Revision: 18608
http://sourceforge.net/p/jmol/code/18608
Author: hansonr
Date: 2013-08-20 22:43:55 +0000 (Tue, 20 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.20c"
bug fix: CIF reader not reading _CCDC_GEOM_BOND_TYPE record
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/simple/FoldingXyzReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-20
18:23:45 UTC (rev 18607)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-20
22:43:55 UTC (rev 18608)
@@ -79,6 +79,10 @@
private CifDataReader tokenizer = new CifDataReader(this);
+ private boolean isMolecular;
+ private boolean filterAssembly;
+ private int configurationPtr = Integer.MIN_VALUE;
+
private String thisDataSetName = "";
private String chemicalName = "";
private String thisStructuralFormula = "";
@@ -86,12 +90,10 @@
private boolean iHaveDesiredModel;
private boolean isPDB = false;
private Map<String, String> htHetero;
- private boolean isMolecular;
private String molecularType = "GEOM_BOND default";
private char lastAltLoc = '\0';
- private int configurationPtr = Integer.MIN_VALUE;
+ private boolean haveAromatic;
private int conformationIndex;
- private boolean filterAssembly;
private int nMolecular = 0;
@@ -122,6 +124,7 @@
configurationPtr = parseIntStr(conf);
isMolecular = checkFilterKey("MOLECUL");
filterAssembly = checkFilterKey("$");
+
if (isMolecular) {
if (!doApplySymmetry) {
doApplySymmetry = true;
@@ -131,7 +134,7 @@
}
molecularType = "filter \"MOLECULAR\"";
}
- initializeMod();
+ initializeModulation();
readCifData();
continuing = false;
}
@@ -281,6 +284,7 @@
atomSetCollection.removeCurrentAtomSet();
else
applySymmetryAndSetTrajectory();
+ finalizeModulation();
if (htSites != null)
addSites(htSites);
int n = atomSetCollection.getAtomSetCount();
@@ -300,6 +304,8 @@
if (header.length() > 0)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader",
header);
+ if (haveAromatic)
+ addJmolScript("calculate aromatic");
}
private void setBiomolecules() {
@@ -560,9 +566,7 @@
if (!doApplySymmetry) {
isMolecular = true;
doApplySymmetry = true;
- latticeCells[0] = 1;
- latticeCells[1] = 1;
- latticeCells[2] = 1;
+ latticeCells[0] = latticeCells[1] = latticeCells[2] = 1;
}
if (isMolecular)
processGeomBondLoopBlock();
@@ -612,6 +616,85 @@
skipLoop();
}
+ private int fieldProperty(int i) {
+ return ((field = tokenizer.loopData[i]).length() > 0
+ && (firstChar = field.charAt(0)) != '\0' ?
+ propertyOf[i] : NONE);
+ }
+
+ private String field;
+ private char firstChar = '\0';
+ private int[] propertyOf = new int[100]; // should be enough
+ private byte[] fieldOf = new byte[100];
+ private String[] fields;
+ private int propertyCount;
+
+
+ /**
+ * sets up arrays and variables for tokenizer.getData()
+ *
+ * @param fields
+ * @throws Exception
+ */
+ private void parseLoopParameters(String[] fields) throws Exception {
+ if (fields == null)
+ fields = this.fields = new String[100];
+ tokenizer.fieldCount = 0;
+ for (int i = fields.length; --i >= 0; )
+ fieldOf[i] = NONE;
+
+ propertyCount = fields.length;
+ while (true) {
+ String str = tokenizer.peekToken();
+ if (str == null) {
+ tokenizer.fieldCount = 0;
+ break;
+ }
+ if (str.charAt(0) != '_')
+ break;
+ tokenizer.getTokenPeeked();
+ propertyOf[tokenizer.fieldCount] = NONE;
+ str = fixKey(str);
+ for (int i = fields.length; --i >= 0;)
+ if (fields[i] == null || str.equals(fields[i])) {
+ propertyOf[tokenizer.fieldCount] = i;
+ fieldOf[i] = (byte) tokenizer.fieldCount;
+ if (fields[i] == null)
+ fields[i] = str;
+ break;
+ }
+ tokenizer.fieldCount++;
+ }
+ if (tokenizer.fieldCount > 0)
+ tokenizer.loopData = new String[tokenizer.fieldCount];
+ }
+
+ /**
+ *
+ * used for turning off fractional or nonfractional coord.
+ *
+ * @param fieldIndex
+ */
+ private void disableField(int fieldIndex) {
+ int i = fieldOf[fieldIndex];
+ if (i != NONE)
+ propertyOf[i] = NONE;
+ }
+
+ /**
+ *
+ * skips all associated loop data
+ *
+ * @throws Exception
+ */
+ private void skipLoop() throws Exception {
+ String str;
+ while ((str = tokenizer.peekToken()) != null && str.charAt(0) == '_')
+ str = tokenizer.getTokenPeeked();
+ while (tokenizer.getNextDataToken() != null) {
+ }
+ }
+
////////////////////////////////////////////////////////////////
// atom type data
////////////////////////////////////////////////////////////////
@@ -1294,160 +1377,7 @@
}
}
-
////////////////////////////////////////////////////////////////
- // bond data
- ////////////////////////////////////////////////////////////////
-
- final private static byte CHEM_COMP_BOND_ATOM_ID_1 = 0;
- final private static byte CHEM_COMP_BOND_ATOM_ID_2 = 1;
- final private static byte CHEM_COMP_BOND_VALUE_ORDER = 2;
- final private static byte CHEM_COMP_BOND_AROMATIC_FLAG = 3;
- final private static String[] chemCompBondFields = {
- "_chem_comp_bond_atom_id_1",
- "_chem_comp_bond_atom_id_2",
- "_chem_comp_bond_value_order",
- "_chem_comp_bond_pdbx_aromatic_flag",
- };
-
- private void processLigandBondLoopBlock() throws Exception {
- parseLoopParameters(chemCompBondFields);
- for (int i = propertyCount; --i >= 0;)
- if (fieldOf[i] == NONE) {
- Logger.warn("?que? missing _chem_comp_bond property:" + i);
- skipLoop();
- return;
- }
- int order = 0;
- boolean isAromatic = false;
- while (tokenizer.getData()) {
- int atomIndex1 = -1;
- int atomIndex2 = -1;
- order = 0;
- isAromatic = false;
- for (int i = 0; i < tokenizer.fieldCount; ++i) {
- switch (fieldProperty(i)) {
- case CHEM_COMP_BOND_ATOM_ID_1:
- atomIndex1 = atomSetCollection.getAtomIndexFromName(field);
- break;
- case CHEM_COMP_BOND_ATOM_ID_2:
- atomIndex2 = atomSetCollection.getAtomIndexFromName(field);
- break;
- case CHEM_COMP_BOND_AROMATIC_FLAG:
- isAromatic = (field.charAt(0) == 'Y');
- break;
- case CHEM_COMP_BOND_VALUE_ORDER:
- order = JmolAdapter.ORDER_COVALENT_SINGLE;
- if (field.equals("SING"))
- order = JmolAdapter.ORDER_COVALENT_SINGLE;
- else if (field.equals("DOUB"))
- order = JmolAdapter.ORDER_COVALENT_DOUBLE;
- else if (field.equals("TRIP"))
- order = JmolAdapter.ORDER_COVALENT_TRIPLE;
- else
- Logger.warn("unknown CIF bond order: " + field);
- break;
- }
- }
- if (atomIndex1 < 0 || atomIndex2 < 0)
- continue;
- if (isAromatic)
- switch (order) {
- case JmolAdapter.ORDER_COVALENT_SINGLE:
- order = JmolAdapter.ORDER_AROMATIC_SINGLE;
- break;
- case JmolAdapter.ORDER_COVALENT_DOUBLE:
- order = JmolAdapter.ORDER_AROMATIC_DOUBLE;
- break;
- }
- atomSetCollection.addNewBondWithOrder(atomIndex1, atomIndex2, order);
- }
- }
-
- final private static byte GEOM_BOND_ATOM_SITE_LABEL_1 = 0;
- final private static byte GEOM_BOND_ATOM_SITE_LABEL_2 = 1;
- final private static byte GEOM_BOND_DISTANCE = 2;
- //final private static byte GEOM_BOND_SITE_SYMMETRY_2 = 3;
-
- final private static String[] geomBondFields = {
- "_geom_bond_atom_site_label_1",
- "_geom_bond_atom_site_label_2",
- "_geom_bond_distance",
- // "_geom_bond_site_symmetry_2",
- };
-
- /**
- *
- * reads bond data -- N_ijk symmetry business is ignored,
- * so we only indicate bonds within the unit cell to just the
- * original set of atoms. "connect" script or "set forceAutoBond"
- * will override these values.
- *
- * @throws Exception
- */
- private void processGeomBondLoopBlock() throws Exception {
- parseLoopParameters(geomBondFields);
- for (int i = propertyCount; --i >= 0;)
- if (fieldOf[i] == NONE) {
- Logger.warn("?que? missing _geom_bond property:" + i);
- skipLoop();
- return;
- }
-
- String name1 = null;
- String name2 = null;
- while (tokenizer.getData()) {
- int atomIndex1 = -1;
- int atomIndex2 = -1;
- float distance = 0;
- float dx = 0;
- //String siteSym2 = null;
- for (int i = 0; i < tokenizer.fieldCount; ++i) {
- switch (fieldProperty(i)) {
- case NONE:
- break;
- case GEOM_BOND_ATOM_SITE_LABEL_1:
- atomIndex1 = atomSetCollection.getAtomIndexFromName(name1 = field);
- break;
- case GEOM_BOND_ATOM_SITE_LABEL_2:
- atomIndex2 = atomSetCollection.getAtomIndexFromName(name2 = field);
- break;
- case GEOM_BOND_DISTANCE:
- distance = parseFloatStr(field);
- int pt = field.indexOf('(');
- if (pt >= 0) {
- char[] data = field.toCharArray();
- // 3.567(12) --> 0.012
- String sdx = field.substring(pt + 1, field.length() - 1);
- int n = sdx.length();
- for (int j = pt; --j >= 0;) {
- if (data[j] == '.')
- --j;
- data[j] = (--n < 0 ? '0' : sdx.charAt(n));
- }
- dx = parseFloatStr(String.valueOf(data));
- if (Float.isNaN(dx)) {
- Logger.info("error reading uncertainty for " + line);
- dx = 0.015f;
- }
- // TODO -- this is the full +/- (dx) in x.xxx(dx) -- is that too
large?
- } else {
- dx = 0.015f;
- }
- break;
- //case GEOM_BOND_SITE_SYMMETRY_2:
- //siteSym2 = field;
- //break;
- }
- }
- if (atomIndex1 < 0 || atomIndex2 < 0)
- continue;
- if (distance > 0)
- bondTypes.addLast(new Object[] { name1, name2,
Float.valueOf(distance), Float.valueOf(dx) });
- }
- }
-
- ////////////////////////////////////////////////////////////////
// HETATM identity
////////////////////////////////////////////////////////////////
@@ -1467,6 +1397,7 @@
*
*/
private String[] hetatmData;
+
private void processNonpolyData() {
if (hetatmData == null)
hetatmData = new String[3];
@@ -1884,86 +1815,175 @@
}
}
- private int fieldProperty(int i) {
- return ((field = tokenizer.loopData[i]).length() > 0
- && (firstChar = field.charAt(0)) != '\0' ?
- propertyOf[i] : NONE);
- }
- String field;
+ ////////////////////////////////////////////////////////////////
+ // bond data
+ ////////////////////////////////////////////////////////////////
+
+ final private static byte CHEM_COMP_BOND_ATOM_ID_1 = 0;
+ final private static byte CHEM_COMP_BOND_ATOM_ID_2 = 1;
+ final private static byte CHEM_COMP_BOND_VALUE_ORDER = 2;
+ final private static byte CHEM_COMP_BOND_AROMATIC_FLAG = 3;
+ final private static String[] chemCompBondFields = {
+ "_chem_comp_bond_atom_id_1",
+ "_chem_comp_bond_atom_id_2",
+ "_chem_comp_bond_value_order",
+ "_chem_comp_bond_pdbx_aromatic_flag",
+ };
- private char firstChar = '\0';
- private int[] propertyOf = new int[100]; // should be enough
- private byte[] fieldOf = new byte[100];
- private String[] fields;
- private int propertyCount;
-
-
- /**
- * sets up arrays and variables for tokenizer.getData()
- *
- * @param fields
- * @throws Exception
- */
- private void parseLoopParameters(String[] fields) throws Exception {
- if (fields == null)
- fields = this.fields = new String[100];
- tokenizer.fieldCount = 0;
- for (int i = fields.length; --i >= 0; )
- fieldOf[i] = NONE;
-
- propertyCount = fields.length;
- while (true) {
- String str = tokenizer.peekToken();
- if (str == null) {
- tokenizer.fieldCount = 0;
- break;
+ private void processLigandBondLoopBlock() throws Exception {
+ parseLoopParameters(chemCompBondFields);
+ for (int i = propertyCount; --i >= 0;)
+ if (fieldOf[i] == NONE) {
+ Logger.warn("?que? missing _chem_comp_bond property:" + i);
+ skipLoop();
+ return;
}
- if (str.charAt(0) != '_')
- break;
- tokenizer.getTokenPeeked();
- propertyOf[tokenizer.fieldCount] = NONE;
- str = fixKey(str);
- for (int i = fields.length; --i >= 0;)
- if (fields[i] == null || str.equals(fields[i])) {
- propertyOf[tokenizer.fieldCount] = i;
- fieldOf[i] = (byte) tokenizer.fieldCount;
- if (fields[i] == null)
- fields[i] = str;
+ int order = 0;
+ boolean isAromatic = false;
+ while (tokenizer.getData()) {
+ int atomIndex1 = -1;
+ int atomIndex2 = -1;
+ order = 0;
+ isAromatic = false;
+ for (int i = 0; i < tokenizer.fieldCount; ++i) {
+ switch (fieldProperty(i)) {
+ case CHEM_COMP_BOND_ATOM_ID_1:
+ atomIndex1 = atomSetCollection.getAtomIndexFromName(field);
break;
+ case CHEM_COMP_BOND_ATOM_ID_2:
+ atomIndex2 = atomSetCollection.getAtomIndexFromName(field);
+ break;
+ case CHEM_COMP_BOND_AROMATIC_FLAG:
+ isAromatic = (field.charAt(0) == 'Y');
+ break;
+ case CHEM_COMP_BOND_VALUE_ORDER:
+ order = getBondOrder(field);
+ break;
}
- tokenizer.fieldCount++;
+ }
+ if (atomIndex1 < 0 || atomIndex2 < 0)
+ continue;
+ if (isAromatic)
+ switch (order) {
+ case JmolAdapter.ORDER_COVALENT_SINGLE:
+ order = JmolAdapter.ORDER_AROMATIC_SINGLE;
+ break;
+ case JmolAdapter.ORDER_COVALENT_DOUBLE:
+ order = JmolAdapter.ORDER_AROMATIC_DOUBLE;
+ break;
+ }
+ atomSetCollection.addNewBondWithOrder(atomIndex1, atomIndex2, order);
}
- if (tokenizer.fieldCount > 0)
- tokenizer.loopData = new String[tokenizer.fieldCount];
}
- /**
- *
- * used for turning off fractional or nonfractional coord.
- *
- * @param fieldIndex
- */
- private void disableField(int fieldIndex) {
- int i = fieldOf[fieldIndex];
- if (i != NONE)
- propertyOf[i] = NONE;
+ private int getBondOrder(String field) {
+ switch (field.charAt(0)) {
+ default:
+ Logger.warn("unknown CIF bond order: " + field);
+ //$FALL-THROUGH$
+ case 'S':
+ return JmolAdapter.ORDER_COVALENT_SINGLE;
+ case 'D':
+ return JmolAdapter.ORDER_COVALENT_DOUBLE;
+ case 'T':
+ return JmolAdapter.ORDER_COVALENT_TRIPLE;
+ case 'A':
+ haveAromatic = true;
+ return JmolAdapter.ORDER_AROMATIC;
+ }
}
+ final private static byte GEOM_BOND_ATOM_SITE_LABEL_1 = 0;
+ final private static byte GEOM_BOND_ATOM_SITE_LABEL_2 = 1;
+ final private static byte GEOM_BOND_DISTANCE = 2;
+ final private static byte CCDC_GEOM_BOND_TYPE = 3;
+
+ //final private static byte GEOM_BOND_SITE_SYMMETRY_2 = 3;
+
+ final private static String[] geomBondFields = {
+ "_geom_bond_atom_site_label_1",
+ "_geom_bond_atom_site_label_2",
+ "_geom_bond_distance",
+ "_ccdc_geom_bond_type"
+ // "_geom_bond_site_symmetry_2",
+ };
+
/**
*
- * skips all associated loop data
+ * reads bond data -- N_ijk symmetry business is ignored,
+ * so we only indicate bonds within the unit cell to just the
+ * original set of atoms. "connect" script or "set forceAutoBond"
+ * will override these values, but see below.
*
* @throws Exception
*/
- private void skipLoop() throws Exception {
- String str;
- while ((str = tokenizer.peekToken()) != null && str.charAt(0) == '_')
- str = tokenizer.getTokenPeeked();
- while (tokenizer.getNextDataToken() != null) {
+ private void processGeomBondLoopBlock() throws Exception {
+ parseLoopParameters(geomBondFields);
+ for (int i = propertyCount; --i >= 0;)
+ if (propertyOf[i] != CCDC_GEOM_BOND_TYPE && fieldOf[i] == NONE) {
+ Logger.warn("?que? missing _geom_bond property:" + i);
+ skipLoop();
+ return;
+ }
+
+ String name1 = null;
+ String name2 = null;
+ Integer order = Integer.valueOf(1);
+ while (tokenizer.getData()) {
+ int atomIndex1 = -1;
+ int atomIndex2 = -1;
+ float distance = 0;
+ float dx = 0;
+ //String siteSym2 = null;
+ for (int i = 0; i < tokenizer.fieldCount; ++i) {
+ switch (fieldProperty(i)) {
+ case NONE:
+ break;
+ case GEOM_BOND_ATOM_SITE_LABEL_1:
+ atomIndex1 = atomSetCollection.getAtomIndexFromName(name1 = field);
+ break;
+ case GEOM_BOND_ATOM_SITE_LABEL_2:
+ atomIndex2 = atomSetCollection.getAtomIndexFromName(name2 = field);
+ break;
+ case GEOM_BOND_DISTANCE:
+ distance = parseFloatStr(field);
+ int pt = field.indexOf('(');
+ if (pt >= 0) {
+ char[] data = field.toCharArray();
+ // 3.567(12) --> 0.012
+ String sdx = field.substring(pt + 1, field.length() - 1);
+ int n = sdx.length();
+ for (int j = pt; --j >= 0;) {
+ if (data[j] == '.')
+ --j;
+ data[j] = (--n < 0 ? '0' : sdx.charAt(n));
+ }
+ dx = parseFloatStr(String.valueOf(data));
+ if (Float.isNaN(dx)) {
+ Logger.info("error reading uncertainty for " + line);
+ dx = 0.015f;
+ }
+ // TODO -- this is the full +/- (dx) in x.xxx(dx) -- is that too
large?
+ } else {
+ dx = 0.015f;
+ }
+ break;
+ case CCDC_GEOM_BOND_TYPE:
+ order = Integer.valueOf(getBondOrder(field));
+ break;
+ //case GEOM_BOND_SITE_SYMMETRY_2:
+ //siteSym2 = field;
+ //break;
+ }
+ }
+ if (atomIndex1 < 0 || atomIndex2 < 0)
+ continue;
+ if (distance > 0)
+ bondTypes.addLast(new Object[] { name1, name2,
Float.valueOf(distance), Float.valueOf(dx), order });
}
- }
-
+ }
+
/////////////////////////////////////
// bonding and molecular
/////////////////////////////////////
@@ -2111,6 +2131,7 @@
Object[] o = bondTypes.get(i);
float distance = ((Float) o[2]).floatValue();
float dx = ((Float) o[3]).floatValue();
+ int order = ((Integer) o[4]).intValue();
int iatom1 = atomSetCollection.getAtomIndexFromName((String) o[0]);
int iatom2 = atomSetCollection.getAtomIndexFromName((String) o[1]);
BS bs1 = bsSets[iatom1 - firstAtom];
@@ -2122,7 +2143,7 @@
if ((!isMolecular || !bsConnected[j + firstAtom].get(k))
&& symmetry.checkDistance(atoms[j + firstAtom], atoms[k
+ firstAtom], distance, dx, 0, 0, 0, ptOffset))
- addNewBond(j + firstAtom, k + firstAtom);
+ addNewBond(j + firstAtom, k + firstAtom, order);
}
}
@@ -2140,7 +2161,7 @@
if (!bsConnected[i].get(k)
&& symmetry.checkDistance(atoms[i], atoms[k], 1.1f, 0, 0, 0,
0, ptOffset))
- addNewBond(i, k);
+ addNewBond(i, k, 1);
}
}
if (!isMolecular)
@@ -2204,9 +2225,10 @@
*
* @param i
* @param j
+ * @param order
*/
- private void addNewBond(int i, int j) {
- atomSetCollection.addNewBond(i, j);
+ private void addNewBond(int i, int j, int order) {
+ atomSetCollection.addNewBondWithOrder(i, j, order);
if (!isMolecular)
return;
bsConnected[i].set(j);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-20 18:23:45 UTC (rev 18607)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-20 22:43:55 UTC (rev 18608)
@@ -84,15 +84,13 @@
protected Map<String, Object> htSubsystems;
- protected void initializeMod() throws Exception {
+ protected void initializeModulation() throws Exception {
modDebug = checkFilterKey("MODDEBUG");
modAxes = getFilter("MODAXES=");
modType = getFilter("MODTYPE="); //ODU
modSelected = parseIntStr("" + getFilter("MOD="));
modVib = checkFilterKey("MODVIB"); // then use MODULATION ON to see
modulation
modAverage = checkFilterKey("MODAVE");
- if (!modVib && !modAverage)
- addJmolScript("modulation on");
checkSpecial = !checkFilterKey("NOSPECIAL");
atomSetCollection.setCheckSpecial(checkSpecial);
allowRotations = !checkFilterKey("NOSYM");
@@ -165,6 +163,11 @@
Logger.debugging = Logger.debuggingHigh = false;
}
+ protected void finalizeModulation() {
+ if (incommensurate && !modVib)
+ addJmolScript("modulation on");
+ }
+
private String suffix;
private P3 getMod(String key) {
return htModulation.get(key + suffix);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/FoldingXyzReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/FoldingXyzReader.java
2013-08-20 18:23:45 UTC (rev 18607)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/FoldingXyzReader.java
2013-08-20 22:43:55 UTC (rev 18608)
@@ -150,7 +150,7 @@
}
}
if (correct && (destination > origin)) {
- atomSetCollection.addNewBond(origin, destination);
+ atomSetCollection.addNewBondWithOrder(origin, destination, 1);
}
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-20 18:23:45 UTC (rev 18607)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-20 22:43:55 UTC (rev 18608)
@@ -46,7 +46,7 @@
@Override
public void initializeReader() throws Exception {
setFractionalCoordinates(true);
- initializeMod();
+ initializeModulation();
atomSetCollection.newAtomSet();
}
@@ -123,6 +123,7 @@
atomSetCollection.getSymmetry().addLatticeVectors(lattvecs);
applySymmetryAndSetTrajectory();
setModulation();
+ finalizeModulation();
finalizeReaderASCR();
}
@@ -221,7 +222,8 @@
String id = name.substring(0, ipt);
ipt = id.lastIndexOf("/");
id = id.substring(ipt + 1);
- BufferedReader r = JmolBinary.getBufferedReaderForString((String)
viewer.getLigandModel(id, name, "_file", "----"));
+ BufferedReader r = JmolBinary.getBufferedReaderForString((String) viewer
+ .getLigandModel(id, name, "_file", "----"));
if (readM40Floats(r).startsWith("command"))
readM40WaveVectors(r);
int nAtoms = (int) floats[0];
@@ -229,8 +231,7 @@
while (readM40Floats(r).length() == 0 || line.charAt(0) == ' '
|| line.charAt(0) == '-') {
}
-
-
+
Atom atom = new Atom();
atom.atomName = line.substring(0, 9).trim();
if (!filterAtom(atom, 0))
@@ -240,9 +241,9 @@
if (!incommensurate)
continue;
String label = ";" + atom.atomName;
- boolean haveCrenel = (getInt(60, 61) > 0);
- boolean haveSawTooth = (getInt(61, 62) > 0);
- boolean haveSomething = (getInt(62, 63) > 0);
+ boolean haveSpecialOcc = (getInt(60, 61) > 0);
+ boolean haveSpecialDisp = (getInt(61, 62) > 0);
+ boolean haveSpecialUij = (getInt(62, 63) > 0);
int nOcc = getInt(65, 68);
int nDisp = getInt(68, 71);
int nUij = getInt(71, 74);
@@ -265,12 +266,12 @@
// read occupancy parameters
P3 pt;
- if (nOcc > 0 && !haveCrenel)
+ if (nOcc > 0 && !haveSpecialOcc)
r.readLine(); //"1.00000"
int wv = 0;
float a1, a2;
for (int j = 0; j < nOcc; j++) {
- if (haveCrenel) {
+ if (haveSpecialOcc) {
float[][] data = readM40FloatLines(2, 1, r);
a1 = data[1][0];
a2 = data[0][0];
@@ -278,17 +279,17 @@
wv = j + 1;
readM40Floats(r);
a1 = floats[1];
- a2 = floats[0];
+ a2 = floats[0];
}
- id = "O_" + wv + "#0" + label;
+ id = "O_" + wv + "#0" + label;
pt = P3.new3(a1, a2, 0);
if (a1 != 0 || a2 != 0)
addModulation(null, id, pt, -1);
}
-
+
// read displacement data
for (int j = 0; j < nDisp; j++) {
- if (haveSawTooth) {
+ if (haveSpecialDisp) {
readM40Floats(r);
float c = floats[3];
float w = floats[4];
@@ -308,11 +309,16 @@
// fourier?
addSinCos(j, "U_", label, r);
} else {
- float[][] data = readM40FloatLines(2, 6, r);
- for (int k = 0, p = 0; k < 6; k++, p+=3)
- addModulation(null, "U_" + (j + 1) + "#"
- + U_LIST.substring(p, p + 3) + label, P3.new3(data[1][k],
- data[0][k], 0), -1);
+ if (haveSpecialUij) {
+ //TODO
+ Logger.error("JanaReader -- not interpreting SpecialUij flag: " +
line);
+ } else {
+ float[][] data = readM40FloatLines(2, 6, r);
+ for (int k = 0, p = 0; k < 6; k++, p += 3)
+ addModulation(null, "U_" + (j + 1) + "#"
+ + U_LIST.substring(p, p + 3) + label, P3.new3(data[1][k],
+ data[0][k], 0), -1);
+ }
}
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-20 18:23:45 UTC (rev 18607)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-20 22:43:55 UTC (rev 18608)
@@ -644,14 +644,6 @@
mapMostRecentAtomSerialNumber();
}
- public Bond addNewBond(int atomIndex1, int atomIndex2) {
- return addNewBondWithOrder(atomIndex1, atomIndex2, 1);
- }
-
- Bond addNewSingleBondFromNames(String atomName1, String atomName2) {
- return addNewBondFromNames(atomName1, atomName2, 1);
- }
-
public Bond addNewBondWithOrder(int atomIndex1, int atomIndex2, int order) {
if (atomIndex1 < 0 || atomIndex1 >= atomCount ||
atomIndex2 < 0 || atomIndex2 >= atomCount)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-20 18:23:45 UTC
(rev 18607)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-20 22:43:55 UTC
(rev 18608)
@@ -11,8 +11,9 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.20"
+___JmolVersion="13.3.4_dev_2013.08.20c"
+bug fix: CIF reader not reading _CCDC_GEOM_BOND_TYPE record
bug fix: File dialog problems with paths having space
bug fix: GAMESS reader not reading energies
bug fix: TRY failure in a load command followed by a successful load
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