from ctypes import *
from pyMMB import *

class ParameterReader_wrapper(Structure):
	_fields_ = [ 
			('mmbID', c_int),
			#('// ParameterReader(const ParameterReader &);', : unknown ctype),
			#('// ParameterReader & operator = (const ParameterReader &);', : unknown ctype),
			#('&)', //// ParameterReader & operator = (const ParameterReader: unknown ctype),
			#('_errorManager', //ErrorManager &: unknown ctype),
			#('// ParameterReader();', : unknown ctype),
			#('ParameterReader()', ////: unknown ctype),
			#('additionalCovalentBondVector', //vector<CovalentBondClass>: unknown ctype),
			#('includeIntraChainInterfaceVector', //vector<IncludeIntraChainInterface>: unknown ctype),
			#('basePairContainer', //BasePairContainer: unknown ctype),
			#('basePairPartners', //map<const ChainResidueIndex, BasePairPartner,twoIndexCmp>: unknown ctype),
			#('Repel.h:', //// variables previously declared and initialized in: unknown ctype),
			('addAllAtomSterics', c_bool),
			('addAllHeavyAtomSterics', c_bool),
			('addBackboneOxygenForces', c_bool),
			('addProteinBackboneSterics', c_bool),
			('addRNABackboneSterics', c_bool),
			('addSelectedAtoms', c_bool),
			('addTestSpring', c_bool),
			('applyC1pSprings', c_bool),
			('calcBaseBodyFramesAtEveryTimeStep', c_int),
			('calcEnergy', c_bool),
			('totalEnergy', c_double),
			('potentialEnergy', c_double),
			('kineticEnergy', c_double),
			('checkSatisfied', c_bool),
			#('constrainRigidSegments', ////bool: unknown ctype),
			('constraintTolerance', c_double),
			('guessCoordinates', c_bool),
			('cutoffRadius', c_double),
			('cutoffAngle', c_double),
			('densityAtomFraction', c_double),
			('densityFileName', c_char_p),
			('electroDensityFileName', c_char_p),
			('densityForceConstant', c_double),
			('electroDensityForceConstant', c_double),
			#('densityMapActivate', ////bool: unknown ctype),
			('excludedVolumeStiffness', c_double),
			#('firstResidueMobilizerType', ////String: unknown ctype),
			('firstStage', c_int),
			('fitDefaultTolerance', c_double),
			('globalAmberImproperTorsionScaleFactor', c_double),
			('globalBondBendScaleFactor', c_double),
			('globalBondStretchScaleFactor', c_double),
			('globalBondTorsionScaleFactor', c_double),
			('globalCoulombScaleFactor', c_double),
			('globalGbsaScaleFactor', c_double),
			('globalVdwScaleFactor', c_double),
			('hardSphereStiffnessMultiplier', c_double),
			('inQVectorFileName', c_char_p),
			('initialSeparation', c_double),
			('integratorAccuracy', c_double),
			('integratorStepSize', c_double),
			('integratorType', c_char_p),
			('kbBackboneTorsionGlobalScaleFactor', c_double),
			('lastStage', c_int),
			('leontisWesthofInFileName', c_char_p),
			('loadTinkerParameterFile', c_bool),
			('outQVectorFileName', c_char_p),
			('magnesiumIonChainId', c_char_p),
			('magnesiumIonRadius', c_double),
			('matchDefaultSkipTopLevelTransform', c_int),
			('matchHydrogenAtomLocations', c_bool),
			('matchPurineN1AtomLocations', c_bool),
			('matchProteinCarboxylOxygenLocations', c_bool),
			('matchExact', c_bool),
			('matchIdealized', c_bool),
			('matchOptimize', c_bool),
			('matchingMinimizerTolerance', c_double),
			('numReportingIntervals', c_int),
			('minimize', c_int),
			('monteCarloRun', c_int),
			('monteCarloTemperature', c_double),
			('monteCarloTemperatureIncrement', c_double),
			('nastGlobalBondTorsionScaleFactor', c_double),
			('noseHooverTime', c_double),
			('numMagnesiumIons', c_int),
			('outMonteCarloFileName', c_char_p),
			('outTrajectoryFileName', c_char_p),
			#('physicsWhereYouWantIt', ////bool: unknown ctype),
			('physicsRadius', c_float),
			('piecewiseRigidify', c_bool),
			('planarityThreshold', c_double),
			('potentialType', c_char_p),
			('prioritize', c_bool),
			('proteinCapping', c_bool),
			('excludedVolumeRadius', c_double),
			('readInQVector', c_int),
			('readPreviousFrameFile', c_bool),
			('readMagnesiumPositionsFromFile', c_int),
			('removeRigidBodyMomentum', c_bool),
			('removeMomentumPeriod', c_double),
			('reportingInterval', c_double),
			('restrainingForceConstant', c_double),
			('restrainingTorqueConstant', c_double),
			('rigidifyFormedHelices', c_bool),
			('rigidifyTermini', c_int),
			('satisfiedBasePairs', c_int),
			('unSatisfiedBasePairs', c_int),
			('scrubberPeriod', c_double),
			('safeParameters', c_bool),
			#('setChiBondAnti', ////int: unknown ctype),
			('setChiBondMobility', c_int),
			#('setDefaultMDParameters', ////int: unknown ctype),
			('setDefaultStructurePredictionParameters', c_int),
			('setDefaultThreadingParameters', c_int),
			('setForceAndStericScrubber', c_bool),
			('setForceScrubber', c_bool),
			('setHelicalStacking', c_bool),
			('setInitialVelocities', c_bool),
			('setLoopBondMobility', c_bool),
			('setOverallBondMobility', c_bool),
			('setRemoveBasePairsInRigidStretch', c_bool),
			('setRepulsiveForce', c_bool),
			('setTemperature', c_bool),
			('smallGroupInertiaMultiplier', c_double),
			('stackAllHelicalResidues', c_bool),
			('thermostatType', c_char_p),
			('tinkerParameterFileName', c_char_p),
			('twoTransformForceMultiplier', c_double),
			('useFixedStepSize', c_bool),
			('useMultithreadedComputation', c_bool),
			('useOpenMMAcceleration', c_bool),
			('vanderWallSphereRadius', c_double),
			('velocityRescalingInterval', c_double),
			('verbose', c_bool),
			('vmdOutput', c_int),
			('waterDropletMake', c_bool),
			('waterDropletRadius', c_double),
			('waterDropletX', c_double),
			('waterDropletY', c_double),
			('waterDropletZ', c_double),
			('waterInertiaMultiplier', c_double),
			('weldToGround', c_bool),
			('wkdpGlobalBondTorsionScaleFactor', c_double),
			('writeCoordinates', c_bool),
			('writeDoublePrecisionTrajectories', c_bool),
			('writeFrameFile', c_bool),
			('writeLastFrameFile', c_bool),
			('workingDirectory', c_char_p),
			('detectConvergence', c_bool),
			('converged', c_bool),
			('convergenceTimeout', c_int),
			('convergenceEpsilon', c_double),
			#('helixBondMobility', //BondMobility::Mobility: unknown ctype),
			#('loopBondMobility', //BondMobility::Mobility: unknown ctype),
			#('overallBondMobility', //BondMobility::Mobility: unknown ctype),
			#('chiBondMobility', //BondMobility::Mobility: unknown ctype),
			#('qVector', //Vector: unknown ctype),
			('lastFrameFileName', c_char_p),
			('previousFrameFileName', c_char_p),
			#('myLeontisWesthofClass', //LeontisWesthofClass: unknown ctype),
			('enforceParallelness', c_int),
			#('Repel.h', //// end of variables improted from: unknown ctype),
			('sequence', c_char_p),
			('proteinSequence', c_char_p),
			('coarseNucleicAcidSequence', c_char_p),
			#('numChains', ////int: unknown ctype),
			('numFirstResidues', c_int),
			('numResetBases', c_int),
			('numProteinFirstResidues', c_int),
			('numProteinChains', c_int),
			('numTemperatures', c_int),
			('numGlobalCoulombScaleFactors', c_int),
			('numGlobalVdwScaleFactors', c_int),
			#('numDutyCycles', ////int: unknown ctype),
			('temperature', c_double),
			('dutyCycle', c_double),
			('periodicallyUpdateParameters', c_int),
			('currentStage', c_int),
			('priority', c_int),
			#('biopolymerVector', ////vector<Biopolymer>: unknown ctype),
			#('chainId', ////vector<String>: unknown ctype),
			#('residueNumber', //vector<int>: unknown ctype),
			#('residueNumberTwo', //map<const ChainResidueIndex, int,twoIndexCmp>: unknown ctype),
			#('temperatureArray', ////vector<double>: unknown ctype),
			#('temperaturePriority', ////vector<int>: unknown ctype),
			#('dutyCycleArray', ////vector<double>: unknown ctype),
			#('dutyCyclePriority', ////vector<int>: unknown ctype),
			#('globalCoulombScaleFactorArray', ///*vector<double>: unknown ctype),
			#('globalCoulombScaleFactorPriority', //vector<int>: unknown ctype),
			#('globalVdwScaleFactorArray', //vector<double>: unknown ctype),
			#('globalVdwScaleFactorPriority', //vector<int>: unknown ctype),
			#('_leontisWesthofClass', //LeontisWesthofClass: unknown ctype),
			#('userVariables', //mutable map<const String,double>: unknown ctype),
			#('myDensityMap', //DensityMap: unknown ctype),
			#('myElectroDensityMap', //DensityMap: unknown ctype),
			#('mobilizerContainer', //MobilizerContainer: unknown ctype),
			#('physicsContainer', //PhysicsContainer: unknown ctype),
			#('constraintToGroundContainer', //ConstraintToGroundContainer: unknown ctype),
			#('displacementContainer', //DisplacementContainer: unknown ctype),
			#('atomSpringContainer', //AtomSpringContainer: unknown ctype),
			#('myBiopolymerClassContainer', //BiopolymerClassContainer: unknown ctype),
			#('moleculeClassContainer', //MoleculeClassContainer: unknown ctype),
			#('waterDropletContainer', //WaterDropletContainer: unknown ctype),
			#('proteinSequences', //map<const String,String>: unknown ctype),
			#('coarseNucleicAcidSequences', //map<const String,String>: unknown ctype),
			#('numRigidSegments', //map<const String, int>: unknown ctype),
			#('firstResidueNumbersIterator', //map<const String,int>::iterator: unknown ctype),
			#('// //void addRingClosingBond(const String chainID, ResidueID residueID1, String atomName1,String bondCenterName1,  ResidueID residueID2, String atomName2,String bondCenterName2);', : unknown ctype),
			#('bondCenterName2)', //// //void addRingClosingBond(const String chainID, ResidueID residueID1, String atomName1,String bondCenterName1, ResidueID residueID2, String atomName2,String: unknown ctype),
			#('// void addC1pSprings (LeontisWesthofClass myLeontisWesthofClass);', : unknown ctype),
			#('myLeontisWesthofClass)', //// void addC1pSprings (LeontisWesthofClass: unknown ctype),
			#('// void applyAtomSprings (SimbodyMatterSubsystem & matter, GeneralForceSubsystem & forces);', : unknown ctype),
			#('forces)', //// void applyAtomSprings (SimbodyMatterSubsystem & matter, GeneralForceSubsystem &: unknown ctype),
			#('// void configureDumm( DuMMForceFieldSubsystem & dumm);', : unknown ctype),
			#('dumm)', //// void configureDumm( DuMMForceFieldSubsystem &: unknown ctype),
			#('// static double myAtoF(map<const String,double> myUserVariables,const char* value );', : unknown ctype),
			#(')', //// //bool chainIsBiopolymer(String myChainId: unknown ctype),
			#('// static bool aToBool( const String& name, const char* value );', : unknown ctype),
			#('// static bool compareUpper( const String& param, const char* symbol );', : unknown ctype),
			#('baseOperationVector', //vector<BasePair>: unknown ctype),
			#('contactContainer', //ContactContainer: unknown ctype),
			#('densityContainer', //DensityContainer: unknown ctype),
			#('electroDensityContainer', //DensityContainer: unknown ctype),
			#('singleBondMobilityVector', //vector<SingleBondMobility>: unknown ctype),
			#('basePairPartnerVector', //vector<BasePairPartner>: unknown ctype),
			#('includeAllNonBondAtomsInResidueVector', ////vector<IncludeAllNonBondAtomsInResidue>: unknown ctype),
			#('includeAllResiduesWithinVector', //vector<AllResiduesWithin>: unknown ctype),
			#('includeNonBondAtomInBiopolymerVector', //vector<IncludeNonBondAtomInBiopolymerStruct>: unknown ctype),
			#('waterDropletAboutResidueVector', //vector <WaterDropletAboutResidueStruct>: unknown ctype),
			#('mobilizerDomainsInterfaceVector', //vector<MobilizerDomainsInterface>: unknown ctype),
			#('// void removeBasePairsInRigidStretch ();', : unknown ctype),
			#('()', //// // void initializeDefaults: unknown ctype),
			#('// void printAllSettings (   ostream  & myOstream = std::cout, String remarkString = "") ;', : unknown ctype),
			#('"")', //// void printAllSettings ( ostream & myOstream = std::cout, String remarkString =: unknown ctype),
			#('// void removeNonPriorityBasePairs (int priorityLevel);', : unknown ctype),
			#('priorityLevel)', //// void removeNonPriorityBasePairs (int: unknown ctype),
			#('// //int getFirstResidueNumbers(const String myChainId) const ;', : unknown ctype),
			#('const', //// // int getNumBasePairs(): unknown ctype),
			#('// // int getProteinFirstResidueNumbers(const String myProteinChainId) const ;', : unknown ctype),
			#('// //int getBasePriority(int baseResidueNumber,String baseChain, String basePairingEdge) const ;', : unknown ctype),
			#('// // int getNumBasePairs() const;', : unknown ctype),
			#('// void updateBasePair(int index,', : unknown ctype),
			#('// String ch1, int res1, String edge1,', : unknown ctype),
			#('// String ch2, int res2, String edge2,', : unknown ctype),
			#('// String orient);', : unknown ctype),
			#('// void updateMobilizerStretch(int index,', : unknown ctype),
			#('// String chainId,', : unknown ctype),
			#('// int startRes,', : unknown ctype),
			#('// int endRes,', : unknown ctype),
			#('// String bondMobility);', : unknown ctype),
			#('// void addAllResiduesWithin(String chainID, int resID, double radius);', : unknown ctype),
			#('radius)', //// void updateAllResiduesWithin(int index, String chainID, int resID, double: unknown ctype),
			#('// void updateAllResiduesWithin(int index, String chainID, int resID, double radius);', : unknown ctype),
			#('// void deleteAllResiduesWithin(int index);', : unknown ctype),
			#('index)', //// void deleteIncludeAllNonBondAtomsInResidue(int: unknown ctype),
			#('// void updateIncludeAllNonBondAtomsInResidue(int index, String chainID, int resID);', : unknown ctype),
			#('resID)', //// void updateIncludeAllNonBondAtomsInResidue(int index, String chainID, int: unknown ctype),
			#('// void deleteIncludeAllNonBondAtomsInResidue(int index);', : unknown ctype),
			#('// //int calcHighestPriority();', : unknown ctype),
			#('calcHighestPriority()', //// //int: unknown ctype),
			#('// //int calcLowestBondingResidue(const String myChainId) ;', : unknown ctype),
			#('myChainId)', //// //bool chainIsMonoAtoms(String: unknown ctype),
			#('// //int calcHighestBondingResidue(const String myChainId);', : unknown ctype),
			#('// void setLeontisWesthofBondRowIndex();', : unknown ctype),
			#('setLeontisWesthofBondRowIndex()', //// void: unknown ctype),
			#('// void parameterStringInterpreter(const String & paramstr);', : unknown ctype),
			#('paramstr)', //// void parameterStringInterpreter(const String &: unknown ctype),
			#('// void parameterStringInterpreter(const ParameterStringClass & parameterStringClass,', : unknown ctype),
			#('// const int readStage = 0,', : unknown ctype),
			#('// const bool readAtOneStageOnly = false,', : unknown ctype),
			#('// const bool readOnlyUntilStage = false,', : unknown ctype),
			#('// const bool readExcept = false);', : unknown ctype),
			#('// void initializeFromFileOnly(const char * parameterFileName = "./commands.dat" ) ;', : unknown ctype),
			#('// void setFirstAndLastStage(const char * parameterFileName = "./commands.dat" ) ;', : unknown ctype),
			#('// void loadSequencesFromPdb(const char * pdbFileName);', : unknown ctype),
			#('pdbFileName)', //// void loadSequencesFromPdb(const char *: unknown ctype),
			#('// //void printRigidSegments();', : unknown ctype),
			#('printRigidSegments()', //// //void: unknown ctype),
			#('// // void printBasePairs();', : unknown ctype),
			#('printBasePairs()', //// // void: unknown ctype),
			#('// // void printBaseAssignments();', : unknown ctype),
			#('printBaseAssignments()', //// // void: unknown ctype),
			#('// void postInitialize();', : unknown ctype),
			#('postInitialize()', //// void: unknown ctype),
			#('// void clearContainers();', : unknown ctype),
			#('clearContainers()', //// void: unknown ctype),
			#('// void clearBiopolymers();', : unknown ctype),
			#('clearBiopolymers()', //// void: unknown ctype),
			#('// void clearForces();', : unknown ctype),
			#('clearForces()', //// void: unknown ctype),
			#('// void clearConstraints();', : unknown ctype),
			#('clearConstraints()', //// void: unknown ctype),
			#('// // void initializeDefaults ();', : unknown ctype),
			#('// void initializeDefaults(const char * leontisWesthofInFileName = "./parameters.csv");', : unknown ctype),
			#('"./parameters.csv")', //// void initializeDefaults(const char * leontisWesthofInFileName =: unknown ctype),
			#('// void initialize(const char * parameterFileName = "./commands.dat" );', : unknown ctype),
			#('// //bool chainIsBiopolymer(String myChainId );', : unknown ctype),
			#('// //bool chainIsMonoAtoms(String myChainId);', : unknown ctype),
			#('// //int getChainIndex(String myChainId , vector<Biopolymer> & tempChain);', : unknown ctype),
			#('tempChain)', //// //int getChainIndex(String myChainId , vector<Biopolymer> &: unknown ctype),
			#('myMonoAtomsContainer', //MonoAtomsContainer: unknown ctype),
			#('// //variables for internal use only:', : unknown ctype),
			#('// int r;', : unknown ctype),
			#('// int ti;', : unknown ctype),
			#('// int gcsfi;', : unknown ctype),
			#('// int gvsfi;', : unknown ctype),
			#('// int d;', : unknown ctype),
			#('// char * s;', : unknown ctype),
			#('// //int numChains ;', : unknown ctype),
			#('// //int numProteinChains ;', : unknown ctype),
			#('// //int prioritize ;', : unknown ctype),
			#('// //temperature = 300;', : unknown ctype),
			#('// //outQVectorFileName;', : unknown ctype),
			#('// //firstStage = 1;', : unknown ctype),
			#('// //lastStage = 0;// calcHighestPriority();', : unknown ctype),
			#('1', ////dutyCycle =: unknown ctype),
			#('0', ////priority =: unknown ctype)
			]

	def __init__(self):
		Structure.__init__(self)
		# print "Init"
		call('updateParameterReader_wrapper', byref(self))
		Structure.__setattr__(self,"nonDefaultParameters",set())

	def __setattr__(self, name, value):
		# print __file__, "Set", name
		#cmd(name + " " + str(value))
		# We synchronize the wrapper with MMB to avoid changing other attributes
		call('updateParameterReader_wrapper', byref(self))
		Structure.__setattr__(self,name, value)
		Structure.__getattribute__(self, "nonDefaultParameters").update(set([name]))
		call('updateParameterReader', byref(self))

	def __getattribute__(self, name):
		# print __file__,  "Get", name
		call('updateParameterReader_wrapper', byref(self))
		return Structure.__getattribute__(self, name)
	
ParameterReader_ptr = POINTER(ParameterReader_wrapper)
MMB.updateParameterReader_wrapper.argtypes = [c_void_p, c_char_p]
MMB.updateParameterReader.argtypes = [c_void_p, c_char_p]