Package com.actelion.research.chem.mmp
Class MMPReader
- java.lang.Object
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- com.actelion.research.chem.mmp.MMPReader
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public class MMPReader extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
MMPReader.DataField
static class
MMPReader.MatchedMolecularPair
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Field Summary
Fields Modifier and Type Field Description static java.util.Comparator<com.actelion.research.chem.mmp.MMPReader.MatchedMolecularPairExamples>
EXAMPLES_SIMILARITY_SORT
static java.util.Comparator<MMPReader.MatchedMolecularPair>
NUMBER_OF_EXAMPLES_SORT
static java.util.Comparator<MMPReader.MatchedMolecularPair>
SIMILARITY_SORT
static java.lang.String
SORT_BY_NUMBER_OF_EXAMPLES
static java.lang.String
SORT_BY_SIMILARITY
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Constructor Summary
Constructors Constructor Description MMPReader(java.io.BufferedReader br, boolean verbose)
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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 idCodejava.lang.Integer[]
fragmentToFragmentIndex(java.lang.String[] fragments)
Return the fragment indexes from one (single cut) or several fragment idCodesjava.lang.Integer
fragmentToFragmentSize(java.lang.String fragment)
Returns the number of heavy atoms of one fragmentjava.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 moleculejava.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 fieldint
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 moleculejava.util.List<java.lang.String>
getDataFields(java.lang.String what)
Returns a list of fieldsjava.lang.String
getIDCodeFromMolName(java.lang.String molName)
Returns the idCode from one compound name, null if the compound is not foundjava.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 fieldsjava.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 fieldsjava.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 Pairsint
getTransformationsSize(java.lang.String value1, int minAtoms, int maxAtoms)
Returns the number of transformations for a defined variable part of a moleculejava.lang.String
getWhat(java.lang.String what)
Returns the requested general information of the data setjava.util.List<java.lang.String[]>
transformationsListToTable(java.lang.String[] keys, java.lang.String value1, int minAtoms, int maxAtoms)
Returns a list of transformations
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Field Detail
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SORT_BY_SIMILARITY
public static final java.lang.String SORT_BY_SIMILARITY
- See Also:
- Constant Field Values
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SORT_BY_NUMBER_OF_EXAMPLES
public static final java.lang.String SORT_BY_NUMBER_OF_EXAMPLES
- See Also:
- Constant Field Values
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NUMBER_OF_EXAMPLES_SORT
public static final java.util.Comparator<MMPReader.MatchedMolecularPair> NUMBER_OF_EXAMPLES_SORT
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SIMILARITY_SORT
public static final java.util.Comparator<MMPReader.MatchedMolecularPair> SIMILARITY_SORT
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EXAMPLES_SIMILARITY_SORT
public static final java.util.Comparator<com.actelion.research.chem.mmp.MMPReader.MatchedMolecularPairExamples> EXAMPLES_SIMILARITY_SORT
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Method Detail
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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
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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
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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
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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
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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.
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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]
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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 moleculekeys
- 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
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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 moleculekeys
- 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
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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 moleculeminAtoms
- 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
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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 moleculekeys
- 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
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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
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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 moleculekeys
- 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
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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
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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
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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
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