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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.chem;

import java.io.*;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.Locale;

public class MolfileCreator {
    private static final float TARGET_AVBL = 1.5f;
	
    private StringBuilder mBuilder;

    /**
     * This creates a new molfile version 2 from the given molecule.
     * If the average bond length is smaller than 1.0 or larger than 3.0,
     * then all coordinates are scaled to achieve an average bond length of 1.5.
     * @param mol
     */
    public MolfileCreator(ExtendedMolecule mol) {
        this(mol, true);
        }
    
    /**
     * This creates a new molfile version 2 from the given molecule.
     * If scale==true and the average bond length is smaller than 1.0 or larger than 3.0,
     * then all coordinates are scaled to achieve an average bond length of 1.5.
     * @param mol
     * @param scale
     */
    public MolfileCreator(ExtendedMolecule mol, boolean scale) {
        this(mol, scale, new StringBuilder(32768));
        }
    
    /**
     * This creates a new molfile version 2 from the given molecule.
     * If scale==true and the average bond length is smaller than 1.0 or larger than 3.0,
     * then all coordinates are scaled to achieve an average bond length of 1.5.
     * If a StringBuilder is given, then the molfile will be appended to that.
     * @param mol
     * @param scale
     * @param builder null or StringBuilder to append to
     */
    public MolfileCreator(ExtendedMolecule mol, boolean scale, StringBuilder builder) {
        mol.ensureHelperArrays(Molecule.cHelperParities);

        boolean isRacemic = true;
        for (int atom=0; atom 3.0f)
            		grafac = TARGET_AVBL / avbl;
            	}
            else { // make the minimum distance between any two atoms twice as long as TARGET_AVBL
                double minDistance = Double.MAX_VALUE;
                for (int atom1=1; atom1 distance)
                            minDistance = distance;
                        }
                    }
                grafac = 2.0f * TARGET_AVBL / minDistance;
	            }
	        }

        for (int atom=0; atom 999) {
            mBuilder.append("  ?");
            return;
            }

        boolean digitFound = false;
        for (int i=0; i<3; i++) {
            int theChar = data / 100;
            if (theChar==0) {
                if (i==2 || digitFound)
                    mBuilder.append((char)'0');
                else
                    mBuilder.append((char)' ');
                }
            else {
                mBuilder.append((char)('0' + theChar));
                digitFound = true;
                }
            data = 10 * (data % 100);
            }
        }

    DecimalFormat df = new DecimalFormat("0.0000", new DecimalFormatSymbols(Locale.ENGLISH)); //English local ('.' for the dot)
    private void appendTenDigitDouble(double theDouble) {
    	String val = df.format(theDouble);  
    	for(int i=val.length(); i<10; i++) mBuilder.append(' ');   
    	mBuilder.append(val);  
        }
	}