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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.chem.io;
import com.actelion.research.chem.MolfileParser;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.UniqueStringList;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.io.BOMSkipper;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.TreeMap;
/**
* Quick and dirty RD-File parser that reads non-hierarchical RD-Files.
*/
public class RDFileParser {
private static final int DEFAULT_RECORDS_TO_INSPECT = 1024;
public static final String cNewLineString = "\n";
private BufferedReader mReader;
private String[] mFieldName;
private String[] mFieldData;
private int mNoOfRecords;
private String mLine,mIRegNo,mERegNo;
private TreeMap mDataMap;
public RDFileParser(String fileName) {
mNoOfRecords = 0;
try {
mReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName), StandardCharsets.UTF_8));
BOMSkipper.skip(mReader);
readHeader();
} catch (IOException e) {
mReader = null;
}
}
public RDFileParser(File file) {
mNoOfRecords = 0;
try {
mReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), StandardCharsets.UTF_8));
BOMSkipper.skip(mReader);
readHeader();
} catch (IOException e) {
mReader = null;
}
}
public RDFileParser(Reader reader) {
mNoOfRecords = 0;
mReader = (reader instanceof BufferedReader) ? (BufferedReader)reader : new BufferedReader(reader);
try { readHeader(); } catch (IOException ioe) {}
}
private void readHeader() throws IOException {
if (!"$RDFILE 1".equals(mReader.readLine()) // check for version 1
|| mReader.readLine() == null // read and skip time stamp
|| (mLine = mReader.readLine()) == null) { // read first reaction tag
mReader.close();
mReader = null;
return;
}
mDataMap = new TreeMap<>();
}
public boolean hasNext() {
return mReader != null;
}
/**
* Only accurate if getFieldNames() or getFieldNames(int) was called earlier
* and if the number of records of the SD-file is smaller than the number
* of records that were examined within the the getFieldNames() method.
* If not all records of the file were seen, then -1 is returned.
* For getRowCount() to reliably return the record count call getFieldNames(Integer.MAX_VALUE) first.
* @return number of rows or -1
*/
public int getRowCount() {
return mNoOfRecords;
}
public TreeMap getFieldData() {
return mDataMap;
}
public String getFieldData(String key) {
return mDataMap.get(key);
}
public String getERegNo() {
return mERegNo;
}
public String getIRegNo() {
return mIRegNo;
}
/**
* RD-files may contains lists of molecules or lists of reactions.
* For RD-files containing reactions use this method.
* @return reaction or null, if the end of the file has been reached
*/
public Reaction getNextReaction() {
if (mReader == null)
return null;
mIRegNo = null;
mERegNo = null;
Reaction rxn = null;
mDataMap.clear();
String key = null;
while (mLine != null) {
if (mLine.startsWith("$REREG ")) {
mERegNo = mLine.substring(7).trim();
}
else if (mLine.startsWith("$RIREG ")) {
mIRegNo = mLine.substring(7).trim();
}
else if (mLine.startsWith("$RFMT")) {
rxn = new Reaction();
try {
if (!new RXNFileParser().parse(rxn, mReader)) {
mReader = null;
return null;
}
}
catch (Exception e) {
mReader = null;
return null;
}
}
else if (mLine.startsWith("$DTYPE ")) {
key = mLine.substring(7).trim();
}
else if (mLine.startsWith("$DATUM ")) {
if (key != null) {
String value = mLine.substring(7).trim();
if (value.length() != 0)
mDataMap.put(key, value);
key = null;
}
}
try {
mLine = mReader.readLine();
if (mLine == null) {
mReader.close();
mReader = null;
}
}
catch (IOException e) {
return null;
}
if (isReactionNext())
break;
}
mNoOfRecords++;
return rxn;
}
public boolean isMoleculeNext() {
return mLine != null && (mLine.startsWith("$MFMT") || mLine.startsWith("$MEGEG") || mLine.startsWith("$MIREG"));
}
public boolean isReactionNext() {
return mLine != null && (mLine.startsWith("$RFMT") || mLine.startsWith("$REGEG") || mLine.startsWith("$RIREG"));
}
/**
* RD-files may contains lists of molecules or lists of reactions.
* For RD-files containing molecule use this method.
* @return molecule or null, if the end of the file has been reached
*/
public StereoMolecule getNextMolecule() {
if (mReader == null)
return null;
mIRegNo = null;
mERegNo = null;
StereoMolecule mol = null;
mDataMap.clear();
String key = null;
while (mLine != null) {
if (mLine.startsWith("$MEREG ")) {
mERegNo = mLine.substring(7).trim();
}
else if (mLine.startsWith("$MIREG ")) {
mIRegNo = mLine.substring(7).trim();
}
else if (mLine.startsWith("$MFMT")) {
mIRegNo = mLine.substring(7).trim();
mol = new StereoMolecule();
try {
if (!new MolfileParser().parse(mol, mReader)) {
mReader = null;
return null;
}
}
catch (Exception e) {
mReader = null;
return null;
}
}
else if (mLine.startsWith("$DTYPE ")) {
key = mLine.substring(7).trim();
}
else if (mLine.startsWith("$DATUM ")) {
if (key != null) {
String value = mLine.substring(7).trim();
if (value.length() != 0)
mDataMap.put(key, value);
key = null;
}
}
try {
mLine = mReader.readLine();
if (mLine == null) {
mReader.close();
mReader = null;
}
}
catch (IOException e) {
return null;
}
if (isMoleculeNext())
break;
}
mNoOfRecords++;
return mol;
}
/**
* Returns a list of field names. If the field names were not passed
* to the constructor of SDFileParser, this method parses the file/reader
* to extract all field names and uses up this SDFileParser. In this case
* one needs to instantiate a new SDFileParser to sequentially iterate
* through the file/reader's records and supply the field name array to
* the constructor.
* @return array of field names
*/
public String[] getFieldNames() {
if (mFieldName == null)
extractAllFieldNames(DEFAULT_RECORDS_TO_INSPECT);
return mFieldName;
}
private void extractAllFieldNames(int recordsToInspect) {
int records = 0;
UniqueStringList fieldNameList = new UniqueStringList();
while (records < recordsToInspect) {
Object chem = isReactionNext() ? getNextReaction() : getNextMolecule();
if (chem == null)
break;
for (String key:mDataMap.keySet())
fieldNameList.addString(key);
records++;
}
mFieldName = fieldNameList.toArray();
}
}