initial commit

import java.io.*;

import java.util.ArrayList;

import java.util.Random;

public class ProteinFactory {

    private static ProteinFactory INSTANCE;

    private ProteinFactory() throws IOException {

    }

    public static ProteinFactory getInstance() throws IOException {

        if (INSTANCE == null) {

            INSTANCE = new ProteinFactory();

        }

        return INSTANCE;

    }

    static Random rng = new Random();

    static final AminoAcid ALANINE;

    static final AminoAcid GLYCINE;

    static {

        try {

            ALANINE = new AminoAcid("testcases/amino_acid/Alanine.txt",

                    2, 12, 10, 5, 4);

            GLYCINE = new AminoAcid("testcases/amino_acid/Glycine.txt",

                    1, 9, 7, 4, 3);

        } catch (IOException e) {

            throw new RuntimeException(e);

        }

    }

    static public class AminoAcid {

        int atomCount;

        StringBuffer atomBuffer;

        int bondCount = 0;

        ArrayList<Integer> bondList = new ArrayList<>();

        String name;

        ArrayList<Integer> termini = new ArrayList<>();

        int terminusC;

        int terminusHN;

        int terminusHO;

        int terminusN;

        int terminusO;

        public AminoAcid(

                String filePath, int terminusC, int terminusHN, int terminusHO, int terminusN, int terminusO)

                throws IOException {

            try (BufferedReader reader = new BufferedReader(new FileReader(filePath))) {

                name = reader.readLine();

                atomCount = Integer.parseInt(reader.readLine());

                atomBuffer = new StringBuffer(atomCount);

                for (int atomIdx = 0; atomIdx < atomCount; atomIdx++) {

                    atomBuffer.append(reader.readLine());

                }

                String bond;

                while ((bond = reader.readLine()) != null) {

                    String[] atoms = bond.split(" ");

                    bondList.add(Integer.parseInt(atoms[0]));

                    bondList.add(Integer.parseInt(atoms[1]));

                    bondCount++;

                }

            }

            termini.add(terminusHN);

            termini.add(terminusHO);

            termini.add(terminusO);

            termini.sort(null);

            this.terminusC = terminusC;

            this.terminusHN = terminusHN;

            this.terminusHO = terminusHO;

            this.terminusN = terminusN;

            this.terminusO = terminusO;

        }

    }

    static public class Protein {

        Integer atomCount;

        StringBuffer atomBuffer = new StringBuffer();

        ArrayList<String> bondList = new ArrayList<>();

        int terminusC;

        boolean complete = false;

        String name;

        public Protein(String name, AminoAcid aminoAcid) {

            int min = Math.min(aminoAcid.terminusHO, aminoAcid.terminusO);

            atomBuffer.append(aminoAcid.atomBuffer, 0, min);

            int max = Math.max(aminoAcid.terminusHO, aminoAcid.terminusO);

            atomBuffer.append(aminoAcid.atomBuffer, min + 1, max);

            atomBuffer.append(aminoAcid.atomBuffer, max + 1, aminoAcid.atomCount);

            atomCount = aminoAcid.atomCount - 2;

            int bondCount = aminoAcid.bondCount;

            int terminusHO = aminoAcid.terminusHO;

            int terminusO = aminoAcid.terminusO;

            for (int bondIdx = 0; bondIdx < bondCount; bondIdx++) {

                int atom0 = aminoAcid.bondList.get(2 * bondIdx);

                if (atom0 == terminusHO || atom0 == terminusO) {

                    continue;

                }

                int atom1 = aminoAcid.bondList.get(2 * bondIdx + 1);

                if (atom1 == terminusHO || atom1 == terminusO) {

                    continue;

                }

                int atomDecrement = 0;

                atomDecrement += (atom0 > terminusHO) ? 1 : 0;

                atomDecrement += (atom0 > terminusO) ? 1 : 0;

                atom0 -= atomDecrement;

                atomDecrement = 0;

                atomDecrement += (atom1 > terminusHO) ? 1 : 0;

                atomDecrement += (atom1 > terminusO) ? 1 : 0;

                atom1 -= atomDecrement;

                bondList.add(String.format("%d %d", atom0, atom1));

            }

            int newTerminusC = aminoAcid.terminusC;

            newTerminusC -= (newTerminusC > terminusHO) ? 1 : 0;

            newTerminusC -= (newTerminusC > terminusO) ? 1 : 0;

            terminusC = newTerminusC;

            this.name = name;

        }

        public void print() {

            System.out.println(atomCount);

            System.out.println(atomBuffer);

            System.out.println(bondList);

            System.out.println(terminusC);

            System.out.println(complete);

        }

        public void write(String folderName) throws IOException {

            BufferedWriter writer = new BufferedWriter(new FileWriter(folderName + "/" + name + ".txt"));

            writer.write(name + "\n");

            writer.write(atomCount.toString());

            writer.write("\n");

            for (int ii = 0; ii < atomCount; ii++) {

                writer.write(atomBuffer.charAt(ii) + "\n");

            }

            for (String b : bondList) {

                writer.write(b + "\n");

            }

            writer.close();

        }

    }

    public static void addAminoAcid(Protein protein, AminoAcid aminoAcid, boolean isLast) {

        if (protein.complete) {

            System.out.println("cannot add to completed protein");

            return;

        }

        if (isLast) {

            int baseIdx = protein.atomCount;

            int indexH = aminoAcid.atomBuffer.indexOf("H");

            protein.atomBuffer.append(aminoAcid.atomBuffer, 0, indexH);

            protein.atomBuffer.append(aminoAcid.atomBuffer, indexH + 1, aminoAcid.atomCount);

            protein.atomCount += aminoAcid.atomCount - 1;

            protein.bondList.add(String.format("%d %d", protein.terminusC, baseIdx + aminoAcid.terminusN));

            int bondCount = aminoAcid.bondCount;

            int terminusHN = aminoAcid.terminusHN;

            for (int bondIdx = 0; bondIdx < bondCount; bondIdx++) {

                int atom0 = aminoAcid.bondList.get(2 * bondIdx);

                if (atom0 == terminusHN) {

                    continue;

                } else if (atom0 > terminusHN) {

                    atom0--;

                }

                int atom1 = aminoAcid.bondList.get(2 * bondIdx + 1);

                if (atom1 == terminusHN) {

                    continue;

                } else if (atom1 > terminusHN) {

                    atom1--;

                }

                protein.bondList.add(String.format("%d %d", baseIdx + atom0, baseIdx + atom1));

            }

            protein.complete = true;

        } else {

            int baseIdx = protein.atomCount;

            int start = -1;

            for (Integer t : aminoAcid.termini) {

                protein.atomBuffer.append(aminoAcid.atomBuffer.substring(start + 1, t));

                start = t;

            }

            protein.atomBuffer.append(aminoAcid.atomBuffer.substring(start + 1));

            protein.atomCount += aminoAcid.atomCount - 3;

            protein.bondList.add(String.format("%d %d", protein.terminusC, baseIdx + aminoAcid.terminusN));

            int bondCount = aminoAcid.bondCount;

            int terminusHN = aminoAcid.terminusHN;

            int terminusHO = aminoAcid.terminusHO;

            int terminusO = aminoAcid.terminusO;

            for (int bondIdx = 0; bondIdx < bondCount; bondIdx++) {

                int atom0 = aminoAcid.bondList.get(2 * bondIdx);

                int atom1 = aminoAcid.bondList.get(2 * bondIdx + 1);

                if (aminoAcid.termini.contains(atom0) || aminoAcid.termini.contains(atom1)) {

                    continue;

                }

                int atomDecrement = 0;

                atomDecrement += (atom0 > terminusHN) ? 1 : 0;

                atomDecrement += (atom0 > terminusHO) ? 1 : 0;

                atomDecrement += (atom0 > terminusO) ? 1 : 0;

                atom0 -= atomDecrement;

                atomDecrement = 0;

                atomDecrement += (atom1 > terminusHN) ? 1 : 0;

                atomDecrement += (atom1 > terminusHO) ? 1 : 0;

                atomDecrement += (atom1 > terminusO) ? 1 : 0;

                atom1 -= atomDecrement;

                protein.bondList.add(String.format("%d %d", baseIdx + atom0, baseIdx + atom1));

            }

            int newTerminusC = aminoAcid.terminusC;

            newTerminusC -= (newTerminusC > terminusHN) ? 1 : 0;

            newTerminusC -= (newTerminusC > terminusHO) ? 1 : 0;

            newTerminusC -= (newTerminusC > terminusO) ? 1 : 0;

            protein.terminusC = newTerminusC;

        }

    }

//    public void addAlanine(Protein protein, boolean isLast) {

//        if (isLast) {

//            protein.atomBuffer.append("CCCOONHHHHHH");

//            protein.atomCount += 12;

//

//            int atomIdx = protein.atomCount;

//            protein.bondList.add(String.format("%d %d", protein.terminusC, atomIdx + 5));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 1));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 6));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 7));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 8));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 2));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 5));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 9));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx + 4, atomIdx + 10));

//            protein.bondList.add(String.format("%d %d", atomIdx + 5, atomIdx + 11));

//

//            protein.complete = true;

//        } else {

//            protein.atomBuffer.append("CCCONHHHHH");

//            protein.atomCount += 10;

//

//            int atomIdx = protein.atomCount;

//            protein.bondList.add(String.format("%d %d", protein.terminusC, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 1));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 5));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 6));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 7));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 2));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 8));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 4, atomIdx + 10));

//

//            protein.terminusC += 2;

//        }

//    }

//

//    public void addArginine(Protein protein, boolean isLast) {

//        if (isLast) {

//            protein.atomBuffer.append("CCCCOONCNCNNHHHHHHHHHHHHH");

//            protein.atomCount += 25;

//

//            int atomIdx = protein.atomCount;

//            protein.bondList.add(String.format("%d %d", protein.terminusC, atomIdx + 11));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 1));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 7));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 12));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 13));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 2));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 14));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 15));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 6));

//            protein.bondList.add(String.format("%d %d", atomIdx + 3, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx + 4, atomIdx + 10));

//            protein.bondList.add(String.format("%d %d", atomIdx + 5, atomIdx + 11));

//

//            protein.complete = true;

//        } else {

//            protein.atomBuffer.append("CCCONHHHHH");

//            protein.atomCount += 10;

//

//            int atomIdx = protein.atomCount;

//            protein.bondList.add(String.format("%d %d", protein.terminusC, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 1));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 5));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 6));

//            protein.bondList.add(String.format("%d %d", atomIdx, atomIdx + 7));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 2));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 4));

//            protein.bondList.add(String.format("%d %d", atomIdx + 1, atomIdx + 8));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 2, atomIdx + 3));

//            protein.bondList.add(String.format("%d %d", atomIdx + 4, atomIdx + 10));

//

//            protein.terminusC += 2;

//        }

//    }

//    public static Protein initProtein(AminoAcid aminoAcid) {

//        Protein protein = new Protein();

//

//        return protein;

//    }

    public void addAminoAcidLast() {

    }

    public void generateProtein(int atomCount) {

    }

    public void generateProteins(int proteinCount, int atomsPerProtein) {

    }

    public static void main(String[] args) throws IOException {

        Protein protein = new Protein("protein1", GLYCINE);

        addAminoAcid(protein, GLYCINE, true);

        protein.write("testcases/protein");

    }

}