Author: scooter
Date: 2010-01-27 14:18:20 -0800 (Wed, 27 Jan 2010)
New Revision: 19050
Modified:
csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
Log:
Remove dead code and workaround cdk bug in the calculation of MW
Modified: csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props 2010-01-27
16:18:45 UTC (rev 19049)
+++ csplugins/trunk/ucsf/scooter/chemViz/resources/plugin.props 2010-01-27
22:18:20 UTC (rev 19050)
@@ -13,7 +13,7 @@
pluginDescription=This plugin provides a variety of cheminformatics
descriptors and visualizations
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.9
+pluginVersion=1.0
# Compatible Cytoscape version
cytoscapeVersion=2.6.3
@@ -28,7 +28,7 @@
# List of authors. Note each author and institution pair are separated by a :
(colon)
# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
-pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF
+pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF;Dazhi Jiao:Indiana
University School of Informatics
# Date this plugin/plugin version was released
releaseDate=January 22, 2010
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2010-01-27 16:18:45 UTC (rev 19049)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2010-01-27 22:18:20 UTC (rev 19050)
@@ -67,6 +67,7 @@
import org.openscience.cdk.Molecule;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
@@ -77,6 +78,7 @@
import org.openscience.cdk.inchi.InChIToStructure;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IIsotope;;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.layout.StructureDiagramGenerator;
@@ -422,9 +424,12 @@
CDKHueckelAromaticityDetector.detectAromaticity(iMolecule);
+ // Make sure we update our implicit hydrogens
+ CDKHydrogenAdder adder =
CDKHydrogenAdder.getInstance(iMolecule.getBuilder());
+ adder.addImplicitHydrogens(iMolecule);
+
// Get our fingerprint
Fingerprinter fp = new Fingerprinter();
-
// Do we need to do the addh here?
fingerPrint =
fp.getFingerprint(addh(iMolecule));
}
@@ -533,10 +538,10 @@
return getAttribute();
case IDENTIFIER:
return getMoleculeString();
- case WEIGHT:
- return getMolecularWeight();
case MASS:
return getExactMass();
+ case WEIGHT:
+ return getMolecularWeight();
case WEINERPATH:
case WEINERPOL:
{
@@ -674,9 +679,25 @@
public double getMolecularWeight() {
if (iMolecule == null) return 0.0f;
-
IMolecularFormula mfa =
MolecularFormulaManipulator.getMolecularFormula(addh(iMolecule));
- return MolecularFormulaManipulator.getTotalMassNumber(mfa);
+ // System.out.println("Formula:
"+MolecularFormulaManipulator.getString(mfa));
+
+ // This method returns the total atomic number, *not* the total
mass number. Do this
+ // by ourselves until this is fixed.
+ // return MolecularFormulaManipulator.getTotalMassNumber(mfa);
+
+ double mass = 0.0;
+ for (IIsotope isotope : mfa.isotopes()) {
+ try {
+ IIsotope isotope2 =
IsotopeFactory.getInstance(mfa.getBuilder()).getMajorIsotope(isotope.getSymbol());
+ // System.out.println("Isotope:
"+isotope.getSymbol()+" has atomic number "+isotope2.getAtomicNumber());
+ // System.out.println("Isotope:
"+isotope.getSymbol()+" has mass number "+isotope2.getMassNumber());
+ mass += isotope2.getMassNumber() *
mfa.getIsotopeCount(isotope);
+ } catch (IOException e) {
+ return 0.0f;
+ }
+ }
+ return mass;
}
/**
@@ -691,57 +712,6 @@
return MolecularFormulaManipulator.getTotalExactMass(mfa);
}
- /**
- * Use the chimeraservices smi2gif service to get a 2D image of this
compound.
- *
- * @return the fetched image
- */
- public Image depictWithUCSFSmi2Gif() {
- if (this.moleculeString == null || "".equals(moleculeString)) {
- return null;
- }
- String url = getDepictURL();
- Image image = null;
- try {
- InputStream in = URLUtil.getInputStream(new URL(url));
- image = ImageIO.read(in);
- } catch (MalformedURLException muex) {
- logger.error("Unable to connect to UCSF SMILES
depiction services: "+muex.getMessage(), muex);
- return null;
- } catch (IOException ioex) {
- logger.error("Unable to connect to UCSF SMILES
depiction services: "+ioex.getMessage(), ioex);
- return null;
- }
- return image;
- }
-
- /**
- * Use the chimeraservices smi2gif service to get a 2D image of a
specific size for this compound.
- *
- * @param width the width of the rendered image
- * @param height the height of the rendered image
- * @param bgcolor the background color of the rendered image
- * @return the fetched image
- */
- public Image depictWithUCSFSmi2Gif(int width, int height, String
bgcolor) {
- if (this.moleculeString == null || "".equals(moleculeString)) {
- return null;
- }
- String url = getDepictURL(width, height, bgcolor);
- Image image = null;
- try {
- InputStream in = URLUtil.getInputStream(new URL(url));
- image = ImageIO.read(in);
- } catch (MalformedURLException muex) {
- logger.error("Unable to connect to UCSF SMILES
depiction services: "+muex.getMessage(), muex);
- return null;
- } catch (IOException ioex) {
- logger.error("Unable to connect to UCSF SMILES
depiction services: "+ioex.getMessage(), ioex);
- return null;
- }
- return image;
- }
-
public Image depictWithCDK(int width, int height, Color background) {
BufferedImage bufferedImage = null;
@@ -834,66 +804,25 @@
InChIGeneratorFactory factory =
InChIGeneratorFactory.getInstance();
InChIToStructure intostruct =
factory.getInChIToStructure(inchi, DefaultChemObjectBuilder.getInstance());
- // Get the structure
- INCHI_RET ret = intostruct.getReturnStatus();
- if (ret == INCHI_RET.WARNING) {
- logger.warning("InChI warning: " +
intostruct.getMessage());
- } else if (ret != INCHI_RET.OKAY) {
- logger.error("Structure generation failed failed: " +
ret.toString()
- + " [" + intostruct.getMessage() + "]");
- return null;
- }
+ // Get the structure
+ INCHI_RET ret = intostruct.getReturnStatus();
+ if (ret == INCHI_RET.WARNING) {
+ logger.warning("InChI warning: " +
intostruct.getMessage());
+ } else if (ret != INCHI_RET.OKAY) {
+ logger.error("Structure generation failed
failed: " + ret.toString()
+ + " [" + intostruct.getMessage() + "]");
+ return null;
+ }
- iMolecule = new Molecule(intostruct.getAtomContainer());
- // Use the molecule to create a SMILES string
- SmilesGenerator sg = new SmilesGenerator();
- return sg.createSMILES(iMolecule);
+ iMolecule = new Molecule(intostruct.getAtomContainer());
+ // Use the molecule to create a SMILES string
+ SmilesGenerator sg = new SmilesGenerator();
+ return sg.createSMILES(iMolecule);
} catch (Exception e) {
logger.error("Structure generation failed failed: " +
e.getMessage());
return null;
}
- /*
- String url =
"http://www.chemspider.com/inchi.asmx/InChIToSMILES?inchi=";
- + inchi.trim();
- String smiles = null;
- try {
- String result = URLUtil.download(new URL(url));
- Pattern pattern =
Pattern.compile(".*<[^>]*>([^<]*)</string>");
- Matcher matcher = pattern.matcher(result);
- if (matcher.find()) {
- smiles = matcher.group(1);
- }
- } catch (MalformedURLException muex) {
- logger.error("Unable to connect to chemspider
conversion services: "+muex.getMessage(), muex);
- return null;
- } catch (IOException ioex) {
- logger.error("Unable to connect to chemspider
conversion services: "+ioex.getMessage(), ioex);
- return null;
- }
- return smiles;
- */
}
- /**
- * Returns the URL to use for getting the rendered image
- */
- private String getDepictURL() {
- String url =
"http://chimeraservices.compbio.ucsf.edu/cgi-bin/smi2gif.cgi?";
- + "smiles=" + this.smilesStr +
"&format=png&width=640&height=640&bgcolor=white&linewidth=2&symbolfontsize=24";
- return url;
- }
-
- /**
- * Returns the URL to use for getting the rendered image
- *
- * @param width the width parameter to put into the URL
- * @param height the height parameter to put into the URL
- * @param bgcolor the bgcolor parameter to put into the URL
- */
- private String getDepictURL(int width, int height, String bgcolor) {
- String url =
"http://chimeraservices.compbio.ucsf.edu/cgi-bin/smi2gif.cgi?";
- + "smiles=" + this.smilesStr + "&width=" + width +
"&height=" + height + "&bgcolor=" + bgcolor;
- return url;
- }
}
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