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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.io.mmcif;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.zip.GZIPOutputStream;
import org.biojava.nbio.core.util.InputStreamProvider;
import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/** This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.
* It is the default way to access these definitions.
* If this provider is called he first time, it will download and install all chemical
* component definitions in a local directory.
* Once the definition files have been installed, it has quick startup time and low memory requirements.
*
* An alternative provider, that keeps all definitions in memory is the {@link AllChemCompProvider}. Another provider, that
* does not require any network access, but only can support a limited set of chemical component definitions, is the {@link ReducedChemCompProvider}.
*
*
* @author Andreas Prlic
*
*/
public class DownloadChemCompProvider implements ChemCompProvider {
private static final Logger logger = LoggerFactory.getLogger(DownloadChemCompProvider.class);
public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";
public static final String SERVER_LOCATION = "http://www.rcsb.org/pdb/files/ligand/";
private static File path;
//private static final String FILE_SEPARATOR = System.getProperty("file.separator");
private static final String NEWLINE = System.getProperty("line.separator");
// flags to make sure there is only one thread running that is loading the dictionary
static AtomicBoolean loading = new AtomicBoolean(false);
static final List protectedIDs = new ArrayList ();
static {
protectedIDs.add("CON");
protectedIDs.add("PRN");
protectedIDs.add("AUX");
protectedIDs.add("NUL");
}
/** by default we will download only some of the files. User has to request that all files should be downloaded...
*
*/
boolean downloadAll = false;
public DownloadChemCompProvider(){
logger.debug("Initialising DownloadChemCompProvider");
// note that path is static, so this is just to make sure that all non-static methods will have path initialised
initPath();
}
public DownloadChemCompProvider(String cacheFilePath){
logger.debug("Initialising DownloadChemCompProvider");
// note that path is static, so this is just to make sure that all non-static methods will have path initialised
path = new File(cacheFilePath);
}
private static void initPath(){
if (path==null) {
UserConfiguration config = new UserConfiguration();
path = new File(config.getCacheFilePath());
}
}
/**
* Checks if the chemical components already have been installed into the PDB directory.
* If not, will download the chemical components definitions file and split it up into small
* subfiles.
*/
public void checkDoFirstInstall(){
if ( ! downloadAll ) {
return;
}
// this makes sure there is a file separator between every component,
// if path has a trailing file separator or not, it will work for both cases
File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
File f = new File(dir, "components.cif.gz");
if ( ! f.exists()) {
downloadAllDefinitions();
} else {
// file exists.. did it get extracted?
FilenameFilter filter =new FilenameFilter() {
@Override
public boolean accept(File dir, String file) {
return file.endsWith(".cif.gz");
}
};
String[] files = dir.list(filter);
if ( files.length < 500) {
// not all did get unpacked
try {
split();
} catch (IOException e) {
logger.error("Could not split file {} into individual chemical component files. Error: {}",
f.toString(), e.getMessage());
}
}
}
}
private void split() throws IOException {
logger.info("Installing individual chem comp files ...");
File dir = new File(path, CHEM_COMP_CACHE_DIRECTORY);
File f = new File(dir, "components.cif.gz");
int counter = 0;
InputStreamProvider prov = new InputStreamProvider();
try( BufferedReader buf = new BufferedReader (new InputStreamReader (prov.getInputStream(f)));
) {
String line = null;
line = buf.readLine ();
StringWriter writer = new StringWriter();
String currentID = null;
while (line != null){
if ( line.startsWith("data_")) {
// a new record found!
if ( currentID != null) {
writeID(writer.toString(), currentID);
counter++;
}
currentID = line.substring(5);
writer = new StringWriter();
}
writer.append(line);
writer.append(NEWLINE);
line = buf.readLine ();
}
// write the last record...
writeID(writer.toString(),currentID);
counter++;
}
logger.info("Created " + counter + " chemical component files.");
}
/**
* Output chemical contents to a file
* @param contents File contents
* @param currentID Chemical ID, used to determine the filename
* @throws IOException
*/
private void writeID(String contents, String currentID) throws IOException{
String localName = DownloadChemCompProvider.getLocalFileName(currentID);
try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {
pw.print(contents.toString());
pw.flush();
}
}
/**
* Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.
*
* @param recordName the ID of the {@link ChemComp}
* @return a new {@link ChemComp} definition.
*/
@Override
public ChemComp getChemComp(String recordName) {
// make sure we work with upper case records
recordName = recordName.toUpperCase().trim();
boolean haveFile = true;
if ( recordName.equals("?")){
return null;
}
if ( ! fileExists(recordName)) {
// check if we should install all components
checkDoFirstInstall();
}
if ( ! fileExists(recordName)) {
// we previously have installed already the definitions,
// just do an incrememntal update
haveFile = downloadChemCompRecord(recordName);
}
// Added check that download was successful and chemical component is available.
if (haveFile) {
String filename = getLocalFileName(recordName);
InputStream inStream = null;
try {
InputStreamProvider isp = new InputStreamProvider();
inStream = isp.getInputStream(filename);
MMcifParser parser = new SimpleMMcifParser();
ChemCompConsumer consumer = new ChemCompConsumer();
// The Consumer builds up the BioJava - structure object.
// you could also hook in your own and build up you own data model.
parser.addMMcifConsumer(consumer);
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
ChemicalComponentDictionary dict = consumer.getDictionary();
ChemComp chemComp = dict.getChemComp(recordName);
return chemComp;
} catch (IOException e) {
logger.error("Could not parse chemical component file {}. Error: {}. "
+ "There will be no chemical component info available for {}", filename, e.getMessage(), recordName);
}
finally{
// Now close it
if(inStream!=null){
try {
inStream.close();
} catch (IOException e) {
// This would be weird...
logger.error("Could not close chemical component file {}. A resource leak could occur!!", filename);
}
}
}
}
// see https://github.com/biojava/biojava/issues/315
// probably a network error happened. Try to use the ReducedChemCOmpProvider
ReducedChemCompProvider reduced = new ReducedChemCompProvider();
return reduced.getChemComp(recordName);
}
/** Returns the file name that contains the definition for this {@link ChemComp}
*
* @param recordName the ID of the {@link ChemComp}
* @return full path to the file
*/
public static String getLocalFileName(String recordName){
if ( protectedIDs.contains(recordName)){
recordName = "_" + recordName;
}
initPath();
File f = new File(path, CHEM_COMP_CACHE_DIRECTORY);
if (! f.exists()){
logger.info("Creating directory " + f);
boolean success = f.mkdir();
// we've checked in initPath that path is writable, so there's no need to check if it succeeds
// in the unlikely case that in the meantime it isn't writable at least we log an error
if (!success) logger.error("Directory {} could not be created",f);
}
File theFile = new File(f,recordName + ".cif.gz");
return theFile.toString();
}
private static boolean fileExists(String recordName){
String fileName = getLocalFileName(recordName);
File f = new File(fileName);
return f.exists();
}
/**
* @param recordName : three-letter name
* @return true if successful download
*/
private static boolean downloadChemCompRecord(String recordName) {
String localName = getLocalFileName(recordName);
File newFile;
try{
newFile = File.createTempFile("chemcomp"+recordName, "cif");
}
catch(IOException e){
logger.error("Could not write to temp directory {} to create the chemical component download temp file", System.getProperty("java.io.tmpdir"));
return false;
}
String u = SERVER_LOCATION + recordName + ".cif";
logger.debug("downloading " + u);
URL url = null;
try {
url = new URL(u);
HttpURLConnection uconn = HTTPConnectionTools.openHttpURLConnection(url);
try( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(newFile)));
BufferedReader fileBuffer = new BufferedReader(new InputStreamReader(uconn.getInputStream()));
) {
String line;
while ((line = fileBuffer.readLine()) != null) {
pw.println(line);
}
pw.flush();
// Now we move this across to where it actually wants to be
boolean couldRename = newFile.renameTo(new File(localName));
if (!couldRename) {
throw new IOException("Could not rename temp file "+newFile.toString()+" to file " + localName);
}
return true;
}
} catch (IOException e){
logger.error("Could not download "+url.toString()+" OR store locally to "+localName+" Error ="+e.getMessage());
newFile.delete();
}
return false;
}
private void downloadAllDefinitions() {
if ( loading.get()){
logger.info("Waiting for other thread to install chemical components...");
}
while ( loading.get() ) {
// another thread is already downloading the components definitions
// wait for the other thread to finish...
try {
// wait half a second
Thread.sleep(500);
} catch (InterruptedException e) {
//e.printStackTrace();
logger.error("Thread interrupted "+e.getMessage());
}
logger.info("Another thread installed the chemical components.");
return;
}
loading.set(true);
long timeS = System.currentTimeMillis();
logger.info("Performing first installation of chemical components.");
logger.info("Downloading components.cif.gz ...");
try {
AllChemCompProvider.downloadFile();
} catch (IOException e){
logger.error("Could not download the all chemical components file. Error: {}. "
+ "Chemical components information won't be available", e.getMessage());
// no point in trying to split if the file could not be downloaded
loading.set(false);
return;
}
try {
split();
} catch (IOException e) {
logger.error("Could not split all chem comp file into individual chemical component files. Error: {}",
e.getMessage());
// no point in reporting time
loading.set(false);
return;
}
long timeE = System.currentTimeMillis();
logger.info("time to install chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");
loading.set(false);
}
/** By default this provider will download only some of the {@link ChemComp} files.
* The user has to request that all files should be downloaded by setting this parameter to true.
*
* @return flag if the all components should be downloaded and installed at startup. (default: false)
*/
public boolean isDownloadAll() {
return downloadAll;
}
/** By default this provider will download only some of the {@link ChemComp} files.
* The user has to request that all files should be downloaded by setting this parameter to true.
*
* @param flag if the all components should be downloaded and installed at startup. (default: false)
*/
public void setDownloadAll(boolean downloadAll) {
this.downloadAll = downloadAll;
}
}
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