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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.io.BOMSkipper;
import java.io.*;
import java.nio.charset.StandardCharsets;
public class SDFileParser extends CompoundFileParser {
private static final int DEFAULT_RECORDS_TO_INSPECT = 10240;
private static final String[] cIDFieldNames = { "Idorsia No", "Actelion No", "ID", "IDNUMBER", "COMPOUND_ID", "NAME", "COMPND" };
public static final String cNewLineString = "\n";
private StringBuilder mMolfileBuffer,mDataBuffer;
private StereoMolecule mMol;
private String[] mFieldName;
private String[] mFieldData;
private int mNoOfRecords,mIDFieldIndex;
public SDFileParser(String fileName) {
this(fileName, null);
}
public SDFileParser(String fileName, String[] fieldName) {
mNoOfRecords = -1;
mFieldName = fieldName;
try {
mReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName), StandardCharsets.UTF_8));
BOMSkipper.skip(mReader);
} catch (IOException e) {
mReader = null;
}
init();
}
public SDFileParser(File file) {
this(file, null);
}
public SDFileParser(File file, String[] fieldName) {
mNoOfRecords = -1;
mFieldName = fieldName;
try {
mReader = new BufferedReader(new InputStreamReader(new FileInputStream(file), StandardCharsets.UTF_8));
BOMSkipper.skip(mReader);
} catch (IOException e) {
mReader = null;
}
init();
}
public SDFileParser(Reader reader) {
this(reader, null);
}
public SDFileParser(Reader reader, String[] fieldName) {
mNoOfRecords = -1;
mFieldName = fieldName;
mReader = (reader instanceof BufferedReader) ? (BufferedReader)reader : new BufferedReader(reader);
init();
}
private void init() {
mMolfileBuffer = new StringBuilder(10240);
mDataBuffer = new StringBuilder(10240);
}
private void extractAllFieldNames(int recordsToInspect) {
int records = 0;
// TreeSet fieldNameList = new TreeSet(); Changed to keep the original order of field names. TLS 6Jan16
UniqueStringList fieldNameList = new UniqueStringList();
while (records < recordsToInspect) {
String line;
try {
line = mReader.readLine();
}
catch (IOException e) {
if (records < recordsToInspect)
mNoOfRecords = records;
break;
}
if (line == null) {
if (records < recordsToInspect)
mNoOfRecords = records;
break;
}
if (line.startsWith("$$$$"))
records++;
if (line.startsWith(">")) {
String fieldName = extractFieldName(line);
if (fieldName != null)
fieldNameList.addString(fieldName);
}
}
try {
mReader.close();
}
catch (IOException e) {}
mFieldName = fieldNameList.toArray();
}
/**
* 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;
}
protected boolean advanceToNext() {
if (mReader == null)
return false;
// removed 13.8.2012 TLS; no need to read molfile in order to advance to the next record
// if (mMolfileBuffer.length() != 0)
// return true;
mMolfileBuffer.setLength(0);
mDataBuffer.setLength(0);
mMol = null;
boolean molfileComplete = false;
int fieldIndex = -1;
String fieldName = null;
String line;
mFieldData = (mFieldName == null) ? null : new String[mFieldName.length];
mIDFieldIndex = -1;
do {
try {
line = mReader.readLine();
if (line == null) {
mMolfileBuffer.setLength(0);
mReader.close();
return false;
}
}
catch (IOException e) {
mMolfileBuffer.setLength(0);
return false;
}
if (!molfileComplete) {
if (line.startsWith(">")) { // to handle sd-record with molfiles without 'M END'
molfileComplete = true;
mMolfileBuffer.append("M END");
mMolfileBuffer.append('\n');
mDataBuffer.append(line);
mDataBuffer.append('\n');
}
else {
mMolfileBuffer.append(line);
mMolfileBuffer.append('\n');
if (line.startsWith("M END"))
molfileComplete = true;
continue;
}
}
else {
mDataBuffer.append(line);
mDataBuffer.append('\n');
}
if (mFieldName != null) {
if (line.length() == 0) {
fieldIndex = -1;
}
else if (fieldIndex == -1) {
fieldName = extractFieldName(line);
if (fieldName != null) {
// find fieldIndex to given fieldName
fieldIndex = -1;
for (int field=0; field records 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(int recordsToInspect) {
if (mFieldName == null)
extractAllFieldNames(recordsToInspect);
return mFieldName;
}
/* public boolean moreRecordsAvailable() {
if (mFieldDataList == null || mFieldDataList.size() == 0)
return false;
mCurrentFieldData = mFieldDataList.get(0);
mFieldDataList.remove(0);
return true;
}
*/
public String getFieldData(int index) {
if (mFieldData == null)
return null;
return mFieldData[index];
}
protected String extractFieldName(String line) {
if (line.length() == 0
|| line.charAt(0) != '>')
return null;
int index = 1;
int openBracket = 0;
int closeBracket = 0;
while (index < line.length()) {
if (line.charAt(index) == '<') {
if (openBracket != 0)
return null;
openBracket = index;
}
else if (line.charAt(index) == '>') {
if (closeBracket != 0)
return null;
closeBracket = index;
}
index++;
}
if (openBracket != 0 && openBracket < closeBracket)
return line.substring(openBracket+1, closeBracket);
// allow for MACCS-II field numbers, which have format DTn
index = line.indexOf("DT", 1);
if (index == -1)
return null;
int i = index+2;
while (line.length()>i && Character.isDigit(line.charAt(i)))
i++;
return (i == index+2) ? null : line.substring(index, i);
}
}