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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* created at Mar 4, 2008
*/
package org.biojava.nbio.structure.io.mmcif;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.vecmath.Matrix4d;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.StructureIOFile;
import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
import org.biojava.nbio.structure.io.mmcif.model.AuditAuthor;
import org.biojava.nbio.structure.io.mmcif.model.Cell;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom;
import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
import org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor;
import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark;
import org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev;
import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
import org.biojava.nbio.structure.io.mmcif.model.Entity;
import org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq;
import org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen;
import org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat;
import org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn;
import org.biojava.nbio.structure.io.mmcif.model.Exptl;
import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor;
import org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier;
import org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly;
import org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme;
import org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList;
import org.biojava.nbio.structure.io.mmcif.model.Refine;
import org.biojava.nbio.structure.io.mmcif.model.Struct;
import org.biojava.nbio.structure.io.mmcif.model.StructAsym;
import org.biojava.nbio.structure.io.mmcif.model.StructConn;
import org.biojava.nbio.structure.io.mmcif.model.StructKeywords;
import org.biojava.nbio.structure.io.mmcif.model.StructNcsOper;
import org.biojava.nbio.structure.io.mmcif.model.StructRef;
import org.biojava.nbio.structure.io.mmcif.model.StructRefSeq;
import org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif;
import org.biojava.nbio.structure.io.mmcif.model.StructSite;
import org.biojava.nbio.structure.io.mmcif.model.StructSiteGen;
import org.biojava.nbio.structure.io.mmcif.model.Symmetry;
import org.biojava.nbio.structure.jama.Matrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A simple mmCif file parser
*
*
* Usage:
*
String file = "path/to/mmcif/file";
StructureIOFile pdbreader = new MMCIFFileReader();
Structure s = pdbreader.getStructure(file);
System.out.println(s);
// you can convert it to a PDB file...
System.out.println(s.toPDB());
*
* For more documentation see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure.
*
* @author Andreas Prlic
* @author Jose Duarte
* @since 1.7
*/
public class SimpleMMcifParser implements MMcifParser {
/**
* The header appearing at the beginning of a mmCIF file.
* A "block code" can be added to it of no more than 32 chars.
* See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf
*/
public static final String MMCIF_TOP_HEADER = "data_";
public static final String COMMENT_CHAR = "#";
public static final String LOOP_START = "loop_";
public static final String FIELD_LINE = "_";
// the following are the 3 valid quoting characters in CIF
/**
* Quoting character '
*/
private static final char S1 = '\'';
/**
* Quoting character "
*/
private static final char S2 = '\"';
/**
* Quoting character ; (multi-line quoting)
*/
public static final String STRING_LIMIT = ";";
private List consumers ;
private Struct struct ;
private static final Logger logger = LoggerFactory.getLogger(SimpleMMcifParser.class);
public SimpleMMcifParser(){
consumers = new ArrayList();
struct = null;
}
@Override
public void addMMcifConsumer(MMcifConsumer consumer) {
consumers.add(consumer);
}
@Override
public void clearConsumers() {
consumers.clear();
}
@Override
public void removeMMcifConsumer(MMcifConsumer consumer) {
consumers.remove(consumer);
}
public static void main(String[] args){
String file = "/Users/andreas/WORK/PDB/mmCif/a9/1a9n.cif.gz";
//String file = "/Users/andreas/WORK/PDB/MMCIF/1gav.mmcif";
//String file = "/Users/andreas/WORK/PDB/MMCIF/100d.cif";
//String file = "/Users/andreas/WORK/PDB/MMCIF/1a4a.mmcif";
System.out.println("parsing " + file);
StructureIOFile pdbreader = new MMCIFFileReader();
try {
Structure s = pdbreader.getStructure(file);
System.out.println(s);
// convert it to a PDB file...
System.out.println(s.toPDB());
} catch (IOException e) {
e.printStackTrace();
}
}
@Override
public void parse(InputStream inStream) throws IOException {
parse(new BufferedReader(new InputStreamReader(inStream)));
}
@Override
public void parse(BufferedReader buf)
throws IOException {
triggerDocumentStart();
// init container objects...
struct = new Struct();
String line = null;
boolean inLoop = false;
boolean inLoopData = false;
List loopFields = new ArrayList();
List lineData = new ArrayList();
Set loopWarnings = new HashSet(); // used only to reduce logging statements
String category = null;
// the first line is a data_PDBCODE line, test if this looks like a mmcif file
line = buf.readLine();
if (line == null || !line.startsWith(MMCIF_TOP_HEADER)){
logger.error("This does not look like a valid mmCIF file! The first line should start with 'data_', but is: '" + line+"'");
triggerDocumentEnd();
return;
}
while ( (line = buf.readLine ()) != null ){
if (line.isEmpty() || line.startsWith(COMMENT_CHAR)) continue;
logger.debug(inLoop + " " + line);
if (line.startsWith(MMCIF_TOP_HEADER)){
// either first line in file, or beginning of new section
if ( inLoop) {
//System.out.println("new data and in loop: " + line);
inLoop = false;
inLoopData = false;
lineData.clear();
loopFields.clear();
}
}
if ( inLoop) {
if ( line.startsWith(LOOP_START)){
loopFields.clear();
inLoop = true;
inLoopData = false;
continue;
}
if ( line.matches("\\s*"+FIELD_LINE+"\\w+.*")) {
if (inLoopData && line.startsWith(FIELD_LINE)) {
logger.debug("Found a field line after reading loop data. Toggling to inLoop=false");
inLoop = false;
inLoopData = false;
loopFields.clear();
// a boring normal line
List data = processLine(line, buf, 2);
if ( data.size() < 1){
// this can happen if empty lines at end of file
lineData.clear();
continue;
}
String key = data.get(0);
int pos = key.indexOf(".");
if ( pos < 0 ) {
// looks like a chem_comp file
// line should start with data, otherwise something is wrong!
if (! line.startsWith(MMCIF_TOP_HEADER)){
logger.warn("This does not look like a valid mmCIF file! The first line should start with 'data_', but is '" + line+"'");
triggerDocumentEnd();
return;
}
// ignore the first line...
category=null;
lineData.clear();
continue;
}
category = key.substring(0,pos);
String value = data.get(1);
loopFields.add(key.substring(pos+1,key.length()));
lineData.add(value);
logger.debug("Found data for category {}: {}", key, value);
continue;
}
// found another field.
String txt = line.trim();
if ( txt.indexOf('.') > -1){
String[] spl = txt.split("\\.");
category = spl[0];
String attribute = spl[1];
loopFields.add(attribute);
logger.debug("Found category: {}, attribute: {}",category, attribute);
if ( spl.length > 2){
logger.warn("Found nested attribute in {}, not supported yet!",txt);
}
} else {
category = txt;
logger.debug("Found category without attribute: {}",category);
}
} else {
// in loop and we found a data line
lineData = processLine(line, buf, loopFields.size());
logger.debug("Found a loop data line with {} data fields", lineData.size());
logger.debug("Data fields: {}", lineData.toString());
if ( lineData.size() != loopFields.size()){
logger.warn("Expected {} data fields, but found {} in line: {}",loopFields.size(),lineData.size(),line);
}
endLineChecks(category, loopFields, lineData, loopWarnings);
lineData.clear();
inLoopData = true;
}
} else {
// not in loop
if ( line.startsWith(LOOP_START)){
if ( category != null)
endLineChecks(category, loopFields, lineData, loopWarnings);
resetBuffers(loopFields, lineData, loopWarnings);
category = null;
inLoop = true;
inLoopData = false;
logger.debug("Detected LOOP_START: '{}'. Toggling to inLoop=true", LOOP_START);
continue;
} else {
logger.debug("Normal line ");
inLoop = false;
// a boring normal line
List data = processLine(line, buf, 2);
if ( data.size() < 1){
// this can happen if empty lines at end of file
lineData.clear();
continue;
}
String key = data.get(0);
int pos = key.indexOf(".");
if ( pos < 0 ) {
// looks like a chem_comp file
// line should start with data, otherwise something is wrong!
if (! line.startsWith(MMCIF_TOP_HEADER)){
logger.warn("This does not look like a valid mmCIF file! The first line should start with 'data_', but is '" + line+"'");
triggerDocumentEnd();
return;
}
// ignore the first line...
category=null;
lineData.clear();
continue;
}
if (category!=null && !key.substring(0,pos).equals(category)) {
// we've changed category: need to flush the previous one
endLineChecks(category, loopFields, lineData, loopWarnings);
resetBuffers(loopFields, lineData, loopWarnings);
}
category = key.substring(0,pos);
String value = data.get(1);
loopFields.add(key.substring(pos+1,key.length()));
lineData.add(value);
logger.debug("Found data for category {}: {}", key, value);
}
}
}
if (category!=null && lineData.size()>0 && lineData.size()==loopFields.size()) {
// the last category in the file will still be missing, we add it now
endLineChecks(category, loopFields, lineData, loopWarnings);
resetBuffers(loopFields, lineData, loopWarnings);
}
if (struct != null){
triggerStructData(struct);
}
triggerDocumentEnd();
}
private void resetBuffers(List loopFields, List lineData, Set loopWarnings) {
loopFields.clear();
lineData.clear();
loopWarnings.clear();
}
private List processSingleLine(String line){
List data = new ArrayList();
if ( line.trim().length() == 0){
return data;
}
if ( line.trim().length() == 1){
if ( line.startsWith(STRING_LIMIT))
return data;
}
boolean inString = false; // semicolon (;) quoting
boolean inS1 = false; // single quote (') quoting
boolean inS2 = false; // double quote (") quoting
String word = "";
for (int i=0; i< line.length(); i++ ){
Character c = line.charAt(i);
Character nextC = null;
if (i < line.length() - 1)
nextC = line.charAt(i+1);
Character prevC = null;
if (i>0)
prevC = line.charAt(i-1);
if (c == ' ') {
if ( ! inString){
if ( ! word.equals(""))
data.add(word.trim());
word = "";
} else {
// we are in a string, add the space
word += c;
}
} else if (c == S1 ) {
if ( inString){
boolean wordEnd = false;
if (! inS2) {
if (nextC==null || Character.isWhitespace(nextC)){
i++;
wordEnd = true;
}
}
if ( wordEnd ) {
// at end of string
if ( ! word.equals(""))
data.add(word.trim());
word = "";
inString = false;
inS1 = false;
} else {
word += c;
}
} else if (prevC==null || prevC==' ') {
// the beginning of a new string
inString = true;
inS1 = true;
} else {
word += c;
}
} else if ( c == S2 ){
if ( inString){
boolean wordEnd = false;
if (! inS1) {
if (nextC==null || Character.isWhitespace(nextC)){
i++;
wordEnd = true;
}
}
if ( wordEnd ) {
// at end of string
if ( ! word.equals(""))
data.add(word.trim());
word = "";
inString = false;
inS2 = false;
} else {
word += c;
}
} else if (prevC==null || prevC==' ') {
// the beginning of a new string
inString = true;
inS2 = true;
} else {
word += c;
}
} else {
word += c;
}
}
if ( ! word.trim().equals(""))
data.add(word);
return data;
}
/**
* Get the content of a cif entry
*
* @param line
* @param buf
* @return
*/
private List processLine(String line,
BufferedReader buf,
int fieldLength)
throws IOException{
//System.out.println("XX processLine " + fieldLength + " " + line);
// go through the line and process each character
List lineData = new ArrayList();
boolean inString = false;
StringBuilder bigWord = null;
while ( true ){
if ( line.startsWith(STRING_LIMIT)){
if (! inString){
inString = true;
if ( line.length() > 1)
bigWord = new StringBuilder(line.substring(1));
else
bigWord = new StringBuilder("");
} else {
// the end of a word
lineData.add(bigWord.toString());
bigWord = null;
inString = false;
}
} else {
if ( inString )
bigWord.append(line);
else {
List dat = processSingleLine(line);
for (String d : dat){
lineData.add(d);
}
}
}
//System.out.println("in process line : " + lineData.size() + " " + fieldLength);
if ( lineData.size() > fieldLength){
logger.warn("wrong data length ("+lineData.size()+
") should be ("+fieldLength+") at line " + line + " got lineData: " + lineData);
return lineData;
}
if ( lineData.size() == fieldLength)
return lineData;
line = buf.readLine();
if ( line == null)
break;
}
return lineData;
}
private void endLineChecks(String category,List loopFields, List lineData, Set loopWarnings ) throws IOException{
logger.debug("Processing category {}, with fields: {}",category,loopFields.toString());
// System.out.println("parsed the following data: " +category + " fields: "+
// loopFields + " DATA: " +
// lineData);
if ( loopFields.size() != lineData.size()){
logger.warn("looks like we got a problem with nested string quote characters:");
throw new IOException("data length ("+ lineData.size() +
") != fields length ("+loopFields.size()+
") category: " +category + " fields: "+
loopFields + " DATA: " +
lineData );
}
if ( category.equals("_entity")){
Entity e = (Entity) buildObject(
Entity.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewEntity(e);
} else if ( category.equals("_struct")){
struct = (Struct) buildObject(
Struct.class.getName(),
loopFields, lineData, loopWarnings);
} else if ( category.equals("_atom_site")){
AtomSite a = (AtomSite) buildObject(
AtomSite.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewAtomSite(a);
} else if ( category.equals("_database_PDB_rev")){
DatabasePDBrev dbrev = (DatabasePDBrev) buildObject(
DatabasePDBrev.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewDatabasePDBrev(dbrev);
} else if ( category.equals("_database_PDB_rev_record")){
DatabasePdbrevRecord dbrev = (DatabasePdbrevRecord) buildObject(
DatabasePdbrevRecord.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewDatabasePDBrevRecord(dbrev);
}else if ( category.equals("_database_PDB_remark")){
DatabasePDBremark remark = (DatabasePDBremark) buildObject(
DatabasePDBremark.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewDatabasePDBremark(remark);
} else if ( category.equals("_exptl")){
Exptl exptl = (Exptl) buildObject(
Exptl.class.getName(),
loopFields,lineData, loopWarnings);
triggerExptl(exptl);
} else if ( category.equals("_cell")){
Cell cell = (Cell) buildObject(
Cell.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewCell(cell);
} else if ( category.equals("_symmetry")){
Symmetry symmetry = (Symmetry) buildObject(
Symmetry.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewSymmetry(symmetry);
} else if ( category.equals("_struct_ncs_oper")) {
// this guy is special because of the [] in the field names
StructNcsOper sNcsOper = getStructNcsOper(loopFields,lineData);
triggerNewStructNcsOper(sNcsOper);
} else if ( category.equals("_struct_ref")){
StructRef sref = (StructRef) buildObject(
StructRef.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewStrucRef(sref);
} else if ( category.equals("_struct_ref_seq")){
StructRefSeq sref = (StructRefSeq) buildObject(
StructRefSeq.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewStrucRefSeq(sref);
} else if ( category.equals("_struct_ref_seq_dif")) {
StructRefSeqDif sref = (StructRefSeqDif) buildObject(
StructRefSeqDif.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewStrucRefSeqDif(sref);
} else if ( category.equals("_struct_site_gen")) {
StructSiteGen sref = (StructSiteGen) buildObject(
StructSiteGen.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewStructSiteGen(sref);
} else if ( category.equals("_struct_site")) {
StructSite sref = (StructSite) buildObject(
StructSite.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewStructSite(sref);
} else if ( category.equals("_entity_poly_seq")){
EntityPolySeq exptl = (EntityPolySeq) buildObject(
EntityPolySeq.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewEntityPolySeq(exptl);
} else if ( category.equals("_entity_src_gen")){
EntitySrcGen entitySrcGen = (EntitySrcGen) buildObject(
EntitySrcGen.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewEntitySrcGen(entitySrcGen);
} else if ( category.equals("_entity_src_nat")){
EntitySrcNat entitySrcNat = (EntitySrcNat) buildObject(
EntitySrcNat.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewEntitySrcNat(entitySrcNat);
} else if ( category.equals("_pdbx_entity_src_syn")){
EntitySrcSyn entitySrcSyn = (EntitySrcSyn) buildObject(
EntitySrcSyn.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewEntitySrcSyn(entitySrcSyn);
} else if ( category.equals("_struct_asym")){
StructAsym sasym = (StructAsym) buildObject(
StructAsym.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewStructAsym(sasym);
} else if ( category.equals("_pdbx_poly_seq_scheme")){
PdbxPolySeqScheme ppss = (PdbxPolySeqScheme) buildObject(
PdbxPolySeqScheme.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewPdbxPolySeqScheme(ppss);
} else if ( category.equals("_pdbx_nonpoly_scheme")){
PdbxNonPolyScheme ppss = (PdbxNonPolyScheme) buildObject(
PdbxNonPolyScheme.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewPdbxNonPolyScheme(ppss);
} else if ( category.equals("_pdbx_entity_nonpoly")){
PdbxEntityNonPoly pen = (PdbxEntityNonPoly) buildObject(
PdbxEntityNonPoly.class.getName(),
loopFields,lineData, loopWarnings
);
triggerNewPdbxEntityNonPoly(pen);
} else if ( category.equals("_struct_keywords")){
StructKeywords kw = (StructKeywords)buildObject(
StructKeywords.class.getName(),
loopFields,lineData, loopWarnings
);
triggerNewStructKeywords(kw);
} else if (category.equals("_refine")){
Refine r = (Refine)buildObject(
Refine.class.getName(),
loopFields,lineData, loopWarnings
);
triggerNewRefine(r);
} else if (category.equals("_chem_comp")){
ChemComp c = (ChemComp)buildObject(
ChemComp.class.getName(),
loopFields, lineData, loopWarnings
);
triggerNewChemComp(c);
} else if (category.equals("_audit_author")) {
AuditAuthor aa = (AuditAuthor)buildObject(
AuditAuthor.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewAuditAuthor(aa);
} else if (category.equals("_pdbx_chem_comp_descriptor")) {
ChemCompDescriptor ccd = (ChemCompDescriptor) buildObject(
ChemCompDescriptor.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewChemCompDescriptor(ccd);
} else if (category.equals("_pdbx_struct_oper_list")) {
// this guy is special since we convert to Matrices and shift vectors...
// and because it contains [] in field names
PdbxStructOperList structOper = getPdbxStructOperList(loopFields,lineData);
triggerNewPdbxStructOper(structOper);
} else if (category.equals("_pdbx_struct_assembly")) {
PdbxStructAssembly sa = (PdbxStructAssembly) buildObject(
PdbxStructAssembly.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewPdbxStructAssembly(sa);
} else if (category.equals("_pdbx_struct_assembly_gen")) {
PdbxStructAssemblyGen sa = (PdbxStructAssemblyGen) buildObject(
PdbxStructAssemblyGen.class.getName(),
loopFields, lineData, loopWarnings);
triggerNewPdbxStructAssemblyGen(sa);
} else if ( category.equals("_chem_comp_atom")){
ChemCompAtom atom = (ChemCompAtom)buildObject(
ChemCompAtom.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewChemCompAtom(atom);
}else if ( category.equals("_chem_comp_bond")){
ChemCompBond bond = (ChemCompBond)buildObject(
ChemCompBond.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewChemCompBond(bond);
} else if ( category.equals("_pdbx_chem_comp_identifier")){
PdbxChemCompIdentifier id = (PdbxChemCompIdentifier)buildObject(
PdbxChemCompIdentifier.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewPdbxChemCompIdentifier(id);
} else if ( category.equals("_pdbx_chem_comp_descriptor")){
PdbxChemCompDescriptor id = (PdbxChemCompDescriptor)buildObject(
PdbxChemCompDescriptor.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewPdbxChemCompDescriptor(id);
} else if ( category.equals("_struct_conn")){
StructConn id = (StructConn)buildObject(
StructConn.class.getName(),
loopFields,lineData, loopWarnings);
triggerNewStructConn(id);
} else {
logger.debug("Using a generic bean for category {}",category);
// trigger a generic bean that can deal with all missing data types...
triggerGeneric(category,loopFields,lineData);
}
}
private PdbxStructOperList getPdbxStructOperList(List loopFields,
List lineData) {
PdbxStructOperList so = new PdbxStructOperList();
//System.out.println(loopFields);
//System.out.println(lineData);
String id = lineData.get(loopFields.indexOf("id"));
so.setId(id);
so.setType(lineData.get(loopFields.indexOf("type")));
Matrix matrix = new Matrix(3,3);
for (int i = 1 ; i <=3 ; i++){
for (int j =1 ; j <= 3 ; j++){
String max = String.format("matrix[%d][%d]",j,i);
String val = lineData.get(loopFields.indexOf(max));
Double d = Double.parseDouble(val);
matrix.set(j-1,i-1,d);
// matrix.set(i-1,j-1,d);
}
}
double[] coords =new double[3];
for ( int i = 1; i <=3 ; i++){
String v = String.format("vector[%d]",i);
String val = lineData.get(loopFields.indexOf(v));
Double d = Double.parseDouble(val);
coords[i-1] = d;
}
so.setMatrix(matrix);
so.setVector(coords);
return so;
}
public void triggerNewPdbxStructOper(PdbxStructOperList structOper) {
for(MMcifConsumer c : consumers){
c.newPdbxStructOperList(structOper);
}
}
private StructNcsOper getStructNcsOper(List loopFields, List lineData) {
StructNcsOper sNcsOper = new StructNcsOper();
int id = Integer.parseInt(lineData.get(loopFields.indexOf("id")));
sNcsOper.setId(id);
sNcsOper.setCode(lineData.get(loopFields.indexOf("code")));
int detailsPos = loopFields.indexOf("details");
if ( detailsPos > -1)
sNcsOper.setDetails(lineData.get(detailsPos));
Matrix4d op = new Matrix4d();
op.setElement(3, 0, 0.0);
op.setElement(3, 1, 0.0);
op.setElement(3, 2, 0.0);
op.setElement(3, 3, 1.0);
for (int i = 1 ; i <=3 ; i++){
for (int j =1 ; j <= 3 ; j++){
String max = String.format("matrix[%d][%d]",i,j);
String val = lineData.get(loopFields.indexOf(max));
Double d = Double.parseDouble(val);
op.setElement(i-1,j-1,d);
}
}
for ( int i = 1; i <=3 ; i++){
String v = String.format("vector[%d]",i);
String val = lineData.get(loopFields.indexOf(v));
Double d = Double.parseDouble(val);
op.setElement(i-1, 3, d);
}
sNcsOper.setOperator(op);
return sNcsOper;
}
public void triggerNewStructNcsOper(StructNcsOper sNcsOper) {
for(MMcifConsumer c : consumers){
c.newStructNcsOper(sNcsOper);
}
}
private Object buildObject(String className, List loopFields, List lineData, Set warnings) {
Object o = null;
Class c = null;
try {
// build up the Entity object from the line data...
c = Class.forName(className);
o = c.newInstance();
} catch (InstantiationException e){
logger.error( "Error while constructing {}: {}", className, e.getMessage());
return null;
} catch (ClassNotFoundException e){
logger.error( "Error while constructing {}: {}", className, e.getMessage());
return null;
} catch (IllegalAccessException e) {
logger.error( "Error while constructing {}: {}", className, e.getMessage());
return null;
}
Method[] methods = c.getMethods();
Map methodMap = new HashMap();
for (Method m : methods) {
methodMap.put(m.getName(),m);
}
int pos = -1 ;
for (String key: loopFields){
pos++;
String val = lineData.get(pos);
// a necessary fix in order to be able to handle keys that contain hyphens (e.g. _symmetry.space_group_name_H-M)
// java can't use hyphens in variable names thus the corresponding bean can't use the hyphen and we replace it by underscore
if (key.contains("-"))
key = key.replace('-', '_');
// building up the setter method name: need to upper case the first letter, leave the rest untouched
String methodName = "set" + key.substring(0,1).toUpperCase() + key.substring(1, key.length());
Method m = methodMap.get(methodName);
if ( m == null) { // no method found in model class with the name found in file
if (!key.contains("[")) { // the fields with square brackets are handled elsewhere, see for instance getStructNcsOper
String warning = "Trying to set field " + key + " in "+ c.getName() +" found in file, but no corresponding field could be found in model class (value:" + val + ")";
String warnkey = key+"-"+c.getName();
// Suppress duplicate warnings or attempts to store empty data
if( val.equals("?") || val.equals(".") || ( warnings != null && warnings.contains(warnkey)) ) {
logger.debug(warning);
} else {
logger.warn(warning);
}
if(warnings != null) {
warnings.add(warnkey);
}
}
continue;
}
// now we populate the object with the values by invoking the corresponding setter method,
// note that all of the mmCif container classes have only one argument (they are beans)
Class[] pType = m.getParameterTypes();
try {
if ( pType[0].getName().equals(Integer.class.getName())) {
if ( val != null && ! val.equals("?") && !val.equals(".")) {
Integer intVal = Integer.parseInt(val);
m.invoke(o, intVal);
}
} else {
// default val is a String
m.invoke(o, val);
}
} catch (IllegalAccessException e) {
logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
} catch (InvocationTargetException e) {
logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
}
}
return o;
}
public void triggerGeneric(String category, List loopFields, List lineData){
for(MMcifConsumer c : consumers){
c.newGenericData(category, loopFields, lineData);
}
}
public void triggerNewEntity(Entity entity){
for(MMcifConsumer c : consumers){
c.newEntity(entity);
}
}
public void triggerNewEntityPolySeq(EntityPolySeq epolseq){
for(MMcifConsumer c : consumers){
c.newEntityPolySeq(epolseq);
}
}
public void triggerNewEntitySrcGen(EntitySrcGen entitySrcGen){
for(MMcifConsumer c : consumers){
c.newEntitySrcGen(entitySrcGen);
}
}
public void triggerNewEntitySrcNat(EntitySrcNat entitySrcNat){
for(MMcifConsumer c : consumers){
c.newEntitySrcNat(entitySrcNat);
}
}
public void triggerNewEntitySrcSyn(EntitySrcSyn entitySrcSyn){
for(MMcifConsumer c : consumers){
c.newEntitySrcSyn(entitySrcSyn);
}
}
public void triggerNewChemComp(ChemComp cc){
for(MMcifConsumer c : consumers){
c.newChemComp(cc);
}
}
public void triggerNewStructAsym(StructAsym sasym){
for(MMcifConsumer c : consumers){
c.newStructAsym(sasym);
}
}
private void triggerStructData(Struct struct){
for(MMcifConsumer c : consumers){
c.setStruct(struct);
}
}
private void triggerNewAtomSite(AtomSite atom){
for(MMcifConsumer c : consumers){
c.newAtomSite(atom);
}
}
private void triggerNewAuditAuthor(AuditAuthor aa){
for(MMcifConsumer c : consumers){
c.newAuditAuthor(aa);
}
}
private void triggerNewDatabasePDBrev(DatabasePDBrev dbrev){
for(MMcifConsumer c : consumers){
c.newDatabasePDBrev(dbrev);
}
}
private void triggerNewDatabasePDBrevRecord(DatabasePdbrevRecord dbrev){
for(MMcifConsumer c : consumers){
c.newDatabasePDBrevRecord(dbrev);
}
}
private void triggerNewDatabasePDBremark(DatabasePDBremark remark){
for(MMcifConsumer c : consumers){
c.newDatabasePDBremark(remark);
}
}
private void triggerExptl(Exptl exptl){
for(MMcifConsumer c : consumers){
c.newExptl(exptl);
}
}
private void triggerNewCell(Cell cell) {
for(MMcifConsumer c : consumers){
c.newCell(cell);
}
}
private void triggerNewSymmetry(Symmetry symmetry) {
for(MMcifConsumer c : consumers){
c.newSymmetry(symmetry);
}
}
private void triggerNewStrucRef(StructRef sref){
for(MMcifConsumer c : consumers){
c.newStructRef(sref);
}
}
private void triggerNewStrucRefSeq(StructRefSeq sref){
for(MMcifConsumer c : consumers){
c.newStructRefSeq(sref);
}
}
private void triggerNewStrucRefSeqDif(StructRefSeqDif sref){
for(MMcifConsumer c : consumers){
c.newStructRefSeqDif(sref);
}
}
private void triggerNewPdbxPolySeqScheme(PdbxPolySeqScheme ppss){
for(MMcifConsumer c : consumers){
c.newPdbxPolySeqScheme(ppss);
}
}
private void triggerNewPdbxNonPolyScheme(PdbxNonPolyScheme ppss){
for(MMcifConsumer c : consumers){
c.newPdbxNonPolyScheme(ppss);
}
}
public void triggerNewPdbxEntityNonPoly(PdbxEntityNonPoly pen){
for (MMcifConsumer c: consumers){
c.newPdbxEntityNonPoly(pen);
}
}
public void triggerNewStructKeywords(StructKeywords kw){
for (MMcifConsumer c: consumers){
c.newStructKeywords(kw);
}
}
public void triggerNewRefine(Refine r){
for (MMcifConsumer c: consumers){
c.newRefine(r);
}
}
public void triggerDocumentStart(){
for(MMcifConsumer c : consumers){
c.documentStart();
}
}
public void triggerDocumentEnd(){
for(MMcifConsumer c : consumers){
c.documentEnd();
}
}
public void triggerNewChemCompDescriptor(ChemCompDescriptor ccd) {
for(MMcifConsumer c : consumers){
c.newChemCompDescriptor(ccd);
}
}
private void triggerNewPdbxStructAssembly(PdbxStructAssembly sa) {
for(MMcifConsumer c : consumers){
c.newPdbxStrucAssembly(sa);
}
}
private void triggerNewPdbxStructAssemblyGen(PdbxStructAssemblyGen sa) {
for(MMcifConsumer c : consumers){
c.newPdbxStrucAssemblyGen(sa);
}
}
private void triggerNewChemCompAtom(ChemCompAtom atom) {
for(MMcifConsumer c : consumers){
c.newChemCompAtom(atom);
}
}
private void triggerNewChemCompBond(ChemCompBond bond) {
for(MMcifConsumer c : consumers){
c.newChemCompBond(bond);
}
}
private void triggerNewPdbxChemCompIdentifier(PdbxChemCompIdentifier id) {
for(MMcifConsumer c : consumers){
c.newPdbxChemCompIndentifier(id);
}
}
private void triggerNewPdbxChemCompDescriptor(PdbxChemCompDescriptor id) {
for(MMcifConsumer c : consumers){
c.newPdbxChemCompDescriptor(id);
}
}
private void triggerNewStructConn(StructConn id) {
for(MMcifConsumer c : consumers){
c.newStructConn(id);
}
}
private void triggerNewStructSiteGen(StructSiteGen id) {
for (MMcifConsumer c : consumers) {
c.newStructSiteGen(id);
}
}
private void triggerNewStructSite(StructSite id) {
for (MMcifConsumer c : consumers) {
c.newStructSite(id);
}
}
}
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