mdlwriter.java

化学图形处理软件

	 * @param   container  Molecule that is written to an OutputStream
	 */
    public void writeMolecule(IMolecule container) throws Exception {
        String line = "";
        // taking care of the $$$$ signs:
        // we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
        if(moleculeNumber == 2) {
          writer.write("$$$$");
          writer.newLine();
        }
        // write header block
        // lines get shortened to 80 chars, that's in the spec
        String title = (String)container.getProperty(CDKConstants.TITLE);
        if (title == null) title = "";
        if(title.length()>80)
          title=title.substring(0,80);
        writer.write(title + "\n");
        
        /* From CTX spec
         * This line has the format:
         * IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
         * (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
         * User's first and last initials (l), program name (P),
         * date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s), 
         * energy (E) if modeling program input, internal registry number (R) 
         * if input through MDL form.
         * A blank line can be substituted for line 2.
         */
        writer.write("  CDK    ");
        writer.write(new SimpleDateFormat("M/d/y,H:m",Locale.US).format(
        		     Calendar.getInstance(TimeZone.getDefault()).getTime())
        );
        writer.write('\n');
        
        String comment = (String)container.getProperty(CDKConstants.REMARK);
        if (comment == null) comment = "";
        if(comment.length()>80)
          comment=comment.substring(0,80);
        writer.write(comment + "\n");
        
        // write Counts line
        line += formatMDLInt(container.getAtomCount(), 3);
        line += formatMDLInt(container.getBondCount(), 3);
        line += "  0  0  0  0  0  0  0  0999 V2000\n";
        writer.write(line);

        // write Atom block
        for (int f = 0; f < container.getAtomCount(); f++) {
        	IAtom atom = container.getAtom(f);
        	line = "";
        	if (atom.getPoint3d() != null) {
        		line += formatMDLFloat((float) atom.getPoint3d().x);
        		line += formatMDLFloat((float) atom.getPoint3d().y);
        		line += formatMDLFloat((float) atom.getPoint3d().z) + " ";
        	} else if (atom.getPoint2d() != null) {
        		line += formatMDLFloat((float) atom.getPoint2d().x);
        		line += formatMDLFloat((float) atom.getPoint2d().y);
        		line += "    0.0000 ";
        	} else {
        		// if no coordinates available, then output a number
        		// of zeros
        		line += formatMDLFloat((float)0.0);
        		line += formatMDLFloat((float)0.0);
        		line += formatMDLFloat((float)0.0) + " ";
        	}
        	if(container.getAtom(f) instanceof IPseudoAtom)
        		line += formatMDLString(((IPseudoAtom) container.getAtom(f)).getLabel(), 3);
        	else
        		line += formatMDLString(container.getAtom(f).getSymbol(), 3); 
        	line += " 0  0  0  0  0  0  0  0  0  0  0  0";
        	writer.write(line);
        	writer.newLine();
        }

        // write Bond block
        Iterator bonds = container.bonds();
        while (bonds.hasNext()) {
            IBond bond = (IBond) bonds.next();

        	if (bond.getAtomCount() != 2) {
        		logger.warn("Skipping bond with more/less than two atoms: " + bond);
        	} else {
        		if (bond.getStereo() == CDKConstants.STEREO_BOND_UP_INV || 
        				bond.getStereo() == CDKConstants.STEREO_BOND_DOWN_INV) {
        			// turn around atom coding to correct for inv stereo
        			line = formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
        			line += formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
        		} else {
        			line = formatMDLInt(container.getAtomNumber(bond.getAtom(0)) + 1,3);
        			line += formatMDLInt(container.getAtomNumber(bond.getAtom(1)) + 1,3);
        		}
        		line += formatMDLInt((int)bond.getOrder(),3);
        		line += "  ";
        		switch(bond.getStereo()){
        		case CDKConstants.STEREO_BOND_UP:
        			line += "1";
        			break;
        		case CDKConstants.STEREO_BOND_UP_INV:
        			line += "1";
        			break;
        		case CDKConstants.STEREO_BOND_DOWN:
        			line += "6";
        			break;
        		case CDKConstants.STEREO_BOND_DOWN_INV:
        			line += "6";
        			break;
        		default:
        			line += "0";
        		}
        		line += "  0  0  0 ";
        		writer.write(line);
        		writer.newLine();
        	}
        }

        // write formal atomic charges
        for (int i = 0; i < container.getAtomCount(); i++) {
        	IAtom atom = container.getAtom(i);
            int charge = atom.getFormalCharge();
            if (charge != 0) {
                writer.write("M  CHG  1 ");
                writer.write(formatMDLInt(i+1,3));
                writer.write(" ");
                writer.write(formatMDLInt(charge,3));
                writer.newLine();
            }
        }
        
        // write formal isotope information
        for (int i = 0; i < container.getAtomCount(); i++) {
        	IAtom atom = container.getAtom(i);
            if (!(atom instanceof IPseudoAtom)) {
                int atomicMass = atom.getMassNumber();
                int majorMass = IsotopeFactory.getInstance(atom.getBuilder()).getMajorIsotope(atom.getSymbol()).getMassNumber();
                if (atomicMass != 0 && atomicMass != majorMass) {
                    writer.write("M  ISO  1 ");
                    writer.write(formatMDLInt(i+1,3));
                    writer.write(" ");
                    writer.write(formatMDLInt(atomicMass,3));
                    writer.newLine();
                }
            }
        }
        
        // close molecule
        writer.write("M  END");
        writer.newLine();
        //write sdfields, if any
        if(sdFields!=null){
          Set set = sdFields.keySet();
          Iterator iterator = set.iterator();
          while (iterator.hasNext()) {
            Object element = iterator.next();
            writer.write("> <"+(String)element+">");
            writer.newLine();
            writer.write(sdFields.get(element).toString());
            writer.newLine();
            writer.newLine();
          }
        }
        // taking care of the $$$$ signs:
        // we write such a sign at the end of all except the first molecule
        if(moleculeNumber != 1) {
          writer.write("$$$$");
          writer.newLine();
        }
        moleculeNumber++;
        writer.flush();
    }

	/**
	 * Formats an int to fit into the connectiontable and changes it 
     * to a String.
	 *
	 * @param   i  The int to be formated
	 * @param   l  Length of the String
	 * @return     The String to be written into the connectiontable
	 */
    private String formatMDLInt(int i, int l) {
        String s = "", fs = "";
        NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
        nf.setParseIntegerOnly(true);
        nf.setMinimumIntegerDigits(1);
        nf.setMaximumIntegerDigits(l);
        nf.setGroupingUsed(false);
        s = nf.format(i);
        l = l - s.length();
        for (int f = 0; f < l; f++)
            fs += " ";
        fs += s;
        return fs;
    }
	
	


	/**
	 * Formats a float to fit into the connectiontable and changes it
     * to a String.
	 *
	 * @param   fl  The float to be formated
	 * @return      The String to be written into the connectiontable
	 */
    private String formatMDLFloat(float fl) {
        String s = "", fs = "";
        int l;
        NumberFormat nf = NumberFormat.getNumberInstance(Locale.ENGLISH);
        nf.setMinimumIntegerDigits(1);
        nf.setMaximumIntegerDigits(4);
        nf.setMinimumFractionDigits(4);
        nf.setMaximumFractionDigits(4);
        nf.setGroupingUsed(false);
        s = nf.format(fl);
        l = 10 - s.length();
        for (int f = 0; f < l; f++)
            fs += " ";
        fs += s;
        return fs;
    }



	/**
	 * Formats a String to fit into the connectiontable.
	 *
	 * @param   s    The String to be formated
	 * @param   le   The length of the String
	 * @return       The String to be written in the connectiontable
	 */
    private String formatMDLString(String s, int le) {
        s = s.trim();
        if (s.length() > le)
            return s.substring(0, le);
        int l;
        l = le - s.length();
        for (int f = 0; f < l; f++)
            s += " ";
        return s;
    }

}