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Open Source Chemistry Library
package com.actelion.research.chem.io.pdb.parser;
import java.util.*;
import com.actelion.research.chem.Molecule3D;
/**
* PDBCoordEntryFile
* Copyright: Idorsia Pharmaceuticals Ltd., Inc. All Rights Reserved
* This software is the proprietary information of Idorsia Pharmaceuticals, Ltd.
* Use is subject to license terms.
* Created by korffmo1 on 20.03.18.
*/
public class PDBCoordEntryFile {
/**
* description of pdb-file format: http://www.wwpdb.org/documentation/file-format
*/
//
// Header information
//
/**
* Classification may be based on function, metabolic role, molecule type, cellular location, etc.
* This record can describe dual functions of a molecules, and when applicable, separated by a
* comma “
*/
private String classification;
private String pdbID;
private Date dateDeposition;
private String obsolete;
private String title;
private String split;
private String caveat;
private String compound;
private String source;
private String keywords;
private String expdata;
private String nummdl;
private String mdltyp;
private String author;
private List liRevdat;
private String sprsde;
private List liJRNL;
private HashMap hmNo_Remark;
private List liDBRef;
private List liDBRef1DBRef2;
private List liSEQADV;
private List liSEQRES;
private List liModRes;
private List liHet;
private HashMap hmId_Name;
private HashMap hmId_Synonyms;
private HashMap hmId_Formula;
private List liHelix;
private List liSheet;
private List liSSBond;
private List liLink;
private List liCisPep;
private HashMap hmId_Site;
private String cryst1;
private String origX1;
private String origX2;
private String origX3;
private String scale1;
private String scale2;
private String scale3;
private List liMtrix1;
private List liMtrix2;
private List liMtrix3;
private List protAtomRecords;
private List hetAtomRecords;
private List liConnect;
private String master;
private boolean end;
public String getClassification() {
return classification;
}
public void setClassification(String classification) {
this.classification = classification;
}
public String getID() {
return pdbID;
}
public void setID(String pdbID) {
this.pdbID = pdbID;
}
public Date getDateDeposition() {
return dateDeposition;
}
public void setDateDeposition(Date dateDeposition) {
this.dateDeposition = dateDeposition;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
public List getProtAtomRecords() {
return protAtomRecords;
}
public void setProtAtomRecords(List protAtomRecords) {
this.protAtomRecords = protAtomRecords;
}
public List getHetAtomRecords() {
return hetAtomRecords;
}
public void setHetAtomRecords(List hetAtomRecords) {
this.hetAtomRecords = hetAtomRecords;
}
public String getObsolete() {
return obsolete;
}
public void setObsolete(String obsolete) {
this.obsolete = obsolete;
}
public String getSplit() {
return split;
}
public void setSplit(String split) {
this.split = split;
}
public String getCaveat() {
return caveat;
}
public void setCaveat(String caveat) {
this.caveat = caveat;
}
public String getCompound() {
return compound;
}
public void setCompound(String compound) {
this.compound = compound;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public String getKeywords() {
return keywords;
}
public void setKeywords(String keywords) {
this.keywords = keywords;
}
public String getExpdata() {
return expdata;
}
public void setExpdata(String expdata) {
this.expdata = expdata;
}
public String getNummdl() {
return nummdl;
}
public void setNummdl(String nummdl) {
this.nummdl = nummdl;
}
public String getMdltyp() {
return mdltyp;
}
public void setMdltyp(String mdltyp) {
this.mdltyp = mdltyp;
}
public String getAuthor() {
return author;
}
public void setAuthor(String author) {
this.author = author;
}
public List getRevdat() {
return liRevdat;
}
public void setRevdat(List liRevdat) {
this.liRevdat = liRevdat;
}
public String getSprsde() {
return sprsde;
}
public void setSprsde(String sprsde) {
this.sprsde = sprsde;
}
public List getJrnl() {
return liJRNL;
}
public void setJrnl(List jrnl) {
this.liJRNL = jrnl;
}
public String getRemark0() {
return hmNo_Remark.get(0);
}
public String getRemark1() {
return hmNo_Remark.get(1);
}
public String getRemark2() {
return hmNo_Remark.get(2);
}
public String getRemark3() {
return hmNo_Remark.get(3);
}
public void setRemarks(HashMap hmNo_Remark) {
this.hmNo_Remark = hmNo_Remark;
}
public String getRemark(int n) {
return hmNo_Remark.get(n);
}
public List getRemarks(){
List liRemarkNo = new ArrayList<>(hmNo_Remark.keySet());
Collections.sort(liRemarkNo);
return liRemarkNo;
}
public List getDBRef() {
return liDBRef;
}
public void setDBRef(List liDBRef) {
this.liDBRef = liDBRef;
}
public List getDBRef1DBRef2() {
return liDBRef1DBRef2;
}
public void setDBRef1DBRef2(List liDBRef1DBRef2) {
this.liDBRef1DBRef2 = liDBRef1DBRef2;
}
public List getSEQADV() {
return liSEQADV;
}
public void setSEQADV(List liSEQADV) {
this.liSEQADV = liSEQADV;
}
public List getSEQRES() {
return liSEQRES;
}
public void setSEQRES(List liSEQRES) {
this.liSEQRES = liSEQRES;
}
public List getModRes() {
return liModRes;
}
public void setModRes(List liModRes) {
this.liModRes = liModRes;
}
public List getHet() {
return liHet;
}
public void setHet(List liHet) {
this.liHet = liHet;
}
public HashMap getHmId_Name() {
return hmId_Name;
}
public void setHmId_Name(HashMap hmId_Name) {
this.hmId_Name = hmId_Name;
}
public List getNameIDs(){
List li = new ArrayList<>(hmId_Name.keySet());
Collections.sort(li);
return li;
}
public String getName(String nameId){
return hmId_Name.get(nameId);
}
public void setHmId_Synonyms(HashMap hm) {
this.hmId_Synonyms = hm;
}
public List getSynonymIDs(){
List li = new ArrayList<>(hmId_Synonyms.keySet());
Collections.sort(li);
return li;
}
public String getSynonyms(String synonymId){
return hmId_Synonyms.get(synonymId);
}
public void setHmId_Formula(HashMap hm) {
this.hmId_Formula = hm;
}
public List getFormulaIDs(){
List li = new ArrayList<>(hmId_Formula.keySet());
Collections.sort(li);
return li;
}
public String getFormula(String formulaId){
return hmId_Formula.get(formulaId);
}
public List getHelix() {
return liHelix;
}
public void setHelix(List liHelix) {
this.liHelix = liHelix;
}
public List getSheet() {
return liSheet;
}
public void setSheet(List liSheet) {
this.liSheet = liSheet;
}
public List getSSBond() {
return liSSBond;
}
public void setSSBond(List liSSBond) {
this.liSSBond = liSSBond;
}
public List getLink() {
return liLink;
}
public void setLink(List liLink) {
this.liLink = liLink;
}
public List getCisPep() {
return liCisPep;
}
public void setCisPep(List liCisPep) {
this.liCisPep = liCisPep;
}
public void setHmId_Site(HashMap hm) {
this.hmId_Site = hm;
}
public List getSiteIDs(){
List li = new ArrayList<>(hmId_Site.keySet());
Collections.sort(li);
return li;
}
public String getSite(String id){
return hmId_Site.get(id);
}
public String getCryst1() {
return cryst1;
}
public void setCryst1(String cryst1) {
this.cryst1 = cryst1;
}
public String getOrigX1() {
return origX1;
}
public void setOrigX1(String origX1) {
this.origX1 = origX1;
}
public String getOrigX2() {
return origX2;
}
public void setOrigX2(String origX2) {
this.origX2 = origX2;
}
public String getOrigX3() {
return origX3;
}
public void setOrigX3(String origX3) {
this.origX3 = origX3;
}
public String getScale1() {
return scale1;
}
public void setScale1(String scale1) {
this.scale1 = scale1;
}
public String getScale2() {
return scale2;
}
public void setScale2(String scale2) {
this.scale2 = scale2;
}
public String getScale3() {
return scale3;
}
public void setScale3(String scale3) {
this.scale3 = scale3;
}
public List getMtrix1() {
return liMtrix1;
}
public void setMtrix1(List liMtrix1) {
this.liMtrix1 = liMtrix1;
}
public List getMtrix2() {
return liMtrix2;
}
public void setMtrix2(List liMtrix2) {
this.liMtrix2 = liMtrix2;
}
public List getMtrix3() {
return liMtrix3;
}
public void setMtrix3(List liMtrix3) {
this.liMtrix3 = liMtrix3;
}
public List getLiConnect() {
return liConnect;
}
public void setLiConnect(List liConnect) {
this.liConnect = liConnect;
}
public String getMaster() {
return master;
}
public void setMaster(String master) {
this.master = master;
}
public boolean isEnd() {
return end;
}
public void setEnd(boolean end) {
this.end = end;
}
public Map> extractMols() {
StructureAssembler assembler = new StructureAssembler(liConnect,protAtomRecords,hetAtomRecords);
return assembler.assemble();
}
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("PDBCoordEntryFile{");
sb.append("classification='").append(classification).append('\'');
sb.append(", pdbID'").append(pdbID).append('\'');
sb.append(", dateDeposition=").append(dateDeposition);
sb.append(", obsolete='").append(obsolete).append('\'');
sb.append(", title='").append(title).append('\'');
sb.append(", split='").append(split).append('\'');
sb.append(", caveat='").append(caveat).append('\'');
sb.append(", compound='").append(compound).append('\'');
sb.append(", source='").append(source).append('\'');
sb.append(", keywords='").append(keywords).append('\'');
sb.append(", expdata='").append(expdata).append('\'');
sb.append(", nummdl='").append(nummdl).append('\'');
sb.append(", mdltyp='").append(mdltyp).append('\'');
sb.append(", author='").append(author).append('\'');
sb.append(", revdat='").append(liRevdat).append('\'');
sb.append(", sprsde='").append(sprsde).append('\'');
sb.append(", jrnl='").append(liJRNL).append('\'');
List liKeyRemark = getRemarks();
for (int key : liKeyRemark) {
String s = getRemark(key);
sb.append(", remark");
sb.append(key);
sb.append("='").append(s).append('\'');;
}
sb.append('}');
return sb.toString();
}
}
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