/* ---------------------------------------------------------------------------- * This file was automatically generated by SWIG (http://www.swig.org). * Version 1.3.31 * * Do not make changes to this file unless you know what you are doing--modify * the SWIG interface file instead. * ----------------------------------------------------------------------------- */ public class OBResidueAtomIter { private long swigCPtr; protected boolean swigCMemOwn; protected OBResidueAtomIter(long cPtr, boolean cMemoryOwn) { swigCMemOwn = cMemoryOwn; swigCPtr = cPtr; } protected static long getCPtr(OBResidueAtomIter obj) { return (obj == null) ? 0 : obj.swigCPtr; } protected void finalize() { delete(); } public synchronized void delete() { if(swigCPtr != 0 && swigCMemOwn) { swigCMemOwn = false; openbabelJNI.delete_OBResidueAtomIter(swigCPtr); } swigCPtr = 0; } public OBResidueAtomIter() { this(openbabelJNI.new_OBResidueAtomIter__SWIG_0(), true); } public OBResidueAtomIter(OBResidue res) { this(openbabelJNI.new_OBResidueAtomIter__SWIG_1(OBResidue.getCPtr(res), res), true); } public OBResidueAtomIter(OBResidueAtomIter ri) { this(openbabelJNI.new_OBResidueAtomIter__SWIG_2(OBResidueAtomIter.getCPtr(ri), ri), true); } public OBAtom __deref__() { long cPtr = openbabelJNI.OBResidueAtomIter___deref__(swigCPtr, this); return (cPtr == 0) ? null : new OBAtom(cPtr, false); } public OBAtom __ref__() { return new OBAtom(openbabelJNI.OBResidueAtomIter___ref__(swigCPtr, this), false); } public void setVisit(boolean value) { openbabelJNI.OBResidueAtomIter_Visit_set(swigCPtr, this, value); } public boolean getVisit() { return openbabelJNI.OBResidueAtomIter_Visit_get(swigCPtr, this); } public boolean Clear() { return openbabelJNI.OBResidueAtomIter_Clear(swigCPtr, this); } public void SetIdx(int idx) { openbabelJNI.OBResidueAtomIter_SetIdx(swigCPtr, this, idx); } public void SetHyb(int hyb) { openbabelJNI.OBResidueAtomIter_SetHyb(swigCPtr, this, hyb); } public void SetAtomicNum(int atomicnum) { openbabelJNI.OBResidueAtomIter_SetAtomicNum(swigCPtr, this, atomicnum); } public void SetIsotope(long iso) { openbabelJNI.OBResidueAtomIter_SetIsotope(swigCPtr, this, iso); } public void SetImplicitValence(int val) { openbabelJNI.OBResidueAtomIter_SetImplicitValence(swigCPtr, this, val); } public void IncrementImplicitValence() { openbabelJNI.OBResidueAtomIter_IncrementImplicitValence(swigCPtr, this); } public void DecrementImplicitValence() { openbabelJNI.OBResidueAtomIter_DecrementImplicitValence(swigCPtr, this); } public void SetFormalCharge(int fcharge) { openbabelJNI.OBResidueAtomIter_SetFormalCharge(swigCPtr, this, fcharge); } public void SetSpinMultiplicity(short spin) { openbabelJNI.OBResidueAtomIter_SetSpinMultiplicity(swigCPtr, this, spin); } public void SetType(String type) { openbabelJNI.OBResidueAtomIter_SetType__SWIG_0(swigCPtr, this, type); } public void SetType(SWIGTYPE_p_std__string type) { openbabelJNI.OBResidueAtomIter_SetType__SWIG_1(swigCPtr, this, SWIGTYPE_p_std__string.getCPtr(type)); } public void SetPartialCharge(double pcharge) { openbabelJNI.OBResidueAtomIter_SetPartialCharge(swigCPtr, this, pcharge); } public void SetVector(vector3 v) { openbabelJNI.OBResidueAtomIter_SetVector__SWIG_0(swigCPtr, this, vector3.getCPtr(v), v); } public void SetVector(double x, double y, double z) { openbabelJNI.OBResidueAtomIter_SetVector__SWIG_1(swigCPtr, this, x, y, z); } public void SetVector() { openbabelJNI.OBResidueAtomIter_SetVector__SWIG_2(swigCPtr, this); } public void SetCoordPtr(SWIGTYPE_p_p_double c) { openbabelJNI.OBResidueAtomIter_SetCoordPtr(swigCPtr, this, SWIGTYPE_p_p_double.getCPtr(c)); } public void SetResidue(OBResidue res) { openbabelJNI.OBResidueAtomIter_SetResidue(swigCPtr, this, OBResidue.getCPtr(res), res); } public void SetParent(OBMol ptr) { openbabelJNI.OBResidueAtomIter_SetParent(swigCPtr, this, OBMol.getCPtr(ptr), ptr); } public void SetAromatic() { openbabelJNI.OBResidueAtomIter_SetAromatic(swigCPtr, this); } public void UnsetAromatic() { openbabelJNI.OBResidueAtomIter_UnsetAromatic(swigCPtr, this); } public void SetClockwiseStereo() { openbabelJNI.OBResidueAtomIter_SetClockwiseStereo(swigCPtr, this); } public void SetAntiClockwiseStereo() { openbabelJNI.OBResidueAtomIter_SetAntiClockwiseStereo(swigCPtr, this); } public void SetPositiveStereo() { openbabelJNI.OBResidueAtomIter_SetPositiveStereo(swigCPtr, this); } public void SetNegativeStereo() { openbabelJNI.OBResidueAtomIter_SetNegativeStereo(swigCPtr, this); } public void UnsetStereo() { openbabelJNI.OBResidueAtomIter_UnsetStereo(swigCPtr, this); } public void SetInRing() { openbabelJNI.OBResidueAtomIter_SetInRing(swigCPtr, this); } public void SetChiral() { openbabelJNI.OBResidueAtomIter_SetChiral(swigCPtr, this); } public void ClearCoordPtr() { openbabelJNI.OBResidueAtomIter_ClearCoordPtr(swigCPtr, this); } public int GetFormalCharge() { return openbabelJNI.OBResidueAtomIter_GetFormalCharge(swigCPtr, this); } public long GetAtomicNum() { return openbabelJNI.OBResidueAtomIter_GetAtomicNum(swigCPtr, this); } public int GetIsotope() { return openbabelJNI.OBResidueAtomIter_GetIsotope(swigCPtr, this); } public int GetSpinMultiplicity() { return openbabelJNI.OBResidueAtomIter_GetSpinMultiplicity(swigCPtr, this); } public double GetAtomicMass() { return openbabelJNI.OBResidueAtomIter_GetAtomicMass(swigCPtr, this); } public double GetExactMass() { return openbabelJNI.OBResidueAtomIter_GetExactMass(swigCPtr, this); } public long GetIdx() { return openbabelJNI.OBResidueAtomIter_GetIdx(swigCPtr, this); } public long GetCoordinateIdx() { return openbabelJNI.OBResidueAtomIter_GetCoordinateIdx(swigCPtr, this); } public long GetCIdx() { return openbabelJNI.OBResidueAtomIter_GetCIdx(swigCPtr, this); } public long GetValence() { return openbabelJNI.OBResidueAtomIter_GetValence(swigCPtr, this); } public long GetHyb() { return openbabelJNI.OBResidueAtomIter_GetHyb(swigCPtr, this); } public long GetImplicitValence() { return openbabelJNI.OBResidueAtomIter_GetImplicitValence(swigCPtr, this); } public long GetHvyValence() { return openbabelJNI.OBResidueAtomIter_GetHvyValence(swigCPtr, this); } public long GetHeteroValence() { return openbabelJNI.OBResidueAtomIter_GetHeteroValence(swigCPtr, this); } public String GetType() { return openbabelJNI.OBResidueAtomIter_GetType(swigCPtr, this); } public double GetX() { return openbabelJNI.OBResidueAtomIter_GetX(swigCPtr, this); } public double GetY() { return openbabelJNI.OBResidueAtomIter_GetY(swigCPtr, this); } public double GetZ() { return openbabelJNI.OBResidueAtomIter_GetZ(swigCPtr, this); } public double x() { return openbabelJNI.OBResidueAtomIter_x(swigCPtr, this); } public double y() { return openbabelJNI.OBResidueAtomIter_y(swigCPtr, this); } public double z() { return openbabelJNI.OBResidueAtomIter_z(swigCPtr, this); } public SWIGTYPE_p_double GetCoordinate() { long cPtr = openbabelJNI.OBResidueAtomIter_GetCoordinate(swigCPtr, this); return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false); } public vector3 GetVector() { return new vector3(openbabelJNI.OBResidueAtomIter_GetVector__SWIG_0(swigCPtr, this), false); } public double GetPartialCharge() { return openbabelJNI.OBResidueAtomIter_GetPartialCharge(swigCPtr, this); } public OBResidue GetResidue() { long cPtr = openbabelJNI.OBResidueAtomIter_GetResidue(swigCPtr, this); return (cPtr == 0) ? null : new OBResidue(cPtr, false); } public OBMol GetParent() { long cPtr = openbabelJNI.OBResidueAtomIter_GetParent(swigCPtr, this); return (cPtr == 0) ? null : new OBMol(cPtr, false); } public boolean GetNewBondVector(vector3 v, double length) { return openbabelJNI.OBResidueAtomIter_GetNewBondVector(swigCPtr, this, vector3.getCPtr(v), v, length); } public OBBond GetBond(OBAtom arg0) { long cPtr = openbabelJNI.OBResidueAtomIter_GetBond(swigCPtr, this, OBAtom.getCPtr(arg0), arg0); return (cPtr == 0) ? null : new OBBond(cPtr, false); } public OBAtom GetNextAtom() { long cPtr = openbabelJNI.OBResidueAtomIter_GetNextAtom(swigCPtr, this); return (cPtr == 0) ? null : new OBAtom(cPtr, false); } public SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator BeginBonds() { return new SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator(openbabelJNI.OBResidueAtomIter_BeginBonds(swigCPtr, this), true); } public SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator EndBonds() { return new SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator(openbabelJNI.OBResidueAtomIter_EndBonds(swigCPtr, this), true); } public OBBond BeginBond(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i) { long cPtr = openbabelJNI.OBResidueAtomIter_BeginBond(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i)); return (cPtr == 0) ? null : new OBBond(cPtr, false); } public OBBond NextBond(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i) { long cPtr = openbabelJNI.OBResidueAtomIter_NextBond(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i)); return (cPtr == 0) ? null : new OBBond(cPtr, false); } public OBAtom BeginNbrAtom(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i) { long cPtr = openbabelJNI.OBResidueAtomIter_BeginNbrAtom(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i)); return (cPtr == 0) ? null : new OBAtom(cPtr, false); } public OBAtom NextNbrAtom(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i) { long cPtr = openbabelJNI.OBResidueAtomIter_NextNbrAtom(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i)); return (cPtr == 0) ? null : new OBAtom(cPtr, false); } public double GetDistance(int index) { return openbabelJNI.OBResidueAtomIter_GetDistance__SWIG_0(swigCPtr, this, index); } public double GetDistance(OBAtom arg0) { return openbabelJNI.OBResidueAtomIter_GetDistance__SWIG_1(swigCPtr, this, OBAtom.getCPtr(arg0), arg0); } public double GetAngle(int b, int c) { return openbabelJNI.OBResidueAtomIter_GetAngle__SWIG_0(swigCPtr, this, b, c); } public double GetAngle(OBAtom b, OBAtom c) { return openbabelJNI.OBResidueAtomIter_GetAngle__SWIG_1(swigCPtr, this, OBAtom.getCPtr(b), b, OBAtom.getCPtr(c), c); } public void NewResidue() { openbabelJNI.OBResidueAtomIter_NewResidue(swigCPtr, this); } public void AddResidue(OBResidue res) { openbabelJNI.OBResidueAtomIter_AddResidue(swigCPtr, this, OBResidue.getCPtr(res), res); } public void DeleteResidue() { openbabelJNI.OBResidueAtomIter_DeleteResidue(swigCPtr, this); } public void AddBond(OBBond bond) { openbabelJNI.OBResidueAtomIter_AddBond(swigCPtr, this, OBBond.getCPtr(bond), bond); } public void InsertBond(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i, OBBond bond) { openbabelJNI.OBResidueAtomIter_InsertBond(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i), OBBond.getCPtr(bond), bond); } public boolean DeleteBond(OBBond bond) { return openbabelJNI.OBResidueAtomIter_DeleteBond(swigCPtr, this, OBBond.getCPtr(bond), bond); } public void ClearBond() { openbabelJNI.OBResidueAtomIter_ClearBond(swigCPtr, this); } public boolean HtoMethyl() { return openbabelJNI.OBResidueAtomIter_HtoMethyl(swigCPtr, this); } public boolean SetHybAndGeom(int arg0) { return openbabelJNI.OBResidueAtomIter_SetHybAndGeom(swigCPtr, this, arg0); } public void ForceNoH() { openbabelJNI.OBResidueAtomIter_ForceNoH(swigCPtr, this); } public boolean HasNoHForced() { return openbabelJNI.OBResidueAtomIter_HasNoHForced(swigCPtr, this); } public long CountFreeOxygens() { return openbabelJNI.OBResidueAtomIter_CountFreeOxygens(swigCPtr, this); } public long ImplicitHydrogenCount() { return openbabelJNI.OBResidueAtomIter_ImplicitHydrogenCount(swigCPtr, this); } public long ExplicitHydrogenCount(boolean ExcludeIsotopes) { return openbabelJNI.OBResidueAtomIter_ExplicitHydrogenCount__SWIG_0(swigCPtr, this, ExcludeIsotopes); } public long ExplicitHydrogenCount() { return openbabelJNI.OBResidueAtomIter_ExplicitHydrogenCount__SWIG_1(swigCPtr, this); } public long MemberOfRingCount() { return openbabelJNI.OBResidueAtomIter_MemberOfRingCount(swigCPtr, this); } public long MemberOfRingSize() { return openbabelJNI.OBResidueAtomIter_MemberOfRingSize(swigCPtr, this); } public long CountRingBonds() { return openbabelJNI.OBResidueAtomIter_CountRingBonds(swigCPtr, this); } public double SmallestBondAngle() { return openbabelJNI.OBResidueAtomIter_SmallestBondAngle(swigCPtr, this); } public double AverageBondAngle() { return openbabelJNI.OBResidueAtomIter_AverageBondAngle(swigCPtr, this); } public long BOSum() { return openbabelJNI.OBResidueAtomIter_BOSum(swigCPtr, this); } public long KBOSum() { return openbabelJNI.OBResidueAtomIter_KBOSum(swigCPtr, this); } public boolean HasResidue() { return openbabelJNI.OBResidueAtomIter_HasResidue(swigCPtr, this); } public boolean IsHydrogen() { return openbabelJNI.OBResidueAtomIter_IsHydrogen(swigCPtr, this); } public boolean IsCarbon() { return openbabelJNI.OBResidueAtomIter_IsCarbon(swigCPtr, this); } public boolean IsNitrogen() { return openbabelJNI.OBResidueAtomIter_IsNitrogen(swigCPtr, this); } public boolean IsOxygen() { return openbabelJNI.OBResidueAtomIter_IsOxygen(swigCPtr, this); } public boolean IsSulfur() { return openbabelJNI.OBResidueAtomIter_IsSulfur(swigCPtr, this); } public boolean IsPhosphorus() { return openbabelJNI.OBResidueAtomIter_IsPhosphorus(swigCPtr, this); } public boolean IsAromatic() { return openbabelJNI.OBResidueAtomIter_IsAromatic(swigCPtr, this); } public boolean IsInRing() { return openbabelJNI.OBResidueAtomIter_IsInRing(swigCPtr, this); } public boolean IsInRingSize(int arg0) { return openbabelJNI.OBResidueAtomIter_IsInRingSize(swigCPtr, this, arg0); } public boolean IsHeteroatom() { return openbabelJNI.OBResidueAtomIter_IsHeteroatom(swigCPtr, this); } public boolean IsNotCorH() { return openbabelJNI.OBResidueAtomIter_IsNotCorH(swigCPtr, this); } public boolean IsConnected(OBAtom arg0) { return openbabelJNI.OBResidueAtomIter_IsConnected(swigCPtr, this, OBAtom.getCPtr(arg0), arg0); } public boolean IsOneThree(OBAtom arg0) { return openbabelJNI.OBResidueAtomIter_IsOneThree(swigCPtr, this, OBAtom.getCPtr(arg0), arg0); } public boolean IsOneFour(OBAtom arg0) { return openbabelJNI.OBResidueAtomIter_IsOneFour(swigCPtr, this, OBAtom.getCPtr(arg0), arg0); } public boolean IsCarboxylOxygen() { return openbabelJNI.OBResidueAtomIter_IsCarboxylOxygen(swigCPtr, this); } public boolean IsPhosphateOxygen() { return openbabelJNI.OBResidueAtomIter_IsPhosphateOxygen(swigCPtr, this); } public boolean IsSulfateOxygen() { return openbabelJNI.OBResidueAtomIter_IsSulfateOxygen(swigCPtr, this); } public boolean IsNitroOxygen() { return openbabelJNI.OBResidueAtomIter_IsNitroOxygen(swigCPtr, this); } public boolean IsAmideNitrogen() { return openbabelJNI.OBResidueAtomIter_IsAmideNitrogen(swigCPtr, this); } public boolean IsPolarHydrogen() { return openbabelJNI.OBResidueAtomIter_IsPolarHydrogen(swigCPtr, this); } public boolean IsNonPolarHydrogen() { return openbabelJNI.OBResidueAtomIter_IsNonPolarHydrogen(swigCPtr, this); } public boolean IsAromaticNOxide() { return openbabelJNI.OBResidueAtomIter_IsAromaticNOxide(swigCPtr, this); } public boolean IsChiral() { return openbabelJNI.OBResidueAtomIter_IsChiral(swigCPtr, this); } public boolean IsAxial() { return openbabelJNI.OBResidueAtomIter_IsAxial(swigCPtr, this); } public boolean IsClockwise() { return openbabelJNI.OBResidueAtomIter_IsClockwise(swigCPtr, this); } public boolean IsAntiClockwise() { return openbabelJNI.OBResidueAtomIter_IsAntiClockwise(swigCPtr, this); } public boolean IsPositiveStereo() { return openbabelJNI.OBResidueAtomIter_IsPositiveStereo(swigCPtr, this); } public boolean IsNegativeStereo() { return openbabelJNI.OBResidueAtomIter_IsNegativeStereo(swigCPtr, this); } public boolean HasChiralitySpecified() { return openbabelJNI.OBResidueAtomIter_HasChiralitySpecified(swigCPtr, this); } public boolean HasChiralVolume() { return openbabelJNI.OBResidueAtomIter_HasChiralVolume(swigCPtr, this); } public boolean IsHbondAcceptor() { return openbabelJNI.OBResidueAtomIter_IsHbondAcceptor(swigCPtr, this); } public boolean IsHbondDonor() { return openbabelJNI.OBResidueAtomIter_IsHbondDonor(swigCPtr, this); } public boolean IsHbondDonorH() { return openbabelJNI.OBResidueAtomIter_IsHbondDonorH(swigCPtr, this); } public boolean HasAlphaBetaUnsat(boolean includePandS) { return openbabelJNI.OBResidueAtomIter_HasAlphaBetaUnsat__SWIG_0(swigCPtr, this, includePandS); } public boolean HasAlphaBetaUnsat() { return openbabelJNI.OBResidueAtomIter_HasAlphaBetaUnsat__SWIG_1(swigCPtr, this); } public boolean HasBondOfOrder(long bo) { return openbabelJNI.OBResidueAtomIter_HasBondOfOrder(swigCPtr, this, bo); } public int CountBondsOfOrder(long bo) { return openbabelJNI.OBResidueAtomIter_CountBondsOfOrder(swigCPtr, this, bo); } public boolean HasNonSingleBond() { return openbabelJNI.OBResidueAtomIter_HasNonSingleBond(swigCPtr, this); } public boolean HasSingleBond() { return openbabelJNI.OBResidueAtomIter_HasSingleBond(swigCPtr, this); } public boolean HasDoubleBond() { return openbabelJNI.OBResidueAtomIter_HasDoubleBond(swigCPtr, this); } public boolean HasAromaticBond() { return openbabelJNI.OBResidueAtomIter_HasAromaticBond(swigCPtr, this); } public boolean MatchesSMARTS(String arg0) { return openbabelJNI.OBResidueAtomIter_MatchesSMARTS(swigCPtr, this, arg0); } public OBBase DoTransformations(SWIGTYPE_p_std__mapTstd__string_std__string_t arg0) { long cPtr = openbabelJNI.OBResidueAtomIter_DoTransformations(swigCPtr, this, SWIGTYPE_p_std__mapTstd__string_std__string_t.getCPtr(arg0)); return (cPtr == 0) ? null : new OBBase(cPtr, false); } public String ClassDescription() { return openbabelJNI.OBResidueAtomIter_ClassDescription(swigCPtr, this); } public boolean HasData(long type) { return openbabelJNI.OBResidueAtomIter_HasData__SWIG_2(swigCPtr, this, type); } public void DeleteData(long type) { openbabelJNI.OBResidueAtomIter_DeleteData__SWIG_0(swigCPtr, this, type); } public void DeleteData(OBGenericData arg0) { openbabelJNI.OBResidueAtomIter_DeleteData__SWIG_1(swigCPtr, this, OBGenericData.getCPtr(arg0), arg0); } public void DeleteData(vectorData arg0) { openbabelJNI.OBResidueAtomIter_DeleteData__SWIG_2(swigCPtr, this, vectorData.getCPtr(arg0), arg0); } public boolean DeleteData(String s) { return openbabelJNI.OBResidueAtomIter_DeleteData__SWIG_3(swigCPtr, this, s); } public void SetData(OBGenericData d) { openbabelJNI.OBResidueAtomIter_SetData(swigCPtr, this, OBGenericData.getCPtr(d), d); } public long DataSize() { return openbabelJNI.OBResidueAtomIter_DataSize(swigCPtr, this); } public OBGenericData GetData(long type) { long cPtr = openbabelJNI.OBResidueAtomIter_GetData__SWIG_0(swigCPtr, this, type); return (cPtr == 0) ? null : new OBGenericData(cPtr, false); } public vectorData GetData() { return new vectorData(openbabelJNI.OBResidueAtomIter_GetData__SWIG_3(swigCPtr, this), false); } public vectorData GetData(DataOrigin source) { return new vectorData(openbabelJNI.OBResidueAtomIter_GetData__SWIG_4(swigCPtr, this, source.swigValue()), true); } public SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator BeginData() { return new SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator(openbabelJNI.OBResidueAtomIter_BeginData(swigCPtr, this), true); } public SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator EndData() { return new SWIGTYPE_p_std__vectorTOpenBabel__OBGenericData_p_t__iterator(openbabelJNI.OBResidueAtomIter_EndData(swigCPtr, this), true); } }