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Cart fixes (#2462)

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* Wrapper fixes: Tversky for De Morgan and java byte functions for ExplicitBitVect

* Wrapper fixes: Tversky for De Morgan and java byte functions for ExplicitBitVect
This commit is contained in:
jones-gareth
2019-05-27 13:29:09 +01:00
committed by Greg Landrum
parent b2a01a09ee
commit ebaa7b64e3
3 changed files with 60 additions and 0 deletions
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43
Code/JavaWrappers/ExplicitBitVect.i
View File

@@ -43,6 +43,34 @@
%ignore ExplicitBitVect::dp_bits;
%ignore ExplicitBitVect::getOnBits (IntVect& v) const;
%ignore ExplicitBitVect::ExplicitBitVect(unsigned int,bool);
#ifdef SWIGJAVA
%template(UChar_Vect) std::vector<unsigned char>;
%typemap(jni) std::string ExplicitBitVect::toByteArray "jbyteArray"
%typemap(jtype) std::string ExplicitBitVect::toByteArray "byte[]"
%typemap(jstype) std::string ExplicitBitVect::toByteArray "byte[]"
%typemap(javaout) std::string ExplicitBitVect::toByteArray {
return $jnicall;
}
%typemap(out) std::string ExplicitBitVect::toByteArray {
$result = JCALL1(NewByteArray, jenv, $1.size());
JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
}
#endif
%typemap(javacode) ExplicitBitVect %{
public static ExplicitBitVect fromByteArray(byte[] fp) {
UChar_Vect vec = new UChar_Vect();
vec.reserve(fp.length);
for (int size=0;size<fp.length;++size) {
vec.add(fp[size]);
}
return new ExplicitBitVect(vec);
}
%}
%include <DataStructs/ExplicitBitVect.h>
%newobject ExplicitBitVect::getOnBits;
%extend ExplicitBitVect {
@@ -53,3 +81,18 @@
}
}
#ifdef SWIGJAVA
%extend ExplicitBitVect {
const std::string toByteArray() {
return ($self)->toString();
}
ExplicitBitVect(const std::vector<unsigned char> & data ) {
std::string str(data.begin(), data.end());
return new ExplicitBitVect(str);
}
}
#endif

4
Code/JavaWrappers/MorganFingerprints.i
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@@ -62,5 +62,9 @@ SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(UInt_Pair_Vect, std::vector< std::pair<unsign
%template(TanimotoSimilaritySIVu32) RDKit::TanimotoSimilarity<boost::uint32_t>;
%template(TanimotoSimilaritySIVi32) RDKit::TanimotoSimilarity<boost::int32_t>;
%template(TanimotoSimilaritySIVi64) RDKit::TanimotoSimilarity<boost::int64_t>;
%template(TverskySimilarity) RDKit::TverskySimilarity<boost::uint32_t>;
%template(TverskySimilarity) RDKit::TverskySimilarity<boost::int32_t>;
%template(TverskySimilarity) RDKit::TverskySimilarity<boost::int64_t>;
%include "MorganFingerprints.h"

13
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/FingerprintsTests.java
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@@ -39,6 +39,7 @@ import org.junit.Test;
public class FingerprintsTests extends GraphMolTest {
public void compareVectors(Int_Vect v1, Int_Vect v2) {
assertEquals(v1.size(), v2.size());
for (int i = 0; i < v1.size(); i++) {
assertEquals(v1.get(i),v2.get(i));
}
@@ -138,6 +139,18 @@ public class FingerprintsTests extends GraphMolTest {
}
}
@Test
public void testToByteArray() {
String smiles = "Cc2nc1ccccc1o2";
ROMol mol = RWMol.MolFromSmiles(smiles);
ExplicitBitVect fp1 = RDKFuncs.PatternFingerprintMol(mol, 2048);
byte[] fpBytes = fp1.toByteArray();
ExplicitBitVect fp2 = ExplicitBitVect.fromByteArray(fpBytes);
Int_Vect fp1Bits = fp1.getOnBits();
Int_Vect fp2Bits = fp2.getOnBits();
compareVectors(fp1Bits, fp2Bits);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.FingerprintsTests");
}