Revision: 20625
http://sourceforge.net/p/jmol/code/20625
Author: hansonr
Date: 2015-07-04 13:47:56 +0000 (Sat, 04 Jul 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.07.03"
bug fix: mmCIF reader does not recognize load MODEL ...
bug fix: PDB reader should be reading load "" [1 3 4] as MODEL record numbers,
not sequential numbers
bug fix: load MODELS "" [1 3 4] does not work (although load "" [1 3 4],
without with MODELS keyword, works)
clarification:
load "" 1 # loads the first model in a file when not PDB or
mmCIF.
load "" 1 # loads the model with MODEL 1 record for a PDB file.
load "" 1 # loads the model with _atom_site.pdbx_PDB_model_num =
1 for an mmCIF file
load "" [1] # same as load "" 1; brackets allow for more than one
model, for instance [1 3 5]
load MODELS ({1}) "" # always loads the SECOND model in a file
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/script/ScriptEval.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 2015-07-03
17:54:59 UTC (rev 20624)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-07-04
13:47:56 UTC (rev 20625)
@@ -50,8 +50,10 @@
/**
* A true line-free CIF file reader for CIF files.
*
- * Subclasses of CIF -- mmCIF/PDBx and msCIF -- are initialized from here.
+ * Subclasses of CIF -- mmCIF/PDBx (pre-initialized) and msCIF (initialized
here).
*
+ * Note that a file can be a PDB file without being
+ *
* Added nonstandard mCIF (magnetic_ tags) 5/2/2014 note that PRELIM keys can
be
* removed at some later time
*
@@ -92,7 +94,7 @@
private String chemicalName = "";
private String thisStructuralFormula = "";
private String thisFormula = "";
- private boolean iHaveDesiredModel;
+ protected boolean iHaveDesiredModel;
protected boolean isMMCIF;
boolean isMagCIF;
private String molecularType = "GEOM_BOND default";
@@ -101,7 +103,7 @@
private int conformationIndex;
private int nMolecular = 0;
private String appendedData;
- private boolean skipping;
+ protected boolean skipping;
protected int nAtoms;
protected int ac;
@@ -470,7 +472,7 @@
Logger.debug(key);
}
- private void nextAtomSet() {
+ protected void nextAtomSet() {
asc.setCurrentModelInfo("isCIF", Boolean.TRUE);
if (asc.iSet >= 0) {
// note that there can be problems with multi-data mmCIF sets each with
@@ -993,7 +995,7 @@
* @throws Exception
*/
boolean processAtomSiteLoopBlock(boolean isLigand) throws Exception {
- int currentModelNo = -1; // PDBX
+ int pdbModelNo = -1; // PDBX
boolean haveCoord = true;
parseLoopParametersFor(FAMILY_ATOM, atomFields);
if (fieldOf[CC_ATOM_X_IDEAL] != NONE) {
@@ -1003,13 +1005,17 @@
disableField(FRACT_X);
disableField(FRACT_Y);
disableField(FRACT_Z);
+ if (fieldOf[GROUP_PDB] != NONE && !isMMCIF) {
+ // this should not happen
+ setIsPDB();
+ isMMCIF = true;
+ }
} else if (fieldOf[FRACT_X] != NONE) {
setFractionalCoordinates(true);
disableField(CARTN_X);
disableField(CARTN_Y);
disableField(CARTN_Z);
- } else if (fieldOf[ANISO_LABEL] != NONE
- || fieldOf[ANISO_MMCIF_ID] != NONE
+ } else if (fieldOf[ANISO_LABEL] != NONE || fieldOf[ANISO_MMCIF_ID] != NONE
|| fieldOf[MOMENT_LABEL] != NONE) {
haveCoord = false;
// no coordinates, but valuable information
@@ -1021,39 +1027,21 @@
int modelField = fieldOf[MODEL_NO];
int siteMult = 0;
while (parser.getData()) {
- if (modelField >= 0) {
- fieldProperty(modelField);
- int modelNo = parseIntStr(field);
- if (modelNo != currentModelNo) {
- if (iHaveDesiredModel && asc.atomSetCount > 0) {
- parser.skipLoop(false);
- // but only this atom loop
- skipping = false;
- continuing = true;
- break;
- }
- currentModelNo = modelNo;
- newModel(modelNo);
- if (!skipping) {
- nextAtomSet();
- if (modelMap == null || asc.ac == 0)
- modelMap = new Hashtable<String, Integer>();
- modelMap.put("" + modelNo, Integer.valueOf(Math.max(0,
asc.iSet)));
- modelMap
- .put("_" + Math.max(0, asc.iSet), Integer.valueOf(modelNo));
- }
- }
- if (skipping)
- continue;
- }
+ if (modelField >= 0) {
+ // mmCIF only
+ pdbModelNo = checkPDBModelField(modelField, pdbModelNo);
+ if (pdbModelNo < 0)
+ break;
+ if (skipping)
+ continue;
+ }
Atom atom = null;
if (haveCoord) {
atom = new Atom();
} else {
if (fieldProperty(fieldOf[ANISO_LABEL]) != NONE
|| fieldProperty(fieldOf[ANISO_MMCIF_ID]) != NONE
- || fieldProperty(fieldOf[MOMENT_LABEL]) != NONE
- ) {
+ || fieldProperty(fieldOf[MOMENT_LABEL]) != NONE) {
if ((atom = asc.getAtomFromName(field)) == null)
continue; // atom has been filtered out
} else {
@@ -1153,15 +1141,15 @@
case ASYM_ID:
assemblyId = field;
if (!useAuthorChainID)
- setChainID(atom, strChain = field);
+ setChainID(atom, strChain = field);
break;
case AUTH_ASYM_ID:
if (useAuthorChainID)
- setChainID(atom, strChain = field);
+ setChainID(atom, strChain = field);
break;
case AUTH_SEQ_ID:
maxSerial = Math.max(maxSerial,
- atom.sequenceNumber = parseIntStr(field));
+ atom.sequenceNumber = parseIntStr(field));
break;
case INS_CODE:
atom.insertionCode = firstChar;
@@ -1182,10 +1170,6 @@
}
break;
case GROUP_PDB:
- if (!isMMCIF) {
- setIsPDB();
- isMMCIF = true;
- }
if ("HETATM".equals(field))
atom.isHetero = true;
break;
@@ -1317,6 +1301,17 @@
return true;
}
+ /**
+ * @param modelField
+ * @param currentModelNo
+ * @return new currentModelNo
+ * @throws Exception
+ */
+ protected int checkPDBModelField(int modelField, int currentModelNo) throws
Exception {
+ // overridden in MMCIF reader
+ return 0;
+ }
+
protected Map<String, String> htHetero;
/**
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-07-03 17:54:59 UTC (rev 20624)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-07-04 13:47:56 UTC (rev 20625)
@@ -41,6 +41,18 @@
import org.jmol.util.SimpleUnitCell;
/**
+ *
+ * mmCIF files are recognized prior to class creation.
+ * Required fields include one of:
+ *
+ * _entry.id
+ * _database_PDB_
+ * _pdbx_
+ * _chem_comp.pdbx_type
+ * _audit_author.name
+ * _atom_site.
+ *
+ *
* @author Bob Hanson (hans...@stolaf.edu)
*
*/
@@ -1060,4 +1072,36 @@
return false;
}
+ private int modelIndex = 0;
+
+ @Override
+ protected int checkPDBModelField(int modelField, int currentModelNo) throws
Exception {
+ // the model field value is only used if
+ // it is indicated AFTER the file name in the load command,
+ // not if we have a MODEL keyword before the file name.
+ //
+ fieldProperty(modelField);
+ int modelNo = parseIntStr(field);
+ if (modelNo != currentModelNo) {
+ if (iHaveDesiredModel && asc.atomSetCount > 0) {
+ parser.skipLoop(false);
+ // but only this atom loop
+ skipping = false;
+ continuing = true;
+ return Integer.MIN_VALUE;
+ }
+ int modelNumberToUse = (useFileModelNumbers ? modelNo : ++modelIndex);
+ newModel(modelNumberToUse);
+ if (!skipping) {
+ nextAtomSet();
+ if (modelMap == null || asc.ac == 0)
+ modelMap = new Hashtable<String, Integer>();
+ modelMap.put("" + modelNo, Integer.valueOf(Math.max(0, asc.iSet)));
+ modelMap
+ .put("_" + Math.max(0, asc.iSet), Integer.valueOf(modelNo));
+ }
+ }
+ return modelNo;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-07-03
17:54:59 UTC (rev 20624)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java 2015-07-04
13:47:56 UTC (rev 20625)
@@ -239,7 +239,7 @@
boolean isAtom = (ptOption == 0 || ptOption == 1);
boolean isModel = (ptOption == 2);
serial = (isAtom ? getSerial(6, 11) : 0);
- boolean isNewModel = ((isTrajectory || isSequential) && !isMultiModel
+ boolean forceNewModel = ((isTrajectory || isSequential) && !isMultiModel
&& isAtom && serial == 1);
if (getHeader) {
if (isAtom || isModel)
@@ -247,12 +247,12 @@
else
readHeader(false);
}
- if (isModel || isNewModel) {
+ if (isModel || forceNewModel) {
isMultiModel = isModel;
getHeader = false;
// PDB is different -- targets actual model number
- int modelNo = (isNewModel ? modelNumber + 1 : getModelNumber());
- modelNumber = (bsModels == null ? modelNo : modelNumber + 1);
+ int modelNo = (forceNewModel ? modelNumber + 1 : getModelNumber());
+ modelNumber = (useFileModelNumbers ? modelNo : modelNumber + 1);
if (!doGetModel(modelNumber, null)) {
handleTlsMissingModels();
boolean isOK = checkLastModel();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-07-03 17:54:59 UTC (rev 20624)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-07-04 13:47:56 UTC (rev 20625)
@@ -180,6 +180,7 @@
protected int vibrationNumber;
public int desiredVibrationNumber = Integer.MIN_VALUE;
protected BS bsModels;
+ protected boolean useFileModelNumbers; // PDB, MMCIF only
protected boolean havePartialChargeFilter;
public String calculationType = "?";
protected String sgName;
@@ -566,6 +567,7 @@
} else if (htParams.containsKey("bsModels")) {
bsModels = (BS) htParams.get("bsModels");
}
+ useFileModelNumbers = htParams.containsKey("useFileModelNumbers");
if (htParams.containsKey("templateAtomCount"))
templateAtomCount = ((Integer) htParams.get("templateAtomCount"))
.intValue();
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-07-03 17:54:59 UTC
(rev 20624)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-07-04 13:47:56 UTC
(rev 20625)
@@ -4429,8 +4429,7 @@
case T.varray:
case T.leftsquare:
case T.spacebeforesquare:
- getLoadModelIndex(i, sOptions, htParams);
- tok = tokAt(i = ++iToken);
+ tok = tokAt(getLoadModelIndex(i, sOptions, htParams));
break;
}
i = getCmdExt().getLoadSymmetryParams(i, sOptions, htParams);
@@ -4673,8 +4672,7 @@
case T.varray:
case T.leftsquare:
case T.spacebeforesquare:
- getLoadModelIndex(i, sOptions, htParams);
- i = iToken + 1;
+ i = getLoadModelIndex(i, sOptions, htParams);
continue;
case T.filter:
filter = stringParameter(++i);
@@ -4757,12 +4755,16 @@
return false;
}
- private void getLoadModelIndex(int i, SB sOptions,
+ private int getLoadModelIndex(int i, SB sOptions,
Map<String, Object> htParams)
throws ScriptException {
+ int n;
switch (tokAt(i)) {
case T.integer:
- int n = intParameter(i);
+ htParams.remove("firstLastStep");
+ htParams.remove("bsModel");
+ htParams.put("useFileModelNumbers", Boolean.TRUE);
+ n = intParameter(i);
sOptions.append(" ").appendI(n);
if (n < 0)
htParams.put("vibrationNumber", Integer.valueOf(-n));
@@ -4772,21 +4774,25 @@
case T.varray:
case T.leftsquare:
case T.spacebeforesquare:
- System.out.println(sOptions);
+ htParams.remove("firstLastStep");
float[] data = floatParameterSet(i, 1, Integer.MAX_VALUE);
i = iToken;
BS bs = new BS();
- for (int j = 0; j < data.length; j++)
- if (data[j] >= 1 && data[j] == (int) data[j])
- bs.set((int) data[j] - 1);
- htParams.remove("firstLastStep");
+ int[] iArray = new int[data.length];
+ for (int j = 0; j < data.length; j++) {
+ n = (int) data[j];
+ if (data[j] >= 1 && data[j] == n)
+ bs.set(n - 1);
+ else
+ invArg();
+ iArray[j] = n;
+ }
+ sOptions.append(" " + Escape.eAI(iArray));
htParams.put("bsModels", bs);
- int[] iArray = new int[bs.cardinality()];
- for (int pt = 0, j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1))
- iArray[pt++] = j + 1;
- sOptions.append(" " + Escape.eAI(iArray));
+ htParams.put("useFileModelNumbers", Boolean.TRUE);
break;
}
+ return iToken + 1;
}
private void finalizeLoad(boolean isAppend, boolean appendNew,
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-03 17:54:59 UTC
(rev 20624)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-07-04 13:47:56 UTC
(rev 20625)
@@ -50,8 +50,20 @@
Jmol.___JmolVersion="14.3.15_2015.07.03"
-bug fix: mmCIF reader does not recognize load model
+bug fix: mmCIF reader does not recognize load MODEL ...
+bug fix: PDB reader should be reading load "" [1 3 4] as MODEL record numbers,
not sequential numbers
+bug fix: load MODELS "" [1 3 4] does not work (although load "" [1 3 4],
without with MODELS keyword, works)
+clarification:
+
+ load "" 1 # loads the first model in a file when not PDB or
mmCIF.
+ load "" 1 # loads the model with MODEL 1 record for a PDB file.
+ load "" 1 # loads the model with _atom_site.pdbx_PDB_model_num =
1 for an mmCIF file
+ load "" [1] # same as load "" 1; brackets allow for more than one
model, for instance [1 3 5]
+ load MODELS ({1}) "" # always loads the SECOND model in a file
+
+
+
JmolVersion="14.3.15_2015.06.30"
bug fix: POVRay and VRML exporters mishandle label backgrounds
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