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Expose additional functionality to SWIG wrappers (#5614)

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* - setenv() should be defined also for MinGW builds, not just MSVC
- fixed getBestRMS signature (ROMol& should be const)
- expose normalizeDepiction(), straightenDepiction(), getBestRMS(), CalcRMS() and getBestAlignmentTransform() to SWIG wrappers
- expose MolFromSmiles() overload taking SmilesParserParams parameter to SWIG wrappers
- expose DoubleVector class to SWIG wrappers as it is needed by alignment functions
- replace std::string with const std::string& in several SWIG wrapper signatures
- build RDKit2DotNet.dll as a 64-bit library on MinGW 64-bit
- add Java tests for the newly exposed SWIG functions
- fixed inconsistent indentation in Chemv2Tests.java

* changes in response to review

* fix typo

* reverted file committed by mistake

Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2022-10-04 05:04:28 +02:00
committed by GitHub
parent e110a5c479
commit 177c09cd6b
8 changed files with 503 additions and 221 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
Code/GraphMol/Chirality.cpp
View File

@@ -766,7 +766,7 @@ const Atom *findHighestCIPNeighbor(const Atom *atom, const Atom *skipAtom) {
namespace Chirality {
#if _MSC_VER
#ifdef _WIN32
int setenv(const char *name, const char *value, int) {
return _putenv_s(name, value);
}

2
Code/GraphMol/MolAlign/AlignMolecules.cpp
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@@ -212,7 +212,7 @@ double getBestAlignmentTransform(const ROMol &prbMol, const ROMol &refMol,
return bestRMS;
}
double getBestRMS(ROMol &prbMol, ROMol &refMol, int prbCid, int refCid,
double getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid, int refCid,
const std::vector<MatchVectType> &map, int maxMatches,
bool symmetrizeConjugatedTerminalGroups,
const RDNumeric::DoubleVector *weights) {

2
Code/GraphMol/MolAlign/AlignMolecules.h
View File

@@ -170,7 +170,7 @@ RDKIT_MOLALIGN_EXPORT double getBestAlignmentTransform(
Best RMSD value found
*/
RDKIT_MOLALIGN_EXPORT double getBestRMS(
ROMol &prbMol, ROMol &refMol, int prbCid = -1, int refCid = -1,
ROMol &prbMol, const ROMol &refMol, int prbCid = -1, int refCid = -1,
const std::vector<MatchVectType> &map = std::vector<MatchVectType>(),
int maxMatches = 1e6, bool symmetrizeConjugatedTerminalGroups = true,
const RDNumeric::DoubleVector *weights = nullptr);

38
Code/JavaWrappers/ROMol.i
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@@ -387,6 +387,15 @@ void setPreferCoordGen(bool);
&referencePattern,acceptFailure,forceRDKit);
}
double normalizeDepiction(int confId=-1, int canonicalize=1,
double scaleFactor=-1.0) {
return RDDepict::normalizeDepiction(*($self), confId, canonicalize, scaleFactor);
}
void straightenDepiction(int confId=-1, bool minimizeRotation=false) {
RDDepict::straightenDepiction(*($self), confId, minimizeRotation);
}
/* From FindRings.cpp, MolOps.h */
int findSSSR(RDKit::VECT_INT_VECT &res) {
return RDKit::MolOps::findSSSR(*($self), res);
@@ -518,7 +527,34 @@ void setPreferCoordGen(bool);
int refCid = -1, const std::vector<std::pair<int,int> > *atomMap = 0,
const RDNumeric::DoubleVector *weights = 0,
bool reflect = false, unsigned int maxIters = 50){
return RDKit::MolAlign::getAlignmentTransform(*($self), refMol, trans, prbCid, refCid, atomMap, weights, reflect, maxIters);
return RDKit::MolAlign::getAlignmentTransform(*($self), refMol, trans, prbCid, refCid, atomMap, weights, reflect, maxIters);
}
double getBestAlignmentTransform(
const RDKit::ROMol &refMol, RDGeom::Transform3D &bestTrans,
std::vector<std::pair<int,int> > &bestMatch, int prbCid = -1, int refCid = -1,
const std::vector<std::vector<std::pair<int,int> > > &map = std::vector<std::vector<std::pair<int,int> > >(),
int maxMatches = 1e6, bool symmetrizeConjugatedTerminalGroups = true,
const RDNumeric::DoubleVector *weights = nullptr, bool reflect = false,
unsigned int maxIters = 50) {
return RDKit::MolAlign::getBestAlignmentTransform(*($self), refMol, bestTrans, bestMatch,
prbCid, refCid, map, maxMatches, symmetrizeConjugatedTerminalGroups, weights, reflect, maxIters);
}
double calcRMS(
const ROMol &refMol, int prbCid = -1, int refCid = -1,
const std::vector<std::vector<std::pair<int,int> > > &map = std::vector<std::vector<std::pair<int,int> > >(),
int maxMatches = 1e6, bool symmetrizeConjugatedTerminalGroups = true,
const RDNumeric::DoubleVector *weights = nullptr) {
return RDKit::MolAlign::CalcRMS(*($self), refMol, prbCid, refCid, map, maxMatches, symmetrizeConjugatedTerminalGroups, weights);
}
double getBestRMS(
const ROMol &refMol, int prbCid = -1, int refCid = -1,
const std::vector<std::vector<std::pair<int,int> > > &map = std::vector<std::vector<std::pair<int,int> > >(),
int maxMatches = 1e6, bool symmetrizeConjugatedTerminalGroups = true,
const RDNumeric::DoubleVector *weights = nullptr) {
return RDKit::MolAlign::getBestRMS(*($self), refMol, prbCid, refCid, map, maxMatches, symmetrizeConjugatedTerminalGroups, weights);
}
/* From GraphMol/MolAlign/AlignMolecules */

30
Code/JavaWrappers/RWMol.i
View File

@@ -54,36 +54,40 @@
%javaconst(1);
#endif
%include <GraphMol/FileParsers/FileParsers.h>
%include <GraphMol/SmilesParse/SmilesParse.h>
%include <GraphMol/RWMol.h>
%extend RDKit::RWMol {
static RDKit::RWMOL_SPTR MolFromSmiles(std::string smi,int debugParse=0,bool sanitize=1,
static RDKit::RWMOL_SPTR MolFromSmiles(const std::string &smi,int debugParse=0,bool sanitize=1,
std::map<std::string,std::string> *replacements=0){
return RDKit::RWMOL_SPTR(RDKit::SmilesToMol(smi, debugParse, sanitize,replacements));
}
static RDKit::RWMOL_SPTR MolFromSmarts(std::string sma,int debugParse=0,bool mergeHs=false,
static RDKit::RWMOL_SPTR MolFromSmiles(const std::string &smi, const RDKit::SmilesParserParams &params){
return RDKit::RWMOL_SPTR(RDKit::SmilesToMol(smi, params));
}
static RDKit::RWMOL_SPTR MolFromSmarts(const std::string &sma,int debugParse=0,bool mergeHs=false,
std::map<std::string,std::string> *replacements=0){
return RDKit::RWMOL_SPTR(RDKit::SmartsToMol(sma, debugParse, mergeHs,replacements));
}
static RDKit::RWMOL_SPTR MolFromMolBlock(std::string molB,
static RDKit::RWMOL_SPTR MolFromMolBlock(const std::string &molB,
bool sanitize=true,bool removeHs=true){
RDKit::RWMol *mol=0;
mol=RDKit::MolBlockToMol(molB,sanitize,removeHs);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromMolFile(std::string filename,
static RDKit::RWMOL_SPTR MolFromMolFile(const std::string &filename,
bool sanitize=true,bool removeHs=true){
RDKit::RWMol *mol=0;
mol=RDKit::MolFileToMol(filename,sanitize,removeHs);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromTPLFile(std::string fName,bool sanitize=true,
static RDKit::RWMOL_SPTR MolFromTPLFile(const std::string &fName,bool sanitize=true,
bool skipFirstConf=false) {
RDKit::RWMol *mol=0;
mol=RDKit::TPLFileToMol(fName, sanitize, skipFirstConf);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromMol2File(std::string fName,bool sanitize=true,bool removeHs=true,
static RDKit::RWMOL_SPTR MolFromMol2File(const std::string &fName,bool sanitize=true,bool removeHs=true,
RDKit::Mol2Type variant=RDKit::CORINA, bool cleanupSubstructures=true) {
RDKit::RWMol *mol=0;
mol=RDKit::Mol2FileToMol(fName, sanitize, removeHs, variant, cleanupSubstructures);
@@ -96,7 +100,7 @@ static RDKit::RWMOL_SPTR MolFromMol2Block(const std::string &molBlock,bool sanit
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromPDBBlock(std::string molB,
static RDKit::RWMOL_SPTR MolFromPDBBlock(const std::string &molB,
bool sanitize=true,bool removeHs=true,
unsigned int flavor=0,bool proximityBonding=true){
RDKit::RWMol *mol=0;
@@ -104,33 +108,33 @@ static RDKit::RWMOL_SPTR MolFromPDBBlock(std::string molB,
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromPDBFile(std::string fName,
static RDKit::RWMOL_SPTR MolFromPDBFile(const std::string &fName,
bool sanitize=true,bool removeHs=true,
unsigned int flavor=0,bool proximityBonding=true){
RDKit::RWMol *mol=0;
mol=RDKit::PDBFileToMol(fName,sanitize,removeHs,flavor,proximityBonding);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromSequence(std::string text,
static RDKit::RWMOL_SPTR MolFromSequence(const std::string &text,
bool sanitize=true,int flavor=0){
RDKit::RWMol *mol=0;
mol=RDKit::SequenceToMol(text,sanitize,flavor);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromFASTA(std::string text,
static RDKit::RWMOL_SPTR MolFromFASTA(const std::string &text,
bool sanitize=true,int flavor=0){
RDKit::RWMol *mol=0;
mol=RDKit::FASTAToMol(text,sanitize,flavor);
return RDKit::RWMOL_SPTR(mol);
}
static RDKit::RWMOL_SPTR MolFromHELM(std::string text,
static RDKit::RWMOL_SPTR MolFromHELM(const std::string &text,
bool sanitize=true){
RDKit::RWMol *mol=0;
mol=RDKit::HELMToMol(text,sanitize);
return RDKit::RWMOL_SPTR(mol);
}
static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(std::string text,
static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(const std::string &text,
bool sanitize=true){
auto res = RDKit::CDXMLToMols(text, sanitize);
std::vector<RDKit::RWMOL_SPTR> mols;
@@ -141,7 +145,7 @@ static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXML(std::string text,
}
static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXMLFile(std::string text,
static std::vector<RDKit::RWMOL_SPTR> MolsFromCDXMLFile(const std::string &text,
bool sanitize=true){
auto res = RDKit::CDXMLFileToMols(text, sanitize);
std::vector<RDKit::RWMOL_SPTR> mols;

21
Code/JavaWrappers/csharp_wrapper/CMakeLists.txt
View File

@@ -24,14 +24,27 @@ else()
SET(COPY_CMD cp -p ${COPY_SOURCE} ${COPY_DEST})
endif()
# Coax SWIG into playing nicely with Apple environments
if(APPLE)
# Coax SWIG into playing nicely with Apple/ARM environments
set(HAS_ARM_PROC FALSE)
string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} LOWERCASE_SYS_PROC)
if(LOWERCASE_SYS_PROC MATCHES "arm")
set(HAS_ARM_PROC TRUE)
endif()
# Based on https://github.com/mono/mono/blob/5d2e3bc3b3c8184d35b2f7801e88d96470d367c4/mcs/mcs/settings.cs#L54
# Mono seems to only support 32-bit ARM
if(APPLE OR HAS_ARM_PROC)
SET(CMAKE_SIZEOF_VOID_P 4)
endif(APPLE)
endif()
if(CMAKE_SIZEOF_VOID_P EQUAL 4)
SET(CMAKE_SWIG_FLAGS -namespace "GraphMolWrap")
if(HAS_ARM_PROC)
SET(PLATFORM "arm")
else()
SET(PLATFORM "x86")
endif()
else()
SET(PLATFORM "x64")
if (WIN32)
SET(CMAKE_SWIG_FLAGS -namespace "GraphMolWrap")
else()
@@ -89,7 +102,7 @@ if(NOT MSVC)
COMMAND ${CMAKE_COMMAND} -E make_directory swig_csharp
## 1. run this custom command only after swig has been run.
COMMAND ${GMCS_EXE} -out:RDKit2DotNet.dll -t:library "swig_csharp/*.cs"
COMMAND ${GMCS_EXE} -platform:${PLATFORM} -out:RDKit2DotNet.dll -t:library "swig_csharp/*.cs"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS "${swig_generated_file_fullname}"
)

628
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/Chemv2Tests.java
View File

@@ -34,232 +34,460 @@
package org.RDKit;
import static org.junit.Assert.*;
import java.io.File;
import java.util.Arrays;
import org.junit.Test;
public class Chemv2Tests extends GraphMolTest {
/* Pickling tests skipped for the time being */
@Test
public void testBasicStuff() {
ROMol m = RWMol.MolFromSmiles("COC(=O)O");
Atom a1 = m.getAtomWithIdx(1);
assertEquals( 8,a1.getAtomicNum() );
assertEquals( 6,m.getAtomWithIdx(2).getAtomicNum() );
Bond b1 = m.getBondWithIdx(1);
assertEquals( Bond.BondType.SINGLE,b1.getBondType() );
assertEquals( Bond.BondType.DOUBLE,m.getBondWithIdx(2).getBondType() );
assertEquals( Bond.BondType.SINGLE,m.getBondBetweenAtoms(0, 1).getBondType() );
}
/* Pickling tests skipped for the time being */
@Test
public void testBasicStuff() {
ROMol m = RWMol.MolFromSmiles("COC(=O)O");
Atom a1 = m.getAtomWithIdx(1);
assertEquals( 8,a1.getAtomicNum() );
assertEquals( 6,m.getAtomWithIdx(2).getAtomicNum() );
Bond b1 = m.getBondWithIdx(1);
assertEquals( Bond.BondType.SINGLE,b1.getBondType() );
assertEquals( Bond.BondType.DOUBLE,m.getBondWithIdx(2).getBondType() );
assertEquals( Bond.BondType.SINGLE,m.getBondBetweenAtoms(0, 1).getBondType() );
}
@Test
public void testEditingPersisting() {
RWMol m = RWMol.MolFromSmiles("COC(=C)O");
Atom a1 = m.getAtomWithIdx(3);
assertEquals("bad atom order",6, a1.getAtomicNum());
a1.setAtomicNum(7);
assertEquals("bad atom order",7, a1.getAtomicNum());
assertEquals("atom order not stored",7, m.getAtomWithIdx(3).getAtomicNum());
}
@Test
public void testEditingPersisting() {
RWMol m = RWMol.MolFromSmiles("COC(=C)O");
Atom a1 = m.getAtomWithIdx(3);
assertEquals("bad atom order",6, a1.getAtomicNum());
a1.setAtomicNum(7);
assertEquals("bad atom order",7, a1.getAtomicNum());
assertEquals("atom order not stored",7, m.getAtomWithIdx(3).getAtomicNum());
}
@Test
public void testSMARTSBasics () {
ROMol m = RWMol.MolFromSmiles("COC(=O)O");
ROMol p = RWMol.MolFromSmarts("CO");
assertTrue(m.hasSubstructMatch(p));
ROMol p2 = RWMol.MolFromSmarts("CS");
assertFalse(m.hasSubstructMatch(p2));
assertEquals( 2,p.getNumAtoms() );
assertEquals( 1,p.getNumBonds() );
assertTrue(m.hasSubstructMatch(p));
Match_Vect_Vect matches = m.getSubstructMatches(p);
assertEquals( 3,matches.size() );
Match_Vect match = matches.get(0);
assertEquals("bad match length", 2, match.size() );
matches = m.getSubstructMatches(p, false);
assertEquals( 3,matches.size() );
match = matches.get(0);
assertEquals("bad match length", 2, match.size() );
@Test
public void testSMARTSBasics () {
ROMol m = RWMol.MolFromSmiles("COC(=O)O");
ROMol p = RWMol.MolFromSmarts("CO");
assertTrue(m.hasSubstructMatch(p));
ROMol p2 = RWMol.MolFromSmarts("CS");
assertFalse(m.hasSubstructMatch(p2));
assertEquals( 2,p.getNumAtoms() );
assertEquals( 1,p.getNumBonds() );
assertTrue(m.hasSubstructMatch(p));
Match_Vect_Vect matches = m.getSubstructMatches(p);
assertEquals( 3,matches.size() );
Match_Vect match = matches.get(0);
assertEquals("bad match length", 2, match.size() );
matches = m.getSubstructMatches(p, false);
assertEquals( 3,matches.size() );
match = matches.get(0);
assertEquals("bad match length", 2, match.size() );
p = RWMol.MolFromSmarts("COC");
assertTrue(m.hasSubstructMatch(p));
assertEquals( 3,p.getNumAtoms() );
assertEquals( 2,p.getNumBonds() );
assertTrue(m.hasSubstructMatch(p));
matches = m.getSubstructMatches(p);
assertEquals( 1,matches.size() );
matches = m.getSubstructMatches(p, false);
assertEquals( 2,matches.size() );
}
p = RWMol.MolFromSmarts("COC");
assertTrue(m.hasSubstructMatch(p));
assertEquals( 3,p.getNumAtoms() );
assertEquals( 2,p.getNumBonds() );
assertTrue(m.hasSubstructMatch(p));
matches = m.getSubstructMatches(p);
assertEquals( 1,matches.size() );
matches = m.getSubstructMatches(p, false);
assertEquals( 2,matches.size() );
}
@Test
public void testDataGetSetSuccess() {
ROMol m = RWMol.MolFromSmiles("CCOC");
m.setProp("foo", "3");
String v = m.getProp("foo");
assertEquals("3",v);
}
@Test
public void testDataGetSetSuccess() {
ROMol m = RWMol.MolFromSmiles("CCOC");
m.setProp("foo", "3");
String v = m.getProp("foo");
assertEquals("3",v);
}
@Test(expected=KeyErrorException.class)
public void testDataGetSetFailure() {
ROMol m = RWMol.MolFromSmiles("CCOC");
m.getProp("monkey");
}
public void testDataGetSetFailure() {
ROMol m = RWMol.MolFromSmiles("CCOC");
m.getProp("monkey");
}
@Test
public void testIssue399() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
assertEquals( Bond.BondDir.BEGINDASH,m.getBondWithIdx(0).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(1).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(2).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(3).getBondDir() );
}
@Test
public void testIssue399() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
assertEquals( Bond.BondDir.BEGINDASH,m.getBondWithIdx(0).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(1).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(2).getBondDir() );
assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(3).getBondDir() );
}
@Test
public void test2DWithSetAtomLocs() {
ROMol m = RWMol.MolFromSmiles("C[C@H]1CO1");
Atom a0 = m.getAtomWithIdx(0);
Int_Point2D_Map coords = new Int_Point2D_Map();
coords.set((int) a0.getIdx(), new Point2D(1.0, 1.5));
RDKFuncs.setPreferCoordGen(false);
long confIdx = m.compute2DCoords(coords);
Conformer c = m.getConformer((int) confIdx);
assertEquals(1.0, c.getAtomPos(a0.getIdx()).getX(), defaultDoubleTol);
assertEquals(1.5, c.getAtomPos(a0.getIdx()).getY(), defaultDoubleTol);
}
@Test
public void test2DWithSetAtomLocs() {
ROMol m = RWMol.MolFromSmiles("C[C@H]1CO1");
Atom a0 = m.getAtomWithIdx(0);
Int_Point2D_Map coords = new Int_Point2D_Map();
coords.set((int) a0.getIdx(), new Point2D(1.0, 1.5));
RDKFuncs.setPreferCoordGen(false);
long confIdx = m.compute2DCoords(coords);
Conformer c = m.getConformer((int) confIdx);
assertEquals(1.0, c.getAtomPos(a0.getIdx()).getX(), defaultDoubleTol);
assertEquals(1.5, c.getAtomPos(a0.getIdx()).getY(), defaultDoubleTol);
}
@Test
public void testMatchingDepictions() {
ROMol template = RWMol.MolFromSmiles("c1nccc2n1ccc2");
template.compute2DCoords();
ROMol m = RWMol.MolFromSmiles("c1cccc2ncn3cccc3c21");
ROMol patt = RWMol.MolFromSmarts("*1****2*1***2");
m.generateDepictionMatching2DStructure(template,-1,patt);
@Test
public void testMatchingDepictions() {
ROMol template = RWMol.MolFromSmiles("c1nccc2n1ccc2");
template.compute2DCoords();
ROMol m = RWMol.MolFromSmiles("c1cccc2ncn3cccc3c21");
ROMol patt = RWMol.MolFromSmarts("*1****2*1***2");
m.generateDepictionMatching2DStructure(template,-1,patt);
// System.out.print(template.MolToMolBlock());
// System.out.print(m.MolToMolBlock());
Conformer c1 = template.getConformer();
Conformer c2 = m.getConformer();
assertEquals(c1.getAtomPos(0).getX(), c2.getAtomPos(6).getX(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getY(), c2.getAtomPos(6).getY(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getZ(), c2.getAtomPos(6).getZ(), defaultDoubleTol);
}
// System.out.print(template.MolToMolBlock());
// System.out.print(m.MolToMolBlock());
Conformer c1 = template.getConformer();
Conformer c2 = m.getConformer();
assertEquals(c1.getAtomPos(0).getX(), c2.getAtomPos(6).getX(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getY(), c2.getAtomPos(6).getY(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getZ(), c2.getAtomPos(6).getZ(), defaultDoubleTol);
}
@Test
public void testGenerateSVG() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
@Test
public void testGenerateSVG() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
String svg=m.ToSVG(8,50);
assertTrue(svg.indexOf("<svg")>-1);
assertTrue(svg.indexOf("</svg>")>-1);
}
}
@Test
public void testMolDraw2DSVG() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
@Test
public void testMolDraw2DSVG() {
ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
}
@Test
public void testMolDraw2DSVGSingleAtomMol() {
ROMol m = RWMol.MolFromSmiles("C");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
}
@Test
public void testNormalizeStraightenDepiction() {
ROMol noradrenalineMJ = RWMol.MolFromMolBlock("\n" +
" MJ201100 \n" +
"\n" +
" 12 12 0 0 1 0 0 0 0 0999 V2000\n" +
" 2.2687 1.0716 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.4437 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.0312 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.4437 -0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 0.2062 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -0.2062 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.0312 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.4437 -1.0716 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.4437 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -2.2687 0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.0312 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -0.2062 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 1 0 0 0 0\n" +
" 3 2 1 0 0 0 0\n" +
" 3 4 1 6 0 0 0\n" +
" 3 5 1 0 0 0 0\n" +
" 5 6 2 0 0 0 0\n" +
" 6 7 1 0 0 0 0\n" +
" 7 8 1 0 0 0 0\n" +
" 7 9 2 0 0 0 0\n" +
" 9 10 1 0 0 0 0\n" +
" 9 11 1 0 0 0 0\n" +
" 11 12 2 0 0 0 0\n" +
" 5 12 1 0 0 0 0\n" +
"M END");
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) < 1.e-5);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 1.875, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 1.513, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -0.321, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 1.340, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -0.773, 1.e-3);
Point3D bond4_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(4));
assertEquals(bond4_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond4_11Conf1.getY(), 1.547, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), 1.547, 1.e-3);
assertEquals(bond10_11Conf2.getY(), 0.0, 1.e-3);
Point3D bond4_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(4));
assertEquals(bond4_11Conf2.getX(), -0.773, 1.e-3);
assertEquals(bond4_11Conf2.getY(), 1.339, 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
}
@Test
public void testMolDraw2DSVGSingleAtomMol() {
ROMol m = RWMol.MolFromSmiles("C");
m.compute2DCoords();
Conformer c = m.getConformer();
m.WedgeMolBonds(c);
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1, -1);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 1.875, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 0.321, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 1.513, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 1.547, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), bond10_11Conf1.getX(), 1.e-3);
assertEquals(bond10_11Conf2.getY(), bond10_11Conf1.getY(), 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
}
@Test
public void testPrepareMolForDrawing() {
RWMol m = RWMol.MolFromSmiles("c1ccccc1");
RDKFuncs.prepareMolForDrawing(m);
assertEquals(m.getNumConformers(), 1);
assertTrue(m.getBondBetweenAtoms(0, 1).getBondType() !=
Bond.BondType.AROMATIC);
assertTrue(m.getBondBetweenAtoms(0, 1).getIsAromatic());
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1, 0, 3.0);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 3.0, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Conformer conformer3 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer3, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 2.475, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 0.0, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 2.143, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -1.237, 1.e-3);
Point3D bond4_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(4));
assertEquals(bond4_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond4_11Conf1.getY(), 2.475, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
Point3D bond10_11Conf3 = conformer3.getAtomPos(11).minus(conformer3.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), bond10_11Conf3.getX(), 1.e-3);
assertEquals(bond10_11Conf2.getY(), bond10_11Conf3.getY(), 1.e-3);
Point3D bond4_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(4));
Point3D bond4_11Conf3 = conformer3.getAtomPos(11).minus(conformer3.getAtomPos(4));
assertEquals(bond4_11Conf2.getX(), bond4_11Conf3.getX(), 1.e-3);
assertEquals(bond4_11Conf2.getY(), bond4_11Conf3.getY(), 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
conformer3.delete();
}
@Test
public void testMolDraw2DHighlight() {
RWMol m = RWMol.MolFromSmiles("CCCCCOC");
RDKFuncs.prepareMolForDrawing(m);
Int_Vect hats = new Int_Vect();
hats.add(0);
hats.add(1);
hats.add(2);
}
Int_Vect hbs = new Int_Vect();
hbs.add(0);
hbs.add(1);
hbs.add(2);
@Test
public void testGetBestRMS() {
String rdpath = System.getenv("RDBASE");
if (rdpath == null)
org.junit.Assert.fail("No definition for RDBASE");
File base = new File(rdpath);
File testFile = new File(base, "Code" + File.separator + "GraphMol"
+ File.separator + "MolAlign" + File.separator + "test_data"
+ File.separator + "probe_mol.sdf");
String fName = testFile.getAbsolutePath();
SDMolSupplier supplier = new SDMolSupplier(fName, true, false);
supplier.next();
ROMol prb = supplier.next();
ROMol ref = supplier.next();
ROMol prbCopy1 = new ROMol(prb);
ROMol prbCopy2 = new ROMol(prb);
ROMol prbCopy3 = new ROMol(prb);
Transform3D bestTrans = new Transform3D();
Match_Vect bestMatch = new Match_Vect();
ColourPalette atCs = new ColourPalette();
atCs.set(0, new DrawColour(1, 1, 0));
atCs.set(1, new DrawColour(1, 0, 1));
atCs.set(2, new DrawColour(0, 1, 1));
ColourPalette bCs = new ColourPalette();
// alignMol() would return this for the rms: 2.50561
// But the best rms is: 2.43449
double rmsdInPlace = prbCopy1.calcRMS(ref);
assertEquals(rmsdInPlace, 2.6026, 1.e-3);
double rmsd = prb.getBestRMS(ref);
assertEquals(rmsd, 2.43449, 1.e-3);
double rmsdCopy = prbCopy1.getBestAlignmentTransform(ref, bestTrans, bestMatch);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), ref.getNumAtoms());
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m, "THE_LEGEND", hats, hbs, atCs, bCs);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
// System.out.print(svg);
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
assertTrue(svg.indexOf("fill:#FFFF00;") > -1);
assertTrue(svg.indexOf("fill:#FF00FF;") > -1);
assertTrue(svg.indexOf("fill:#00FFFF;") > -1);
// default line color:
assertTrue(svg.indexOf("stroke:#FF7F7F;") > -1);
SmilesParserParams params = new SmilesParserParams();
params.setRemoveHs(false);
RWMol scaffold = RWMol.MolFromSmiles("N1C([H])([H])C([H])([H])C([H])([H])[N+]([H])([H])C([H])([H])C1([H])[H]", params);
Match_Vect scaffoldMatch = ref.getSubstructMatch(scaffold);
assertFalse(scaffoldMatch.isEmpty());
int nAtoms = (int)ref.getNumAtoms();
boolean[] scaffoldIndices = new boolean[nAtoms];
Arrays.fill(scaffoldIndices, false);
for (int i = 0; i < scaffoldMatch.size(); ++i) {
int pairSecond = scaffoldMatch.get(i).getSecond();
scaffoldIndices[pairSecond] = true;
}
@Test
public void testMolDraw2DContours() {
// really just a test to make sure this can be called
RWMol m = RWMol.MolFromSmiles("CCCCCOC");
RDKFuncs.prepareMolForDrawing(m);
Point2D_Vect cents = new Point2D_Vect();
Double_Vect weights = new Double_Vect();
Double_Vect widths = new Double_Vect();
for(int i=0;i<m.getNumAtoms();++i){
cents.add(new Point2D(m.getConformer().getAtomPos(i)));
weights.add(1.0);
widths.add(0.4);
}
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.clearDrawing();
RDKFuncs.ContourAndDrawGaussians(drawer,cents,weights,widths,10);
drawer.drawOptions().setClearBackground(false);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
System.out.print(svg);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.Chemv2Tests");
}
Match_Vect_Vect matches = ref.getSubstructMatches(prb, false);
Match_Vect_Vect matchesPruned = new Match_Vect_Vect(matches.size());
for (int i = 0; i < matches.size(); ++i) {
Match_Vect match = matches.get(i);
Match_Vect matchPruned = new Match_Vect();
for (int j = 0; j < match.size(); ++j) {
int pairSecond = match.get(j).getSecond();
if (scaffoldIndices[pairSecond]) {
matchPruned.add(match.get(j));
}
}
matchesPruned.set(i, matchPruned);
matchPruned.delete();
}
rmsdInPlace = prbCopy2.calcRMS(ref, -1, -1, matchesPruned);
assertEquals(rmsdInPlace, 2.5672, 1.e-3);
rmsd = prb.getBestRMS(ref, -1, -1, matchesPruned);
assertEquals(rmsd, 1.14329, 1.e-3);
rmsdCopy = prbCopy2.getBestAlignmentTransform(ref, bestTrans, bestMatch, -1, -1, matchesPruned);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), scaffoldMatch.size());
DoubleVector weights = new DoubleVector(nAtoms, 1.0);
for (int i = 0; i < nAtoms; ++i) {
if (scaffoldIndices[i]) {
weights.setVal(i, 100.0);
}
}
rmsdInPlace = prbCopy3.calcRMS(ref, -1, -1, matches, 1000, true, weights);
assertEquals(rmsdInPlace, 17.7959, 1.e-3);
rmsd = prb.getBestRMS(ref, -1, -1, matches, 1000, true, weights);
assertEquals(rmsd, 10.9681, 1.e-3);
rmsdCopy = prbCopy3.getBestAlignmentTransform(ref, bestTrans, bestMatch, -1, -1, matches, 1000, true, weights);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), ref.getNumAtoms());
supplier.delete();
prbCopy1.delete();
prbCopy2.delete();
prbCopy3.delete();
params.delete();
matchesPruned.delete();
weights.delete();
}
@Test
public void testPrepareMolForDrawing() {
RWMol m = RWMol.MolFromSmiles("c1ccccc1");
RDKFuncs.prepareMolForDrawing(m);
assertEquals(m.getNumConformers(), 1);
assertTrue(m.getBondBetweenAtoms(0, 1).getBondType() !=
Bond.BondType.AROMATIC);
assertTrue(m.getBondBetweenAtoms(0, 1).getIsAromatic());
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
}
@Test
public void testMolDraw2DHighlight() {
RWMol m = RWMol.MolFromSmiles("CCCCCOC");
RDKFuncs.prepareMolForDrawing(m);
Int_Vect hats = new Int_Vect();
hats.add(0);
hats.add(1);
hats.add(2);
Int_Vect hbs = new Int_Vect();
hbs.add(0);
hbs.add(1);
hbs.add(2);
ColourPalette atCs = new ColourPalette();
atCs.set(0, new DrawColour(1, 1, 0));
atCs.set(1, new DrawColour(1, 0, 1));
atCs.set(2, new DrawColour(0, 1, 1));
ColourPalette bCs = new ColourPalette();
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.drawMolecule(m, "THE_LEGEND", hats, hbs, atCs, bCs);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
// System.out.print(svg);
assertTrue(svg.indexOf("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -1);
assertTrue(svg.indexOf("fill:#FFFF00;") > -1);
assertTrue(svg.indexOf("fill:#FF00FF;") > -1);
assertTrue(svg.indexOf("fill:#00FFFF;") > -1);
// default line color:
assertTrue(svg.indexOf("stroke:#FF7F7F;") > -1);
}
@Test
public void testMolDraw2DContours() {
// really just a test to make sure this can be called
RWMol m = RWMol.MolFromSmiles("CCCCCOC");
RDKFuncs.prepareMolForDrawing(m);
Point2D_Vect cents = new Point2D_Vect();
Double_Vect weights = new Double_Vect();
Double_Vect widths = new Double_Vect();
for(int i=0;i<m.getNumAtoms();++i){
cents.add(new Point2D(m.getConformer().getAtomPos(i)));
weights.add(1.0);
widths.add(0.4);
}
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.clearDrawing();
RDKFuncs.ContourAndDrawGaussians(drawer,cents,weights,widths,10);
drawer.drawOptions().setClearBackground(false);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
System.out.print(svg);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.Chemv2Tests");
}
}

1
Code/JavaWrappers/transforms.i
View File

@@ -53,6 +53,7 @@
%template(IntSymmMatrix) RDNumeric::SymmMatrix<int>;
%template(DoubleSymmMatrix) RDNumeric::SymmMatrix<double>;
%template(DoubleSquareMatrix) RDNumeric::SquareMatrix<double>;
%template(DoubleVector) RDNumeric::Vector<double>;
%include <Geometry/Transform.h>
%include <Geometry/Transform2D.h>