Metadata-Version: 2.1
Name: MutationChecker
Version: 0.1.7
Summary: Package for the computation of distances from a residue to the catalytic active residues.
Home-page: UNKNOWN
Author: RMolina
Author-email: ruben.molina-fernandez@upf.edu
License: UNKNOWN
Description: # Mutation_Checker
        
        Python package for checking the distance of a mutation from an active center of a protein.
        
        ## Installation
        
        Run the following to install:
        
        ```python
        pip3 install MutationChecker
        ```
        
        ## Usage
        
        This package consists of several modules: MAPPER, EMBL, PROSITE and STRUCTURE. Each one has it's own methods.
        
        ## MAPPER MODULE
        
        The mapper module consist of 3 functions. GeneToUniprot, GeneToPDB and GeneToFasta. These functions are
        used for converting identifiers between main databases.
        
        ### GeneToUniprot
        This function takes the name of a gene and maps it into a Uniprot Reviewed ID. By default uses the human
        specie. 
        
        @ input - gene (str) Name of Gene
        @ input - specie (str) Name of the Specie. Default: Human
        @ output - Uniprot ID (str) - Uniprot ID Code
        
        Example: Generate info for EIF2B5 gene
        
        ```python
        from MutationChecker.mapper import GeneToUniprot
        GeneToUniprot("EIF2B5")
        ```
        
        ### GeneToPDB
        
        This function takes the name of a gene and maps it into a list of PDB id's
        By default uses the human specie. 
        
        @ input - gene (str) Name of Gene
        @ input - specie (str) Name of the Specie. Default: Human
        @ output - PDB ID (list of str) - PDB ID Codes
        
        Example: Generate PDB Code for EIF2B5 gene
        
        ```python
        from MutationChecker.mapper import GeneToPDBMapper
        GeneToPDB("EIF2B5")
        ```
        
        ### GeneToFasta
        
        This function takes the name of a gene, and extract its sequence from Uniprot.
        
        @ input - gene (str) Name of Gene
        @ input - specie (str) Name of the Specie. Default: Human
        @ output - Uniprot Fasta (str)
        
        Example: Generate Fasta for EIF2B5 gene
        
        ```python
        from MutationChecker.mapper import GeneToFasta
        GeneToFasta("EIF2B5")
        ```
        
        ## STRUCTURE MODULE
        
        This module contains methods related to computations of the PDB structure file of a protein. 
        
        ### DownloadPDB
        
        This function takes a list of str (or one str) of PDB Codes and downloads the file into the working folder.
        It accepts a list of PDB to download the longest PDB structure.. 
        
        @ input - List of Strings (or standalone str) - Code of PDBs
        @ output - PDB ID (str) - Path of the downloaded file.
        
        Example: Download 1UBQ
        
        ```python
        from MutationChecker.structure import DownloadPDB
        DownloadPDB("1UBQ")
        ```
        
        ### PDBtoSequence
        
        This function takes a PDB file and extracts the sequence of the structure.
        
        @ input - PDB File path (str)
        @ output - Fasta Sequence (str) - Sequence of the structure.
        
        Example: Get sequence for 1UBQ file
        
        ```python
        from MutationChecker.structure import PDBtoSequence
        ExtractPDBSequence("./1UBQ")
        ```
        
        ### MapUniprotToPDB
        
        This function takes a sequence of uniprot, a sequence of PDB (of the same protein) and a uniprot residue number, and
        returns you the residue number on the structure. 
        
        @ input - Uniprot Fasta (str), can be obtained with the method GeneToFasta
        @ input - PDB Fasta (str), can be obtained with the method PDBtoSequence
        @ input - uniprot residue number (int)
        @ output - PDB residue number that match the uniprot residue number given (int)
        
        ```python
        from MutationChecker.structure import MapUniprotToPDB
        MapUniprotToPDB(GeneToFasta("EIF2B5"), PDBtoSequence("3JUI"), 45)
        ```
        
        ### CheckDistances
        
        This function takes a residue number , a list of another residue numbers, and a PDB structure file, and compute
        the physical distance between the first residue to the residues on the list
        
        @ input - PDB residue number (int)
        @ input - List of PDB residue numbers (list)
        @ output - List of distances between the first input residue, to the ones in the list (float)
        
        ```python
        from MutationChecker.structure import CheckDistances
        CheckDistances(1, [5, 6, 7], "./pdb3jui.ent")
        ```
        
        ## PROSITE MODULE
        
        This module has methods to search and parse the prosite database.
        
        ### PrositeRequest
        
        This function takes an uniprot id, and returns a JSON with information about the domains and motifs of the protein.
        
        @ input - Uniprot ID (str)
        @ output - Information about protein domains (json)
        
        ```python
        from MutationChecker.prosite import PrositeRequest
        PrositeRequest("Q13144")
        ```
        
        ### CheckMutationProsite
        
        This function takes a number of the residue in the sequence according to uniprot, and a uniprot ID of the protein.
        It search the Prosite database to extract the motifs, and checks if the mutation falls in place.
        
        @ input - num_residue (int) - Number of the residue to check in the sequence
                uniprot_id (str) - String of the uniprot identifier of the protein to check.
        
        @ output - Bool - The "num_residue" falls into the domain found by Prosite
        
        ```python
        from MutationChecker.prosite import CheckMutationProsite
        CheckMutationProsite(45, "Q13144")
        ```
        
        ### RetrieveDomain
        
        This function takes a number of the residue in the sequence according to uniprot, and a uniprot ID of the protein.
        It search the Prosite database to extract the motifs, and checks if the mutation falls in place.
        
        @ input - num_residue (int) - Number of the residue to check in the sequence
                  uniprot_id (str) - String of the uniprot identifier of the protein to check.
        
        @ output - tupple of str - Tupple with the parameters (Name of the domain found at num_residue, Accession code of Prosite of the domain.)
        
        ```python
        from MutationChecker.prosite import RetrieveDomain
        RetrieveDomain(45, "Q13144")
        ```
        
        ## EMBL MODULE
        
        This module has function related to the parse of the active site described on EMBL
        
        ### ObtainActiveCenterResidues
        
        This function takes the Uniprot ID of a protein, and returns a list of
        residue numbers that conforms the active site based on EMBL-EBI
        
        @ input - gene (str) Name of Gene
        @ output - List of Strings - Active Site residue numbers.
        
        If the protein has not an active site mapped on EMBL-EBI it returns None.
        
        Example: Get Active Site residues for LTA4H
        
        ```python
        from MutationChecker.embl import ObtainActiveCenterResidues
        from MutationChecker.mapper import GeneToUniprot, GeneToFasta
        
        UniprotID = GeneToUniprot("LTA4H")
        ObtainActiveCenterResidues(UniprotID)
        ```
        
        ### CheckDistanceToActiveSite
        
        This function takes a name of the Gene, and a residue number, and
        computes the physical distance in amstrongs between the residue number and the
        active site residues.
        
        @ input - gene (str) Name of the gene
        @ input - residue number (int) - Number of residue to check
        @ output - List of tupples (Name of active site residue, number)
        
        Example: Get distances to the Active site from ASN488 in LTA4H
        
        ```python
        from MutationChecker.embl import CheckDistanceToActiveSite
        CheckDistanceToActiveSite("LTA4H")
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
