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P

parseCommandLine(String[], String, boolean) - Static method in class tools.progressbar.Utils
Usefull for parsing command line arguments.
Pattern - Class in tools.tree.trie.pattern
 
Pattern() - Constructor for class tools.tree.trie.pattern.Pattern
 
PatternContainer - Class in tools.tree.trie.pattern
 
PatternContainer() - Constructor for class tools.tree.trie.pattern.PatternContainer
 
PatternGenerator - Class in tools.tree.trie.pattern
 
PatternGenerator() - Constructor for class tools.tree.trie.pattern.PatternGenerator
 
PatternString - Class in tools.tree.trie.pattern
 
PatternString() - Constructor for class tools.tree.trie.pattern.PatternString
 
PharmacophorePointAssigner - Class in tools.moltyping
 
PharmacophorePointAssigner() - Constructor for class tools.moltyping.PharmacophorePointAssigner
 
PotentialPharmacophorePoint - Class in tools.moltyping.pharmacophore
 
PotentialPharmacophorePoint(String, String, String) - Constructor for class tools.moltyping.pharmacophore.PotentialPharmacophorePoint
 
PotentialPharmacophorePointPair - Class in tools.moltyping.pharmacophore
 
PotentialPharmacophorePointPair(PotentialPharmacophorePoint, int, PotentialPharmacophorePoint, int) - Constructor for class tools.moltyping.pharmacophore.PotentialPharmacophorePointPair
 
PPPDefinitionFileReader - Class in tools.moltyping.pharmacophore
 
PPPDefinitionFileReader() - Constructor for class tools.moltyping.pharmacophore.PPPDefinitionFileReader
 
prepareMoleculeConserveHydrogens(Molecule) - Static method in class io.reader.MoleculePreprocessor
types the molecule, leaves the hydrogens attached
prepareMoleculeRemoveHydrogens(Molecule) - Static method in class io.reader.MoleculePreprocessor
standard preparation protocol: remove hydrogens, types, ring detection
print() - Method in class fingerprinters.features.FeatureMap
 
printFeatureMapStatistics(List<FeatureMap>) - Static method in class fingerprinters.features.FeatureMapHelper
 
printInfo(double, double, double) - Static method in class io.writer.ExporterHelper
 
printMinMaxInfNaN(double[]) - Static method in class tools.progressbar.Utils
 
ProgressBar - Class in tools.progressbar
Draws a nice graphical ASCII/ANSI Prograss bar on the console.
ProgressBar(int) - Constructor for class tools.progressbar.ProgressBar
Initialize the progressBar object
ProgressBar(long) - Constructor for class tools.progressbar.ProgressBar
Initialize the progressBar object
ProgressBar(int, boolean) - Constructor for class tools.progressbar.ProgressBar
 

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