Smiles2Monomers | A tool to rely chemical structures to biological structures | Genomics library

 by   yoann-dufresne Java Version: Current License: AGPL-3.0

kandi X-RAY | Smiles2Monomers Summary

kandi X-RAY | Smiles2Monomers Summary

Smiles2Monomers is a Java library typically used in Artificial Intelligence, Genomics applications. Smiles2Monomers has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However Smiles2Monomers build file is not available. You can download it from GitHub.

Smiles2Monomers is a software to infer monomeric structures from atomic structures of polymers. The structures are predicted by a two-step algorithm. First, all the candidates monomers are independantly searched and second, all the founded monomers are putted together in a non-overlapping tiling. For more details, please read the article. For speed performances during the search, we decided to pre-compute an index of the best way to search each monomer in polymers. So, each monomer have to be carve by boundary rules and ordered using frequences of atoms.
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            kandi-support Support

              Smiles2Monomers has a low active ecosystem.
              It has 3 star(s) with 4 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              Smiles2Monomers has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of Smiles2Monomers is current.

            kandi-Quality Quality

              Smiles2Monomers has no bugs reported.

            kandi-Security Security

              Smiles2Monomers has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              Smiles2Monomers is licensed under the AGPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              Smiles2Monomers releases are not available. You will need to build from source code and install.
              Smiles2Monomers has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are available. Examples and code snippets are not available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Smiles2Monomers and discovered the below as its top functions. This is intended to give you an instant insight into Smiles2Monomers implemented functionality, and help decide if they suit your requirements.
            • Command - line parser
            • Calculate the coverage for a given Polymer
            • Match all families in the polymer
            • Recursive modulation
            • Command line parser
            • Generate a set of residues from a monomer
            • Generate a residue from a rule
            • Create a DFS from an atom node
            • Extracts a Residue from a JSON representation
            • Returns the coverage of a particular family
            • Check if two segments are compatible
            • Adds all hydrogens from the chem object
            • Returns a string representation of the molecule
            • Entry point for testing
            • Command line entry point
            • Main method for testing
            • Extracts a Polymer object from a JSON object
            • Create a bond
            • Builds a contract for unknown nodes
            • Create the monomers list
            • Construct a FamilyRecords object from a JSON object
            • Generate JSON array for residues
            • Creates the pepideInfos
            • Extracts a coverage object from a JSON object
            • Performs a match for a given family
            • Main method to read all the peptides from the command line arguments
            Get all kandi verified functions for this library.

            Smiles2Monomers Key Features

            No Key Features are available at this moment for Smiles2Monomers.

            Smiles2Monomers Examples and Code Snippets

            No Code Snippets are available at this moment for Smiles2Monomers.

            Community Discussions

            QUESTION

            search for regex match between two files using python
            Asked 2022-Apr-09 at 00:49

            I´m working with two text files that look like this: File 1

            ...

            ANSWER

            Answered 2022-Apr-09 at 00:49

            Perhaps you are after this?

            Source https://stackoverflow.com/questions/71789818

            QUESTION

            Is there a way to permute inside using to variables in bash?
            Asked 2021-Dec-09 at 23:50

            I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

            This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

            The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

            1. Input files: Highland.ped - Midland.ped - Lowland.ped
            2. Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
            3. Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

            The general code is:

            ...

            ANSWER

            Answered 2021-Dec-09 at 23:50

            Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

            Source https://stackoverflow.com/questions/70298074

            QUESTION

            BigQuery Regex to extract string between two substrings
            Asked 2021-Dec-09 at 01:11

            From this example string:

            ...

            ANSWER

            Answered 2021-Dec-09 at 01:11

            use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

            if applied to sample data in your question - output is

            Source https://stackoverflow.com/questions/70283253

            QUESTION

            how to stop letter repeating itself python
            Asked 2021-Nov-25 at 18:33

            I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

            ...

            ANSWER

            Answered 2021-Nov-25 at 18:33

            As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

            Source https://stackoverflow.com/questions/70112201

            QUESTION

            Split multiallelic to biallelic in vcf by plink 1.9 and its variant name
            Asked 2021-Nov-17 at 13:56

            I am trying to use plink1.9 to split multiallelic into biallelic. The input is that

            ...

            ANSWER

            Answered 2021-Nov-17 at 09:45

            QUESTION

            Delete specific letter in a FASTA sequence
            Asked 2021-Oct-12 at 21:00

            I have a FASTA file that has about 300000 sequences but some of the sequences are like these

            ...

            ANSWER

            Answered 2021-Oct-12 at 20:28

            You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

            For example:

            Source https://stackoverflow.com/questions/69545912

            QUESTION

            How to get the words within the first single quote in r using regex?
            Asked 2021-Oct-04 at 22:27

            For example, I have two strings:

            ...

            ANSWER

            Answered 2021-Oct-04 at 22:27

            For your example your pattern would be:

            Source https://stackoverflow.com/questions/69442717

            QUESTION

            Does Apache Spark 3 support GPU usage for Spark RDDs?
            Asked 2021-Sep-23 at 05:53

            I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

            I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

            On querying in Hail forum, I got the response that

            That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

            So, does Spark3 not support GPU usage for RDD interfaces?

            ...

            ANSWER

            Answered 2021-Sep-23 at 05:53

            As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

            Source: Link

            Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

            Here, an answer from spark-rapids team

            Source: Link

            We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

            Source https://stackoverflow.com/questions/69273205

            QUESTION

            Aggregating and summing columns across 1500 files by matching IDs in R (or bash)
            Asked 2021-Sep-07 at 13:09

            I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:

            ...

            ANSWER

            Answered 2021-Sep-07 at 11:10

            QUESTION

            Usage of compression IO functions in apache arrow
            Asked 2021-Jun-02 at 18:58

            I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

            ...

            ANSWER

            Answered 2021-Jun-02 at 18:58

            Here is an example program that inflates a compressed zlib file and reads it as CSV.

            Source https://stackoverflow.com/questions/67799265

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

            Vulnerabilities

            No vulnerabilities reported

            Install Smiles2Monomers

            You can download it from GitHub.
            You can use Smiles2Monomers 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 Smiles2Monomers 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 .

            Support

            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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            https://github.com/yoann-dufresne/Smiles2Monomers.git

          • CLI

            gh repo clone yoann-dufresne/Smiles2Monomers

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            git@github.com:yoann-dufresne/Smiles2Monomers.git

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