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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.
*
* @author Modest v. Korff
*/
package com.actelion.research.chem.io.pdb.parser;
import java.io.*;
import java.net.URI;
import java.net.URLConnection;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.AbstractMap.SimpleEntry;
import java.util.stream.IntStream;
import java.util.zip.GZIPInputStream;
/**
* PDBFileParser
* Created by korffmo1 on 20.03.18.
*/
public class PDBFileParser {
// 05-FEB-18
public static final String DATE_FORMAT = "dd-MMM-yy";
public static final String TAG_HEADER = "HEADER";
public static final String TAG_OBSOLTE = "OBSLTE";
public static final String TAG_TITLE = "TITLE";
public static final String TAG_SPLIT = "SPLIT";
public static final String TAG_CAVEAT = "CAVEAT";
// Mandatory
public static final String TAG_COMPND = "COMPND";
// Mandatory
public static final String TAG_SOURCE = "SOURCE";
// Mandatory
public static final String TAG_KEYWDS = "KEYWDS";
// Mandatory
public static final String TAG_EXPDTA = "EXPDTA";
// Optional Mandatory for NMR ensemble entries.
public static final String TAG_NUMMDL = "NUMMDL";
// Optional Mandatory for NMR minimized average Structures or when the entire polymer chain contains C alpha or P atoms only.
public static final String TAG_MDLTYP = "MDLTYP";
// Mandatory
public static final String TAG_AUTHOR = "AUTHOR";
// Mandatory
public static final String TAG_REVDAT = "REVDAT";
// Optional Mandatory for a replacement entry.
public static final String TAG_SPRSDE = "SPRSDE";
// Optional Mandatory for a publication describes the experiment.
public static final String TAG_JRNL = "JRNL";
// Remark has format 'other'
public static final String TAG_REMARK = "REMARK";
// Optional Mandatory for a re-refined structure
public static final String TAG_REMARK0 = "REMARK 0";
// Optional
public static final String TAG_REMARK1 = "REMARK 1";
// Mandatory
public static final String TAG_REMARK2 = "REMARK 2";
// Mandatory
public static final String TAG_REMARK3 = "REMARK 3";
// Optional
public static final String TAG_REMARK_N = "REMARK N";
// Optional Mandatory for all polymers.
public static final String TAG_DBREF = "DBREF";
// Optional Mandatory when certain sequence database accession and/or sequence numbering does not fit preceding DBREF format.
public static final String TAG_DBREF1_DBREF2 = "DBREF1/DBREF2";
// Optional Mandatory if sequence conflict exists.
public static final String TAG_SEQADV = "SEQADV";
// Mandatory if ATOM records exist.
public static final String TAG_SEQRES = "SEQRES";
// Optional Mandatory if modified group exists in the coordinates.
public static final String TAG_MODRES = "MODRES";
// Optional Mandatory if a non-standard group other than water appears in the coordinates.
public static final String TAG_HET = "HET";
// Optional Mandatory if
public static final String TAG_HETNAM = "HETNAM";
// Optional
public static final String TAG_HETSYN = "HETSYN";
// Optional
public static final String TAG_FORMUL = "FORMUL";
// Optional
public static final String TAG_HELIX = "HELIX";
// Optional
public static final String TAG_SHEET = "SHEET";
// Optional Mandatory if a disulfide bond is present.
public static final String TAG_SSBOND = "SSBOND";
// Optional Mandatory if non-standard residues appear in a polymer
public static final String TAG_LINK = "LINK";
// Optional
public static final String TAG_CISPEP = "CISPEP";
// Optional
public static final String TAG_SITE = "SITE";
// Mandatory
public static final String TAG_CRYST1 = "CRYST1";
// Mandatory
public static final String TAG_ORIGX1 = "ORIGX1";
// Mandatory
public static final String TAG_ORIGX2 = "ORIGX2";
// Mandatory
public static final String TAG_ORIGX3 = "ORIGX3";
// Mandatory
public static final String TAG_SCALE1 = "SCALE1";
// Mandatory
public static final String TAG_SCALE2 = "SCALE2";
// Mandatory
public static final String TAG_SCALE3 = "SCALE3";
//
public static final String TAG_MTRIX1 = "MTRIX1";
public static final String TAG_MTRIX2 = "MTRIX2";
// Optional Mandatory if the complete asymmetric unit must be generated from the given coordinates using non-crystallographic symmetry.
public static final String TAG_MTRIX3 = "MTRIX3";
// Optional Mandatory if more than one model is present in the entry.
public static final String TAG_MODEL = "MODEL";
// Optional Mandatory if standard residues exist.
public static final String TAG_ATOM = "ATOM";
// Optional
public static final String TAG_ANISOU = "ANISOU";
// Optional Mandatory if ATOM records exist.
public static final String TAG_TER = "TER";
// Optional Mandatory if non-standard group exists.
public static final String TAG_HETATM = "HETATM";
// Optional Mandatory if MODEL appears.
public static final String TAG_ENDMDL = "ENDMDL";
// Optional Mandatory if non-standard group appears and if LINK or SSBOND records exist.
public static final String TAG_CONECT = "CONECT";
// Mandatory
public static final String TAG_MASTER = "MASTER";
// Mandatory
public static final String TAG_END = "END";
private final DateFormat dfDateDeposition;
private final HetNameParser hetNameParser;
private final HetSynonymParser hetSynonymParser;
private final FormulaParser formulaParser;
private final SiteParser siteParser;
private final ModelParser modelParser;
public PDBCoordEntryFile getFromPDB(String pdbID) throws Exception {
URLConnection con = new URI("https://files.rcsb.org/download/"+pdbID+".pdb.gz").toURL().openConnection();
return new PDBFileParser().parse(new BufferedReader(new InputStreamReader(new GZIPInputStream(con.getInputStream()))));
}
public PDBFileParser() {
dfDateDeposition = new SimpleDateFormat(DATE_FORMAT);
RemarkParser remarkParser = new RemarkParser();
hetNameParser = new HetNameParser();
hetSynonymParser = new HetSynonymParser();
formulaParser = new FormulaParser();
siteParser = new SiteParser();
modelParser = new ModelParser();
}
public PDBCoordEntryFile parse(File fiPDB) throws IOException, ParseException {
return parse(new BufferedReader(new FileReader(fiPDB)));
}
public PDBCoordEntryFile parse(BufferedReader br) throws IOException, ParseException {
PDBCoordEntryFile pdbCoordEntryFile = new PDBCoordEntryFile();
ArrayList liRaw = new ArrayList();
String sCurrentLine;
while ((sCurrentLine = br.readLine()) != null) {
liRaw.add(sCurrentLine);
}
int indexLine = 0;
String lHeader = liRaw.get(indexLine);
if(lHeader.startsWith(TAG_HEADER)) {
try {
indexLine = parseHeader(lHeader, pdbCoordEntryFile);}
catch(Exception e) {
indexLine++;
}
}
String data = liRaw.get(indexLine);
while((!data.startsWith(TAG_ATOM) && !data.startsWith(TAG_HETATM)) && indexLine siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_OBSOLTE);
pdbCoordEntryFile.setObsolete(siIndex.getKey());
indexLine = siIndex.getValue();
}
if(liRaw.get(indexLine).startsWith(TAG_TITLE)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_TITLE);
pdbCoordEntryFile.setTitle(siIndex.getKey());
indexLine = siIndex.getValue();
}
//} else {
// throw new RuntimeException("Missing " + TAG_TITLE);
//}
// Not mandatory
if(liRaw.get(indexLine).startsWith(TAG_SPLIT)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_SPLIT);
pdbCoordEntryFile.setSplit(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Not mandatory
if(liRaw.get(indexLine).startsWith(TAG_CAVEAT)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_CAVEAT);
pdbCoordEntryFile.setSplit(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_COMPND)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_COMPND);
pdbCoordEntryFile.setCompound(siIndex.getKey());
indexLine = siIndex.getValue();
}
//} else {
// throw new RuntimeException("Missing " + TAG_COMPND);
//}
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_SOURCE)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_SOURCE);
pdbCoordEntryFile.setSource(siIndex.getKey());
indexLine = siIndex.getValue();
}
//} else {
// throw new RuntimeException("Missing " + TAG_SOURCE);
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_KEYWDS)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_KEYWDS);
pdbCoordEntryFile.setKeywords(siIndex.getKey());
indexLine = siIndex.getValue();
} //else {
//throw new RuntimeException("Missing " + TAG_KEYWDS);
//}
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_EXPDTA)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_EXPDTA);
pdbCoordEntryFile.setExpdata(siIndex.getKey());
indexLine = siIndex.getValue();
} //else {
// throw new RuntimeException("Missing " + TAG_EXPDTA);
//}
// Optional Mandatory for NMR ensemble entries.
if(liRaw.get(indexLine).startsWith(TAG_NUMMDL)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_NUMMDL);
pdbCoordEntryFile.setNummdl(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Optional Mandatory for NMR minimized average Structures or when the entire polymer chain contains C alpha or P atoms only.
if(liRaw.get(indexLine).startsWith(TAG_MDLTYP)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_MDLTYP);
pdbCoordEntryFile.setMdltyp(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_AUTHOR)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_AUTHOR);
pdbCoordEntryFile.setAuthor(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Mandatory
if(liRaw.get(indexLine).startsWith(TAG_REVDAT)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_REVDAT);
pdbCoordEntryFile.setRevdat(liIndex.getLi());
indexLine = liIndex.getId();
} //else {
// throw new RuntimeException("Missing " + TAG_REVDAT);
//}
// Optional Mandatory for a replacement entry.
if(liRaw.get(indexLine).startsWith(TAG_SPRSDE)) {
SimpleEntry siIndex = parseOneTimeMultipleLines(liRaw, indexLine, TAG_SPRSDE);
pdbCoordEntryFile.setSprsde(siIndex.getKey());
indexLine = siIndex.getValue();
}
// Optional Mandatory for a publication describes the experiment.
if(liRaw.get(indexLine).startsWith(TAG_JRNL)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_JRNL);
pdbCoordEntryFile.setJrnl(liIndex.getLi());
indexLine = liIndex.getId();
}
/*
remarkParser.parse(liRaw, indexLine);
HashMap hmNo_Remark = remarkParser.getHmNo_Remark();
indexLine = remarkParser.getIndexLine();
pdbCoordEntryFile.setRemarks(hmNo_Remark);
*/
// Mandatory for all polymers.
if(liRaw.get(indexLine).startsWith(TAG_DBREF)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_DBREF);
pdbCoordEntryFile.setDBRef(liIndex.getLi());
indexLine = liIndex.getId();
}
// Mandatory for all polymers.
if(liRaw.get(indexLine).startsWith(TAG_DBREF1_DBREF2)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_DBREF1_DBREF2);
pdbCoordEntryFile.setDBRef1DBRef2(liIndex.getLi());
indexLine = liIndex.getId();
}
// Mandatory if sequence conflict exists.
if(liRaw.get(indexLine).startsWith(TAG_SEQADV)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_SEQADV);
pdbCoordEntryFile.setSEQADV(liIndex.getLi());
indexLine = liIndex.getId();
}
// Mandatory if ATOM records exist.
// Primary sequence of backbone residues.
if(liRaw.get(indexLine).startsWith(TAG_SEQRES)) {
ListInteger liIndexChains = parseMultipleTimesMultipleLinesSEQRES(liRaw, indexLine, TAG_SEQRES);
pdbCoordEntryFile.setSEQRES(liIndexChains.getLi());
indexLine = liIndexChains.getId();
}
// Mandatory if modified group exists in the coordinates.
// Identification of modifications to standard residues.
if(liRaw.get(indexLine).startsWith(TAG_MODRES)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_MODRES);
pdbCoordEntryFile.setModRes(liIndex.getLi());
indexLine = liIndex.getId();
}
// Mandatory if a non-standard group other than water appears in the coordinates.
// Identification of non-standard groups heterogens).
String patternHET = TAG_HET + " ";
if(liRaw.get(indexLine).startsWith(patternHET)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, patternHET);
pdbCoordEntryFile.setHet(liIndex.getLi());
indexLine = liIndex.getId();
}
//
// Compound name of the heterogens.
if(liRaw.get(indexLine).startsWith(TAG_HETNAM)) {
hetNameParser.parse(liRaw, indexLine);
HashMap hmId_Name = hetNameParser.getHMId_Name();
pdbCoordEntryFile.setHmId_Name(hmId_Name);
indexLine = hetNameParser.getIndexLine();
}
if(liRaw.get(indexLine).startsWith(TAG_HETSYN)) {
hetSynonymParser.parse(liRaw, indexLine);
HashMap hmId_Synonyms = hetSynonymParser.getHMId_Synonyms();
pdbCoordEntryFile.setHmId_Synonyms(hmId_Synonyms);
indexLine = hetSynonymParser.getIndexLine();
}
if(liRaw.get(indexLine).startsWith(TAG_FORMUL)) {
formulaParser.parse(liRaw, indexLine);
HashMap hmId_Formula = formulaParser.getHMId_Formula();
pdbCoordEntryFile.setHmId_Formula(hmId_Formula);
indexLine = formulaParser.getIndexLine();
}
if(liRaw.get(indexLine).startsWith(TAG_HELIX)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_HELIX);
pdbCoordEntryFile.setHelix(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_SHEET)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_SHEET);
pdbCoordEntryFile.setSheet(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_SSBOND)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_SSBOND);
pdbCoordEntryFile.setSSBond(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_LINK)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_LINK);
pdbCoordEntryFile.setLink(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_CISPEP)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_CISPEP);
pdbCoordEntryFile.setCisPep(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_SITE)) {
siteParser.parse(liRaw, indexLine);
HashMap hmId_Site = siteParser.getHMId_Site();
pdbCoordEntryFile.setHmId_Site(hmId_Site);
indexLine = siteParser.getIndexLine();
}
if(liRaw.get(indexLine).startsWith(TAG_CRYST1)) {
pdbCoordEntryFile.setCryst1(liRaw.get(indexLine).substring(6));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_CRYST1);
//}
if(liRaw.get(indexLine).startsWith(TAG_ORIGX1)) {
pdbCoordEntryFile.setOrigX1(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_ORIGX1);
//}
if(liRaw.get(indexLine).startsWith(TAG_ORIGX2)) {
pdbCoordEntryFile.setOrigX2(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_ORIGX2);
//}
if(liRaw.get(indexLine).startsWith(TAG_ORIGX3)) {
pdbCoordEntryFile.setOrigX3(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_ORIGX3);
//}
if(liRaw.get(indexLine).startsWith(TAG_SCALE1)) {
pdbCoordEntryFile.setScale1(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_SCALE1);
//}
if(liRaw.get(indexLine).startsWith(TAG_SCALE2)) {
pdbCoordEntryFile.setScale2(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_SCALE2);
//}
if(liRaw.get(indexLine).startsWith(TAG_SCALE3)) {
pdbCoordEntryFile.setScale3(liRaw.get(indexLine).substring(10));
indexLine++;
} //else {
// throw new RuntimeException("Missing " + TAG_SCALE3);
//}
if(liRaw.get(indexLine).startsWith(TAG_MTRIX1)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_MTRIX1);
pdbCoordEntryFile.setMtrix1(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_MTRIX2)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_MTRIX2);
pdbCoordEntryFile.setMtrix2(liIndex.getLi());
indexLine = liIndex.getId();
}
if(liRaw.get(indexLine).startsWith(TAG_MTRIX3)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_MTRIX3);
pdbCoordEntryFile.setMtrix3(liIndex.getLi());
indexLine = liIndex.getId();
}
else {
indexLine++;
}
data = liRaw.get(indexLine);
//
// Parsing atoms and their coordinates
//
}
//indexLine--;
List hetAtomRecords = new ArrayList();
List protAtomRecords = new ArrayList();
modelParser.parse(liRaw, indexLine,protAtomRecords,hetAtomRecords);
pdbCoordEntryFile.setProtAtomRecords(protAtomRecords);
pdbCoordEntryFile.setHetAtomRecords(hetAtomRecords);
//List liModelModel = modelParser.getLiModelModel();
//pdbCoordEntryFile.setLiModelModel(liModelModel);
indexLine = modelParser.getIndexLine();
//
// Parsing atom connections
//
List bonds = new ArrayList();
if(liRaw.get(indexLine).startsWith(TAG_CONECT)) {
ListInteger liIndex = parseMultipleTimesOneLine(liRaw, indexLine, TAG_CONECT);
for(String bondInfo:liIndex.getLi()) {
bondInfo = bondInfo.trim();
String[] strArr = bondInfo.split("\\s+");
try {
int firstAtom = Integer.parseInt(strArr[0]);
IntStream.range(1,strArr.length).forEach(e -> {
int[] bond = new int[2];
bond[0] = firstAtom;
bond[1] = Integer.parseInt(strArr[e]);
bonds.add(bond);
});
}
catch(Exception e) {
continue;
}
}
indexLine = liIndex.getId();
}
pdbCoordEntryFile.setLiConnect(bonds);
if(liRaw.get(indexLine).startsWith(TAG_MASTER)) {
pdbCoordEntryFile.setMaster(liRaw.get(indexLine).substring(10).trim());
indexLine++;
}
if(liRaw.get(indexLine).startsWith(TAG_END)) {
pdbCoordEntryFile.setEnd(true);
} else {
pdbCoordEntryFile.setEnd(false);
}
return pdbCoordEntryFile;
}
private int parseHeader(String lHeader, PDBCoordEntryFile pdbCoordEntryFile) throws ParseException {
int length = lHeader.length();
pdbCoordEntryFile.setClassification(lHeader.substring (10, Math.min(length,50)).trim() );
Date date = dfDateDeposition.parse(lHeader.substring (50, Math.min(length,59)).trim() );
pdbCoordEntryFile.setDateDeposition(date);
pdbCoordEntryFile.setID(lHeader.substring (62, Math.min(length,66)).trim() );
return 1;
}
/**
* One time, multiple lines: There are records that conceptually exist only once in an entry, but the
information content may exceed the number of columns available. These records are therefore
continued on subsequent lines.
* @param liRaw
* @param indexLine
* @return
* @throws ParseException
*/
private AbstractMap.SimpleEntry parseOneTimeMultipleLines(List liRaw, int indexLine, String tag) throws ParseException {
String l0 = liRaw.get(indexLine);
if(!l0.startsWith(tag)) {
throw new RuntimeException("Error in parsing " + tag);
}
String titleSub0 = l0.substring(tag.length()).trim();
StringBuilder sb = new StringBuilder(titleSub0);
indexLine++;
int start = indexLine;
for (int i = start; i < liRaw.size(); i++) {
String l = liRaw.get(i);
if(l.startsWith(tag)) {
String [] arr = l.split("[ ]+");
sb.append(" ");
for (int j = 1; 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;
}
private ListInteger parseMultipleTimesOneLine(List liRaw, int indexLine, String tag) throws ParseException {
int skipFirst = 1;
String l0 = liRaw.get(indexLine);
if(!l0.startsWith(tag)) {
throw new RuntimeException("Error in parsing " + tag);
}
String titleSub0 = l0.substring(tag.length()).trim();
List liTxt = new ArrayList<>();
liTxt.add(titleSub0);
indexLine++;
int start = indexLine;
for (int i = start; i < liRaw.size(); i++) {
String l = liRaw.get(i);
if(l.startsWith(tag)) {
StringBuilder sb = new StringBuilder();
String [] arr = l.split("[ ]+");
sb.append(" ");
for (int j = skipFirst; j < arr.length; j++) {
sb.append(arr[j]);
if(j < arr.length-1) {
sb.append(" ");
}
}
liTxt.add(sb.toString());
indexLine++;
} else {
break;
}
}
ListInteger liTextIndex = new ListInteger(liTxt, indexLine);
return liTextIndex;
}
private static ListInteger parseMultipleTimesMultipleLinesSEQRES(List liRaw, int indexLine, String tag) throws ParseException {
String l0 = liRaw.get(indexLine);
if(!l0.startsWith(tag)) {
throw new RuntimeException("Error in parsing " + tag);
}
StringBuilder sb = new StringBuilder();
int start = indexLine;
String chainId = l0.substring(11, 12);
int numResidues = Integer.parseInt(l0.substring(13,17).trim());
List liChain = new ArrayList<>();
for (int i = start; i < liRaw.size(); i++) {
String l = liRaw.get(i);
if(!l.startsWith(tag)) {
break;
}
String chainIdLine = l.substring(11, 12);
int numResiduesLine = Integer.parseInt(l.substring(13,17).trim());
if(!chainId.equals(chainIdLine)) {
String chain = sb.toString();
liChain.add(chain);
chainId = chainIdLine;
numResidues = numResiduesLine;
sb = new StringBuilder();
}
if(sb.length()>0){
sb.append(" ");
}
/*
if(numResidues!=numResiduesLine) {
throw new RuntimeException("Number of residues differs!");
}
*/
String chainLine = l.substring(19).trim();
sb.append(chainLine);
indexLine++;
}
if(sb.length()>0){
String chain = sb.toString();
liChain.add(chain);
}
ListInteger listIndexLineChain = new ListInteger(liChain, indexLine);
return listIndexLineChain;
}
}