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* src/atom.h, src/base.h, src/bond.h, src/residue.h, src/mol.h,

Browse Source 
src/ring.h, src/mol.cpp, src/base.cpp, src/obiter.h: Remove
  OBNodeBase, OBEdgeBase, and OBGraphBase classes, contributed by
  Gerd Menche.

  * tools/obprop.cpp: Ditto. Example of changing iterators to new format.

  * scripts/*: Updated based on above changes.
This commit is contained in:
Geoffrey Hutchison
2006-11-20 18:43:41 +00:00
parent 0fd1813a26
commit 8dad311517
88 changed files with 43343 additions and 16533 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/java/OBSmartsPattern.java
+25 -25
View File
@@ -27,105 +27,105 @@ public class OBSmartsPattern {
public synchronized void delete() {
if(swigCPtr != 0 && swigCMemOwn) {
swigCMemOwn = false;
net.sourceforge.openbabelJNI.delete_OBSmartsPattern(swigCPtr);
openbabelJNI.delete_OBSmartsPattern(swigCPtr);
}
swigCPtr = 0;
}
public OBSmartsPattern() {
this(net.sourceforge.openbabelJNI.new_OBSmartsPattern__SWIG_0(), true);
this(openbabelJNI.new_OBSmartsPattern__SWIG_0(), true);
}
public OBSmartsPattern(OBSmartsPattern cp) {
this(net.sourceforge.openbabelJNI.new_OBSmartsPattern__SWIG_1(OBSmartsPattern.getCPtr(cp), cp), true);
this(openbabelJNI.new_OBSmartsPattern__SWIG_1(OBSmartsPattern.getCPtr(cp), cp), true);
}
public long NumMatches() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_NumMatches(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_NumMatches(swigCPtr, this);
}
public long NumAtoms() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_NumAtoms(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_NumAtoms(swigCPtr, this);
}
public long NumBonds() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_NumBonds(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_NumBonds(swigCPtr, this);
}
public int GetAtomicNum(int arg0) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_GetAtomicNum(swigCPtr, this, arg0);
return openbabelJNI.OBSmartsPattern_GetAtomicNum(swigCPtr, this, arg0);
}
public void GetBond(SWIGTYPE_p_int arg0, SWIGTYPE_p_int arg1, SWIGTYPE_p_int arg2, int arg3) {
net.sourceforge.openbabelJNI.OBSmartsPattern_GetBond(swigCPtr, this, SWIGTYPE_p_int.getCPtr(arg0), SWIGTYPE_p_int.getCPtr(arg1), SWIGTYPE_p_int.getCPtr(arg2), arg3);
openbabelJNI.OBSmartsPattern_GetBond(swigCPtr, this, SWIGTYPE_p_int.getCPtr(arg0), SWIGTYPE_p_int.getCPtr(arg1), SWIGTYPE_p_int.getCPtr(arg2), arg3);
}
public int GetCharge(int arg0) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_GetCharge(swigCPtr, this, arg0);
return openbabelJNI.OBSmartsPattern_GetCharge(swigCPtr, this, arg0);
}
public String GetSMARTS() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_GetSMARTS__SWIG_0(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_GetSMARTS__SWIG_0(swigCPtr, this);
}
public int GetVectorBinding(int idx) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_GetVectorBinding(swigCPtr, this, idx);
return openbabelJNI.OBSmartsPattern_GetVectorBinding(swigCPtr, this, idx);
}
public boolean Empty() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_Empty(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_Empty(swigCPtr, this);
}
public boolean IsValid() {
return net.sourceforge.openbabelJNI.OBSmartsPattern_IsValid(swigCPtr, this);
return openbabelJNI.OBSmartsPattern_IsValid(swigCPtr, this);
}
public boolean Init(String arg0) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_Init__SWIG_0(swigCPtr, this, arg0);
return openbabelJNI.OBSmartsPattern_Init__SWIG_0(swigCPtr, this, arg0);
}
public void WriteMapList(SWIGTYPE_p_std__ostream arg0) {
net.sourceforge.openbabelJNI.OBSmartsPattern_WriteMapList(swigCPtr, this, SWIGTYPE_p_std__ostream.getCPtr(arg0));
openbabelJNI.OBSmartsPattern_WriteMapList(swigCPtr, this, SWIGTYPE_p_std__ostream.getCPtr(arg0));
}
public boolean Match(OBMol mol, boolean single) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_Match__SWIG_0(swigCPtr, this, OBMol.getCPtr(mol), mol, single);
return openbabelJNI.OBSmartsPattern_Match__SWIG_0(swigCPtr, this, OBMol.getCPtr(mol), mol, single);
}
public boolean Match(OBMol mol) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_Match__SWIG_1(swigCPtr, this, OBMol.getCPtr(mol), mol);
return openbabelJNI.OBSmartsPattern_Match__SWIG_1(swigCPtr, this, OBMol.getCPtr(mol), mol);
}
public boolean RestrictedMatch(OBMol mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t pairs, boolean single) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_0(swigCPtr, this, OBMol.getCPtr(mol), mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t.getCPtr(pairs), single);
return openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_0(swigCPtr, this, OBMol.getCPtr(mol), mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t.getCPtr(pairs), single);
}
public boolean RestrictedMatch(OBMol mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t pairs) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_1(swigCPtr, this, OBMol.getCPtr(mol), mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t.getCPtr(pairs));
return openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_1(swigCPtr, this, OBMol.getCPtr(mol), mol, SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t.getCPtr(pairs));
}
public boolean RestrictedMatch(OBMol mol, OBBitVec bv, boolean single) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_2(swigCPtr, this, OBMol.getCPtr(mol), mol, OBBitVec.getCPtr(bv), bv, single);
return openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_2(swigCPtr, this, OBMol.getCPtr(mol), mol, OBBitVec.getCPtr(bv), bv, single);
}
public boolean RestrictedMatch(OBMol mol, OBBitVec bv) {
return net.sourceforge.openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_3(swigCPtr, this, OBMol.getCPtr(mol), mol, OBBitVec.getCPtr(bv), bv);
return openbabelJNI.OBSmartsPattern_RestrictedMatch__SWIG_3(swigCPtr, this, OBMol.getCPtr(mol), mol, OBBitVec.getCPtr(bv), bv);
}
public vvInt GetMapList() {
return new vvInt(net.sourceforge.openbabelJNI.OBSmartsPattern_GetMapList(swigCPtr, this), false);
return new vvInt(openbabelJNI.OBSmartsPattern_GetMapList(swigCPtr, this), false);
}
public vvInt GetUMapList() {
return new vvInt(net.sourceforge.openbabelJNI.OBSmartsPattern_GetUMapList(swigCPtr, this), false);
return new vvInt(openbabelJNI.OBSmartsPattern_GetUMapList(swigCPtr, this), false);
}
public SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator BeginMList() {
return new SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator(net.sourceforge.openbabelJNI.OBSmartsPattern_BeginMList(swigCPtr, this), true);
return new SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator(openbabelJNI.OBSmartsPattern_BeginMList(swigCPtr, this), true);
}
public SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator EndMList() {
return new SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator(net.sourceforge.openbabelJNI.OBSmartsPattern_EndMList(swigCPtr, this), true);
return new SWIGTYPE_p_std__vectorTstd__vectorTint_t_t__iterator(openbabelJNI.OBSmartsPattern_EndMList(swigCPtr, this), true);
}
}