symmetry | : ferris_wheel : Detect , analyze , and visualize protein | Machine Learning library
kandi X-RAY | symmetry Summary
kandi X-RAY | symmetry Summary
This project collects tools to detect, analyze, and visualize protein symmetry. This includes the CE-Symm tool for internal symmetry, a tool for quaternary symmetry, and other experiments relating to symmetry. This project serves dual purposes. First, it acts as an incubator for new methods and contains RCSB-specific or other non-production ready code. Stable methods have been moved to the biojava library, where they are accessible for programatic use. Second, user interfaces are built here following each BioJava release. See releases for the latest CE-Symm executable.
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Top functions reviewed by kandi - BETA
- The main entry point
- Parses the given file into a list of structure names
- Verifies if the parameters are compatible
- Creates the options
- Main method for testing
- Reverses a set of CA atoms
- Calculate the trace fragment
- Returns the angle between two AFPs
- Dump the symmetry of an assembly
- Create the options
- Test the chain ordering of the protein
- Saves a graph into a file
- Calculates the number of peaks in a chain
- Calculates the order of the AFPChain
- Calculates the order of the residues in the AFPChain
- Refine a MultipleAlignment
- Runs the analysis
- Creates a sample dataset
- Calculates the preferred ordering for the AFPChain
- Write result to file
- Detects asymmetric symmetry in the given structure
- Writes a result to the table
- Creates and returns a sample chart for the given category
- Write a result
- Entry point for testing
- Calculate the order of the Triangle wave wave
symmetry Key Features
symmetry Examples and Code Snippets
Community Discussions
Trending Discussions on symmetry
QUESTION
Nearly i tried to finish a Codewars task called "Alphabet symmetry".
Here is the link: https://www.codewars.com/kata/59d9ff9f7905dfeed50000b0/train/javascript
I tried finish it on JavaScript language.
So my code is working and it passes all the tests, except one:
ANSWER
Answered 2021-Jan-15 at 02:34The problem is a logic one:
QUESTION
I'm trying to detect if two square tiles are symmetries of each other, by iterating over the 8 symmetries of the square, applying each of the symmetry transforms to one of the tiles, and comparing the result of that with the other tile.
All of the transforms have the same inputs and outputs. I'd like to loop over them.
I'm using the image crate, which exports the transforms I need, with signatures like this:
...ANSWER
Answered 2021-Jun-04 at 15:12As documented in the Reference under Function item types (emphasis added):
When referred to, a function item, or the constructor of a tuple-like struct or enum variant, yields a zero-sized value of its function item type. That type explicitly identifies the function - its name, its type arguments, and its early-bound lifetime arguments (but not its late-bound lifetime arguments, which are only assigned when the function is called) - so the value does not need to contain an actual function pointer, and no indirection is needed when the function is called.
There is no syntax that directly refers to a function item type, but the compiler will display the type as something like
fn(u32) -> i32 {fn_name}
in error messages.Because the function item type explicitly identifies the function, the item types of different functions - different items, or the same item with different generics - are distinct, and mixing them will create a type error:
QUESTION
I have to solve the equality between 2 matrices 12x12 containing a lot of symbolic variables and with which I perform inversion of the matrix. There are only one unknown called SIGAM_O, and FISH_O_SYM(1,1), FISH_O_SYM(1,2) and FISH_O_SYM(2,2) (FISH_O_SYM(2,1) = FISH_O_SYM(1,2)
.
My system is solved fastly when I take for example 2 matrices 2x2, the inversion is pretty direct.
Now, with the case of 2 matrices 12x12, I need before actually to inverse a 31x31 matrix of symbolic variables (I marginalize after), since inversion takes a lot of time.
I would like to benefit from my GPU NVIDIA card to achieve this inversion faster but the GPU optimization is not supported currently for Symbolic arrays.
Below the script where you will find the line of inversion:
...ANSWER
Answered 2021-May-02 at 10:23(Posted answer on behalf of the question author in order to move it to the answer space).
I resolve this issue by doing simply:
QUESTION
I have more than 20 images that I want to classify based on pixel correlation. I am able to perform all the procedures but the problem is just saving the image into the corresponding class.
Suppose that the pixel correlation values are[0.48, 0.20, 0.57, 0.53, 0.06, 0.52, 0.55, 0.57, 0.51, 0.49, ..., 0.25]
And I want to use each index of the above values based on some thresholds to classify the images into Normal, Abnormal and Ambiguous classes. With this snippet below, I achieved the following results however, The saved images are in an unsupported format
...ANSWER
Answered 2021-May-24 at 08:22Are you asking how to correct the format of the saved images? Or why the saved images are different than your input ones?
In case you are asking the later:
Assuming your snippet is inside a loop that reads each image separately:
I believe your error is on img[index]. You are saving the image as a column, including all of the rows thus creating an image as shown. Keep in mind that an image is a 2d array and with [] you can specify which values you want to manipulate.
Image[columns, rows]
Since openvcv documentation says that imwrite takes parameters first the filename and second the image, change your code to:
QUESTION
Apologies in advance for my inefficient code, still learning! I'm trying to create a loop that (1) takes items from a list of semantic characters, copying the ones that are relevant into a new matrix, and (2) deleting the items I copy as I go. I achieved part 1, but cannot get part 2 to work. It only works for the first two rows and then I get a "Error in a[[n]] : subscript out of bounds".
Here is the code that achieves part 1:
...ANSWER
Answered 2021-May-18 at 20:35I am not 100% sure that I understand what you are trying to do, however, the reason that you are getting an out-of-bounds error is that
- You establish the value
x
here:
QUESTION
I was trying to recreate a simplified version of the natural numbers, for learning purposes (as it involves inductive definitions, recursive functions, etc...). In that process however, I got stuck in something that I thought would be very trivial.
Basically, I have a definition for natural numbers 'natt
' and a definition for the '<
' relation:
ANSWER
Answered 2021-May-12 at 22:34After some tips from user9716869, it's clear that my main problem was the lack of knowledge about the arbitrary
option in induction
. Using (induction _ arbitrary: _)
and (cases _)
(see the reference manual for details), the proofs are quite straight forward.
Since these are made for educational purposes, the following proofs are not meant to be concise, but to make every step very clear. Most of these could be vastly reduced if more automation is desired, and some can be done in one line (which I left as a comment below the lemma).
Note: In these proofs, we are using an implicit lemma about inductive types, their injectivity (which implies (Succ a = Succ b) ≡ (a = b)
and Zero ≠ Succ a
). Furthermore, (Succ a < Succ b) ≡ (a < b)
by definition.
First, we prove 2 useful lemmas:
a < b ⟹ b ≠ Zero
b ≠ Zero ⟷ (∃ b'. b = Succ b')
QUESTION
I would like to test the simetry in the response of an observer to a contrast stimuli with different polarity, positive (white) and negative (black). I took the reaction time (RT) as dependent variable, along four different contrasts. It is known that the response time follows a Pieron curve whose asymptotas are placed (1) at observer threshold (Inf) and (2) at a base RT placed somewere between 250 and 450 msec. The knowledge allows us to linearize the relationship transforming the independent variable (effective contrast EC) as 1/EC^2 (tEC), so the equation linking RT to EC becomes:
RT = m * tEC + RT0
To test the symmetry I established the criteria: same slope and same intercept in the two polarities implies symmetry. To obtain the coefficients I made a linear model with interaction (coding trough a dummy variable for Polarity: Positive or Negative). The output of lm is clear to me, but some colegues prefer somthing more similar to an ANOVA output. So I decided to use emmeans to make the contrasts. With the slope is all right, but when computing the interceps starts the problem. The intercepts computed by lm are very different from the output of emmeans, and the conclusions are also different. In what follows I reproduce the example. The question is two fold: It is possible to use emmeans to solve my problem? If not, it is possible to make the contrasts through other packages (which one)?
Data RT1000 EC tEC Polarity 596.3564 -25 0.001600 Negative 648.2471 -20 0.002500 Negative 770.7602 -17 0.003460 Negative 831.2971 -15 0.004444 Negative 1311.3331 15 0.004444 Positive 1173.8942 17 0.003460 Positive 1113.7240 20 0.002500 Positive 869.3635 25 0.001600 Positive Code ...ANSWER
Answered 2021-Apr-30 at 16:28What you are calling the intercepts are not; they are the model predictions at the mean value of tEC
. If you want the intercepts, use instead:
QUESTION
I am, specifically concerned with obeying the symmetry part of the general contract established in Object#equals(Object)
where, given two non-null objects x
and y
, the result of x.equals(y)
and y.equals(x)
should be the same.
Suppose you have two classes, PurchaseOrder
and InternationalPurchaseOrder
where the latter extends the former. In the basic case, it makes sense that comparing an instance of each against the other shall return consistently false
for x.equals(y)
and y.equals(x)
simply because a PurchaseOrder
is not always an InternationalPurchaseOrder
and therefore, the additional fields in InternationalPurchaseOrder
objects will not be present in instances of PurchaseOrder
.
Now, suppose you upcast an instance of InternationalPurchaseOrder
.
ANSWER
Answered 2021-Mar-08 at 11:45I think the misconception here is that upcasting actually changes the type of an object.
Any type of casting is just a pointer to the compiler to treat a variable as having a certain type, for the developers benefit. So upcasting a variable with type InternationalPurchaseOrder
to a PurchaseOrder
might change the way you see it and can interact with it (as you mentioned, fields being restricted), but the variable still references an InternationalPurchaseOrder
Therefore to concretely answer your question, comparing classes will use the equals
method declared to their actual type, not the type you have marked it as.
QUESTION
I am wondering what is an elegant and effective way of simplifying the following snippet of code. Since I have many more buttons and their mechanics all behave in the same way, the symmetry of the methods, and the alternation from
color.green -> color.red
suggests there may exist a way of simplifying this down to a function?
I have been scratching my head on this design problem for a while, the way I am coding it seems definitely wrong and cumbersome.
GameFrame Class ...ANSWER
Answered 2021-Apr-26 at 01:55Any number of ways you might do this, but one might be to take the common state information you need and apply it to a method, for example...
QUESTION
In a magic rectangle of dimensions m x n, every entry is the XOR of the row and column, zero-indexed. Example (8 x 5):
...ANSWER
Answered 2021-Apr-25 at 14:49We can divide the matrix into four sub metrices and leverage sum_range(start, m-1) * n
over and over. For simplicity I'll explain using recursion, you can easily convert it to non recursive solution using queue.
Let's consider small worse case scenario, a 7x7 matrix. Where, m=7(columns), n=7(rows). Sum 168.
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Install symmetry
You can use symmetry like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the symmetry component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .
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