incompatible types: Rating cannot be converted to RatingModels".
The code I am done so far:
...ANSWER
Answered 2020-Apr-28 at 13:35You have different types
QUESTION
I am making a change to a record in a sqlite3 database using Django, and the save() function doesn't seem to work.
I am able to save changes using the graphical admin app however.
Here is the code to the specific model I'm trying to do the save in:
...ANSWER
Answered 2020-Jan-09 at 12:55To understand why your model isn't saving, you must first understand how querysets are evaluated. Essentially, anytime you iterate over them, or slice them, they will hit the database, however there are caveats to this.
Consider the following abstract example:
QUESTION
Being a beginner I started with the form, and I would like to make ONE form but fill it out on several pages.
To do this I would like to know how to save the data entered on page 1, to use it on page 2? In order to avoid the problem of the following picture [Probleme - Page 2][1] The values on page 1 are correctly retrieved.
To do this, I created two controllers that each have their own pages.
Page 1 : SimulationController.php and simulation.html.twig
...ANSWER
Answered 2019-Oct-18 at 14:46I have not used it myself so cannot attest to how good it is but there is a bundle available to help you build multi-page forms here: https://github.com/craue/CraueFormFlowBundle
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install foyer
SMARTS-based atomtyping
Supported SMARTS Grammar
Defining force field parameters
Force field file validation
https://github.com/mosdef-hub/foyer/tree/master/foyer/forcefields
https://github.com/chrisiacovella/OPLSaa_perfluoroalkanes
https://github.com/mosdef-hub/forcefield_perfluoroethers
https://github.com/summeraz/OPLSaa_alkylsilanes
https://github.com/mosdef-hub/forcefield_template
Basic usage examples
Detailed Jupyter notebook tutorials, including integration with mBuild
Jupyter notebook tutorials, from our paper
Installation instructions
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
