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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/
*
* Created on 2013-06-13 Created by Douglas Myers-Turnbull
*
* @since 3.0.6
*/
package org.biojava.nbio.structure.rcsb;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
/**
* Fetches information from RCSB's RESTful Web Service
* Interface. A factory for {@link RCSBLigands RCSBLigands} from {@code ligandInfo} XML files. The factory methods
* will return null if the data was not found (rather than throwing an exception); client code should test for this.
* This is for consistency: if the factory could not read some part (corresponding to a field in a class in
* {@code rcsb.descriptions}) of the XML file, either because it was blank or contained an error that could not be
* safely ignored, that field will simply be null. This holds even for numerical values. On some parse errors, the error
* will additionally be printed to standard error.
*
* Example usage:
*
*
* RCSBLigands ligands = RCSBLigandsFactory.getFromPdbIds("1w0p");
* List<RCSBLigand> list = ligands.getLigands();
* System.out.println(list.get(0).getFormula()); // prints "CA 2"
* System.out.println(list.get(1).getFormula()); // prints "C11 H19 N O9"
*
*
* @see RCSB RESTful
*
* @author dmyerstu
* @since 3.0.6
*/
public class RCSBLigandsFactory {
private static final String HET_URL_STUB = "http://www.pdb.org/pdb/rest/describeHet?chemicalID=";
private static final Logger logger = Logger.getLogger(RCSBLigandsFactory.class.getPackage().getName());
private static final String PDB_URL_STUB = "http://www.pdb.org/pdb/rest/ligandInfo?structureId=";
/**
* @return A list of {@link RCSBLigand RCSBLigands} from the XML file loaded as {@code stream}. Prefer calling
* {@link #getFromHeteroAtomId(String)} if you want data directly from RCSB's RESTful service.
* @see RCSBDescriptionFactory#get(String)
*/
public static RCSBLigand getFromHeteroAtomId(InputStream stream) {
return getFromHeteroAtomIds(stream).get(0);
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid"}. This is the preferred factory method,
* unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static RCSBLigand getFromHeteroAtomId(String heteroAtomId) {
return getFromHeteroAtomIds(heteroAtomId).get(0);
}
/**
* @return A list of {@link RCSBLigand RCSBLigands} from the XML file loaded as {@code stream}. Prefer calling
* {@link #getFromHeteroAtomId(String)} if you want data directly from RCSB's RESTful service.
* @see RCSBDescriptionFactory#get(String)
*/
public static List getFromHeteroAtomIds(InputStream stream) {
NodeList data;
try {
data = ReadUtils.getNodes(stream);
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't parse XML", e);
return null;
}
List ligands = new ArrayList();
// first get the ligandInfo
Element structureIdE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
structureIdE = (Element) data.item(i);
if (structureIdE.getNodeName().equals("ligandInfo")) {
break;
}
}
// now get individual ligands
data = structureIdE.getChildNodes();
Element ligandE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
ligandE = (Element) data.item(i);
if (ligandE.getNodeName().equals("ligand")) {
RCSBLigand ligand = makeLigand(ligandE);
ligands.add(ligand);
}
}
return ligands;
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid"}. This is the preferred factory method,
* unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static List getFromHeteroAtomIds(List heteroAtomIds) {
String[] x = new String[heteroAtomIds.size()];
heteroAtomIds.toArray(x);
return getFromHeteroAtomIds(x); // somewhat cheating here
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid"}. This is the preferred factory method,
* unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static List getFromHeteroAtomIds(String... heteroAtomIds) {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < heteroAtomIds.length; i++) {
if (i > 0) sb.append(",");
sb.append(heteroAtomIds[i]);
}
InputStream is;
try {
URL url = new URL(HET_URL_STUB + sb.toString());
is = url.openConnection().getInputStream();
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't open connection", e);
return null;
}
return getFromHeteroAtomIds(is);
}
/**
* @return An {@link RCSBLigands} from the XML file loaded as {@code stream}. Prefer calling
* {@link #getFromPdbId(String)} if you want data directly from RCSB's RESTful service.
* @see RCSBDescriptionFactory#get(String)
*/
public static RCSBLigands getFromPdbId(InputStream stream) {
NodeList data;
try {
data = ReadUtils.getNodes(stream);
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't parse XML", e);
return null;
}
// first get the ligandInfo
RCSBLigands ligands = new RCSBLigands();
Element structureIdE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
structureIdE = (Element) data.item(i);
if (structureIdE.getNodeName().equals("ligandInfo")) {
break;
}
}
// now get individual ligands
data = structureIdE.getChildNodes();
Element ligandE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
ligandE = (Element) data.item(i);
if (ligandE.getNodeName().equals("ligand")) {
if (ligands.getPdbId() == null) {
ligands.setPdbId(ligandE.getAttribute("structureId"));
}
RCSBLigand ligand = makeLigand(ligandE);
ligands.addLigand(ligand);
}
}
return ligands;
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId"}. This is the preferred factory
* method, unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static RCSBLigands getFromPdbId(String pdbId) {
InputStream is;
try {
URL url = new URL(PDB_URL_STUB + pdbId);
is = url.openConnection().getInputStream();
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't open connection", e);
return null;
}
return getFromPdbId(is);
}
/**
* @return An {@link RCSBLigands} from the XML file loaded as {@code stream}. Prefer calling
* {@link #getFromPdbId(String)} if you want data directly from RCSB's RESTful service.
* @see RCSBDescriptionFactory#get(String)
*/
public static List getFromPdbIds(InputStream stream) {
NodeList dataaa;
try {
dataaa = ReadUtils.getNodes(stream);
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't parse XML", e);
return null;
}
// first we have to handle the element "ligandsInEntry", which is not present if we have only 1 structure
List ligandsList = new ArrayList();
Element structureIdE = null;
for (int k = 0; k < dataaa.getLength(); k++) {
if (dataaa.item(k).getNodeType() != 1) continue;
structureIdE = (Element) dataaa.item(k);
if (structureIdE.getNodeName().equals("structureId")) {
// now get the ligandInfo
NodeList data = structureIdE.getChildNodes();
RCSBLigands ligands = new RCSBLigands();
Element ligandIdE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
ligandIdE = (Element) data.item(i);
if (ligandIdE.getNodeName().equals("ligandInfo")) {
break;
}
}
// now get individual ligands
data = ligandIdE.getChildNodes();
Element ligandE = null;
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
ligandE = (Element) data.item(i);
if (ligandE.getNodeName().equals("ligand")) {
if (ligands.getPdbId() == null) {
ligands.setPdbId(ligandE.getAttribute("structureId"));
}
RCSBLigand ligand = makeLigand(ligandE);
ligands.addLigand(ligand);
}
}
ligandsList.add(ligands);
}
}
return ligandsList;
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId"}. This is the preferred factory
* method, unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static List getFromPdbIds(List pdbIds) {
String[] x = new String[pdbIds.size()];
pdbIds.toArray(x);
return getFromPdbIds(x);
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId"}. This is the preferred factory
* method, unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static RCSBLigands getFromPdbIds(String pdbId) {
InputStream is;
try {
URL url = new URL(PDB_URL_STUB + pdbId);
is = url.openConnection().getInputStream();
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't open connection", e);
return null;
}
return getFromPdbId(is);
}
/**
* @return An {@link RCSBLigands} from the XML file at
* {@code "http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId"}. This is the preferred factory
* method, unless a different URL or input source is required.
* @see RCSBDescriptionFactory#get(InputStream)
*/
public static List getFromPdbIds(String... pdbIds) {
InputStream is;
StringBuilder sb = new StringBuilder();
for (int i = 0; i < pdbIds.length; i++) {
if (i > 0) sb.append(",");
sb.append(pdbIds[i]);
}
try {
URL url = new URL(PDB_URL_STUB + sb.toString());
is = url.openConnection().getInputStream();
} catch (IOException e) {
logger.log(Level.WARNING,"Couldn't open connection", e);
return null;
}
return getFromPdbIds(is);
}
private static RCSBLigand makeLigand(Element ligandE) {
RCSBLigand ligand = new RCSBLigand();
ligand.setId(ligandE.getAttribute("chemicalID"));
ligand.setType(ligandE.getAttribute("type"));
ligand.setWeight(ReadUtils.toDouble(ligandE.getAttribute("molecularWeight")));
Element element = null;
NodeList data = ligandE.getChildNodes();
for (int i = 0; i < data.getLength(); i++) {
if (data.item(i).getNodeType() != 1) continue;
element = (Element) data.item(i);
if (element.getNodeName().equals("chemicalName")) {
ligand.setName(element.getTextContent());
} else if (element.getNodeName().equals("formula")) {
ligand.setFormula(element.getTextContent());
} else if (element.getNodeName().equals("InChIKey")) {
ligand.setInChIKey(element.getTextContent());
} else if (element.getNodeName().equals("InChI")) {
ligand.setInChI(element.getTextContent());
} else if (element.getNodeName().equals("smiles")) {
ligand.setSmiles(element.getTextContent());
}
}
return ligand;
}
}
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