[Jmol-commits] SF.net SVN: jmol: [4681] trunk/Jmol/src/org/jmol/viewer/Eval.java
Revision: 4681
Author: hansonr
Date: 2006-03-22 04:29:28 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4681&view=rev
Log Message:
---
Eval: just adding some error traps; some may be unnecessary.
Modified Paths:
--
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===
--- trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-22 02:43:59 UTC (rev
4680)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-22 12:29:28 UTC (rev
4681)
@@ -738,6 +738,10 @@
evalError("variable undefined:" + varName);
}
+ void endOfStatementUnexpected() throws ScriptException {
+evalError("unexpected end of script command");
+ }
+
void badArgumentCount() throws ScriptException {
evalError("bad argument count");
}
@@ -1769,6 +1773,8 @@
Hashtable variables = new Hashtable();
void define() throws ScriptException {
+if (statementLength == 1)
+ keywordExpected();
String variable = (String) statement[1].value;
variables.put(variable, (expression(statement, 2)));
}
@@ -1813,6 +1819,8 @@
int i = 1;
// ignore optional file format
String filename = "fileset";
+if (statementLength == 1)
+ filenameExpected();
if (statement[i].tok == Token.identifier)
++i;
if (statement[i].tok != Token.string)
@@ -2148,6 +2156,8 @@
}
void script() throws ScriptException {
+if (statementLength == 1)
+ endOfStatementUnexpected();
if (statement[1].tok != Token.string)
filenameExpected();
pushContext();
@@ -2173,6 +2183,8 @@
}
void translate() throws ScriptException {
+if (statementLength <3)
+ endOfStatementUnexpected();
if (statement[2].tok != Token.integer)
integerExpected();
int percent = statement[2].intValue;
@@ -2198,6 +2210,8 @@
}
void zoom() throws ScriptException {
+if (statementLength == 1)
+ endOfStatementUnexpected();
if (statement[1].tok == Token.integer) {
int percent = statement[1].intValue;
if (percent < 5 || percent > Viewer.MAXIMUM_ZOOM_PERCENTAGE)
@@ -2220,6 +2234,8 @@
void delay() throws ScriptException {
long timeBegin = System.currentTimeMillis();
long millis = 0;
+if (statementLength == 1)
+ endOfStatementUnexpected();
Token token = statement[1];
switch (token.tok) {
case Token.integer:
@@ -2315,6 +2331,8 @@
}
void slab() throws ScriptException {
+if (statementLength == 1)
+ endOfStatementUnexpected();
if (statement[1].tok == Token.integer) {
int percent = statement[1].intValue;
if (percent < 0 || percent > 100)
@@ -2612,6 +2630,8 @@
}
void dots() throws ScriptException {
+if (statementLength == 1)
+ endOfStatementUnexpected();
short mad = 0;
switch (statement[1].tok) {
case Token.on:
@@ -2638,6 +2658,9 @@
void proteinShape(int shapeType) throws ScriptException {
short mad = 0;
+if (statementLength == 1)
+ endOfStatementUnexpected();
+
int tok = statement[1].tok;
switch (tok) {
case Token.on:
@@ -2883,6 +2906,8 @@
*/
void set() throws ScriptException {
+if (statementLength == 1)
+ endOfStatementUnexpected();
switch (statement[1].tok) {
case Token.axes:
setAxes();
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[Jmol-commits] SF.net SVN: jmol: [4682] trunk/Jmol-datafiles
Revision: 4682
Author: migueljmol
Date: 2006-03-22 08:52:15 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4682&view=rev
Log Message:
---
sample data file and resolver work for MDL v3000 format
Modified Paths:
--
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
Added Paths:
---
trunk/Jmol-datafiles/v3000/
trunk/Jmol-datafiles/v3000/WO0119816T.sdf
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2006-03-22
12:29:28 UTC (rev 4681)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2006-03-22
16:52:15 UTC (rev 4682)
@@ -103,6 +103,8 @@
LimitedLineReader llr = new LimitedLineReader(bufferedReader, 16384);
for (int i = 0; i < lines.length; ++i)
lines[i] = llr.readLineWithNewline();
+if (checkV3000(lines))
+ return "V3000";
if (checkMol(lines))
return "Mol";
if (checkXyz(lines))
@@ -142,12 +144,20 @@
// file types that need special treatment
+ static boolean checkV3000(String[] lines) {
+if (lines[3].length() >= 6) {
+ String line4trimmed = lines[3].trim();
+ if (line4trimmed.endsWith("V3000"))
+return true;
+}
+return false;
+ }
+
static boolean checkMol(String[] lines) {
if (lines[3].length() >= 6) {
String line4trimmed = lines[3].trim();
if (line4trimmed.endsWith("V2000") ||
- line4trimmed.endsWith("v2000") ||
- line4trimmed.endsWith("V3000"))
+ line4trimmed.endsWith("v2000"))
return true;
try {
Integer.parseInt(lines[3].substring(0, 3).trim());
Added: trunk/Jmol-datafiles/v3000/WO0119816T.sdf
===
--- trunk/Jmol-datafiles/v3000/WO0119816T.sdf (rev 0)
+++ trunk/Jmol-datafiles/v3000/WO0119816T.sdf 2006-03-22 16:52:15 UTC (rev
4682)
@@ -0,0 +1,368 @@
+
+ 02260622002D 0 0.0 0.0 0
+HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved.
+ 0 0 0 0 0999 V3000
+M V30 BEGIN CTAB
+M V30 COUNTS 7 6 0 0 0
+M V30 BEGIN ATOM
+M V30 1 S 0.75 2.25 0 0
+M V30 2 C 2.04904 3 0 0
+M V30 3 C 3.34808 2.25 0 0 CFG=2
+M V30 4 N 3.34808 0.75 0 0
+M V30 5 C 4.64711 3 0 0
+M V30 6 O 5.94615 2.25 0 0
+M V30 7 O 4.64711 4.5 0 0
+M V30 END ATOM
+M V30 BEGIN BOND
+M V30 1 1 1 2
+M V30 2 1 2 3
+M V30 3 1 3 4 CFG=1
+M V30 4 1 3 5
+M V30 5 2 5 6
+M V30 6 1 5 7
+M V30 END BOND
+M V30 BEGIN COLLECTION
+M V30 MDLV30/STEABS ATOMS=(1 3)
+M V30 END COLLECTION
+M V30 END CTAB
+M END
+>
+CYSTEINE
+
+
+
+ 02260622002D 0 0.0 0.0 0
+HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved.
+ 0 0 0 0 0999 V3000
+M V30 BEGIN CTAB
+M V30 COUNTS 11 11 0 0 0
+M V30 BEGIN ATOM
+M V30 1 N 3.75 0.750001 0 0
+M V30 2 C 3 2.04904 0 0 CFG=2
+M V30 3 C 1.5 2.04904 0 0
+M V30 4 O 0.750001 0.75 0 0
+M V30 5 O 0.75 3.34808 0 0
+M V30 6 C 3.75 3.34808 0 0
+M V30 7 C 5.25 3.34808 0 0
+M V30 8 C 6.13168 4.5616 0 0
+M V30 9 N 7.55826 4.09808 0 0
+M V30 10 C 7.55827 2.59808 0 0
+M V30 11 N 6.13168 2.13455 0 0
+M V30 END ATOM
+M V30 BEGIN BOND
+M V30 1 1 2 1 CFG=3
+M V30 2 1 2 3
+M V30 3 1 2 6
+M V30 4 2 3 4
+M V30 5 1 3 5
+M V30 6 1 6 7
+M V30 7 2 7 8
+M V30 8 1 7 11
+M V30 9 1 8 9
+M V30 10 1 9 10
+M V30 11 2 10 11
+M V30 END BOND
+M V30 BEGIN COLLECTION
+M V30 MDLV30/STEABS ATOMS=(1 2)
+M V30 END COLLECTION
+M V30 END CTAB
+M END
+>
+histidine
+
+
+
+
+ 02260622012D 0 0.0 0.0 0
+HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved.
+ 0 0 0 0 0999 V3000
+M V30 BEGIN CTAB
+M V30 COUNTS 12 12 0 0 0
+M V30 BEGIN ATOM
+M V30 1 N 4.64711 3.75 0 0
+M V30 2 C 3.34808 3 0 0 CFG=2
+M V30 3 C 2.04904 3.75 0 0
+M V30 4 O 0.75 3 0 0
+M V30 5 O 2.04904 5.25 0 0
+M V30 6 C 3.34808 1.5 0 0
+M V30 7 C 5.94615 3 0 0 CFG=3
+M V30 8 C 7.24519 3.75 0 0
+M V30 9 C 8.54423 3 0 0
+M V30 10 C 8.54423 1.5 0 0
+M V30 11 C 7.2452 0.75 0 0
+M V30 12 C 5.94616 1.5 0 0
+M V30 END ATOM
+M V30 BEGIN BOND
+M V30 1 1 1 2
+M V30 2 1 1 7
+M V30 3 1 2 3
+M V30 4 1 2 6 CFG=1
+M V30 5 2 3 4
+M V30 6 1 3 5
+M V30 7 1 7 8
+M V30 8 1 7 12
+M V30 9 1 8 9
+M V30 10 1 9 10
+M V30 11 1 10 11
+M V30 12 1 11 12
+M V30 END BOND
+M V30 BEGIN COLLECTION
+M V30 MDLV30/STEABS ATOMS=(1 2)
+M V30 END COLLECTION
+M V30 END CTAB
+M END
+>
+cyclohexyl alanine
+
+
+
+ 02260622032D 0 0.0 0.0 0
+HDR: RoxyName (Build 030), Copyright (c) 2001-2005. All rights reserved.
+ 0 0 0 0 0999 V3000
+M V30 BEGIN CTAB
+M V30 COUNTS 25 27 0 0 0
+M V30 BEGIN
[Jmol-commits] SF.net SVN: jmol: [4683] trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
Revision: 4683
Author: migueljmol
Date: 2006-03-22 10:33:25 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4683&view=rev
Log Message:
---
simple version of V3000 reader that only reads atoms
Added Paths:
---
trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
Added: trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
===
--- trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java2006-03-22
18:33:25 UTC (rev 4683)
@@ -0,0 +1,122 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-03-15 08:52:29 -0500 (Wed, 15 Mar 2006) $
+ * $Revision: 4614 $
+ *
+ * Copyright (C) 2006 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.smarter;
+
+import org.jmol.api.JmolAdapter;
+
+import java.io.BufferedReader;
+
+/**
+ * A reader for MDL V3000 files
+ *
+ *
+ * http://www.mdli.com/downloads/public/ctfile/ctfile.jsp
+ *
+ *
+ */
+class V3000Reader extends AtomSetCollectionReader {
+
+ int headerAtomCount;
+ int headerBondCount;
+
+ AtomSetCollection readAtomSetCollection(BufferedReader reader)
+throws Exception {
+atomSetCollection = new AtomSetCollection("v3000");
+processCtab(reader);
+return atomSetCollection;
+ }
+
+ void processCtab(BufferedReader reader) throws Exception {
+String line;
+do {
+ line = reader.readLine();
+ if (line == null)
+return;
+} while (! line.startsWith("M V30 BEGIN CTAB"));
+line = reader.readLine();
+while (line != null && ! line.startsWith("M END")) {
+ if (line.startsWith("M V30 COUNTS")) {
+processCounts(line);
+line = reader.readLine();
+continue;
+ }
+ if (line.startsWith("M V30 BEGIN ATOM")) {
+line = processAtomBlock(reader);
+continue;
+ }
+ /*
+ if (line.startsWith("M V30 BEGIN BOND")) {
+line = processBond(reader);
+continue;
+ }
+ */
+ line = reader.readLine();
+}
+ }
+
+ void processCounts(String line) {
+headerAtomCount = parseInt(line, 13);
+headerBondCount = parseInt(line, ichNextParse);
+ }
+
+ String processAtomBlock(BufferedReader reader) throws Exception {
+for (int i = headerAtomCount; --i >= 0; ) {
+ String line = readLineWithContinuation(reader);
+ if (line == null || (! line.startsWith("M V30 ")))
+throw new Exception("unrecognized atom");
+ Atom atom = atomSetCollection.addNewAtom();
+ atom.atomSerial = parseInt(line, 7);
+ atom.elementSymbol = parseToken(line, ichNextParse);
+ atom.x = parseFloat(line, ichNextParse);
+ atom.y = parseFloat(line, ichNextParse);
+ atom.z = parseFloat(line, ichNextParse);
+ parseInt(line, ichNextParse); // discard aamap
+ while (true) {
+String option = parseToken(line, ichNextParse);
+if (option == null)
+ break;
+if (option.startsWith("CHG="))
+ atom.formalCharge = parseInt(option, 4);
+ }
+}
+String line = reader.readLine();
+if (line == null || ! line.startsWith("M V30 END ATOM"))
+ throw new Exception("M V30 END ATOM not found");
+return line;
+ }
+
+ String readLineWithContinuation(BufferedReader reader) throws Exception {
+String line = reader.readLine();
+if (line != null && line.length() > 7) {
+ while (line.charAt(line.length() - 1) == '-') {
+String line2 = reader.readLine();
+if (line2 == null || ! line.startsWith("M V30 "))
+ throw new Exception("Invalid line continuation");
+line += line2.substring(7);
+ }
+}
+return line;
+ }
+}
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[Jmol-commits] SF.net SVN: jmol: [4684] trunk/Jmol/src/org/jmol/adapter/smarter
Revision: 4684
Author: migueljmol
Date: 2006-03-22 19:18:30 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4684&view=rev
Log Message:
---
more work on V3000 reader ... but must be integrated with MolReader because
an .sdf file can contain a mixture of V3000 and V2000 stuff :-(
Modified Paths:
--
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-03-22 18:33:25 UTC (rev 4683)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-03-23 03:18:30 UTC (rev 4684)
@@ -148,7 +148,7 @@
for (int i = atomCount; --i >= 0; )
atoms[i] = null;
atomCount = 0;
-atomNameMap.clear();
+atomSymbolicMap.clear();
atomSetCount = 0;
currentAtomSetIndex = -1;
for (int i = atomSetNumbers.length; --i >= 0; ) {
@@ -231,6 +231,11 @@
mapMostRecentAtomName();
}
+ void addAtomWithMappedSerialNumber(Atom atom) {
+addAtom(atom);
+mapMostRecentAtomSerialNumber();
+ }
+
Bond addNewBond(int atomIndex1, int atomIndex2) {
return addNewBond(atomIndex1, atomIndex2, 1);
}
@@ -240,6 +245,9 @@
}
Bond addNewBond(int atomIndex1, int atomIndex2, int order) {
+if (atomIndex1 < 0 || atomIndex1 >= atomCount ||
+atomIndex2 < 0 || atomIndex2 >= atomCount)
+ return null;
Bond bond = new Bond(atomIndex1, atomIndex2, order);
addBond(bond);
return bond;
@@ -251,6 +259,13 @@
order);
}
+ Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2,
+ int order) {
+return addNewBond(getAtomSerialNumberIndex(atomSerial1),
+ getAtomSerialNumberIndex(atomSerial2),
+ order);
+ }
+
void addBond(Bond bond) {
/*
System.out.println("I see a bond:" + bond.atomIndex1 + "-" +
@@ -285,28 +300,45 @@
}
}
- Hashtable atomNameMap = new Hashtable();
+ Hashtable atomSymbolicMap = new Hashtable();
void mapMostRecentAtomName() {
if (atomCount > 0) {
int index = atomCount - 1;
String atomName = atoms[index].atomName;
if (atomName != null)
-atomNameMap.put(atomName, new Integer(atomCount - 1));
+atomSymbolicMap.put(atomName, new Integer(index));
}
}
+ void mapMostRecentAtomSerialNumber() {
+if (atomCount > 0) {
+ int index = atomCount - 1;
+ int atomSerial = atoms[index].atomSerial;
+ if (atomSerial != Integer.MIN_VALUE)
+atomSymbolicMap.put(new Integer(atomSerial), new Integer(index));
+}
+ }
+
void mapAtomName(String atomName, int atomIndex) {
-atomNameMap.put(atomName, new Integer(atomIndex));
+atomSymbolicMap.put(atomName, new Integer(atomIndex));
}
-
+
int getAtomNameIndex(String atomName) {
int index = -1;
-Object value = atomNameMap.get(atomName);
+Object value = atomSymbolicMap.get(atomName);
if (value != null)
index = ((Integer)value).intValue();
return index;
}
+
+ int getAtomSerialNumberIndex(int serialNumber) {
+int index = -1;
+Object value = atomSymbolicMap.get(new Integer(serialNumber));
+if (value != null)
+ index = ((Integer)value).intValue();
+return index;
+ }
/**
* Sets a property for the AtomSetCollection
@@ -334,7 +366,6 @@
void newAtomSet() {
-//System.out.println("newAtomSet()");
currentAtomSetIndex = atomSetCount++;
if (atomSetCount > atomSetNumbers.length) {
atomSetNumbers = AtomSetCollectionReader.doubleLength(atomSetNumbers);
@@ -347,6 +378,11 @@
(Hashtable[])
AtomSetCollectionReader.doubleLength(atomSetAuxiliaryInfo);
}
atomSetNumbers[currentAtomSetIndex] = atomSetCount;
+// miguel 2006 03 22
+// added this clearing of the atomSymbolicMap to support V3000
+// seems that it should have been here all along, but apparently
+// noone else needed it
+atomSymbolicMap.clear();
}
/**
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java
===
--- trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java2006-03-22
18:33:25 UTC (rev 4683)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/V3000Reader.java2006-03-23
03:18:30 UTC (rev 4684)
@@ -44,36 +44,43 @@
AtomSetCollection readAtomSetCollection(BufferedReader reader)
throws Exception {
atomSetCollection = new AtomSetCollection("v3000");
-processCtab(reader);
+boolean startNewAtomSet = false;
+String line;
+while (true) {
+ line = processCtab(reader, startNewAtomSet)
[Jmol-commits] SF.net SVN: jmol: [4685] trunk/Jmol/src/org/jmol/viewer
Revision: 4685
Author: hansonr
Date: 2006-03-22 20:18:56 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4685&view=rev
Log Message:
---
Eval: cleaning up code; moving to appropriate locations
and accessing via Viewer.
Philosophy:
1. If all of the method calls in a method are
methods in frame, this method should be in frame.
2. Eval should not be doing model selection/bitset creation
functions that are not unique to scripts.
3. Moving these methods opens up more possibilities for
applet-applet communication via more direct methods than script.
Modified Paths:
--
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Frame.java
trunk/Jmol/src/org/jmol/viewer/ModelManager.java
trunk/Jmol/src/org/jmol/viewer/SelectionManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===
--- trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 03:18:30 UTC (rev
4684)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 04:18:56 UTC (rev
4685)
@@ -30,8 +30,6 @@
import java.util.BitSet;
import java.util.Vector;
import java.util.Hashtable;
-import javax.vecmath.AxisAngle4f;
-import javax.vecmath.Matrix3f;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
@@ -942,15 +940,6 @@
return bs;
}
- int firstAtomOf(BitSet bs) {
-int numberOfAtoms = viewer.getAtomCount();
-for (int i = numberOfAtoms; --i >= 0;)
- if (bs.get(i)) {
-return i;
- }
-return -1;
- }
-
int endOfExpression;
BitSet expression(Token[] code, int pcStart) throws ScriptException {
@@ -1014,55 +1003,41 @@
stack[sp++] = copyBitSet(viewer.getVisibleSet());
break;
case Token.hetero:
-stack[sp++] = getHeteroSet();
-break;
case Token.hydrogen:
-stack[sp++] = getHydrogenSet();
+ case Token.protein:
+ case Token.nucleic:
+ case Token.dna:
+ case Token.rna:
+ case Token.purine:
+ case Token.pyrimidine:
+stack[sp++] = viewer.getAtomBits((String) instruction.value);
break;
case Token.spec_name_pattern:
-stack[sp++] = getSpecName((String) instruction.value);
+stack[sp++] = viewer.getAtomBits("SpecName", (String)
instruction.value);
break;
case Token.spec_resid:
-stack[sp++] = getSpecResid(instruction.intValue);
+stack[sp++] = viewer.getAtomBits("SpecResid", instruction.intValue);
break;
case Token.spec_seqcode:
-stack[sp++] = getSpecSeqcode(instruction.intValue);
+stack[sp++] = viewer.getAtomBits("SpecSeqcode",instruction.intValue);
break;
case Token.spec_seqcode_range:
int seqcodeA = instruction.intValue;
int seqcodeB = ((Integer) instruction.value).intValue();
-stack[sp++] = getSpecSeqcodeRange(seqcodeA, seqcodeB);
+stack[sp++] = viewer.getAtomBits("SpecSeqcodeRange", seqcodeA,
seqcodeB);
break;
case Token.spec_chain:
-stack[sp++] = getSpecChain((char) instruction.intValue);
+stack[sp++] = viewer.getAtomBits("SpecChain", instruction.intValue);
break;
case Token.spec_atom:
-stack[sp++] = getSpecAtom((String) instruction.value);
+stack[sp++] = viewer.getAtomBits("SpecAtom", (String)
instruction.value);
break;
case Token.spec_alternate:
-stack[sp++] = getSpecAlternate((String) instruction.value);
+stack[sp++] = viewer.getAtomBits("SpecAlternate", (String)
instruction.value);
break;
case Token.spec_model:
-stack[sp++] = getSpecModel((String) instruction.value);
+stack[sp++] = viewer.getAtomBits("SpecModel", (String)
instruction.value);
break;
- case Token.protein:
-stack[sp++] = getProteinSet();
-break;
- case Token.nucleic:
-stack[sp++] = getNucleicSet();
-break;
- case Token.dna:
-stack[sp++] = getDnaSet();
-break;
- case Token.rna:
-stack[sp++] = getRnaSet();
-break;
- case Token.purine:
-stack[sp++] = getPurineSet();
-break;
- case Token.pyrimidine:
-stack[sp++] = getPyrimidineSet();
-break;
case Token.y:
case Token.amino:
case Token.backbone:
@@ -1070,7 +1045,7 @@
case Token.identifier:
case Token.sidechain:
case Token.surface:
-stack[sp++] = lookupIdentifierValue((String) instruction.value);
+stack[sp++] = viewer.getAtomBits("IdentifierValue", (String)
instruction.value);
break;
case Token.opLT:
case Token.opLE:
@@ -1090,6 +1065,15 @@
return stack[0];
}
+ void notSet(BitSet bs) {
+for (int i = viewer.getAtomCount(); --i >= 0;) {
+
[Jmol-commits] SF.net SVN: jmol: [4686] trunk/Jmol/src/org/jmol/viewer/Eval.java
Revision: 4686
Author: hansonr
Date: 2006-03-22 21:16:53 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4686&view=rev
Log Message:
---
removing unnecessary statementLength checks;
leaves necessary ones in -- load and translate, for example.
Modified Paths:
--
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===
--- trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 04:18:56 UTC (rev
4685)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 05:16:53 UTC (rev
4686)
@@ -1927,8 +1927,7 @@
}
void script() throws ScriptException {
-if (statementLength == 1)
- endOfStatementUnexpected();
+// token allows for only 1 parameter
if (statement[1].tok != Token.string)
filenameExpected();
pushContext();
@@ -1946,7 +1945,7 @@
void translate() throws ScriptException {
if (statementLength <3)
- endOfStatementUnexpected();
+ badArgumentCount();
if (statement[2].tok != Token.integer)
integerExpected();
int percent = statement[2].intValue;
@@ -1972,8 +1971,7 @@
}
void zoom() throws ScriptException {
-if (statementLength == 1)
- endOfStatementUnexpected();
+// token has ondefault1
if (statement[1].tok == Token.integer) {
int percent = statement[1].intValue;
if (percent < 5 || percent > Viewer.MAXIMUM_ZOOM_PERCENTAGE)
@@ -1996,8 +1994,7 @@
void delay() throws ScriptException {
long timeBegin = System.currentTimeMillis();
long millis = 0;
-if (statementLength == 1)
- endOfStatementUnexpected();
+//token has ondefault1
Token token = statement[1];
switch (token.tok) {
case Token.integer:
@@ -2041,8 +2038,7 @@
}
void slab() throws ScriptException {
-if (statementLength == 1)
- endOfStatementUnexpected();
+//token has ondefault1
if (statement[1].tok == Token.integer) {
int percent = statement[1].intValue;
if (percent < 0 || percent > 100)
@@ -2340,8 +2336,7 @@
}
void dots() throws ScriptException {
-if (statementLength == 1)
- endOfStatementUnexpected();
+// token has onDefault1
short mad = 0;
switch (statement[1].tok) {
case Token.on:
@@ -2368,9 +2363,7 @@
void proteinShape(int shapeType) throws ScriptException {
short mad = 0;
-if (statementLength == 1)
- endOfStatementUnexpected();
-
+//token has ondefault1
int tok = statement[1].tok;
switch (tok) {
case Token.on:
@@ -2616,8 +2609,6 @@
*/
void set() throws ScriptException {
-if (statementLength == 1)
- endOfStatementUnexpected();
switch (statement[1].tok) {
case Token.axes:
setAxes();
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---
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[Jmol-commits] SF.net SVN: jmol: [4687] trunk/Jmol/src/org/jmol/viewer/Eval.java
Revision: 4687
Author: hansonr
Date: 2006-03-22 21:31:26 -0800 (Wed, 22 Mar 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=4687&view=rev
Log Message:
---
Eval quick fix.
Modified Paths:
--
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===
--- trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 05:16:53 UTC (rev
4686)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java2006-03-23 05:31:26 UTC (rev
4687)
@@ -1045,7 +1045,7 @@
case Token.identifier:
case Token.sidechain:
case Token.surface:
-stack[sp++] = viewer.getAtomBits("IdentifierValue", (String)
instruction.value);
+stack[sp++] = lookupIdentifierValue((String) instruction.value);
break;
case Token.opLT:
case Token.opLE:
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
---
This SF.Net email is sponsored by xPML, a groundbreaking scripting language
that extends applications into web and mobile media. Attend the live webcast
and join the prime developer group breaking into this new coding territory!
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
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