com.actelion.research.chem.io.pdb.parser.RemarkParser Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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.
*
* @author Modest v. Korff
*/
package com.actelion.research.chem.io.pdb.parser;
import java.text.ParseException;
import java.util.AbstractMap;
import java.util.HashMap;
import java.util.List;
import java.util.AbstractMap.SimpleEntry;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* RemarkParser
* Created by korffmo1 on 09.04.18.
*/
public class RemarkParser {
private int indexLine;
private HashMap hmNo_Remark;
public RemarkParser() {
}
void parse(List liRaw, int indexLine) throws ParseException {
this.indexLine = indexLine;
hmNo_Remark = new HashMap<>();
int ccRemark = 0;
// Optional Mandatory for a re-refined structure
if(RemarkParser.getMatcherRemark(ccRemark, liRaw.get(indexLine)).find()) {
SimpleEntry siIndex = parseRemark(liRaw, indexLine, ccRemark);
hmNo_Remark.put(ccRemark, siIndex.getKey());
indexLine = siIndex.getValue();
}
ccRemark++;
if(RemarkParser.getMatcherRemark(ccRemark, liRaw.get(indexLine)) .find()) {
SimpleEntry siIndex = parseRemark(liRaw, indexLine, ccRemark);
hmNo_Remark.put(ccRemark, siIndex.getKey());
indexLine = siIndex.getValue();
}
// Remark 2 mandatory
ccRemark++;
if(RemarkParser.getMatcherRemark(ccRemark, liRaw.get(indexLine)) .find()) {
SimpleEntry siIndex = parseRemark(liRaw, indexLine, ccRemark);
hmNo_Remark.put(ccRemark, siIndex.getKey());
indexLine = siIndex.getValue();
} //else {
// throw new RuntimeException("Missing " + PDBFileParser.TAG_REMARK2);
//}
// Remark 3 mandatory
ccRemark++;
if(RemarkParser.getMatcherRemark(ccRemark, liRaw.get(indexLine)) .find()) {
SimpleEntry siIndex = parseRemark(liRaw, indexLine, ccRemark);
hmNo_Remark.put(ccRemark, siIndex.getKey());
indexLine = siIndex.getValue();
} //else {
// throw new RuntimeException("Missing " + PDBFileParser.TAG_REMARK3);
//}
Pattern p = getPatternRemark();
boolean searchRemarks = true;
while (searchRemarks) {
String line = liRaw.get(indexLine);
Matcher matcher = p.matcher(line);
if(matcher.find()) {
String [] arr = line.split("[ ]+");
ccRemark = Integer.parseInt(arr[1]);
SimpleEntry siIndex = parseRemark(liRaw, indexLine, ccRemark);
hmNo_Remark.put(ccRemark, siIndex.getKey());
indexLine = siIndex.getValue();
} else {
searchRemarks = false;
}
}
this.indexLine = indexLine;
}
public int getIndexLine() {
return indexLine;
}
public HashMap getHmNo_Remark() {
return hmNo_Remark;
}
private static SimpleEntry parseRemark(List liRaw, int indexLine, int indexRemark) throws ParseException {
Pattern pattern = RemarkParser.getPatternRemark(indexRemark);
// String titleSub0 = l0.substring(tag.length()).trim();
StringBuilder sb = new StringBuilder();
int start = indexLine;
for (int i = start; i < liRaw.size(); i++) {
String l = liRaw.get(i);
Matcher matcher = pattern.matcher(l);
if(matcher.find()) {
String [] arr = l.split("[ ]+");
sb.append(" ");
for (int j = 2; j < arr.length; j++) {
sb.append(arr[j]);
if(j < arr.length-1) {
sb.append(" ");
}
}
indexLine++;
} else {
break;
}
}
AbstractMap.SimpleEntry siTextIndex = new AbstractMap.SimpleEntry<>(sb.toString(), indexLine);
return siTextIndex;
}
static Pattern getPatternRemark() {
String p = PDBFileParser.TAG_REMARK + "[ ]+";
return Pattern.compile(p);
}
static Pattern getPatternRemark(int index) {
String p = PDBFileParser.TAG_REMARK + "[ ]+" + index;
return Pattern.compile(p);
}
static Matcher getMatcherRemark(int indexRemark, String s){
Pattern p = getPatternRemark(indexRemark);
Matcher matcher = p.matcher(s);
return matcher;
}
}