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additional functionality required by the knime nodes

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This commit is contained in:
Greg Landrum
2011-04-12 10:07:52 +00:00
parent 9ebc0a67d3
commit 800a4c2149
6 changed files with 66 additions and 5 deletions
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13
Code/JavaWrappers/ChemReactions.i
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@@ -43,7 +43,8 @@
%include <GraphMol/ChemReactions/Reaction.h>
%include <GraphMol/ChemReactions/ReactionParser.h>
%ignore RDKit::ChemicalReaction::validate;
%ignore RDKit::ChemicalReaction::validate(unsigned int &,unsigned int &,bool);
%ignore RDKit::ChemicalReaction::validate(unsigned int &,unsigned int &);
%extend RDKit::ChemicalReaction {
static RDKit::ChemicalReaction *ReactionFromSmarts(std::string sma){
@@ -100,7 +101,7 @@ static RDKit::ChemicalReaction *RxnFromBinary(std::vector<int> pkl){
};
/* A Java-accessible validation function */
std::pair<int,int> *Validate(bool silent=false) {
std::pair<int,int> *validateReaction(bool silent=false) {
std::pair<int,int> *res = new std::pair<int,int>();
// Use some local unsigned ints so that we don't create a new and useless type at the Java
// level.
@@ -110,6 +111,12 @@ static RDKit::ChemicalReaction *RxnFromBinary(std::vector<int> pkl){
res->first = (int) first;
res->second = (int) second;
return res;
}
};
bool validate() {
unsigned int nErr=0,nWarn=0;
bool res=$self->validate(nErr,nWarn);
return res;
};
}

2
Code/JavaWrappers/MorganFingerprints.i
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@@ -48,6 +48,8 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(UInt_Pair_Vect, std::vector< std::pair<unsign
%newobject RDKit::MorganFingerprints::getFingerprint;
%rename(MorganFingerprintMol) RDKit::MorganFingerprints::getFingerprint;
%newobject RDKit::MorganFingerprints::getFingerprintAsBitVect;
%rename(getMorganFingerprintAsBitVect) RDKit::MorganFingerprints::getFingerprintAsBitVect;
%include <GraphMol/Fingerprints/MorganFingerprints.h>
%include <DataStructs/BitOps.h>

40
Code/JavaWrappers/ROMol.i
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@@ -56,6 +56,7 @@
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include "Depict.h"
%}
%template(ROMol_Vect) std::vector< boost::shared_ptr<RDKit::ROMol> >;
@@ -212,6 +213,25 @@
permuteDeg4Nodes);
}
unsigned int compute2DCoords(RDKit::ROMol &templ){
RDKit::MatchVectType matchVect;
if(templ.getNumConformers() && SubstructMatch(*($self),templ,matchVect)){
RDGeom::INT_POINT2D_MAP coordMap;
RDKit::Conformer conf=templ.getConformer();
for(RDKit::MatchVectType::const_iterator iter=matchVect.begin();
iter!=matchVect.end();++iter){
RDGeom::Point2D pt;
pt.x = conf.getAtomPos(iter->first).x;
pt.y = conf.getAtomPos(iter->first).y;
coordMap[iter->second]=pt;
}
return RDDepict::compute2DCoords(*($self),&coordMap);
} else {
return RDDepict::compute2DCoords(*($self),0);
}
}
unsigned int compute2DCoordsMimicDistMat(const RDDepict::DOUBLE_SMART_PTR *dmat=0,
bool canonOrient=true,
bool clearConfs=true,
@@ -336,3 +356,23 @@
}
}
%extend RDKit::ROMol {
std::string ToSVG(int lineWidthMult=2,int fontSize=50){
if(lineWidthMult<0) lineWidthMult *=2;
if(fontSize<0) fontSize*=2;
std::vector<int> drawing=MolToDrawing(*($self),0);
std::string svg=DrawingToSVG(drawing,lineWidthMult,fontSize);
return svg;
}
std::string ToSVG(const std::vector<int> &highlightAtoms,
int lineWidthMult=2,int fontSize=50){
if(lineWidthMult<0) lineWidthMult *=2;
if(fontSize<0) fontSize*=2;
std::vector<int> drawing=MolToDrawing(*($self),&highlightAtoms);
std::string svg=DrawingToSVG(drawing,lineWidthMult,fontSize);
return svg;
}
}

4
Code/JavaWrappers/gmwrapper/CMakeLists.txt
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@@ -21,6 +21,10 @@ INCLUDE_DIRECTORIES(${JNI_INCLUDE_DIRS})
SET_SOURCE_FILES_PROPERTIES(GraphMolJava.i PROPERTIES CPLUSPLUS ON )
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../*.java COPY_SOURCE)
FILE(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/org/RDKit COPY_DEST)
# Setup a few variables for environment-specific things
if(WIN32)
ADD_DEFINITIONS("/W3 /wd4716")

8
Code/JavaWrappers/gmwrapper/GraphMolJava.i
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@@ -46,6 +46,7 @@
/* Include the base types before anything that will utilize them */
%include "stdint.i"
%include "std_string.i"
%include "std_list.i"
%include "std_vector.i"
%include "std_map.i"
%include "std_pair.i"
@@ -173,6 +174,8 @@ typedef unsigned long long int uintmax_t;
%include "../transforms.i"
%include "../DistGeom.i"
%include "../ForceField.i"
%include "../ChemTransforms.i"
%include "../Subgraphs.i"
// Create a class to throw various sorts of errors for testing. Required for unit tests in ErrorHandlingTests.java
#ifdef INCLUDE_ERROR_GENERATOR
@@ -207,6 +210,7 @@ typedef unsigned long long int uintmax_t;
%template(Int_Int_Map) std::map<int,int>;
%template(Int_Point2D_Map) std::map<int, RDGeom::Point2D>;
%template(Int_Point3D_Map) std::map<int, RDGeom::Point3D>;
%template(Int_Int_Vect_List_Map) std::map<int,std::list<std::vector<int> > >;
/* vector pair */
%template(UInt_Pair_Vect) std::vector<std::pair<boost::uint32_t,int> >;
@@ -216,6 +220,10 @@ typedef unsigned long long int uintmax_t;
/* vector vector */
%template(Int_Vect_Vect) std::vector<std::vector<int> >;
/* list */
%template(Int_Vect_List) std::list<std::vector<int> >;
/* other */
%template(Match_Vect_Vect) std::vector<std::vector<std::pair<int,int> > >;
%template(Flagged_Atomic_Params_Vect) std::pair<std::vector<const ForceFields::UFF::AtomicParams *>,bool>;

4
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ChemReactionTests.java
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@@ -291,13 +291,13 @@ public class ChemReactionTests extends GraphMolTest {
public void test5Validation() {
ChemicalReaction rxn = ChemicalReaction.ReactionFromSmarts("[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn);
Int_Pair validationResults = rxn.Validate();
Int_Pair validationResults = rxn.validateReaction();
assertEquals(0, validationResults.getFirst());
assertEquals(0, validationResults.getSecond());
rxn = ChemicalReaction.ReactionFromSmarts("[C:1](=[O:1])O.[N:3]>>[C:1](=[O:2])[N:3]");
assertNotNull(rxn);
validationResults = rxn.Validate();
validationResults = rxn.validateReaction();
assertEquals(0, validationResults.getFirst());
assertEquals(2, validationResults.getSecond());