Package com.actelion.research.chem.mmp

Class MMPReader

  • public class MMPReader
extends java.lang.Object

    • Constructor Summary

      Constructors 
      Constructor Description
      MMPReader​(java.io.BufferedReader br, boolean verbose)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.Integer fragmentToFragmentIndex​(java.lang.String fragment)
      Returns the fragment index from one fragment idCode
      java.lang.Integer[] fragmentToFragmentIndex​(java.lang.String[] fragments)
      Return the fragment indexes from one (single cut) or several fragment idCodes
      java.lang.Integer fragmentToFragmentSize​(java.lang.String fragment)
      Returns the number of heavy atoms of one fragment
      java.util.List<java.lang.String> getChemicalSpace​(java.lang.String[] keys, java.lang.String value, java.lang.String dataField)
      Returns the list of idCode & molecules names representing the chemical space of one constant part of a molecule
      java.lang.String getChemicalSpaceDWAR​(java.lang.String moleculeIDCode, java.lang.String[] keys, java.lang.String dataField)
      Generates the DWAR file for the chemical space for a specific 'key' and data field
      int getChemicalSpaceSize​(java.lang.String key)
      Returns the size of the chemical space corresponding to a specific 'key' (constant part of a molecule)
      int getChemicalSpaceSize​(java.lang.String[] keys)
      Returns the size of the chemical space corresponding to one constant part of a molecule
      java.util.List<java.lang.String> getDataFields​(java.lang.String what)
      Returns a list of fields
      java.lang.String getIDCodeFromMolName​(java.lang.String molName)
      Returns the idCode from one compound name, null if the compound is not found
      java.lang.String getMMPsDWAR​(java.lang.String moleculeIDCode, java.lang.String[] keys, java.lang.String value1, java.lang.String value2, int replacementSize, java.util.List<java.lang.String> properties)
      Generates the DWAR file for the Matched Molecular Pairs corresponding to a specific seed 'value', target 'value', and list of data fields
      java.lang.String getTransformationsDWAR​(java.lang.String moleculeIDCode, java.lang.String[] keys, java.lang.String value1, int minAtoms, int maxAtoms, java.lang.Integer environmentSize, java.util.List<java.lang.String> properties)
      Generates the DWAR file for the Transformations corresponding to a specific seed 'value', number of atoms for the replacement, environment size, and list of data fields
      java.lang.String getTransformationsJSON​(java.lang.String moleculeIDCode, java.lang.String[] keys, java.lang.String value1, int minAtoms, int maxAtoms, java.lang.String sortBy)
      Generates the main JSON file for Transformations and Matched Molecular Pairs
      int getTransformationsSize​(java.lang.String value1, int minAtoms, int maxAtoms)
      Returns the number of transformations for a defined variable part of a molecule
      java.lang.String getWhat​(java.lang.String what)
      Returns the requested general information of the data set
      java.util.List<java.lang.String[]> transformationsListToTable​(java.lang.String[] keys, java.lang.String value1, int minAtoms, int maxAtoms)
      Returns a list of transformations

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • SORT_BY_SIMILARITY

        public static final java.lang.String SORT_BY_SIMILARITY
        See Also:
        Constant Field Values

      • SORT_BY_NUMBER_OF_EXAMPLES

        public static final java.lang.String SORT_BY_NUMBER_OF_EXAMPLES
        See Also:
        Constant Field Values

      • EXAMPLES_SIMILARITY_SORT

        public static final java.util.Comparator<com.actelion.research.chem.mmp.MMPReader.MatchedMolecularPairExamples> EXAMPLES_SIMILARITY_SORT

    • Constructor Detail

      • MMPReader

        public MMPReader​(java.io.BufferedReader br,
                 boolean verbose)
          throws java.io.IOException,
                 java.lang.Exception
        Throws:
        java.io.IOException
        java.lang.Exception

    • Method Detail

      • fragmentToFragmentIndex

        public java.lang.Integer fragmentToFragmentIndex​(java.lang.String fragment)
        Returns the fragment index from one fragment idCode
        Parameters:
        fragment - idCode of a fragment
        Returns:
        fragment index

      • fragmentToFragmentIndex

        public java.lang.Integer[] fragmentToFragmentIndex​(java.lang.String[] fragments)
        Return the fragment indexes from one (single cut) or several fragment idCodes
        Parameters:
        fragments - List of fragment idCodes
        Returns:
        List of fragment indexes

      • fragmentToFragmentSize

        public java.lang.Integer fragmentToFragmentSize​(java.lang.String fragment)
        Returns the number of heavy atoms of one fragment
        Parameters:
        fragment - idCode of a fragment
        Returns:
        number of heavy atoms

      • getChemicalSpaceSize

        public int getChemicalSpaceSize​(java.lang.String key)
        Returns the size of the chemical space corresponding to a specific 'key' (constant part of a molecule)
        Parameters:
        key - idCode of the 'key' (constant part of a molecule)
        Returns:
        the size of the chemical space

      • getChemicalSpaceSize

        public int getChemicalSpaceSize​(java.lang.String[] keys)
        Returns the size of the chemical space corresponding to one constant part of a molecule
        Parameters:
        keys - array of one (single cut) or two (double cut) IDCodes of the 'keys' (constant part of the molecule)
        Returns:
        the size of the chemical space.

      • getChemicalSpace

        public java.util.List<java.lang.String> getChemicalSpace​(java.lang.String[] keys,
                                                         java.lang.String value,
                                                         java.lang.String dataField)
        Returns the list of idCode & molecules names representing the chemical space of one constant part of a molecule
        Parameters:
        keys - array of one (single cut) or two (double cut) IDCodes of the 'keys' (constant part of the molecule)
        value - the variable part of the molecule; not used yet but might be used to identify the current compound
        Returns:
        an array of tab-delimited idCode, idCoord, molecule names [and data]

      • getChemicalSpaceDWAR

        public java.lang.String getChemicalSpaceDWAR​(java.lang.String moleculeIDCode,
                                             java.lang.String[] keys,
                                             java.lang.String dataField)
        Generates the DWAR file for the chemical space for a specific 'key' and data field
        Parameters:
        moleculeIDCode - idCode of the seed molecule
        keys - Array of one (single cut) or two (double cut) 'keys' idCodes (constant part of the molecule)
        dataField - null or short name of a data field
        Returns:
        the whole string of the generated DWAR file

      • getMMPsDWAR

        public java.lang.String getMMPsDWAR​(java.lang.String moleculeIDCode,
                                    java.lang.String[] keys,
                                    java.lang.String value1,
                                    java.lang.String value2,
                                    int replacementSize,
                                    java.util.List<java.lang.String> properties)
        Generates the DWAR file for the Matched Molecular Pairs corresponding to a specific seed 'value', target 'value', and list of data fields
        Parameters:
        moleculeIDCode - idCode of the seed molecule
        keys - Array of one or two 'keys' idCodes (constant part of the molecule)
        value1 - seed 'value' (variable part of the molecule)
        value2 - target 'value' (variable part of the molecule)
        replacementSize - size of the replacement (number of heavy atoms)
        properties - List of data fields for which data should be retrieved
        Returns:
        the whole string of the generated DWAR file

      • getTransformationsSize

        public int getTransformationsSize​(java.lang.String value1,
                                  int minAtoms,
                                  int maxAtoms)
        Returns the number of transformations for a defined variable part of a molecule
        Parameters:
        value1 - IDCode of the variable part of a molecule
        minAtoms - minimal number of atoms in the replacement (relative to value1Atoms)
        maxAtoms - maximal number of atoms in the replacement (relative to value1Atoms)
        Returns:
        an integer corresponding to the number of transformations

      • getTransformationsDWAR

        public java.lang.String getTransformationsDWAR​(java.lang.String moleculeIDCode,
                                               java.lang.String[] keys,
                                               java.lang.String value1,
                                               int minAtoms,
                                               int maxAtoms,
                                               java.lang.Integer environmentSize,
                                               java.util.List<java.lang.String> properties)
        Generates the DWAR file for the Transformations corresponding to a specific seed 'value', number of atoms for the replacement, environment size, and list of data fields
        Parameters:
        moleculeIDCode - idCode of the seed molecule
        keys - Array of 'keys' idCodes (constant part of the molecule)
        value1 - seed 'value' idCode (variable part of the molecule)
        minAtoms - minimal number of atoms in the replacement (relative to value1Atoms)
        maxAtoms - maximal number of atoms in the replacement (relative to value1Atoms)
        environmentSize - size of the environment (0-5)
        properties - List of numerical data fields
        Returns:
        String of the whole DWAR file

      • transformationsListToTable

        public java.util.List<java.lang.String[]> transformationsListToTable​(java.lang.String[] keys,
                                                                     java.lang.String value1,
                                                                     int minAtoms,
                                                                     int maxAtoms)
        Returns a list of transformations
        Parameters:
        keys - Array of 'keys' idCodes (constant part of the molecule)
        value1 - seed 'value' idCode (variable part of the molecule)
        minAtoms - minimal number of atoms in the replacement (relative to value1Atoms)
        maxAtoms - maximal number of atoms in the replacement (relative to value1Atoms)
        Returns:
        List of transformations

      • getTransformationsJSON

        public java.lang.String getTransformationsJSON​(java.lang.String moleculeIDCode,
                                               java.lang.String[] keys,
                                               java.lang.String value1,
                                               int minAtoms,
                                               int maxAtoms,
                                               java.lang.String sortBy)
        Generates the main JSON file for Transformations and Matched Molecular Pairs
        Parameters:
        moleculeIDCode - idCode of the seed molecule
        keys - Array of 'keys' idCodes (constant part of the molecule)
        value1 - seed 'value' idCode (variable part of the molecule)
        minAtoms - minimal number of atoms in the replacement (relative to value1Atoms)
        maxAtoms - maximal number of atoms in the replacement (relative to value1Atoms)
        sortBy - SORT_BY_SIMILARITY, SORT_BY_NUMBER_OF_EXAMPLES
        Returns:
        JSON string

      • getIDCodeFromMolName

        public java.lang.String getIDCodeFromMolName​(java.lang.String molName)
        Returns the idCode from one compound name, null if the compound is not found
        Parameters:
        molName - name of a compound
        Returns:
        null or idCode

      • getDataFields

        public java.util.List<java.lang.String> getDataFields​(java.lang.String what)
        Returns a list of fields
        Parameters:
        what - Requested data (fieldName, longFieldName, categoryName, percentile5, percentile95)
        Returns:
        List of fields

      • getWhat

        public java.lang.String getWhat​(java.lang.String what)
        Returns the requested general information of the data set
        Parameters:
        what - Requested information (datasetName, date, numberOfMolecules, randomMoleculeName)
        Returns:
        the requested information