Package uk.ac.cam.ch.wwmm.ptclib.cdk

Examples of uk.ac.cam.ch.wwmm.ptclib.cdk.Molecule2Png.renderMolecule()

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                "no".equals(request.getParameter("colourAtoms")))) {
          m2p.colourAtoms = false;
        }

        OutputStream os = response.getOutputStream();
        m2p.renderMolecule(mol, os, makeStructure);
        os.close();
      } catch (Exception e) {
        response.setContentType("image/png");
        try {
          m2p.renderMolecule(null, response.getOutputStream());       
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        m2p.renderMolecule(mol, os, makeStructure);
        os.close();
      } catch (Exception e) {
        response.setContentType("image/png");
        try {
          m2p.renderMolecule(null, response.getOutputStream());       
        } catch (Exception ee) {
          //e.printStackTrace();
        }       
      }
      m2p = null;
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        StructureConverter.configureMolecule(mol);
        Molecule2Png m2p = new Molecule2Png();
        m2p.fixedWidthAndHeight = true;
        m2p.height = 300;
        m2p.width = 300;
        m2p.renderMolecule(mol, new File(paperDir, id+".png").toString());
      } catch (Exception ee) {
       
      }
    }
    try {
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      Molecule blank = new Molecule();
      Molecule2Png m2p = new Molecule2Png();
      m2p.fixedWidthAndHeight = true;
      m2p.height = 300;
      m2p.width = 300;
      m2p.renderMolecule(blank, new File(paperDir, "blank.png").toString());     
    } catch (Exception ee) {
     
    }
    trans.transform(new StreamSource(new File(paperDir, "markedup.xml")), new StreamResult(new File(paperDir, "markedup.html")));
    System.out.println(paperDir);
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