# FEATURE
# See COPYING and AUTHORS for copyright and license agreement terms.

# $Id: Makefile.am 363 2005-05-27 05:43:42Z mliang $

## Process this file with automake to produce Makefile.in

# this is where everything gets installed
featuredir = $(prefix)/@PACKAGE@
featurehtmldir = $(featuredir)/html

# compiler options
CWARN = -Wall -pedantic
AM_CXXFLAGS = $(CWARN)

# these are the executable files that will be installed
feature_PROGRAMS = training scan evaluation featurize scorefeatures scoreit buildmodel findfile featuretosvm
feature_SCRIPTS = convert_files.py protein_amber.py protein_residues.py
# test programs (not installed)
check_PROGRAMS = testNeighbor testResidueHelper testResidueTemplate \
    testForceFieldParameters testAssignAtomType testSTLTypes
# data files to be installed
feature_DATA = amberM2_params.dat amberM_params.dat amber_params.dat \
    residue_templates.dat
featurehtml_DATA = README.html Feature-diagram.jpg ViewFeature-diagram2.jpg 
EXTRA_DIST = $(feature_DATA) $(featurehtml_DATA) $(feature_SCRIPTS)

training_SOURCES = training.cc \
    AssignAtomType.cc AssignAtomType.h CAllSitesFile.cc CAllSitesFile.h \
    CAtomArray.cc CAtomArray.h CBayes.cc CBayes.h CBinaryFile.cc CBinaryFile.h \
    CDouble.h CFile.cc CFile.h CGrid.cc CGrid.h CHashTable.cc CHashTable.h \
    CObArray.cc CObArray.h CObject.h CParser.cc CParser.h CPropertiesArray.cc \
    CPropertiesArray.h CProperty.cc CProperty.h CProtein.cc CProtein.h \
    CProteinObject.cc CProteinObject.h CPtrArray.cc CPtrArray.h \
    CScanningGrid.cc CScanningGrid.h CScoreBins.cc CScoreBins.h CScoreFile.cc \
    CScoreFile.h CStatisticsFile.cc CStatisticsFile.h CString.cc CString.h \
    File.cc File.h FileExt.h ForceFieldParameters.cc ForceFieldParameters.h \
    MathConst.h Message.cc Message.h Neighbor.cc Neighbor.h Parse.cc Parse.h \
    PropertyConstants.h PropertyList.cc PropertyList.h Random.cc Random.h \
    RankSum.cc RankSum.h ResidueHelper.cc ResidueHelper.h ResidueTemplate.cc \
    ResidueTemplate.h SAtom.cc SAtom.h SAtomProperties.cc SAtomProperties.h \
    SBox.cc SBox.h SPoint3D.cc SPoint3D.h SPoint3DList.cc SPoint3DList.h \
    SPropertyScoreData.h SPropertyStatData.cc SPropertyStatData.h \
    SPropertyValues.cc SPropertyValues.h SSSBond.cc SSSBond.h SSite.cc \
    SSite.h Utilities.cc Utilities.h const.cc const.h logutils.cc logutils.h \
    stl_types.cc stl_types.h

scan_SOURCES = scan.cc \
    AssignAtomType.cc AssignAtomType.h CAllSitesFile.cc CAllSitesFile.h \
    CAtomArray.cc CAtomArray.h CBayes.cc CBayes.h CBinaryFile.cc \
    CBinaryFile.h CDouble.h CFile.cc CFile.h CGrid.cc CGrid.h CHashTable.cc \
    CHashTable.h CObArray.cc CObArray.h CObject.h CParser.cc CParser.h \
    CPropertiesArray.cc CPropertiesArray.h CProperty.cc CProperty.h \
    CProtein.cc CProtein.h CProteinObject.cc CProteinObject.h CPtrArray.cc \
    CPtrArray.h CScanningGrid.cc CScanningGrid.h CScanningGridCache.cc \
    CScanningGridCache.h CScoreBins.cc CScoreBins.h CScoreFile.cc \
    CScoreFile.h CStatisticsFile.cc CStatisticsFile.h CString.cc CString.h \
    File.cc File.h FileExt.h ForceFieldParameters.cc ForceFieldParameters.h \
    MathConst.h Message.cc Message.h Neighbor.cc Neighbor.h Parse.cc Parse.h \
    PropertyConstants.h PropertyList.cc PropertyList.h Random.cc Random.h \
    RankSum.cc RankSum.h ResidueHelper.cc ResidueHelper.h ResidueTemplate.cc \
    ResidueTemplate.h SAtom.cc SAtom.h SAtomProperties.cc SAtomProperties.h \
    SBox.cc SBox.h SPoint3D.cc SPoint3D.h SPoint3DList.cc SPoint3DList.h \
    SPropertyScoreData.h SPropertyStatData.cc SPropertyStatData.h \
    SPropertyValues.cc SPropertyValues.h SSSBond.cc SSSBond.h SSite.cc \
    SSite.h Utilities.cc Utilities.h const.cc const.h logutils.cc logutils.h \
    stl_types.cc stl_types.h

evaluation_SOURCES = evalScore.cc \
    CAllSitesFile.cc CAllSitesFile.h CDouble.h CFile.cc CFile.h \
    CObArray.cc CObArray.h CObject.h CParser.cc CParser.h CProteinObject.cc \
    CProteinObject.h CString.cc CString.h File.cc File.h FileExt.h Parse.cc \
    Parse.h SPoint3D.cc SPoint3D.h Utilities.cc Utilities.h const.cc const.h \
    logutils.cc logutils.h

featurize_SOURCES = featurize.cc \
    AssignAtomType.cc AssignAtomType.h CAtomArray.cc CAtomArray.h CBayes.cc \
    CBayes.h CBinaryFile.cc CBinaryFile.h CFile.cc CFile.h CGrid.cc CGrid.h \
    CHashTable.cc CHashTable.h CNeighborhood.h CObArray.cc CObArray.h \
    CObject.h CParser.cc CParser.h CPropertiesArray.cc CPropertiesArray.h \
    CProperty.cc CProperty.h CProtein.cc CProtein.h CProteinObject.cc \
    CProteinObject.h CPtrArray.cc CPtrArray.h CScoreBins.cc CScoreBins.h \
    CScoreFile.cc CScoreFile.h CStatisticsFile.cc CStatisticsFile.h \
    CString.cc CString.h EnvironmentList.cc EnvironmentList.h File.cc \
    File.h FileExt.h ForceFieldParameters.cc ForceFieldParameters.h \
    MathConst.h Message.cc Message.h Neighbor.cc Neighbor.h Parse.cc \
    Parse.h PointList.cc PointList.h PropertyConstants.h PropertyList.cc \
    PropertyList.h Random.cc Random.h RankSum.cc RankSum.h ResidueHelper.cc \
    ResidueHelper.h ResidueTemplate.cc ResidueTemplate.h SAtom.cc SAtom.h \
    SAtomProperties.cc SAtomProperties.h SBox.cc SBox.h SPoint3D.cc SPoint3D.h \
    SPoint3DList.cc SPoint3DList.h SPropertyScoreData.h SPropertyStatData.cc \
    SPropertyStatData.h SPropertyValues.cc SPropertyValues.h SSSBond.cc \
    SSSBond.h SSite.cc SSite.h Utilities.cc Utilities.h const.cc const.h \
    hashstring.hpp logutils.cc logutils.h stl_types.cc stl_types.h

scorefeatures_SOURCES = scorefeatures.cc \
    AssignAtomType.cc AssignAtomType.h CAllSitesFile.cc CAllSitesFile.h \
    CAtomArray.cc CAtomArray.h CBayes.cc CBayes.h CBinaryFile.cc \
    CBinaryFile.h CDouble.h CFile.cc CFile.h CGrid.cc CGrid.h CHashTable.cc \
    CHashTable.h CObArray.cc CObArray.h CObject.h CParser.cc CParser.h \
    CPropertiesArray.cc CPropertiesArray.h CProperty.cc CProperty.h \
    CProtein.cc CProtein.h CProteinObject.cc CProteinObject.h CPtrArray.cc \
    CPtrArray.h CScanningGrid.cc CScanningGrid.h CScanningGridCache.cc \
    CScanningGridCache.h CScoreBins.cc CScoreBins.h CScoreFile.cc CScoreFile.h \
    CStatisticsFile.cc CStatisticsFile.h CString.cc CString.h File.cc \
    File.h FileExt.h ForceFieldParameters.cc ForceFieldParameters.h \
    MathConst.h Message.cc Message.h Neighbor.cc Neighbor.h Parse.cc \
    Parse.h PointList.cc PointList.h PropertyConstants.h PropertyList.cc \
    PropertyList.h Random.cc Random.h RankSum.cc RankSum.h ResidueHelper.cc \
    ResidueHelper.h ResidueTemplate.cc ResidueTemplate.h SAtom.cc SAtom.h \
    SAtomProperties.cc SAtomProperties.h SBox.cc SBox.h SPoint3D.cc SPoint3D.h \
    SPoint3DList.cc SPoint3DList.h SPropertyScoreData.h SPropertyStatData.cc \
    SPropertyStatData.h SPropertyValues.cc SPropertyValues.h SSSBond.cc \
    SSSBond.h SSite.cc SSite.h Utilities.cc Utilities.h const.cc const.h \
    logutils.cc logutils.h stl_types.cc stl_types.h

scoreit_SOURCES = scoreit.cc \
    CAtomArray.cc CAtomArray.h CBayes.cc CBayes.h CBinaryFile.cc CBinaryFile.h \
    CFile.cc CFile.h CGrid.cc CGrid.h CHashTable.cc CHashTable.h CObArray.cc \
    CObArray.h CObject.h CParser.cc CParser.h CPropertiesArray.cc \
    CPropertiesArray.h CProperty.cc CProperty.h CProteinObject.cc \
    CProteinObject.h CPtrArray.cc CPtrArray.h CScoreBins.cc CScoreBins.h \
    CScoreFile.cc CScoreFile.h CStatisticsFile.cc CStatisticsFile.h CString.cc \
    CString.h EnvironmentList.cc EnvironmentList.h File.cc File.h FileExt.h \
    MathConst.h Message.cc Message.h Parse.cc Parse.h PropertyConstants.h \
    PropertyList.cc PropertyList.h Random.cc Random.h RankSum.cc RankSum.h \
    SAtom.cc SAtom.h SAtomProperties.cc SAtomProperties.h SBox.cc SBox.h \
    SPoint3D.cc SPoint3D.h SPropertyScoreData.h SPropertyStatData.cc \
    SPropertyStatData.h SPropertyValues.cc SPropertyValues.h Utilities.cc \
    Utilities.h const.cc const.h logutils.cc logutils.h stl_types.cc \
    stl_types.h

buildmodel_SOURCES = buildmodel.cc \
    CAtomArray.cc CAtomArray.h CBayes.cc CBayes.h CBinaryFile.cc CBinaryFile.h \
    CFile.cc CFile.h CGrid.cc CGrid.h CHashTable.cc CHashTable.h CObArray.cc \
    CObArray.h CObject.h CParser.cc CParser.h CPropertiesArray.cc \
    CPropertiesArray.h CProperty.cc CProperty.h CProteinObject.cc \
    CProteinObject.h CPtrArray.cc CPtrArray.h CScoreBins.cc CScoreBins.h \
    CScoreFile.cc CScoreFile.h CStatisticsFile.cc CStatisticsFile.h CString.cc \
    CString.h EnvironmentList.cc EnvironmentList.h File.cc File.h FileExt.h \
    MathConst.h Message.cc Message.h Parse.cc Parse.h PropertyConstants.h \
    PropertyList.cc PropertyList.h Random.cc Random.h RankSum.cc RankSum.h \
    SAtom.cc SAtom.h SAtomProperties.cc SAtomProperties.h SBox.cc SBox.h \
    SPoint3D.cc SPoint3D.h SPropertyScoreData.h SPropertyStatData.cc \
    SPropertyStatData.h SPropertyValues.cc SPropertyValues.h Utilities.cc \
    Utilities.h const.cc const.h logutils.cc logutils.h stl_types.cc \
    stl_types.h

findfile_SOURCES = findfile.cc \
    Utilities.cc Utilities.h logutils.cc logutils.h

featuretosvm_SOURCES = featuretosvm.cc

testNeighbor_SOURCES = testNeighbor.cc \
    CObject.h Neighbor.h Neighbor.cc SPoint3D.h SPoint3D.cc SPoint3DList.h \
    SPoint3DList.cc stl_types.h stl_types.cc

testResidueHelper_SOURCES = testResidueHelper.cc \
    AssignAtomType.h AssignAtomType.cc CAtomArray.h CAtomArray.cc CFile.h \
    CFile.cc CObArray.h CObArray.cc CObject.h CParser.h CParser.cc \
    CProtein.h CProtein.cc CProteinObject.h CProteinObject.cc CString.h \
    CString.cc File.h File.cc FileExt.h ForceFieldParameters.h \
    ForceFieldParameters.cc MathConst.h Message.h Message.cc Neighbor.h \
    Neighbor.cc Parse.h Parse.cc Random.h Random.cc ResidueHelper.h \
    ResidueHelper.cc ResidueTemplate.h ResidueTemplate.cc SAtom.h SAtom.cc \
    SBox.h SBox.cc SPoint3D.h SPoint3D.cc SPoint3DList.h SPoint3DList.cc \
    SSSBond.h SSSBond.cc SSite.h SSite.cc Utilities.h Utilities.cc const.h \
    const.cc stl_types.h stl_types.cc logutils.h logutils.cc

testResidueTemplate_SOURCES = testResidueTemplate.cc \
    ResidueTemplate.h ResidueTemplate.cc Utilities.h Utilities.cc \
    stl_types.h stl_types.cc logutils.h logutils.cc

testForceFieldParameters_SOURCES = testForceFieldParameters.cc \
    ForceFieldParameters.h ForceFieldParameters.cc Utilities.h Utilities.cc \
    stl_types.h stl_types.cc logutils.h logutils.cc

testAssignAtomType_SOURCES = testAssignAtomType.cc \
    AssignAtomType.h AssignAtomType.cc CAtomArray.h CAtomArray.cc CFile.h \
    CFile.cc CObArray.h CObArray.cc CObject.h CParser.h CParser.cc \
    CProtein.h CProtein.cc CProteinObject.h CProteinObject.cc CString.h \
    CString.cc File.h File.cc FileExt.h ForceFieldParameters.h \
    ForceFieldParameters.cc MathConst.h Message.h Message.cc Neighbor.h \
    Neighbor.cc Parse.h Parse.cc Random.h Random.cc ResidueHelper.h \
    ResidueHelper.cc ResidueTemplate.h ResidueTemplate.cc SAtom.h SAtom.cc \
    SBox.h SBox.cc SPoint3D.h SPoint3D.cc SPoint3DList.h SPoint3DList.cc \
    SSSBond.h SSSBond.cc SSite.h SSite.cc Utilities.h Utilities.cc const.h \
    const.cc stl_types.h stl_types.cc logutils.h logutils.cc

testSTLTypes_SOURCES = testSTLTypes.cc \
    stl_types.h stl_types.cc