symmetry | : ferris_wheel : Detect , analyze , and visualize protein | Machine Learning library

 by   rcsb Java Version: symmetry-2.2.1 License: LGPL-2.1

kandi X-RAY | symmetry Summary

kandi X-RAY | symmetry Summary

symmetry is a Java library typically used in Artificial Intelligence, Machine Learning applications. symmetry has no bugs, it has no vulnerabilities, it has build file available, it has a Weak Copyleft License and it has high support. You can download it from GitHub.

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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              symmetry has a highly active ecosystem.
              It has 22 star(s) with 17 fork(s). There are 24 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 10 open issues and 49 have been closed. On average issues are closed in 263 days. There are no pull requests.
              It has a positive sentiment in the developer community.
              The latest version of symmetry is symmetry-2.2.1

            kandi-Quality Quality

              symmetry has 0 bugs and 0 code smells.

            kandi-Security Security

              symmetry has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              symmetry code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              symmetry is licensed under the LGPL-2.1 License. This license is Weak Copyleft.
              Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

            kandi-Reuse Reuse

              symmetry releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              symmetry saves you 2119 person hours of effort in developing the same functionality from scratch.
              It has 4646 lines of code, 160 functions and 42 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed symmetry and discovered the below as its top functions. This is intended to give you an instant insight into symmetry implemented functionality, and help decide if they suit your requirements.
            • 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
            Get all kandi verified functions for this library.

            symmetry Key Features

            No Key Features are available at this moment for symmetry.

            symmetry Examples and Code Snippets

            Symmetry in Protein Structures,Building
            Javadot img1Lines of Code : 1dot img1License : Weak Copyleft (LGPL-2.1)
            copy iconCopy
            mvn package
              

            Community Discussions

            QUESTION

            Codewars: Alphabet symmetry
            Asked 2021-Jun-07 at 13:23

            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 02:34

            The problem is a logic one:

            Source https://stackoverflow.com/questions/65729401

            QUESTION

            Iterate over a collection of function items with generic bounds of associated types
            Asked 2021-Jun-04 at 15:12

            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 15:12

            As 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:

            Source https://stackoverflow.com/questions/67832671

            QUESTION

            Large substitution from symbolic matrix to numerical values while keeping 4 unknowns into the new matrix
            Asked 2021-Jun-01 at 09:14

            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:

            Source https://stackoverflow.com/questions/67252491

            QUESTION

            How to use a loop to save images in different folders in python-opencv
            Asked 2021-May-27 at 02:28

            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 08:22

            Are 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:

            Source https://stackoverflow.com/questions/67668659

            QUESTION

            Deleting items off a list as I go in R loop
            Asked 2021-May-18 at 20:35

            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 20:35

            I 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

            1. You establish the value x here:

            Source https://stackoverflow.com/questions/67593088

            QUESTION

            Proving basic properties of recursive "less than" definition for naturals in Isabelle
            Asked 2021-May-12 at 22:34

            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 22:34

            After 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')

            Source https://stackoverflow.com/questions/67479214

            QUESTION

            Failed to contrast intercepts through emmeans in R
            Asked 2021-Apr-30 at 16:28

            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 16:28

            What 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:

            Source https://stackoverflow.com/questions/67334851

            QUESTION

            What should be the result of overridden "Object#equals(Object)" when instance is upcasted?
            Asked 2021-Apr-27 at 11:57

            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 11:45

            I 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.

            Source https://stackoverflow.com/questions/66520914

            QUESTION

            Java simplifying a repetitive code snippet to a function within ActionListener
            Asked 2021-Apr-26 at 02:03

            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 01:55

            Any 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...

            Source https://stackoverflow.com/questions/67259873

            QUESTION

            XOR Magic Rectangle
            Asked 2021-Apr-25 at 14:49
            The Problem:

            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 14:49

            We 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.

            Source https://stackoverflow.com/questions/67249122

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install symmetry

            You can download it from GitHub.
            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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            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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