/**
* KEGG get names by cpd id.
*
* @param identifier the identifier
* @return the string
*/
public static String[] KEGGgetNameByCpd(String identifier) {
String ret = "";
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
// get molecule by accession ID
String str = "cpd:" + identifier;
ret = serv.bget(str);
} catch (Exception e) {
System.err.println(e.toString());
}
// System.out.println(ret);
String names = ret.substring(ret.indexOf("NAME") + 12, ret.indexOf("FORMULA") - 1);
// System.out.println(names);
// find white spaces
Pattern p = Pattern.compile("\\s+");
Matcher m = p.matcher(names);
String cleanedNames = m.replaceAll(" ");
// System.out.println(cleanedNames);
String[] namesArr = cleanedNames.split(";");
for (int i = 0; i < namesArr.length; i++) {
Pattern p1 = Pattern.compile("^\\s+");
Matcher m1 = p1.matcher(namesArr[i]);
namesArr[i] = m1.replaceAll("");
}
return namesArr;
}
/**
* Gets the mol file from a specified KEGG ID.
*
* @param accessionID the accession id (e.g. C00509)
* @return the string
* @throws CDKException
*/
public static IAtomContainer getMol(String accessionID, String keggPath, boolean getAll)
throws CDKException {
String ret = "";
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
// get molecule by accession ID
String str = "-f m cpd:" + accessionID;
boolean webservice = false;
String mol = "";
try {
// Open the file that is the first
// command line parameter
FileInputStream fstream = new FileInputStream(keggPath + accessionID + ".mol");
// Get the object of DataInputStream
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
// Read File Line By Line
String line;
while ((line = br.readLine()) != null) {
// Print the content on the console
mol += line + "\n";
}
// Close the input stream
in.close();
} catch (FileNotFoundException e) {
webservice = true;
}
// if this file is not found use webservice...otherwise use local molfile
if (webservice) ret = serv.bget(str);
else ret = mol;
} catch (Exception e) {
System.err.println(e.toString());
}
MDLReader reader;
List<IAtomContainer> containersList;
reader = new MDLReader(new StringReader(ret));
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IAtomContainer molecule = containersList.get(0);
if (getAll) return molecule;
if (!MolecularFormulaTools.isBiologicalCompound(molecule)) molecule = null;
return molecule;
}
/**
* Gets the mol file from a specified KEGG ID.
*
* @param accessionID the accession id (e.g. C00509)
* @return the string
*/
public static String KEGGgetMol(String accessionID, String keggPath) {
String ret = "";
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
// get molecule by accession ID
String str = "-f m cpd:" + accessionID;
boolean webservice = false;
String mol = "";
try {
// Open the file that is the first
// command line parameter
FileInputStream fstream = new FileInputStream(keggPath + accessionID + ".mol");
// Get the object of DataInputStream
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
// Read File Line By Line
String line;
while ((line = br.readLine()) != null) {
// Print the content on the console
mol += line + "\n";
}
// Close the input stream
in.close();
} catch (FileNotFoundException e) {
webservice = true;
}
// if this file is not found use webservice...otherwise use local molfile
if (webservice) ret = serv.bget(str);
else ret = mol;
} catch (Exception e) {
System.err.println(e.toString());
}
return ret;
}
/**
* KEGG by sum formula.
*
* @param sumFormula the sum formula
* @return the vector< string>
*/
public static Vector<String> KEGGbySumFormula(String sumFormula) {
Vector<String> KEGGCandidates = new Vector<String>();
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
String[] results = serv.search_compounds_by_composition(sumFormula);
for (int i = 0; i < results.length; i++) {
System.out.println(results[i]);
KEGGCandidates.add(results[i]);
}
} catch (Exception e) {
System.err.println(e.toString());
}
return KEGGCandidates;
}
/**
* KEGG search by mass. TODO: Get candidates through webservice...bget
*
* @param mass the mass
* @param error the error
* @return the vector< string>
*/
public static Vector<String> KEGGbyMass(double mass, double error) {
Vector<String> KEGGCandidates = new Vector<String>();
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
String[] results = serv.search_compounds_by_mass((float) mass, (float) error);
for (int i = 0; i < results.length; i++) {
System.out.println(results[i]);
KEGGCandidates.add(results[i]);
}
} catch (Exception e) {
// System.err.println(e.toString());
e.printStackTrace();
}
return KEGGCandidates;
}