crystals | Data structures , algorithms , and parsing for crystallography
kandi X-RAY | crystals Summary
kandi X-RAY | crystals Summary
crystals is a library of data structure and algorithms to manipulate abstract crystals in a Pythonic way. crystals helps with reading crystallographic files (like .cif and .pdb), provides access to atomic positions, scattering utilities, allows for symmetry determination, and indexing of diffraction peaks. Although crystals can be used on its own, it was made to be integrated into larger projects (like [scikit-ued] Take a look at the [documentation] for more information and examples.
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Top functions reviewed by kandi - BETA
- Return the atoms in the structure
- Affine transformation matrix
- Convert a complex coordinates to a fractional basis
- Transform a 3x3 matrix
- List of symmetry operations
- Return the Hall symbol
- Write to a XYZ file
- Write XYZ to a file
- Calculate the ratio of reflections
- Compute the miller index of the scattering vector
- List of atoms
- Returns the list of lattice vectors
- Construct a Project from a MPJ file
- Performs symmetry expansion on atoms
- Create a Castro instance from a COD file
- The symmetry operation of the unit cell
- Return the structure block
- The cartesian coordinates of the lattice
- List of secondary structures
- Compute the minimum distance between two images
- Construct a molecule from a sequence of atoms
- Return a new atom with the given matrices
- Return a rotation matrix
- Try to guess a constructor for a given type
- Return symmetry operations from equiv site
- Create a molecule from a PDB file
crystals Key Features
crystals Examples and Code Snippets
Community Discussions
Trending Discussions on crystals
QUESTION
Here are my fields:
...ANSWER
Answered 2021-May-14 at 17:36Like David Zimmerman says, put e.printStackTrace() in catch block to see the exception. Also I suspect that you are executing wrong the method. With your implementation you have to do something like this:
QUESTION
I've been given these source files and headers. In the README.md the authors explain how to launch the test executables without the need of a proper installation. It is just a make command to run. They explain how to generate the .so files. I think these latter are meant to be used if I wanted to install the APIs at a system level (the definitions should be in api.h). My question is: where should I copy the shared objects generated by the Makefile and the api.h header? I aim to write a source file from scratch where I use those APIs (e.g. crypto_sign()) just including the headers, if it is possible. Thanks
ANSWER
Answered 2021-Mar-31 at 10:32where should I copy the shared objects generated by the Makefile and the api.h header? I aim to write a source file from scratch where I use those APIs (e.g. crypto_sign()) just including the headers, if it is possible
Nowhere.
The project comes with CMake support. Use CMake in your project and just add_subdirectory the repository directory.
Anyway, if you really wish to install the library system-wide, then FHS specifies directory structure on linux. For local system administration use /usr/local/lib for local libraries .so files and /usr/local/include for local C header files.
QUESTION
I'm trying to capture rows for a specific group and then convert them into columns naming the script's headers.
This is an example of data:
...ANSWER
Answered 2020-Oct-16 at 12:36You might use Dynamic Pivot including ROW_NUMBER() function with values grouped by formulas ordered by instructions column in order to number the column names along with iteration of that analytic function :
QUESTION
I want to create a gif from the following images: (I don't have enough reputation to embed them)
...ANSWER
Answered 2020-Oct-26 at 18:55ImageMagick quantization by default uses dithering. Your Night.png image has more than 256 colors and GIF only allows 256. So when quantized to 256 colors the spots get created from the dithering. You can disable the dithering and get a smoother result by adding +dither to your command. This works for me on IM 6.9.11.34 Q16 Mac OSX.
QUESTION
I have 2 MongoDB Collections: crystals & cleanses
Crystal Schema:
...ANSWER
Answered 2020-Oct-06 at 23:42Updated the return Object.assign() to get the correct results:
QUESTION
Essentially, what I am trying to accomplish is I want to cd into a specific directory containing all my lighthouse folders. I want to loop through each line of urls.txt and for every URL execute the npm lighthouse command and output the results into a CSV to analyze later.
...ANSWER
Answered 2020-Sep-22 at 03:19The following will probably get you a bit closer. At least, it's valid AppleScript for what I think you're trying to do (never having used lighthouse before). I'm assuming that you want that given URL in the do shell script to be the URL stored in each line of the file, right?
The quoted form of command makes sure that paths are properly quoted for unix, saving you some headaches. I've used the full path to npm, because do shell script doesn't import your interactive shell PATH variable and won't find that utility. if you ever want to know wether do shell script will be able to find a utility, run do shell script "which utilityname"; if the command errors out, use the full path.
QUESTION
I am trying to put together a function to build tables and their relationships using SQLAlchemy. The problem is that I am working with tables with many columns and many foreign keys. Some of the relationships are many-to-one, but some others are many-to-many. Since there are many parties interested in the outcome of the database, there will be for sure additional columns added in the future. Hence, being able to build tables from a function is desirable. This is what I have after a couple of days looking around:
...ANSWER
Answered 2020-Sep-05 at 15:22You have an issue in the arguments to relationship(). When you look at the documentation, you will see that the first argument is the target table, and the second is the secondary table for many-to-many relationships. The important part of the function signature is:
QUESTION
I have an image with a light gray background that is filled with black and white crystals:
.
My goal is to create a binary mask that turns the white crystals into a white foreground and merges the black crystals and the gray background into a black background.
I am using the opencv library in python. I have tried to sharpen the image using a laplacian filter, smooth it with a gaussian filter and finally apply OTSU thresholding to create the mask with the following code:
...ANSWER
Answered 2020-Sep-02 at 16:40QUESTION
I am quite new to html and CSS, and currently I am doing a hobby website project. On my portfolio page I have some images that also work as links, however the clickable area of the link is larger than the image itself. I have looked through different answers here on stackoverflow, which has helped a bit, but the problem has not been resolved yet.
I would greatly appreciate if someone could have a look at my code, and lead me in the right direction.
...ANSWER
Answered 2020-Jul-17 at 11:42Your images have margin so all the space created by the margin is also clickable because they are inside your a tag
QUESTION
I want to use machine learning techniques to categorise "images" of energy released in an electromagnetic calorimeter, using a keras CNN. In order to import the data I'm using a Pandas DataFrame, however the data isn't formatted in the necessary way.
The calorimeter can be considered a 28x28 crystal square, however the data that I receive only show the energy in crystals that have been triggered, on average about 10-15 crystals per event.
...ANSWER
Answered 2020-Jun-17 at 14:46Your arr shape is actually (4,) and what you want is an array of (1,4) if I didn't misunderstood. You could doarr=np.array([[event,xi,yi,0]]) to have the good shape.
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