spice | SPiCe - Sequence-based Protein Classification | Machine Learning library
kandi X-RAY | spice Summary
kandi X-RAY | spice Summary
The spice package can be used for calculating sequence-based protein features, visualizing the obtained features, and training and testing of protein classifiers using these features. This featext.py module can be used for sequence-based protein feature extraction. it uses the featmat.py module to manage the labeled feature matrix, an m x n matrix for m proteins and n features, and the dataset.py module to manage the set of proteins and their corresponding labels. The classification.py module is a layer on top of scikit-learn that can be used to construct protein classifiers and the classify.py module can be used to test new protein sequences on an allready trained classifier. The project\_management.py module is used by the SPiCE website to manage user projects.
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Top functions reviewed by kandi - BETA
- Create a heatmap plot
- Calculate heatmap
- Create labels for the given axes
- A colormap
- Load features from directory
- Add a labeling object
- Add new features
- Return a JSON representation of a feature
- Standardize a matrix
- Calculate the feature vector
- Calculate the peak peaks for a given interval
- Removes specified features from the feature matrix
- T - test t test
- Calculate the entropy for a given position
- Save the data
- Classify the classifier
- Get the clustdist of the dataset
- Set the object ids
- Calculate missense features for a feature category
- Return the backbone angles in the protein
- Saves a histogram
- Get the solv access vector
- Calculate protein features associated with a feature category
- Count the number of atoms in the structure
- Save a scatter plot
- Get the path to the clustered dataset
spice Key Features
spice Examples and Code Snippets
Community Discussions
Trending Discussions on spice
QUESTION
I'm using bert pre-trained model for question and answering. It's returning correct result but with lot of spaces between the text
The code is below :
...ANSWER
Answered 2021-Jun-15 at 17:14You can just use the tokenizer decode function:
QUESTION
I'm using Python requests and am trying to access the values that I am getting from a GET request that I have made. The output is a JSON response (I think it's called a 2D array as there are arrays within the array). I want to store these values so that I can access them in the next function.
Here is the Python:
...ANSWER
Answered 2021-Jun-06 at 15:21To get the ids of the jsResponse, just do:
QUESTION
Problem statement: When I open a file with .sp extention with vim it opens with spice syntax which the same file with .sim/.cir extension does not open with spice syntax.
My efforts: I tried by added the below line in .vimrc but it's not working.
au BufRead *.sim setfiletype spice
Details: I have the following lines in .vimrc
syntax on
filetype on
Looking for: I am looking for an option that we can add in .vimrc to enable a set of file extensions(sim/cir/sp) to open with a spice syntax.
Thanks.
...ANSWER
Answered 2021-May-16 at 10:31If it doesn't already exist, create the following directory:
QUESTION
So I have a function, where I want to return (resolve- upon promise completion) a set of key-value pairs, which I cannot.
...ANSWER
Answered 2021-May-15 at 21:34You create your promise wrong:
QUESTION
I keep getting the error:
...ANSWER
Answered 2021-May-10 at 09:55In Java, Enum only has private constructors. Hence can’t be instantiated by Spring
QUESTION
ANSWER
Answered 2021-May-07 at 07:37You are trying to create an instance of a class Curry you just don't have. Instead, you have a class Spice with a name and a spiciness. If you want an instance of, say Red Curry, you would have to instantiate a Spice and give it the desired name: Spice("Red Curry", "kinda hot").
A good practice for that spiciness (at least a better one than just a String) would be an enum class Spiciness...
Here's a simple example:
QUESTION
I wrote 2 functions and I executed them nested. But one of my functions is not working properly. It's first line is working fine but other lines are not working. Output does not show anything. The main idea of my code is price / quality comparison. So i created 2 list and put the qualities and prices. Note: GreenGroce, Bakery etc. are the list of the prices.
...ANSWER
Answered 2021-Apr-30 at 17:41The comparing() function only prints something if i == 4:, but it never is. Inside the for i in range(0, 4, 1): loop the values of i are 0 → 3.
So I believe you are mistakenly thinking the shopping() function not working.
QUESTION
Excuse me for the length of the title please but this is a pretty specific question. I'm currently simulating a launch of a rocket to mars in the 2022 launch window and I noticed that my rocket is a far distance away from Mars, even though it's traveling in the right direction. After simplifying my code to narrow down the problem, I simply plotted the orbits of the Earth and Mars (Using data from NASA's SPICE library) and propagated the position and velocity given to me by the lambert solver I implemented (Universal variables) to plot the final orbit of the rocket.
I'm only letting the Sun's gravity effect the rocket, not the Earth or Mars, to minimize my problem space. Yet even though I've simplified my problem so far, the intersection between Mars' and my rocket's orbits happens well before the time of flight has been simulated all the way, and the minimum distance between the two bodies is more than a million kilometers at all times.
That being said, something must be wrong but I cannot find the problem. I've made sure the lambert solver code I copied is correct by comparing it to Dario Izzo's method and both gave the same results. Furthermore, I've also checked that my orbit propagator works by propagating Mars' and the Earth's orbits and comparing those ellipses to the data from SPICE.
In conclusion, I assume this must be a stupid little mistake I made somewhere, but cannot find because I lack experience in this field. Thank you for any help! :)
This is the JupyterLab notebook I used:
...ANSWER
Answered 2021-Apr-28 at 14:29So, I managed to figure out what the problem was after much head-scratching. I was simply not taking into account that the Sun is not located at (0,0,0) in my coordinate system. I thought this was negligible, but that is what made the difference. In the end, I simply passed the difference between the Earth and Mars's and the Sun's position vectors and passed those into the Lambert solver. This finally gave me the desired results.
The reason that the error ended up being so "small" (It didn't seem like an obvious bug at first) was because my coordinates are centered at the solar system barycenter which is a few million kilometers away from the Sun, as one would expect.
Thanks for the comments!
QUESTION
These are the grocery store lists:
...ANSWER
Answered 2021-Apr-26 at 13:06Make sure you are using item.lower() and not item.lower. I would also use a dictionary, where the key is the name of the aisle, and the value is a list of items in that aisle.
QUESTION
I have one requirement to iterate through list of items which has n-level of hierarchy and I would like to get bottom-up elements for the selected item ID.
For e.g. below is the raw data
...ANSWER
Answered 2021-Apr-21 at 10:42Without any code, I can only give you a "default" answer for your problem.
To solve your problem, you must implement a function in your classes to get the parent of your instance.
To get the absolute parent (object has no parent itself) you must implement a function which calls itself as long as it has a parent.
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