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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-09-16 09:53:18 -0500 (Sat, 16 Sep 2006) $
* $Revision: 5561 $
*
* Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
*
* Contact: [email protected]
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.jmol.adapter.readers.xml;
import org.jmol.adapter.smarter.Bond;
import org.jmol.adapter.smarter.Atom;
import java.util.Hashtable;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Properties;
import java.util.StringTokenizer;
import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.BS;
import org.jmol.api.JmolAdapter;
import org.jmol.util.BSUtil;
import org.jmol.util.Logger;
/**
* A CML2 Reader -
* If passed a bufferedReader (from a file or inline string), we
* generate a SAX parser and use callbacks to construct an
* AtomSetCollection.
* If passed a JSObject (from LiveConnect) we treat it as a JS DOM
* tree, and walk the tree, (using the same processing as the SAX
* parser) to construct the AtomSetCollection.
*
* symmetry added by Bob Hanson:
*
* setSpaceGroupName()
* setUnitCellItem()
* setFractionalCoordinates()
* setAtomCoord()
* applySymmetryAndSetTrajectory()
*
*
* "isotope" added 4/6/2009 Bob Hanson
*
*/
/* TODO 9/06
*
*
* We need to implement the capability to load a specific
* model as well as indicate the number of unit cells to load.
*
* Follow the equivalent in CIF files to see how this is done.
*
*/
public class XmlCmlReader extends XmlReader {
public XmlCmlReader() {
}
private String scalarDictRef;
//String scalarDictKey;
private String scalarDictValue;
private String scalarTitle;
private String cellParameterType;
private boolean checkedSerial;
private boolean isSerial;
// counter that is incremented each time a molecule element is started and
// decremented when finished. Needed so that only 1 atomSet created for each
// parent molecule that exists.
private int moleculeNesting = 0;
private int latticeVectorPtr = 0;
private boolean embeddedCrystal = false;
private Properties atomIdNames;
////////////////////////////////////////////////////////////////
// Main body of class; variables & functions shared by DOM & SAX alike.
protected String[] tokens = new String[16];
// the same atom array gets reused
// it will grow to the maximum length;
// ac holds the current number of atoms
private int aaLen;
private Atom[] atomArray = new Atom[100];
private int bondCount;
private Bond[] bondArray = new Bond[100];
// the same string array gets reused
// tokenCount holds the current number of tokens
// see breakOutTokens
private int tokenCount;
//private int nModules = 0;
private int moduleNestingLevel = 0;
private boolean haveMolecule = false;
private String localSpaceGroupName;
protected boolean processing = true;
protected int state = START;
private int atomIndex0;
private Lst joinList;
private Map mapRtoA;
private BS deleteAtoms;
protected String moleculeID;
protected Map htModelAtomMap;
private boolean optimize2d;
/**
* state constants
*/
final static protected int START = 0,
CML = 1,
CRYSTAL = 2,
CRYSTAL_SCALAR = 3,
CRYSTAL_SYMMETRY = 4,
CRYSTAL_SYMMETRY_TRANSFORM3 = 5,
MOLECULE = 6,
MOLECULE_ATOM_ARRAY = 7,
MOLECULE_ATOM = 8,
MOLECULE_ATOM_SCALAR = 9,
MOLECULE_BOND_ARRAY = 10,
MOLECULE_BOND = 11,
MOLECULE_BOND_STEREO = 12,
MOLECULE_FORMULA = 13,
MOLECULE_ATOM_BUILTIN = 14,
MOLECULE_BOND_BUILTIN = 15,
MODULE = 16,
SYMMETRY = 17,
LATTICE_VECTOR = 18,
ASSOCIATION = 19;
/**
* the current state
*/
/*
* added 2/2007 Bob Hanson:
*
*
4.592100143433e0 4.592100143433e0 2.957400083542e0
9.000000000000e1 9.000000000000e1 9.000000000000e1
*
*/
@Override
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
optimize2d = parent.checkFilterKey("2D");
processXml2(parent, saxReader);
if (optimize2d)
set2D();
}
@Override
public void processStartElement(String name, String nodeName) {
if (!processing)
return;
processStart2(name);
}
protected void processStart2(String name) {
name = name.toLowerCase();
String val;
switch (state) {
case START:
if (name.equals("molecule")) {
moleculeID = atts.get("id");
state = MOLECULE;
haveMolecule = true;
if (moleculeNesting == 0)
createNewAtomSet();
moleculeNesting++;
} else if (name.equals("crystal")) {
state = CRYSTAL;
} else if (name.equals("symmetry")) {
state = SYMMETRY;
if ((val = atts.get("spacegroup")) != null) {
localSpaceGroupName = val;
} else {
localSpaceGroupName = "P1";
parent.clearUnitCell();
}
} else if (name.equals("module")) {
moduleNestingLevel++;
//nModules++;
} else if (name.equals("latticevector")) {
state = LATTICE_VECTOR;
setKeepChars(true);
}
break;
case CRYSTAL:
// we force this to be NOT serialized by number, because we might have a1 and a1_....
checkedSerial = true;
isSerial = false;
if (name.equals("scalar")) {
state = CRYSTAL_SCALAR;
setKeepChars(true);
scalarTitle = atts.get("title");
getDictRefValue();
} else if (name.equals("symmetry")) {
state = CRYSTAL_SYMMETRY;
if ((val = atts.get("spacegroup")) != null) {
localSpaceGroupName = val;
for (int i = 0; i < localSpaceGroupName.length(); i++)
if (localSpaceGroupName.charAt(i) == '_')
localSpaceGroupName = localSpaceGroupName.substring(0, i)
+ localSpaceGroupName.substring((i--) + 1);
}
} else if (name.equals("cellparameter")) {
if ((val = atts.get("parametertype")) != null) {
cellParameterType = val;
setKeepChars(true);
}
}
break;
case LATTICE_VECTOR:
/*
* 1.980499982834e0
* 3.430000066757e0 0.000000000000e0 -1.980499982834e0
* 3.430000066757e0 0.000000000000e0 0.000000000000e0
* 0.000000000000e0 4.165999889374e0
*/
setKeepChars(true);
break;
case SYMMETRY:
case CRYSTAL_SCALAR:
case CRYSTAL_SYMMETRY:
if (name.equals("transform3")) {
state = CRYSTAL_SYMMETRY_TRANSFORM3;
setKeepChars(true);
}
break;
case CRYSTAL_SYMMETRY_TRANSFORM3:
case MOLECULE:
if (name.equals("fragmentlist")) {
joinList = new Lst();
mapRtoA = new Hashtable();
if (deleteAtoms == null)
deleteAtoms = new BS();
} else if (name.equals("crystal")) {
state = CRYSTAL;
embeddedCrystal = true;
} else if (name.equals("molecule")) {
state = MOLECULE;
moleculeNesting++;
} else if (name.equals("join")) {
int order = -1;
tokenCount = 0;
if ((val = atts.get("atomrefs2")) != null) {
breakOutTokens(val);
if ((val = atts.get("order")) != null)
order = parseBondToken(val);
if (tokenCount == 2 && order > 0)
joinList.addLast(new String[] { tokens[0], tokens[1], "" + order });
}
} else if (name.equals("bondarray")) {
state = MOLECULE_BOND_ARRAY;
bondCount = 0;
if ((val = atts.get("order")) != null) {
breakOutBondTokens(val);
for (int i = tokenCount; --i >= 0;)
bondArray[i].order = parseBondToken(tokens[i]);
}
if ((val = atts.get("atomref1")) != null) {
breakOutBondTokens(val);
for (int i = tokenCount; --i >= 0;)
bondArray[i].atomIndex1 = getAtomIndex(tokens[i]);
}
if ((val = atts.get("atomref2")) != null) {
breakOutBondTokens(val);
for (int i = tokenCount; --i >= 0;)
bondArray[i].atomIndex2 = getAtomIndex(tokens[i]);
}
} else if (name.equals("atomarray")) {
state = MOLECULE_ATOM_ARRAY;
aaLen = 0;
boolean coords3D = false;
if ((val = atts.get("atomid")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].atomName = tokens[i];
}
boolean is3d = (!optimize2d && (val = atts.get("x3")) != null);
if (is3d) {
is3d = true;
coords3D = true;
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].x = parseFloatStr(tokens[i]);
if ((val = atts.get("y3")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].y = parseFloatStr(tokens[i]);
}
if ((val = atts.get("z3")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].z = parseFloatStr(tokens[i]);
}
} else {
if ((val = atts.get("x2")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].x = parseFloatStr(tokens[i]);
}
if ((val = atts.get("y2")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].y = parseFloatStr(tokens[i]);
}
}
if ((val = atts.get("elementtype")) != null) {
breakOutAtomTokens(val);
for (int i = tokenCount; --i >= 0;)
atomArray[i].elementSymbol = tokens[i];
}
for (int i = aaLen; --i >= 0;) {
Atom atom = atomArray[i];
if (!coords3D)
atom.z = 0;
addAtom(atom);
}
} else if (name.equals("formula")) {
state = MOLECULE_FORMULA;
} else if (name.equals("association")) {
state = ASSOCIATION;
}
break;
case MOLECULE_BOND_ARRAY:
if (name.equals("bond")) {
state = MOLECULE_BOND;
int order = -1;
tokenCount = 0;
if ((val = atts.get("atomrefs2")) != null)
breakOutTokens(val);
if ((val = atts.get("order")) != null)
order = parseBondToken(val);
if (tokenCount == 2 && order > 0) {
addNewBond(tokens[0], tokens[1], order);
}
}
break;
case MOLECULE_ATOM_ARRAY:
if (name.equals("atom")) {
state = MOLECULE_ATOM;
atom = new Atom();
parent.setFractionalCoordinates(false);
String id = atts.get("id");
if ((val = atts.get("name")) != null)
atom.atomName = val;
else if ((val = atts.get("title")) != null)
atom.atomName = val;
else if ((val = atts.get("label")) != null)
atom.atomName = val;
else
atom.atomName = id;
if (!checkedSerial) {
// this is important because the atomName may not be unique
// (as in PDB files)
// but it causes problems in cif-derived files that involve a1 and a1_1, for instance
isSerial = (id != null && id.length() > 1 && id.startsWith("a") && PT
.parseInt(id.substring(1)) != Integer.MIN_VALUE);
checkedSerial = true;
}
if (isSerial)
atom.atomSerial = PT.parseInt(id.substring(1));
if ((val = atts.get("xfract")) != null
&& (parent.iHaveUnitCell || !atts.containsKey("x3"))) {
parent.setFractionalCoordinates(true);
atom.set(parseFloatStr(val), parseFloatStr(atts.get("yfract")),
parseFloatStr(atts.get("zfract")));
} else if ((val = atts.get("x3")) != null) {
atom.set(parseFloatStr(val), parseFloatStr(atts.get("y3")),
parseFloatStr(atts.get("z3")));
} else if ((val = atts.get("x2")) != null) {
atom.set(parseFloatStr(val), parseFloatStr(atts.get("y2")), 0);
}
if ((val = atts.get("elementtype")) != null) {
String sym = val;
if ((val = atts.get("isotope")) != null)
atom.elementNumber = (short) ((parseIntStr(val) << 7) + JmolAdapter
.getElementNumber(sym));
atom.elementSymbol = sym;
}
if ((val = atts.get("formalcharge")) != null)
atom.formalCharge = parseIntStr(val);
}
break;
case MOLECULE_BOND:
if ((val = atts.get("builtin")) != null) {
setKeepChars(true);
state = MOLECULE_BOND_BUILTIN;
scalarDictValue = val;
} else if (name.equals("bondstereo")) {
state = MOLECULE_BOND_STEREO;
}
break;
case MOLECULE_BOND_STEREO:
setKeepChars(true);
state = MOLECULE_BOND_STEREO;
break;
case MOLECULE_ATOM:
if (name.equals("scalar")) {
state = MOLECULE_ATOM_SCALAR;
setKeepChars(true);
scalarTitle = atts.get("title");
getDictRefValue();
} else if ((val = atts.get("builtin")) != null) {
setKeepChars(true);
state = MOLECULE_ATOM_BUILTIN;
scalarDictValue = val;
}
break;
case MOLECULE_ATOM_SCALAR:
break;
case MOLECULE_FORMULA:
break;
case MOLECULE_ATOM_BUILTIN:
break;
case MOLECULE_BOND_BUILTIN:
break;
}
}
private int getAtomIndex(String label) {
return asc.getAtomIndex(isSerial ? label.substring(1) : label);
}
final private static String[] unitCellParamTags = { "a", "b", "c", "alpha",
"beta", "gamma" };
@Override
void processEndElement(String name) {
// if (!uri.equals(NAMESPACE_URI))
// return;
//System.out.println("END: " + name);
if (!processing)
return;
processEnd2(name);
}
public void processEnd2(String name) {
name = name.toLowerCase();
switch (state) {
case START:
if (name.equals("module")) {
if (--moduleNestingLevel == 0) {
if (parent.iHaveUnitCell)
applySymmetryAndSetTrajectory();
setAtomNames();
}
}
break;
case ASSOCIATION:
if (name.equals("association"))
state = MOLECULE;
break;
case CRYSTAL:
if (name.equals("crystal")) {
if (embeddedCrystal) {
state = MOLECULE;
embeddedCrystal = false;
} else {
state = START;
}
} else if (name.equals("cellparameter") && keepChars) {
String[] tokens = PT.getTokens(chars.toString());
setKeepChars(false);
if (tokens.length != 3 || cellParameterType == null) {
} else if (cellParameterType.equals("length")) {
for (int i = 0; i < 3; i++)
parent.setUnitCellItem(i, parseFloatStr(tokens[i]));
break;
} else if (cellParameterType.equals("angle")) {
for (int i = 0; i < 3; i++)
parent.setUnitCellItem(i + 3, parseFloatStr(tokens[i]));
break;
}
// if here, then something is wrong
Logger.error("bad cellParameter information: parameterType="
+ cellParameterType + " data=" + chars);
parent.setFractionalCoordinates(false);
}
break;
case CRYSTAL_SCALAR:
if (name.equals("scalar")) {
state = CRYSTAL;
if (scalarTitle != null)
checkUnitCellItem(unitCellParamTags, scalarTitle);
else if (scalarDictRef != null)
checkUnitCellItem(JmolAdapter.cellParamNames, (scalarDictValue
.startsWith("_") ? scalarDictValue : "_" + scalarDictValue));
}
setKeepChars(false);
scalarTitle = null;
scalarDictRef = null;
break;
case CRYSTAL_SYMMETRY_TRANSFORM3:
if (name.equals("transform3")) {
// setSymmetryOperator("xyz matrix: " + chars);
// the problem is that these matricies are in CARTESIAN coordinates, not
// ijk coordinates
setKeepChars(false);
state = CRYSTAL_SYMMETRY;
}
break;
case LATTICE_VECTOR:
float[] values = getTokensFloat(chars.toString(), null, 3);
parent.addExplicitLatticeVector(latticeVectorPtr, values, 0);
latticeVectorPtr = (latticeVectorPtr + 1) % 3;
setKeepChars(false);
state = START;
break;
case CRYSTAL_SYMMETRY:
case SYMMETRY:
if (name.equals("symmetry"))
state = (state == CRYSTAL_SYMMETRY ? CRYSTAL : START);
if (moduleNestingLevel == 0 && parent.iHaveUnitCell && !embeddedCrystal)
applySymmetryAndSetTrajectory();
break;
case MOLECULE:
if (name.equals("fragmentlist")) {
for (int i = joinList.size(); --i >= 0;) {
String[] join = joinList.get(i);
Atom r1 = asc.getAtomFromName(fixSerialName(join[0]));
Atom r2 = asc.getAtomFromName(fixSerialName(join[1]));
if (r1 != null && r2 != null) {
deleteAtoms.set(r1.index);
deleteAtoms.set(r2.index);
addNewBond(mapRtoA.get(r1), mapRtoA.get(r2), parseIntStr(join[2]));
}
}
joinList = null;
mapRtoA = null;
}
if (name.equals("molecule")) {
if (--moleculeNesting == 0) {
// if is within , then
// we have to wait until the end of all s to
// apply symmetry.
applySymmetryAndSetTrajectory();
setAtomNames();
state = START;
} else {
state = MOLECULE;
}
}
break;
case MOLECULE_BOND_ARRAY:
if (name.equals("bondarray")) {
state = MOLECULE;
for (int i = 0; i < bondCount; ++i)
addBond(bondArray[i]);
parent.applySymmetryToBonds = true;
}
break;
case MOLECULE_ATOM_ARRAY:
if (name.equals("atomarray")) {
state = MOLECULE;
// for (int i = 0; i < aaLen; ++i)
// addAtom(atomArray[i]);
}
break;
case MOLECULE_BOND:
if (name.equals("bond")) {
state = MOLECULE_BOND_ARRAY;
}
break;
case MOLECULE_ATOM:
if (name.equals("atom")) {
state = MOLECULE_ATOM_ARRAY;
addAtom(atom);
atom = null;
}
break;
case MOLECULE_ATOM_SCALAR:
if (name.equals("scalar")) {
state = MOLECULE_ATOM;
if ("jmol:charge".equals(scalarDictRef)) {
atom.partialCharge = parseFloatStr(chars.toString());
} else if (scalarDictRef != null
&& "_atom_site_label".equals(scalarDictValue)) {
if (atomIdNames == null)
atomIdNames = new Properties();
atomIdNames.put(atom.atomName, chars.toString());
}
}
setKeepChars(false);
scalarTitle = null;
scalarDictRef = null;
break;
case MOLECULE_ATOM_BUILTIN:
state = MOLECULE_ATOM;
if (scalarDictValue.equals("x3"))
atom.x = parseFloatStr(chars.toString());
else if (scalarDictValue.equals("y3"))
atom.y = parseFloatStr(chars.toString());
else if (scalarDictValue.equals("z3"))
atom.z = parseFloatStr(chars.toString());
else if (scalarDictValue.equals("elementType"))
atom.elementSymbol = chars.toString();
setKeepChars(false);
break;
case MOLECULE_BOND_STEREO:
String stereo = chars.toString();
if (bond.order == 1)
bond.order = (stereo.equals("H") ? JmolAdapter.ORDER_STEREO_FAR : JmolAdapter.ORDER_STEREO_NEAR);
setKeepChars(false);
state = MOLECULE_BOND;
break;
case MOLECULE_BOND_BUILTIN: // ACD Labs
state = MOLECULE_BOND;
if (scalarDictValue.equals("atomRef")) {
if (tokenCount == 0)
tokens = new String[2];
if (tokenCount < 2)
tokens[tokenCount++] = chars.toString();
} else if (scalarDictValue.equals("order")) {
int order = parseBondToken(chars.toString());
if (order > 0 && tokenCount == 2)
addNewBond(tokens[0], tokens[1], order);
}
setKeepChars(false);
break;
case MOLECULE_FORMULA:
state = MOLECULE;
break;
}
}
private void addBond(Bond bond) {
Atom a1 = asc.atoms[bond.atomIndex1];
Atom a2 = asc.atoms[bond.atomIndex2];
if (joinList != null && !checkBondToR(a1.atomName, a2.atomName))
asc.addBond(bond);
}
/**
* Checks to see if we have a bond to R and, if so, adds this R atom
* as a key to its attached atom
* @param a1name
* @param a2name
* @return true if handled so no need to add a bond
*/
private boolean checkBondToR(String a1name, String a2name) {
Atom a1 = asc.getAtomFromName(a1name);
Atom a2 = asc.getAtomFromName(a2name);
if (a1 == null || a2 == null)
return true;
if ("R".equals(a1.elementSymbol)) {
mapRtoA.put(a1, a2.atomName);
return true;
} else if ("R".equals(a2.elementSymbol)) {
mapRtoA.put(a2, a1.atomName);
return true;
}
return false;
}
private void setAtomNames() {
// for CML reader "a3" --> "N3"
if (atomIdNames == null)
return;
String s;
Atom[] atoms = asc.atoms;
for (int i = atomIndex0; i < asc.ac; i++)
if ((s = atomIdNames.getProperty(atoms[i].atomName)) != null)
atoms[i].atomName = s;
atomIdNames = null;
atomIndex0 = asc.ac;
}
private void addNewBond(String a1, String a2, int order) {
if (a1 == null || a2 == null)
return;
parent.applySymmetryToBonds = true;
a1 = fixSerialName(a1);
a2 = fixSerialName(a2);
if (joinList == null || !checkBondToR(a1, a2)) {
asc.addNewBondFromNames(a1, a2, order);
bond = asc.bonds[asc.bondCount - 1];
}
}
private String fixSerialName(String a) {
return (isSerial ? a.substring(1) : a);
}
private void getDictRefValue() {
scalarDictRef = atts.get("dictref");
if (scalarDictRef != null) {
int iColon = scalarDictRef.indexOf(":");
scalarDictValue = scalarDictRef.substring(iColon + 1);
}
}
private void checkUnitCellItem(String[] tags, String value) {
for (int i = tags.length; --i >= 0;)
if (value.equals(tags[i])) {
parent.setUnitCellItem(i, parseFloatStr(chars.toString()));
return;
}
}
private void addAtom(Atom atom) {
if ((atom.elementSymbol == null && atom.elementNumber < 0)
|| Float.isNaN(atom.z))
return;
parent.setAtomCoord(atom);
if (htModelAtomMap != null)
htModelAtomMap.put(moleculeID + atom.atomName, atom);
if (isSerial)
asc.addAtomWithMappedSerialNumber(atom);
else
asc.addAtomWithMappedName(atom);
}
private int parseBondToken(String str) {
float floatOrder = parseFloatStr(str);
if (Float.isNaN(floatOrder) && str.length() >= 1) {
str = str.toUpperCase();
switch (str.charAt(0)) {
case 'S':
return JmolAdapter.ORDER_COVALENT_SINGLE;
case 'D':
return JmolAdapter.ORDER_COVALENT_DOUBLE;
case 'T':
return JmolAdapter.ORDER_COVALENT_TRIPLE;
case 'A':
return JmolAdapter.ORDER_AROMATIC;
case 'P':
//TODO: Note, this could be elaborated more specifically
return JmolAdapter.ORDER_PARTIAL12;
}
return parseIntStr(str);
}
if (floatOrder == 1.5)
return JmolAdapter.ORDER_AROMATIC;
if (floatOrder == 2)
return JmolAdapter.ORDER_COVALENT_DOUBLE;
if (floatOrder == 3)
return JmolAdapter.ORDER_COVALENT_TRIPLE;
return JmolAdapter.ORDER_COVALENT_SINGLE;
}
//this routine breaks out all the tokens in a string
// results ar e placed into the tokens array
private void breakOutTokens(String str) {
StringTokenizer st = new StringTokenizer(str);
tokenCount = st.countTokens();
if (tokenCount > tokens.length)
tokens = new String[tokenCount];
for (int i = 0; i < tokenCount; ++i) {
try {
tokens[i] = st.nextToken();
} catch (NoSuchElementException nsee) {
tokens[i] = null;
}
}
}
void breakOutAtomTokens(String str) {
breakOutTokens(str);
checkAtomArrayLength(tokenCount);
}
void checkAtomArrayLength(int newAtomCount) {
if (aaLen == 0) {
if (newAtomCount > atomArray.length)
atomArray = new Atom[newAtomCount];
for (int i = newAtomCount; --i >= 0;)
atomArray[i] = new Atom();
aaLen = newAtomCount;
} else if (newAtomCount != aaLen) {
throw new IndexOutOfBoundsException("bad atom attribute length");
}
}
void breakOutBondTokens(String str) {
breakOutTokens(str);
checkBondArrayLength(tokenCount);
}
void checkBondArrayLength(int newBondCount) {
if (bondCount == 0) {
if (newBondCount > bondArray.length)
bondArray = new Bond[newBondCount];
for (int i = newBondCount; --i >= 0;)
bondArray[i] = new Bond(-1, -1, 1);
bondCount = newBondCount;
} else if (newBondCount != bondCount) {
throw new IndexOutOfBoundsException("bad bond attribute length");
}
}
private void createNewAtomSet() {
asc.newAtomSet();
String val;
if (htModelAtomMap != null)
htModelAtomMap.put("" + asc.iSet, "" + moleculeID);
String collectionName = ((val = atts.get("title")) != null
|| (val = atts.get("id")) != null ? val : null);
if (collectionName != null) {
asc.setAtomSetName(collectionName);
}
}
@Override
public void applySymmetryAndSetTrajectory() {
if (moduleNestingLevel > 0 || !haveMolecule || localSpaceGroupName == null)
return;
parent.setSpaceGroupName(localSpaceGroupName);
parent.iHaveSymmetryOperators = iHaveSymmetryOperators;
parent.applySymmetryAndSetTrajectory();
}
@Override
public void endDocument() {
// CML reader uses this
if (deleteAtoms != null) {
BS bs = (asc.bsAtoms == null ? asc.bsAtoms = BSUtil.newBitSet2(0, asc.ac) : asc.bsAtoms);
bs.andNot(deleteAtoms);
}
}
}
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