mirror of
https://github.com/openbabel/openbabel.git
synced 2025-02-25 18:55:23 -06:00
785 lines
26 KiB
Java
785 lines
26 KiB
Java
/* ----------------------------------------------------------------------------
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* This file was automatically generated by SWIG (http://www.swig.org).
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* Version 1.3.31
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*
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* Do not make changes to this file unless you know what you are doing--modify
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* the SWIG interface file instead.
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* ----------------------------------------------------------------------------- */
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public class OBMol extends OBBase {
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private long swigCPtr;
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protected OBMol(long cPtr, boolean cMemoryOwn) {
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super(openbabelJNI.SWIGOBMolUpcast(cPtr), cMemoryOwn);
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swigCPtr = cPtr;
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}
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protected static long getCPtr(OBMol obj) {
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return (obj == null) ? 0 : obj.swigCPtr;
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}
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protected void finalize() {
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delete();
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}
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public synchronized void delete() {
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if(swigCPtr != 0 && swigCMemOwn) {
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swigCMemOwn = false;
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openbabelJNI.delete_OBMol(swigCPtr);
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}
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swigCPtr = 0;
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super.delete();
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}
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public OBMol() {
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this(openbabelJNI.new_OBMol__SWIG_0(), true);
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}
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public OBMol(OBMol arg0) {
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this(openbabelJNI.new_OBMol__SWIG_1(OBMol.getCPtr(arg0), arg0), true);
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}
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public void ReserveAtoms(int natoms) {
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openbabelJNI.OBMol_ReserveAtoms(swigCPtr, this, natoms);
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}
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public OBAtom CreateAtom() {
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long cPtr = openbabelJNI.OBMol_CreateAtom(swigCPtr, this);
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return (cPtr == 0) ? null : new OBAtom(cPtr, false);
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}
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public OBBond CreateBond() {
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long cPtr = openbabelJNI.OBMol_CreateBond(swigCPtr, this);
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return (cPtr == 0) ? null : new OBBond(cPtr, false);
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}
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public OBResidue CreateResidue() {
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long cPtr = openbabelJNI.OBMol_CreateResidue(swigCPtr, this);
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return (cPtr == 0) ? null : new OBResidue(cPtr, false);
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}
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public void DestroyAtom(OBAtom arg0) {
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openbabelJNI.OBMol_DestroyAtom(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
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}
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public void DestroyBond(OBBond arg0) {
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openbabelJNI.OBMol_DestroyBond(swigCPtr, this, OBBond.getCPtr(arg0), arg0);
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}
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public void DestroyResidue(OBResidue arg0) {
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openbabelJNI.OBMol_DestroyResidue(swigCPtr, this, OBResidue.getCPtr(arg0), arg0);
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}
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public boolean AddAtom(OBAtom arg0) {
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return openbabelJNI.OBMol_AddAtom(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
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}
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public boolean InsertAtom(OBAtom arg0) {
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return openbabelJNI.OBMol_InsertAtom(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
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}
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public boolean AddBond(int beginIdx, int endIdx, int order, int flags, int insertpos) {
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return openbabelJNI.OBMol_AddBond__SWIG_0(swigCPtr, this, beginIdx, endIdx, order, flags, insertpos);
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}
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public boolean AddBond(int beginIdx, int endIdx, int order, int flags) {
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return openbabelJNI.OBMol_AddBond__SWIG_1(swigCPtr, this, beginIdx, endIdx, order, flags);
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}
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public boolean AddBond(int beginIdx, int endIdx, int order) {
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return openbabelJNI.OBMol_AddBond__SWIG_2(swigCPtr, this, beginIdx, endIdx, order);
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}
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public boolean AddBond(OBBond arg0) {
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return openbabelJNI.OBMol_AddBond__SWIG_3(swigCPtr, this, OBBond.getCPtr(arg0), arg0);
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}
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public boolean AddResidue(OBResidue arg0) {
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return openbabelJNI.OBMol_AddResidue(swigCPtr, this, OBResidue.getCPtr(arg0), arg0);
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}
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public OBAtom NewAtom() {
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long cPtr = openbabelJNI.OBMol_NewAtom(swigCPtr, this);
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return (cPtr == 0) ? null : new OBAtom(cPtr, false);
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}
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public OBBond NewBond() {
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long cPtr = openbabelJNI.OBMol_NewBond(swigCPtr, this);
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return (cPtr == 0) ? null : new OBBond(cPtr, false);
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}
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public OBResidue NewResidue() {
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long cPtr = openbabelJNI.OBMol_NewResidue(swigCPtr, this);
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return (cPtr == 0) ? null : new OBResidue(cPtr, false);
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}
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public boolean DeleteAtom(OBAtom arg0) {
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return openbabelJNI.OBMol_DeleteAtom(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
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}
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public boolean DeleteBond(OBBond arg0) {
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return openbabelJNI.OBMol_DeleteBond(swigCPtr, this, OBBond.getCPtr(arg0), arg0);
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}
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public boolean DeleteResidue(OBResidue arg0) {
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return openbabelJNI.OBMol_DeleteResidue(swigCPtr, this, OBResidue.getCPtr(arg0), arg0);
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}
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public void BeginModify() {
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openbabelJNI.OBMol_BeginModify(swigCPtr, this);
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}
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public void EndModify(boolean nukePerceivedData) {
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openbabelJNI.OBMol_EndModify__SWIG_0(swigCPtr, this, nukePerceivedData);
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}
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public void EndModify() {
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openbabelJNI.OBMol_EndModify__SWIG_1(swigCPtr, this);
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}
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public int GetMod() {
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return openbabelJNI.OBMol_GetMod(swigCPtr, this);
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}
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public void IncrementMod() {
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openbabelJNI.OBMol_IncrementMod(swigCPtr, this);
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}
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public void DecrementMod() {
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openbabelJNI.OBMol_DecrementMod(swigCPtr, this);
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}
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public int GetFlags() {
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return openbabelJNI.OBMol_GetFlags(swigCPtr, this);
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}
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public String GetTitle() {
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return openbabelJNI.OBMol_GetTitle(swigCPtr, this);
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}
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public long NumAtoms() {
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return openbabelJNI.OBMol_NumAtoms(swigCPtr, this);
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}
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public long NumBonds() {
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return openbabelJNI.OBMol_NumBonds(swigCPtr, this);
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}
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public long NumHvyAtoms() {
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return openbabelJNI.OBMol_NumHvyAtoms(swigCPtr, this);
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}
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public long NumResidues() {
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return openbabelJNI.OBMol_NumResidues(swigCPtr, this);
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}
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public long NumRotors() {
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return openbabelJNI.OBMol_NumRotors(swigCPtr, this);
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}
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public OBAtom GetAtom(int idx) {
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long cPtr = openbabelJNI.OBMol_GetAtom(swigCPtr, this, idx);
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return (cPtr == 0) ? null : new OBAtom(cPtr, false);
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}
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public OBAtom GetFirstAtom() {
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long cPtr = openbabelJNI.OBMol_GetFirstAtom(swigCPtr, this);
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return (cPtr == 0) ? null : new OBAtom(cPtr, false);
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}
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public OBBond GetBond(int idx) {
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long cPtr = openbabelJNI.OBMol_GetBond__SWIG_0(swigCPtr, this, idx);
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return (cPtr == 0) ? null : new OBBond(cPtr, false);
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}
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public OBBond GetBond(int a, int b) {
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long cPtr = openbabelJNI.OBMol_GetBond__SWIG_1(swigCPtr, this, a, b);
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return (cPtr == 0) ? null : new OBBond(cPtr, false);
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}
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public OBBond GetBond(OBAtom bgn, OBAtom end) {
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long cPtr = openbabelJNI.OBMol_GetBond__SWIG_2(swigCPtr, this, OBAtom.getCPtr(bgn), bgn, OBAtom.getCPtr(end), end);
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return (cPtr == 0) ? null : new OBBond(cPtr, false);
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}
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public OBResidue GetResidue(int arg0) {
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long cPtr = openbabelJNI.OBMol_GetResidue(swigCPtr, this, arg0);
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return (cPtr == 0) ? null : new OBResidue(cPtr, false);
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}
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public SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t GetInternalCoord() {
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return new SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t(openbabelJNI.OBMol_GetInternalCoord(swigCPtr, this), true);
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}
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public double GetTorsion(int arg0, int arg1, int arg2, int arg3) {
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return openbabelJNI.OBMol_GetTorsion__SWIG_0(swigCPtr, this, arg0, arg1, arg2, arg3);
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}
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public double GetTorsion(OBAtom a, OBAtom b, OBAtom c, OBAtom d) {
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return openbabelJNI.OBMol_GetTorsion__SWIG_1(swigCPtr, this, OBAtom.getCPtr(a), a, OBAtom.getCPtr(b), b, OBAtom.getCPtr(c), c, OBAtom.getCPtr(d), d);
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}
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public double GetAngle(OBAtom a, OBAtom b, OBAtom c) {
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return openbabelJNI.OBMol_GetAngle(swigCPtr, this, OBAtom.getCPtr(a), a, OBAtom.getCPtr(b), b, OBAtom.getCPtr(c), c);
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}
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public String GetFormula() {
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return openbabelJNI.OBMol_GetFormula(swigCPtr, this);
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}
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public String GetSpacedFormula(int ones, String sp) {
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return openbabelJNI.OBMol_GetSpacedFormula__SWIG_0(swigCPtr, this, ones, sp);
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}
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public String GetSpacedFormula(int ones) {
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return openbabelJNI.OBMol_GetSpacedFormula__SWIG_1(swigCPtr, this, ones);
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}
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public String GetSpacedFormula() {
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return openbabelJNI.OBMol_GetSpacedFormula__SWIG_2(swigCPtr, this);
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}
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public double GetEnergy() {
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return openbabelJNI.OBMol_GetEnergy(swigCPtr, this);
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}
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public double GetMolWt() {
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return openbabelJNI.OBMol_GetMolWt(swigCPtr, this);
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}
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public double GetExactMass() {
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return openbabelJNI.OBMol_GetExactMass(swigCPtr, this);
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}
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public int GetTotalCharge() {
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return openbabelJNI.OBMol_GetTotalCharge(swigCPtr, this);
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}
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public long GetTotalSpinMultiplicity() {
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return openbabelJNI.OBMol_GetTotalSpinMultiplicity(swigCPtr, this);
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}
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public int GetDimension() {
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return openbabelJNI.OBMol_GetDimension(swigCPtr, this);
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}
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public SWIGTYPE_p_double GetCoordinates() {
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long cPtr = openbabelJNI.OBMol_GetCoordinates(swigCPtr, this);
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return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
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}
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public SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t GetSSSR() {
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return new SWIGTYPE_p_std__vectorTOpenBabel__OBRing_p_t(openbabelJNI.OBMol_GetSSSR(swigCPtr, this), false);
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}
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public boolean AutomaticFormalCharge() {
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return openbabelJNI.OBMol_AutomaticFormalCharge(swigCPtr, this);
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}
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public boolean AutomaticPartialCharge() {
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return openbabelJNI.OBMol_AutomaticPartialCharge(swigCPtr, this);
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}
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public void SetTitle(String title) {
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openbabelJNI.OBMol_SetTitle__SWIG_0(swigCPtr, this, title);
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}
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public void SetTitle(SWIGTYPE_p_std__string title) {
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openbabelJNI.OBMol_SetTitle__SWIG_1(swigCPtr, this, SWIGTYPE_p_std__string.getCPtr(title));
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}
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public void SetFormula(String molFormula) {
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openbabelJNI.OBMol_SetFormula(swigCPtr, this, molFormula);
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}
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public void SetEnergy(double energy) {
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openbabelJNI.OBMol_SetEnergy(swigCPtr, this, energy);
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}
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public void SetDimension(int d) {
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openbabelJNI.OBMol_SetDimension(swigCPtr, this, d);
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}
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public void SetTotalCharge(int charge) {
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openbabelJNI.OBMol_SetTotalCharge(swigCPtr, this, charge);
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}
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public void SetTotalSpinMultiplicity(long spin) {
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openbabelJNI.OBMol_SetTotalSpinMultiplicity(swigCPtr, this, spin);
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}
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public void SetInternalCoord(SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t int_coord) {
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openbabelJNI.OBMol_SetInternalCoord(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t.getCPtr(int_coord));
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}
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public void SetAutomaticFormalCharge(boolean val) {
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openbabelJNI.OBMol_SetAutomaticFormalCharge(swigCPtr, this, val);
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}
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public void SetAutomaticPartialCharge(boolean val) {
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openbabelJNI.OBMol_SetAutomaticPartialCharge(swigCPtr, this, val);
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}
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public void SetAromaticPerceived() {
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openbabelJNI.OBMol_SetAromaticPerceived(swigCPtr, this);
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}
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public void SetSSSRPerceived() {
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openbabelJNI.OBMol_SetSSSRPerceived(swigCPtr, this);
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}
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public void SetRingAtomsAndBondsPerceived() {
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openbabelJNI.OBMol_SetRingAtomsAndBondsPerceived(swigCPtr, this);
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}
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public void SetAtomTypesPerceived() {
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openbabelJNI.OBMol_SetAtomTypesPerceived(swigCPtr, this);
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}
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public void SetChainsPerceived() {
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openbabelJNI.OBMol_SetChainsPerceived(swigCPtr, this);
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}
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public void SetChiralityPerceived() {
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openbabelJNI.OBMol_SetChiralityPerceived(swigCPtr, this);
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}
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public void SetPartialChargesPerceived() {
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openbabelJNI.OBMol_SetPartialChargesPerceived(swigCPtr, this);
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}
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public void SetHybridizationPerceived() {
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openbabelJNI.OBMol_SetHybridizationPerceived(swigCPtr, this);
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}
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public void SetImplicitValencePerceived() {
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openbabelJNI.OBMol_SetImplicitValencePerceived(swigCPtr, this);
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}
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public void SetKekulePerceived() {
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openbabelJNI.OBMol_SetKekulePerceived(swigCPtr, this);
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}
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public void SetClosureBondsPerceived() {
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openbabelJNI.OBMol_SetClosureBondsPerceived(swigCPtr, this);
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}
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public void SetHydrogensAdded() {
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openbabelJNI.OBMol_SetHydrogensAdded(swigCPtr, this);
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}
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public void SetCorrectedForPH() {
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openbabelJNI.OBMol_SetCorrectedForPH(swigCPtr, this);
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}
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public void SetAromaticCorrected() {
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openbabelJNI.OBMol_SetAromaticCorrected(swigCPtr, this);
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}
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public void SetSpinMultiplicityAssigned() {
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openbabelJNI.OBMol_SetSpinMultiplicityAssigned(swigCPtr, this);
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}
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public void SetFlags(int flags) {
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openbabelJNI.OBMol_SetFlags(swigCPtr, this, flags);
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}
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public void UnsetAromaticPerceived() {
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openbabelJNI.OBMol_UnsetAromaticPerceived(swigCPtr, this);
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}
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public void UnsetPartialChargesPerceived() {
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openbabelJNI.OBMol_UnsetPartialChargesPerceived(swigCPtr, this);
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}
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public void UnsetImplicitValencePerceived() {
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openbabelJNI.OBMol_UnsetImplicitValencePerceived(swigCPtr, this);
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}
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public void UnsetHydrogensAdded() {
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openbabelJNI.OBMol_UnsetHydrogensAdded(swigCPtr, this);
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}
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public void UnsetFlag(int flag) {
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openbabelJNI.OBMol_UnsetFlag(swigCPtr, this, flag);
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}
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public OBBase DoTransformations(SWIGTYPE_p_std__mapTstd__string_std__string_t pOptions) {
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long cPtr = openbabelJNI.OBMol_DoTransformations(swigCPtr, this, SWIGTYPE_p_std__mapTstd__string_std__string_t.getCPtr(pOptions));
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return (cPtr == 0) ? null : new OBBase(cPtr, false);
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}
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public static String ClassDescription() {
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return openbabelJNI.OBMol_ClassDescription();
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}
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public boolean Clear() {
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return openbabelJNI.OBMol_Clear(swigCPtr, this);
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}
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public void RenumberAtoms(SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t arg0) {
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openbabelJNI.OBMol_RenumberAtoms(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t.getCPtr(arg0));
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}
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public void ToInertialFrame(int conf, SWIGTYPE_p_double rmat) {
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openbabelJNI.OBMol_ToInertialFrame__SWIG_0(swigCPtr, this, conf, SWIGTYPE_p_double.getCPtr(rmat));
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}
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public void ToInertialFrame() {
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openbabelJNI.OBMol_ToInertialFrame__SWIG_1(swigCPtr, this);
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}
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public void Translate(vector3 v) {
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openbabelJNI.OBMol_Translate__SWIG_0(swigCPtr, this, vector3.getCPtr(v), v);
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}
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public void Translate(vector3 v, int conf) {
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openbabelJNI.OBMol_Translate__SWIG_1(swigCPtr, this, vector3.getCPtr(v), v, conf);
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}
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public void Rotate(SWIGTYPE_p_a_3__double u) {
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openbabelJNI.OBMol_Rotate__SWIG_0(swigCPtr, this, SWIGTYPE_p_a_3__double.getCPtr(u));
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}
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public void Rotate(SWIGTYPE_p_double m) {
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openbabelJNI.OBMol_Rotate__SWIG_1(swigCPtr, this, SWIGTYPE_p_double.getCPtr(m));
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}
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public void Rotate(SWIGTYPE_p_double m, int nconf) {
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openbabelJNI.OBMol_Rotate__SWIG_2(swigCPtr, this, SWIGTYPE_p_double.getCPtr(m), nconf);
|
|
}
|
|
|
|
public void Center() {
|
|
openbabelJNI.OBMol_Center__SWIG_0(swigCPtr, this);
|
|
}
|
|
|
|
public boolean Kekulize() {
|
|
return openbabelJNI.OBMol_Kekulize(swigCPtr, this);
|
|
}
|
|
|
|
public boolean PerceiveKekuleBonds() {
|
|
return openbabelJNI.OBMol_PerceiveKekuleBonds(swigCPtr, this);
|
|
}
|
|
|
|
public void NewPerceiveKekuleBonds() {
|
|
openbabelJNI.OBMol_NewPerceiveKekuleBonds(swigCPtr, this);
|
|
}
|
|
|
|
public boolean DeleteHydrogens() {
|
|
return openbabelJNI.OBMol_DeleteHydrogens__SWIG_0(swigCPtr, this);
|
|
}
|
|
|
|
public boolean DeleteHydrogens(OBAtom arg0) {
|
|
return openbabelJNI.OBMol_DeleteHydrogens__SWIG_1(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public boolean DeleteNonPolarHydrogens() {
|
|
return openbabelJNI.OBMol_DeleteNonPolarHydrogens(swigCPtr, this);
|
|
}
|
|
|
|
public boolean DeleteHydrogen(OBAtom arg0) {
|
|
return openbabelJNI.OBMol_DeleteHydrogen(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public boolean AddHydrogens(boolean polaronly, boolean correctForPH) {
|
|
return openbabelJNI.OBMol_AddHydrogens__SWIG_0(swigCPtr, this, polaronly, correctForPH);
|
|
}
|
|
|
|
public boolean AddHydrogens(boolean polaronly) {
|
|
return openbabelJNI.OBMol_AddHydrogens__SWIG_1(swigCPtr, this, polaronly);
|
|
}
|
|
|
|
public boolean AddHydrogens() {
|
|
return openbabelJNI.OBMol_AddHydrogens__SWIG_2(swigCPtr, this);
|
|
}
|
|
|
|
public boolean AddHydrogens(OBAtom arg0) {
|
|
return openbabelJNI.OBMol_AddHydrogens__SWIG_3(swigCPtr, this, OBAtom.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public boolean AddPolarHydrogens() {
|
|
return openbabelJNI.OBMol_AddPolarHydrogens(swigCPtr, this);
|
|
}
|
|
|
|
public boolean StripSalts() {
|
|
return openbabelJNI.OBMol_StripSalts(swigCPtr, this);
|
|
}
|
|
|
|
public vectorMol Separate(int StartIndex) {
|
|
return new vectorMol(openbabelJNI.OBMol_Separate__SWIG_0(swigCPtr, this, StartIndex), true);
|
|
}
|
|
|
|
public vectorMol Separate() {
|
|
return new vectorMol(openbabelJNI.OBMol_Separate__SWIG_1(swigCPtr, this), true);
|
|
}
|
|
|
|
public boolean ConvertDativeBonds() {
|
|
return openbabelJNI.OBMol_ConvertDativeBonds(swigCPtr, this);
|
|
}
|
|
|
|
public boolean CorrectForPH() {
|
|
return openbabelJNI.OBMol_CorrectForPH(swigCPtr, this);
|
|
}
|
|
|
|
public boolean AssignSpinMultiplicity() {
|
|
return openbabelJNI.OBMol_AssignSpinMultiplicity(swigCPtr, this);
|
|
}
|
|
|
|
public vector3 Center(int nconf) {
|
|
return new vector3(openbabelJNI.OBMol_Center__SWIG_1(swigCPtr, this, nconf), true);
|
|
}
|
|
|
|
public void SetTorsion(OBAtom arg0, OBAtom arg1, OBAtom arg2, OBAtom arg3, double arg4) {
|
|
openbabelJNI.OBMol_SetTorsion(swigCPtr, this, OBAtom.getCPtr(arg0), arg0, OBAtom.getCPtr(arg1), arg1, OBAtom.getCPtr(arg2), arg2, OBAtom.getCPtr(arg3), arg3, arg4);
|
|
}
|
|
|
|
public void FindSSSR() {
|
|
openbabelJNI.OBMol_FindSSSR(swigCPtr, this);
|
|
}
|
|
|
|
public void FindRingAtomsAndBonds() {
|
|
openbabelJNI.OBMol_FindRingAtomsAndBonds(swigCPtr, this);
|
|
}
|
|
|
|
public void FindChiralCenters() {
|
|
openbabelJNI.OBMol_FindChiralCenters(swigCPtr, this);
|
|
}
|
|
|
|
public void FindChildren(vectorInt children, int bgnIdx, int endIdx) {
|
|
openbabelJNI.OBMol_FindChildren__SWIG_0(swigCPtr, this, vectorInt.getCPtr(children), children, bgnIdx, endIdx);
|
|
}
|
|
|
|
public void FindChildren(SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t children, OBAtom bgn, OBAtom end) {
|
|
openbabelJNI.OBMol_FindChildren__SWIG_1(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t.getCPtr(children), OBAtom.getCPtr(bgn), bgn, OBAtom.getCPtr(end), end);
|
|
}
|
|
|
|
public void FindLargestFragment(OBBitVec frag) {
|
|
openbabelJNI.OBMol_FindLargestFragment(swigCPtr, this, OBBitVec.getCPtr(frag), frag);
|
|
}
|
|
|
|
public void ContigFragList(vvInt arg0) {
|
|
openbabelJNI.OBMol_ContigFragList(swigCPtr, this, vvInt.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public void Align(OBAtom arg0, OBAtom arg1, vector3 arg2, vector3 arg3) {
|
|
openbabelJNI.OBMol_Align(swigCPtr, this, OBAtom.getCPtr(arg0), arg0, OBAtom.getCPtr(arg1), arg1, vector3.getCPtr(arg2), arg2, vector3.getCPtr(arg3), arg3);
|
|
}
|
|
|
|
public void ConnectTheDots() {
|
|
openbabelJNI.OBMol_ConnectTheDots(swigCPtr, this);
|
|
}
|
|
|
|
public void PerceiveBondOrders() {
|
|
openbabelJNI.OBMol_PerceiveBondOrders(swigCPtr, this);
|
|
}
|
|
|
|
public void FindAngles() {
|
|
openbabelJNI.OBMol_FindAngles(swigCPtr, this);
|
|
}
|
|
|
|
public void FindTorsions() {
|
|
openbabelJNI.OBMol_FindTorsions(swigCPtr, this);
|
|
}
|
|
|
|
public boolean GetGTDVector(vectorInt arg0) {
|
|
return openbabelJNI.OBMol_GetGTDVector(swigCPtr, this, vectorInt.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public void GetGIVector(vectorUnsignedInt arg0) {
|
|
openbabelJNI.OBMol_GetGIVector(swigCPtr, this, vectorUnsignedInt.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public void GetGIDVector(vectorUnsignedInt arg0) {
|
|
openbabelJNI.OBMol_GetGIDVector(swigCPtr, this, vectorUnsignedInt.getCPtr(arg0), arg0);
|
|
}
|
|
|
|
public boolean Has2D() {
|
|
return openbabelJNI.OBMol_Has2D(swigCPtr, this);
|
|
}
|
|
|
|
public boolean Has3D() {
|
|
return openbabelJNI.OBMol_Has3D(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasNonZeroCoords() {
|
|
return openbabelJNI.OBMol_HasNonZeroCoords(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasAromaticPerceived() {
|
|
return openbabelJNI.OBMol_HasAromaticPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasSSSRPerceived() {
|
|
return openbabelJNI.OBMol_HasSSSRPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasRingAtomsAndBondsPerceived() {
|
|
return openbabelJNI.OBMol_HasRingAtomsAndBondsPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasAtomTypesPerceived() {
|
|
return openbabelJNI.OBMol_HasAtomTypesPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasChiralityPerceived() {
|
|
return openbabelJNI.OBMol_HasChiralityPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasPartialChargesPerceived() {
|
|
return openbabelJNI.OBMol_HasPartialChargesPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasHybridizationPerceived() {
|
|
return openbabelJNI.OBMol_HasHybridizationPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasImplicitValencePerceived() {
|
|
return openbabelJNI.OBMol_HasImplicitValencePerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasKekulePerceived() {
|
|
return openbabelJNI.OBMol_HasKekulePerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasClosureBondsPerceived() {
|
|
return openbabelJNI.OBMol_HasClosureBondsPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasChainsPerceived() {
|
|
return openbabelJNI.OBMol_HasChainsPerceived(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasHydrogensAdded() {
|
|
return openbabelJNI.OBMol_HasHydrogensAdded(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasAromaticCorrected() {
|
|
return openbabelJNI.OBMol_HasAromaticCorrected(swigCPtr, this);
|
|
}
|
|
|
|
public boolean IsCorrectedForPH() {
|
|
return openbabelJNI.OBMol_IsCorrectedForPH(swigCPtr, this);
|
|
}
|
|
|
|
public boolean HasSpinMultiplicityAssigned() {
|
|
return openbabelJNI.OBMol_HasSpinMultiplicityAssigned(swigCPtr, this);
|
|
}
|
|
|
|
public boolean IsChiral() {
|
|
return openbabelJNI.OBMol_IsChiral(swigCPtr, this);
|
|
}
|
|
|
|
public boolean Empty() {
|
|
return openbabelJNI.OBMol_Empty(swigCPtr, this);
|
|
}
|
|
|
|
public int NumConformers() {
|
|
return openbabelJNI.OBMol_NumConformers(swigCPtr, this);
|
|
}
|
|
|
|
public void SetConformers(SWIGTYPE_p_std__vectorTdouble_p_t v) {
|
|
openbabelJNI.OBMol_SetConformers(swigCPtr, this, SWIGTYPE_p_std__vectorTdouble_p_t.getCPtr(v));
|
|
}
|
|
|
|
public void AddConformer(SWIGTYPE_p_double f) {
|
|
openbabelJNI.OBMol_AddConformer(swigCPtr, this, SWIGTYPE_p_double.getCPtr(f));
|
|
}
|
|
|
|
public void SetConformer(int i) {
|
|
openbabelJNI.OBMol_SetConformer(swigCPtr, this, i);
|
|
}
|
|
|
|
public void CopyConformer(SWIGTYPE_p_double c, int nconf) {
|
|
openbabelJNI.OBMol_CopyConformer(swigCPtr, this, SWIGTYPE_p_double.getCPtr(c), nconf);
|
|
}
|
|
|
|
public void DeleteConformer(int nconf) {
|
|
openbabelJNI.OBMol_DeleteConformer(swigCPtr, this, nconf);
|
|
}
|
|
|
|
public SWIGTYPE_p_double GetConformer(int i) {
|
|
long cPtr = openbabelJNI.OBMol_GetConformer(swigCPtr, this, i);
|
|
return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
|
|
}
|
|
|
|
public SWIGTYPE_p_double BeginConformer(SWIGTYPE_p_std__vectorTdouble_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_BeginConformer(swigCPtr, this, SWIGTYPE_p_std__vectorTdouble_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
|
|
}
|
|
|
|
public SWIGTYPE_p_double NextConformer(SWIGTYPE_p_std__vectorTdouble_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_NextConformer(swigCPtr, this, SWIGTYPE_p_std__vectorTdouble_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTdouble_p_t GetConformers() {
|
|
return new SWIGTYPE_p_std__vectorTdouble_p_t(openbabelJNI.OBMol_GetConformers(swigCPtr, this), false);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator BeginAtoms() {
|
|
return new SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator(openbabelJNI.OBMol_BeginAtoms(swigCPtr, this), true);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator EndAtoms() {
|
|
return new SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator(openbabelJNI.OBMol_EndAtoms(swigCPtr, this), true);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator BeginBonds() {
|
|
return new SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator(openbabelJNI.OBMol_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.OBMol_EndBonds(swigCPtr, this), true);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator BeginResidues() {
|
|
return new SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator(openbabelJNI.OBMol_BeginResidues(swigCPtr, this), true);
|
|
}
|
|
|
|
public SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator EndResidues() {
|
|
return new SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator(openbabelJNI.OBMol_EndResidues(swigCPtr, this), true);
|
|
}
|
|
|
|
public OBAtom BeginAtom(SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_BeginAtom(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new OBAtom(cPtr, false);
|
|
}
|
|
|
|
public OBAtom NextAtom(SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_NextAtom(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBAtom_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new OBAtom(cPtr, false);
|
|
}
|
|
|
|
public OBBond BeginBond(SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_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.OBMol_NextBond(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBBond_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new OBBond(cPtr, false);
|
|
}
|
|
|
|
public OBResidue BeginResidue(SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_BeginResidue(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new OBResidue(cPtr, false);
|
|
}
|
|
|
|
public OBResidue NextResidue(SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_NextResidue(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBResidue_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new OBResidue(cPtr, false);
|
|
}
|
|
|
|
public SWIGTYPE_p_OpenBabel__OBInternalCoord BeginInternalCoord(SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_BeginInternalCoord(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new SWIGTYPE_p_OpenBabel__OBInternalCoord(cPtr, false);
|
|
}
|
|
|
|
public SWIGTYPE_p_OpenBabel__OBInternalCoord NextInternalCoord(SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator i) {
|
|
long cPtr = openbabelJNI.OBMol_NextInternalCoord(swigCPtr, this, SWIGTYPE_p_std__vectorTOpenBabel__OBInternalCoord_p_t__iterator.getCPtr(i));
|
|
return (cPtr == 0) ? null : new SWIGTYPE_p_OpenBabel__OBInternalCoord(cPtr, false);
|
|
}
|
|
|
|
}
|