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Removed the dependency on the data module, by adding the IChemObjectB…
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…uilder to the API

Change-Id: I05dc82cee22450879bec44bbbd8c98c58c9b7d75
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
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@egonw @johnmay
egonw authored and johnmay committed Dec 21, 2013
1 parent e596106 commit b569dec
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Showing 12 changed files with 67 additions and 73 deletions.
1 change: 0 additions & 1 deletion src/META-INF/forcefield.cdkdepends
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@@ -1,6 +1,5 @@
cdk-annotation.jar
cdk-core.jar
cdk-data.jar
cdk-interfaces.jar
cdk-io.jar
cdk-standard.jar
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
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Expand Up @@ -72,7 +72,7 @@ public MMFF94PartialCharges() { }
*/
public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws Exception {
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.setForceFieldConfigurator("mmff94", ac.getBuilder());
ffc.assignAtomTyps(ac);
Map<String,Object> parameterSet = ffc.getParameterSet();
// for this calculation,
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15 changes: 8 additions & 7 deletions src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
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Expand Up @@ -41,6 +41,7 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
Expand Down Expand Up @@ -127,7 +128,7 @@ public boolean checkForceFieldType(String ffname) {
* @param ffname name of the force field data file
*/
@TestMethod("testSetForceFieldConfigurator")
public void setForceFieldConfigurator(String ffname) throws CDKException {
public void setForceFieldConfigurator(String ffname, IChemObjectBuilder builder) throws CDKException {
ffname=ffname.toLowerCase();
boolean check=false;

Expand All @@ -145,7 +146,7 @@ public void setForceFieldConfigurator(String ffname) throws CDKException {
mm2.setInputStream(ins);
//logger.debug("ForceFieldConfigurator: mm2 set input stream ... READY");
try{
this.setMM2Parameters();
this.setMM2Parameters(builder);
}catch (Exception ex1){
throw new CDKException("Problems with set MM2Parameters due to "+ex1.toString(), ex1);
}
Expand All @@ -158,7 +159,7 @@ public void setForceFieldConfigurator(String ffname) throws CDKException {

mmff94.setInputStream(ins);
try{
this.setMMFF94Parameters();
this.setMMFF94Parameters(builder);
}catch (Exception ex2){
throw new CDKException("Problems with set MM2Parameters due to"+ex2.toString(), ex2);
}
Expand Down Expand Up @@ -190,22 +191,22 @@ public void setParameters(Map<String, Object> parameterset) {
* Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
*/
@TestMethod("testSetMM2Parameters")
public void setMM2Parameters() throws CDKException{
public void setMM2Parameters(IChemObjectBuilder builder) throws CDKException{
try{
if(mm2 == null)
mm2 = new MM2BasedParameterSetReader();
mm2.readParameterSets();
mm2.readParameterSets(builder);
}catch(Exception ex1){
throw new CDKException("Problem within readParameterSets due to:"+ex1.toString(), ex1);
}
parameterSet = mm2.getParamterSet();
atomTypes = mm2.getAtomTypes();
}
@TestMethod("testSetMMFF94Parameters")
public void setMMFF94Parameters() throws Exception{
public void setMMFF94Parameters(IChemObjectBuilder builder) throws Exception{
if(mmff94 == null)
mmff94 = new MMFF94BasedParameterSetReader();
mmff94.readParameterSets();
mmff94.readParameterSets(builder);
parameterSet = mmff94.getParamterSet();
atomTypes = mmff94.getAtomTypes();
}
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19 changes: 6 additions & 13 deletions src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,5 @@
/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2005-2007 Christian Hoppe <chhoppe@users.sf.net>
/* Copyright (C) 2005-2007 Christian Hoppe <chhoppe@users.sf.net>
* 2013 Egon Willighagen <egonw@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
Expand Down Expand Up @@ -40,8 +36,6 @@
import java.util.StringTokenizer;
import java.util.Vector;

import org.openscience.cdk.AtomType;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.config.Isotopes;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
Expand Down Expand Up @@ -266,7 +260,7 @@ private void setForceFieldDefinitions() throws Exception {
*
* @exception Exception Description of the Exception
*/
private void setAtomTypes() throws Exception {
private void setAtomTypes(IChemObjectBuilder builder) throws Exception {
String name = "";
String rootType = "";
int an = 0;
Expand Down Expand Up @@ -294,7 +288,7 @@ private void setAtomTypes() throws Exception {
"Malformed Number");
}

IAtomType atomType = new AtomType(name, rootType);
IAtomType atomType = builder.newInstance(IAtomType.class, name, rootType);
atomType.setAtomicNumber(an);
atomType.setExactMass(mass);
atomType.setMassNumber(massNumber(an, mass));
Expand Down Expand Up @@ -810,7 +804,7 @@ private void setPiBond() throws Exception {
*
* @exception Exception Description of the Exception
*/
public void readParameterSets() throws Exception {
public void readParameterSets(IChemObjectBuilder builder) throws Exception {
//vdW,vdWp,bond,bond4,bond3,angle,angle4,angle3,
//strbond,opbend,torsion,torsion4,charge,dipole,
//dipole3,piatom,pibond,dipole3
Expand Down Expand Up @@ -840,7 +834,7 @@ public void readParameterSets() throws Exception {
a[0]++;
} else if (s.startsWith("atom") & nt <= 8) {
a[0]++;
setAtomTypes();
setAtomTypes(builder);
} else if (s.startsWith("vdw ") & nt <= 5) {
setvdWaals();
a[1]++;
Expand Down Expand Up @@ -909,7 +903,6 @@ public void readParameterSets() throws Exception {
*/
private Integer massNumber(int atomicNumber, double exactMass) throws IOException {
String symbol = PeriodicTable.getSymbol(atomicNumber);
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IIsotope isotope = Isotopes.getInstance()
.getIsotope(symbol,
exactMass,
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10 changes: 5 additions & 5 deletions src/main/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,9 @@
import java.util.StringTokenizer;
import java.util.Vector;

import org.openscience.cdk.AtomType;
import org.openscience.cdk.config.Isotopes;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.tools.periodictable.PeriodicTable;

Expand Down Expand Up @@ -177,7 +177,7 @@ private void setAtomTypeData() throws Exception {
*
* @exception Exception Description of the Exception
*/
private void setAtomTypes() throws Exception {
private void setAtomTypes(IChemObjectBuilder builder) throws Exception {
String name = "";
String rootType = "";
//int an = 0;
Expand Down Expand Up @@ -207,7 +207,7 @@ private void setAtomTypes() throws Exception {
"Malformed Number");
}

AtomType atomType = new AtomType(name, rootType);
IAtomType atomType = builder.newInstance(IAtomType.class, name, rootType);
atomType.setAtomicNumber(atomNr);
atomType.setExactMass(mass);
atomType.setMassNumber(massNumber(atomNr, mass));
Expand Down Expand Up @@ -450,7 +450,7 @@ private void setDefaultStrBnd() throws Exception {
*
* @exception Exception Description of the Exception
*/
public void readParameterSets() throws Exception {
public void readParameterSets(IChemObjectBuilder builder) throws Exception {
//vdW,bond,angle,strbond,opbend,torsion,data
//logger.debug("------ Read MMFF94 ParameterSets ------");

Expand Down Expand Up @@ -498,7 +498,7 @@ public void readParameterSets() throws Exception {
st = new StringTokenizer(s,"\t; ");
int nt = st.countTokens();
if (s.startsWith("atom") & nt <= 8) {
setAtomTypes();
setAtomTypes(builder);
a[0]++;
} else if (s.startsWith("bond") & nt == 9) {
setBond();
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17 changes: 9 additions & 8 deletions src/main/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.layout.AtomPlacer;
import org.openscience.cdk.ringsearch.RingPartitioner;
Expand Down Expand Up @@ -92,28 +93,28 @@ public class ModelBuilder3D {
* @param templateHandler templateHandler Object
* @param ffname name of force field
*/
private ModelBuilder3D(TemplateHandler3D templateHandler, String ffname) throws CDKException {
private ModelBuilder3D(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder builder) throws CDKException {
setTemplateHandler(templateHandler);
setForceField(ffname);
setForceField(ffname, builder);
}

public static ModelBuilder3D getInstance(TemplateHandler3D templateHandler, String ffname) throws CDKException {
public static ModelBuilder3D getInstance(TemplateHandler3D templateHandler, String ffname, IChemObjectBuilder chemObjectBuilder) throws CDKException {
if (ffname == null || ffname.length() == 0) throw new CDKException("The given ffname is null or empty!");
if (templateHandler == null) throw new CDKException("The given template handler is null!");

String builderCode = templateHandler.getClass().getName()+ "#" + ffname;
if (!memyselfandi.containsKey(builderCode)) {
ModelBuilder3D builder = new ModelBuilder3D(
templateHandler, ffname
templateHandler, ffname, chemObjectBuilder
);
memyselfandi.put(builderCode, builder);
return builder;
}
return memyselfandi.get(builderCode);
}

public static ModelBuilder3D getInstance() throws CDKException {
return getInstance(TemplateHandler3D.getInstance(), "mm2");
public static ModelBuilder3D getInstance(IChemObjectBuilder builder) throws CDKException {
return getInstance(TemplateHandler3D.getInstance(), "mm2", builder);
}

/**
Expand All @@ -131,13 +132,13 @@ public String[] getFfTypes(){
*
* @param ffname forceField name
*/
private void setForceField(String ffname) throws CDKException {
private void setForceField(String ffname, IChemObjectBuilder builder) throws CDKException {
if (ffname == null) {
ffname = "mm2";
}
try {
forceFieldName = ffname;
ffc.setForceFieldConfigurator(ffname);
ffc.setForceFieldConfigurator(ffname, builder);
parameterSet = ffc.getParameterSet();
} catch (CDKException ex1) {
logger.error("Problem with ForceField configuration due to>" + ex1.getMessage());
Expand Down
26 changes: 13 additions & 13 deletions src/test/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ public void testCheckForceFieldType_String() {
@Test
public void testSetForceFieldConfigurator_String() throws CDKException {
String forceFieldName = "mmff94";
forceFieldConfigurator.setForceFieldConfigurator(forceFieldName);
forceFieldConfigurator.setForceFieldConfigurator(forceFieldName, DefaultChemObjectBuilder.getInstance());
List<IAtomType> mmff94AtomTypes = forceFieldConfigurator.getAtomTypes();
assertNotNull(mmff94AtomTypes);
IAtomType atomtype0 = mmff94AtomTypes.get(0);
Expand All @@ -75,7 +75,7 @@ public void testSetForceFieldConfigurator_String() throws CDKException {
assertEquals("Csp2", atomtype1.getAtomTypeName());

forceFieldName = "mm2";
forceFieldConfigurator.setForceFieldConfigurator(forceFieldName);
forceFieldConfigurator.setForceFieldConfigurator(forceFieldName, DefaultChemObjectBuilder.getInstance());
List<IAtomType> mm2AtomTypes = forceFieldConfigurator.getAtomTypes();
assertNotNull(mm2AtomTypes);
IAtomType atomtype2 = mm2AtomTypes.get(2);
Expand All @@ -87,7 +87,7 @@ public void testSetForceFieldConfigurator_String() throws CDKException {

@Test
public void testSetMM2Parameters() throws CDKException {
forceFieldConfigurator.setMM2Parameters();
forceFieldConfigurator.setMM2Parameters(DefaultChemObjectBuilder.getInstance());
assertNotNull(forceFieldConfigurator.getParameterSet());
List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes();
IAtomType atomtype1 = atomtypeList.get(1);
Expand All @@ -98,7 +98,7 @@ public void testSetMM2Parameters() throws CDKException {

@Test
public void testSetMMFF94Parameters() throws Exception {
forceFieldConfigurator.setMMFF94Parameters();
forceFieldConfigurator.setMMFF94Parameters(DefaultChemObjectBuilder.getInstance());
assertNotNull(forceFieldConfigurator.getParameterSet());
List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes();
IAtomType atomtype4 = atomtypeList.get(4);
Expand Down Expand Up @@ -130,7 +130,7 @@ public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_hydroxyurea() thro
SmilesParser parser = new SmilesParser(builder);
IAtomContainer hu = parser.parseSmiles(husmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.setForceFieldConfigurator("mmff94", builder);
IAtom N1= hu.getAtom(0);
IAtom N2 = hu.getAtom(3);
ffc.configureAtom(N1,
Expand All @@ -151,7 +151,7 @@ public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_propanamide() thro
SmilesParser parser = new SmilesParser(builder);
IAtomContainer pa = parser.parseSmiles(pasmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.setForceFieldConfigurator("mmff94", builder);
IAtom amideN = pa.getAtom(0);
ffc.configureMMFF94BasedAtom(amideN,
new HOSECodeGenerator().getHOSECode(pa, amideN, 3),
Expand All @@ -170,7 +170,7 @@ public void testConfigureMMFF94BasedAtom_IAtom_String_boolean_urea() throws CDKE
SmilesParser parser = new SmilesParser(builder);
IAtomContainer urea = parser.parseSmiles(usmi);
ForceFieldConfigurator ffc = new ForceFieldConfigurator();
ffc.setForceFieldConfigurator("mmff94");
ffc.setForceFieldConfigurator("mmff94", builder);
IAtom amideN = urea.getAtom(0);
ffc.configureMMFF94BasedAtom(amideN,
new HOSECodeGenerator().getHOSECode(urea, amideN, 3),
Expand Down Expand Up @@ -199,7 +199,7 @@ public void testAssignAtomTyps_test4_hydroxyurea() throws CDKException {
for(int i=0; i<molecule.getAtomCount(); i++) {
assertEquals(originalAtomTypes[i],molecule.getAtom(i).getAtomTypeName());
}
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IRingSet moleculeRingSet = forceFieldConfigurator.assignAtomTyps(molecule);
//no rings
assertEquals(0, moleculeRingSet.getAtomContainerCount());
Expand All @@ -221,7 +221,7 @@ public void testAssignAtomTyps_bug() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
SmilesParser parser = new SmilesParser(builder);
IAtomContainer bugmol = parser.parseSmiles(smiles);
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IAtom amideN = bugmol.getAtom(11);
forceFieldConfigurator.configureMMFF94BasedAtom(amideN,
new HOSECodeGenerator().getHOSECode(bugmol, amideN, 3),
Expand All @@ -239,7 +239,7 @@ public void testAssignAtomTyps_bug_no2() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
SmilesParser parser = new SmilesParser(builder);
IAtomContainer bugmol = parser.parseSmiles(smiles);
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IAtom amideN = bugmol.getAtom(2);
forceFieldConfigurator.configureMMFF94BasedAtom(amideN,
new HOSECodeGenerator().getHOSECode(bugmol, amideN, 3),
Expand All @@ -259,7 +259,7 @@ public void testAssignAtomTyps_bug_so2() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
SmilesParser parser = new SmilesParser(builder);
IAtomContainer bugmol = parser.parseSmiles(smiles);
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IAtom sulphur = bugmol.getAtom(1);
HOSECodeGenerator hscodegen = new HOSECodeGenerator();
forceFieldConfigurator.configureAtom(sulphur,
Expand All @@ -276,7 +276,7 @@ public void testAssignAtomTyps_bug_nitrogenatomType() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
SmilesParser parser = new SmilesParser(builder);
IAtomContainer bugmol = parser.parseSmiles(smiles);
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IAtom nitrogen1 = bugmol.getAtom(1);
IAtom nitrogen2 = bugmol.getAtom(4);
IAtom nitrogen3 = bugmol.getAtom(6);
Expand All @@ -301,7 +301,7 @@ public void testAssignAtomTyps_bug_amideRingAtomType() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
SmilesParser parser = new SmilesParser(builder);
IAtomContainer bugmol = parser.parseSmiles(smiles);
forceFieldConfigurator.setForceFieldConfigurator("mmff94");
forceFieldConfigurator.setForceFieldConfigurator("mmff94", builder);
IAtom nitrogen1 = bugmol.getAtom(2);
HOSECodeGenerator hscodegen = new HOSECodeGenerator();
forceFieldConfigurator.configureAtom(nitrogen1,
Expand Down
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