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Hyun Soo Kim authoredHyun Soo Kim authored
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ProteinFactory.java 12.33 KiB
import java.io.*;
import java.util.ArrayList;
public class ProteinFactory {
public ProteinFactory() {
}
static final AminoAcid ALANINE;
static final AminoAcid CYSTEINE;
static final AminoAcid GLYCINE;
static final AminoAcid LEUCINE;
static final AminoAcid ISOLEUCINE;
static final AminoAcid METHIONINE;
static final AminoAcid PROLINE;
static final AminoAcid SERINE;
static final AminoAcid THREONINE;
static final AminoAcid VALINE;
static {
try {
ALANINE = new AminoAcid("src/amino_acid/Alanine.txt",
2, 12, 10, 5, 4);
CYSTEINE = new AminoAcid("src/amino_acid/Cysteine.txt",
2, 12, 10, 5, 4);
GLYCINE = new AminoAcid("src/amino_acid/Glycine.txt",
1, 9, 7, 4, 3);
LEUCINE = new AminoAcid("src/amino_acid/Leucine.txt",
5, 21, 19, 8, 7);
ISOLEUCINE = new AminoAcid("src/amino_acid/l-Isoleucine.txt",
5, 21, 19, 8, 7);
METHIONINE = new AminoAcid("src/amino_acid/Methionine.txt",
5, 19, 17, 8, 7);
PROLINE = new AminoAcid("src/amino_acid/Proline.txt",
5, 13, 16, 3, 7);
SERINE = new AminoAcid("src/amino_acid/Serine.txt",
2, 12, 10, 5, 4);
THREONINE = new AminoAcid("src/amino_acid/Threonine.txt",
3, 15, 13, 6, 5);
VALINE = new AminoAcid("src/amino_acid/Valine.txt",
4, 18, 16, 7, 6);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
static public void initAminoAcids() {
ALANINE.symbol1 = "A";
CYSTEINE.symbol1 = "C";
GLYCINE.symbol1 = "G";
ISOLEUCINE.symbol1 = "I";
LEUCINE.symbol1 = "L";
METHIONINE.symbol1 = "M";
PROLINE.symbol1 = "P";
SERINE.symbol1 = "S";
THREONINE.symbol1 = "T";
VALINE.symbol1 = "V";
}
static final int AMINO_ACID_COUNT = 10;
static public class AminoAcid {
int atomCount;
StringBuffer atomBuffer;
int bondCount = 0;
ArrayList<Integer> bondList = new ArrayList<>();
String name;
String symbol1;
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<>();
boolean complete = false;
String name;
int terminusC;
public Protein(AminoAcid aminoAcid) {
name = aminoAcid.symbol1;
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;
}
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;
}
protein.name += aminoAcid.symbol1;
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 = baseIdx + newTerminusC;
}
}
public static AminoAcid getAminoAcid(int id) {
return switch (id) {
case 9 -> LEUCINE; // 22
case 8 -> ISOLEUCINE; // 22
case 7 -> METHIONINE; // 20
case 6 -> VALINE; // 19
case 5 -> THREONINE; // 17
case 4 -> PROLINE; // 17
case 3 -> SERINE; // 14
case 2 -> CYSTEINE; // 14
case 1 -> ALANINE; // 13
default -> GLYCINE; // 10
};
}
public static Protein generateProtein(int seed, int chainLen) {
Protein protein = new Protein(getAminoAcid(seed % AMINO_ACID_COUNT));
for (int ii = 0; ii < chainLen - 2; ii++) {
seed /= AMINO_ACID_COUNT;
addAminoAcid(protein, getAminoAcid(seed % AMINO_ACID_COUNT), false);
}
seed /= AMINO_ACID_COUNT;
addAminoAcid(protein, getAminoAcid(seed % AMINO_ACID_COUNT), true);
return protein;
}
public static void manySimpleProteins() throws IOException {
int simpleIdx = 0;
File simpleDir = new File("../simple");
for (int ii = 0; ii < 100; ii++) {
System.out.println(ii + "% done generating simple proteins (< 137 atoms)");
File simpleDirNested = new File(simpleDir, "simple" + ii);
if (simpleDirNested.mkdirs()) {
System.out.println("made new directory: " + simpleDirNested);
}
for (int jj = 0; jj < 100000; jj++) {
Protein protein = generateProtein(simpleIdx, 7);
protein.write(simpleDirNested.toString());
simpleIdx++;
}
}
System.out.println("done");
}
public static void fewComplexProteins() throws IOException {
int complexIdx = 0;
File complexDir = new File("../complex");
for (int ii = 0; ii < 10; ii++) {
System.out.println(ii + "0% done generating complex proteins (>= 10006 atoms)");
File complexDirNested = new File(complexDir, "complex" + ii);
if (complexDirNested.mkdirs()) {
System.out.println("made new directory: " + complexDirNested);
}
for (int jj = 0; jj < 1000; jj++) {
Protein protein = generateProtein(complexIdx, 1429);
protein.name = "protein" + complexIdx;
protein.write(complexDirNested.toString());
complexIdx++;
}
}
System.out.println("done");
}
public static void main(String[] args) throws IOException {
System.out.println("hello world");
manySimpleProteins();
fewComplexProteins();
System.out.println("goodbye");
}
}