mbuild | A hierarchical , component based molecule builder
kandi X-RAY | mbuild Summary
kandi X-RAY | mbuild Summary
With just a few lines of mBuild code, you can assemble reusable components into complex molecular systems for molecular dynamics simulations. To learn more, get started or contribute, check out our website. If you use this package, please cite our paper. The BibTeX reference is. The mBuild package is part of the Molecular Simulation Design Framework (MoSDeF) project. Libraries in the MoSDeF ecosystem are designed to provide utilities neccessary to streamline a researcher's simulation workflow. When setting up simulation studies, we also recommend users to follow the TRUE (Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common practices meant to improve the reproducibility of computational simulation research.
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Top functions reviewed by kandi - BETA
- Fill a box
- Return a list of all ports
- Update port locations of all ports
- Update the coordinates of the Compound
- Write a GOMC control file
- Write the control file
- Convert a dictionary of keys to a list
- Save a compound
- Convert compound to compound
- Save the molecule to file
- Checks if input_variables_dict is a string or a string
- Clone this Compound
- Write a GOMD structure to a GSM file
- Transform a molecule into equivalent atoms
- Check if the input_variable_dict is a string or float
- Convert a Compound object to a MD trajectory
- Prints the valid input variables
- Convert a Compound to an InterMole object
- Convert angle vectors and angles to vector
- Fill a sphere
- Fill a region using packmol
- Writes a homoomd XML file
- Converts a Compound to ParmEd format
- Solvate a molecule using packmol
- Load an object from a file or file
- Save the molecule to a file
- Convert a BioBabel object to a PyBabel object
mbuild Key Features
mbuild Examples and Code Snippets
Lines of Code : 51License : Strong Copyleft (CC BY-SA 4.0)
Copypicked=print(random.choice(Classes))
picked = random.choice(Classes)
print(picked)
import random
Classes=["Demon Hunter","Monk","Crusader","Barbarian","Necromancer","Wizard","Witch Doctor"%rename("getVersion") _getVersion_Swig;
%inline %{
std::string _getVersion_Swig()
{
Version v = getVersion();
return v.asString();
}
%}
Community Discussions
Trending Discussions on mbuild
QUESTION
PROBLEM: WANT TO USE A MATLAB DLL IN LABVIEW
ISSUE: BELOW ERR
...ANSWER
Answered 2021-Feb-04 at 20:15Running it in a single line solev this issue 😂
QUESTION
i have a edittext in Alert Dialog.....my operation is performing well if ediitext is not empty.....i want to set focus when ediitext is empty in alertdialog ..
need help thanks in advance
i tried the following code please have a look:---
...ANSWER
Answered 2020-Aug-17 at 08:05
NumberFormatExceptionis an Exception that might be thrown when you try to convert a String into a number, where that number might be an int , a float , or any other Java numeric type.
QUESTION
I try to run an activity after taping a button, but instead of the activity I expected to have, a blank activity runs. The logcat indicates :
...ANSWER
Answered 2020-Mar-18 at 09:47It seems Like you did not called setContentView() inside the onCreate() of your AddBase Activity.
QUESTION
I used Ubuntu to install software, but I can not find it.
Someone told me :
pip --user installs things into a directory called ~/.local/bin, but this might not be on your bash search path.
Can you check the content of $PATH and add ~/.local/bin in your .bashrc if neccessary.
How can I write the command?
Thanks in advance for any great help!
Best,
Yue
...ANSWER
Answered 2019-Dec-18 at 18:40echo $PATH will check the current value of the PATH variable
QUESTION
MBuild can use response files to save and run commands. But why is it called response file? What is it responding to?
(Also in an MsBuild file the task elements are called Target. What is 'target' refering too?)
...ANSWER
Answered 2019-May-17 at 14:27A target represents a collection of things you want to do. In an msbuild file, it is represented by an xml element that can have various child xml elements called tasks. Conceptually it looks like this:
QUESTION
I am trying to make a thing that picks a class and a build for my next character in a game. I can get it to pick the class, but I can't figure out why it wont pick the build. I am still really new so this probably isn't the cleanest or easiest way to do this.
...ANSWER
Answered 2018-Oct-23 at 17:37The problem was where you were trying to set the return of a print to a variable, which you can't do
QUESTION
I have a C++ function
...ANSWER
Answered 2018-Jun-29 at 22:18%rename only renames the function for the target language -- that is, %rename("getVersionHidden") getVersion; will create a Python function (getVersionHidden) which forwards the getVersion() defined in C/C++.
Instead, you should create a new function and then rename that to override the getVersion that would otherwise get generated automatically:
QUESTION
I'm currently working with the USGS's EarthExplorer to setup some batch downloads of Landsat scenes based on spatial coordinates. They provide a wonderful handy script to do this at https://earthexplorer.usgs.gov/inventory/example/json-download_data-pl which is great. I'm working on a cluster, and despite installing all perl modules properly, when I run the script I get the following output:
...ANSWER
Answered 2017-Sep-15 at 04:22Your code doesn't check for errors. You should have something like
QUESTION
I have a problem with Session on Perl.
I am trying to fix this error
...ANSWER
Answered 2017-May-30 at 08:38The error you are getting is:
Can't locate Session.pm in @INC (you may need to install the Session module)
As the message says, the solution to this problem is to install the Session module from CPAN. For some reason, you have tried to solve it by installing the Apache::Session module from CPAN. Session and Apache::Session are two completely different modules. You cannot expect to solve a missing module problem by installing the wrong module.
(Although, I see that Session is a thin wrapper around Apache::Session - so you will need the Apache::Session module installed as well.)
I suggest that you install Session in order to fix your problem.
However, I should point out that the Session module has a single release (version 0.01) which was released in 2003, by someone who hasn't released anything to CPAN since 2005. I'd, therefore, suggest that the chances of getting any support for this module are tiny and I would recommend avoiding the module if at all possible.
QUESTION
I'm creating an app in that I'm allow client to rate the app.
I have two issues
FIRST.
I have added Rating bar in Alert dialog but dont know why its getting overwrite on button which i have created for submit the ratings. I have tried with margin-top for button still its not working
Second.
On submit it also not showing toast message.
Code for Alert Dialog
...ANSWER
Answered 2017-Jan-13 at 14:08you have fixed the size of dialog which is not allowing rating bar to fit into it.
replace dialog.getWindow().setLayout(600, 400);
with dialog.getWindow().setLayout(800, 600);
In your Activity
create class variable :-
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No vulnerabilities reported
Install mbuild
You can use mbuild 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.
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