Revision: 18669
http://sourceforge.net/p/jmol/code/18669
Author: hansonr
Date: 2013-09-18 23:09:05 +0000 (Wed, 18 Sep 2013)
Log Message:
-----------
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
Removed Paths:
-------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/PqrReader.java
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-09-18 23:07:12 UTC (rev 18668)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-09-18 23:09:05 UTC (rev 18669)
@@ -26,10 +26,12 @@
import java.io.BufferedReader;
import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
import org.jmol.util.JmolList;
-
-
-
import org.jmol.util.TextFormat;
import org.jmol.adapter.readers.molxyz.MolReader;
@@ -96,7 +98,7 @@
public class JcampdxReader extends MolReader {
- private String modelID;
+ private String thisModelID;
private AtomSetCollection models;
private String modelIdList = "";
private JmolList<String> peakData = new JmolList<String>();
@@ -152,7 +154,9 @@
if (label.equals("##$MODELS"))
return readModels();
if (label.equals("##$PEAKS"))
- return readPeaks();
+ return (readPeaks(false) > 0);
+ if (label.equals("##$SIGNALS"))
+ return (readPeaks(true) > 0);
return true;
}
@@ -180,7 +184,7 @@
// load xxx.jdx 0 will mean "load only the base model(s)"
models = null;
line = "";
- modelID = "";
+ thisModelID = "";
boolean isFirst = true;
while (true) {
int model0 = atomSetCollection.getCurrentAtomSetIndex();
@@ -208,11 +212,11 @@
private void updateModelIDs(int model0, boolean isFirst) {
int n = atomSetCollection.getAtomSetCount();
if (isFirst && n == model0 + 2) {
- atomSetCollection.setAtomSetAuxiliaryInfo("modelID", modelID);
+ atomSetCollection.setAtomSetAuxiliaryInfo("modelID", thisModelID);
return;
}
for (int pt = 0, i = model0; ++i < n;) {
- atomSetCollection.setAtomSetAuxiliaryInfoForSet("modelID", modelID + "."
+ atomSetCollection.setAtomSetAuxiliaryInfoForSet("modelID", thisModelID +
"."
+ (++pt), i);
}
}
@@ -223,10 +227,10 @@
}
private AtomSetCollection getModelAtomSetCollection() throws Exception {
- lastModel = modelID;
- modelID = getAttribute(line, "id");
+ lastModel = thisModelID;
+ thisModelID = getAttribute(line, "id");
// read model only once for a given ID
- String key = ";" + modelID + ";";
+ String key = ";" + thisModelID + ";";
if (modelIdList.indexOf(key) >= 0) {
discardLinesUntilContains("</ModelData>");
return null;
@@ -276,7 +280,7 @@
for (int i = a.getAtomCount(); --i >= 0;)
atoms[i].scaleVector(vibScale);
}
- Logger.info("jdx model=" + modelID + " type=" + a.getFileTypeName());
+ Logger.info("jdx model=" + thisModelID + " type=" + a.getFileTypeName());
return a;
}
@@ -312,23 +316,171 @@
}
}
- private boolean readPeaks() throws Exception {
- if (line.indexOf("<Peaks") < 0)
- discardLinesUntilContains2("<Peaks", "##");
- if (line.indexOf("<Peaks") < 0)
- return false;
- String type = getAttribute(line, "type").toUpperCase();
- if (type.equals("HNMR"))
- type = "1HNMR";
- else if (type.equals("CNMR"))
- type = "13CNMR";
- while (readLine() != null && !(line = line.trim()).startsWith("</Peaks>"))
- if (line.startsWith("<PeakData"))
- peakData.addLast("<PeakData file=" + peakFilePath + " index=\"" +
(++peakIndex[0]) + "\"" + " type=\"" + type + "\" " + line.substring(9).trim());
- return true;
+ String piUnitsX, piUnitsY;
+
+ /**
+ * read a <Peaks> or <Signals> block See similar method in
+ * JSpecViewLib/src/jspecview/source/FileReader.java
+ *
+ * @param isSignals
+ * @return true if successful
+ * @throws Exception
+ */
+ private int readPeaks(boolean isSignals) throws Exception {
+ JcampdxReader reader = this;
+ Object spectrum = null;
+
+ try {
+ int offset = (isSignals ? 1 : 0);
+ String tag1 = (isSignals ? "Signals" : "Peaks");
+ String tag2 = (isSignals ? "<Signal" : "<PeakData");
+ String line = discardUntil(reader, tag1);
+ if (line.indexOf("<" + tag1) < 0)
+ line = discardUntil(reader, "<" + tag1);
+ if (line.indexOf("<" + tag1) < 0)
+ return 0;
+
+ String file = getPeakFilePath();
+ String model = getQuotedAttribute(line, "model");
+ model = " model=" + escape(model == null ? thisModelID : model);
+ String type = getQuotedAttribute(line, "type");
+ if ("HNMR".equals(type))
+ type = "1HNMR";
+ else if ("CNMR".equals(type))
+ type = "13CNMR";
+ type = (type == null ? "" : " type=" + escape(type));
+ piUnitsX = getQuotedAttribute(line, "xLabel");
+ piUnitsY = getQuotedAttribute(line, "yLabel");
+ Map<String, Object[]> htSets = new Hashtable<String, Object[]>();
+ List<Object[]> list = new ArrayList<Object[]>();
+ while ((line = reader.readLine()) != null
+ && !(line = line.trim()).startsWith("</" + tag1)) {
+ if (line.startsWith(tag2)) {
+ info(line);
+ String title = getQuotedAttribute(line, "title");
+ if (title == null) {
+ title = (type == "1HNMR" ? "atom%S%: %ATOMS%; integration:
%NATOMS%" : "");
+ title = " title=" + escape(title);
+ } else {
+ title = "";
+ }
+ String stringInfo = "<PeakData "
+ + file
+ + " index=\"%INDEX%\""
+ + title
+ + type
+ + (getQuotedAttribute(line, "model") == null ? model
+ : "") + " " + line.substring(tag2.length()).trim();
+ String atoms = getQuotedAttribute(stringInfo, "atoms");
+ if (atoms != null)
+ stringInfo = simpleReplace(stringInfo, "atoms=\""
+ + atoms + "\"", "atoms=\"%ATOMS%\"");
+ String key = ((int) (parseFloatStr(getQuotedAttribute(line, "xMin"))
* 100))
+ + "_"
+ + ((int) (parseFloatStr(getQuotedAttribute(line,
+ "xMax")) * 100));
+ Object[] o = htSets.get(key);
+ if (o == null) {
+ o = new Object[] { stringInfo,
+ (atoms == null ? null : new BS()) };
+ htSets.put(key, o);
+ list.add(o);
+ }
+ BS bs = (BS) o[1];
+ if (bs != null) {
+ atoms = atoms.replace(',', ' ');
+ bs.or(unescapeBitSet("({" + atoms + "})"));
+ }
+ }
+ }
+ int nH = 0;
+ int n = list.size();
+ for (int i = 0; i < n; i++) {
+ Object[] o = list.get(i);
+ String stringInfo = (String) o[0];
+ stringInfo = simpleReplace(stringInfo, "%INDEX%", ""
+ + getPeakIndex());
+ BS bs = (BS) o[1];
+ if (bs != null) {
+ String s = "";
+ for (int j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1))
+ s += "," + (j + offset);
+ int na = bs.cardinality();
+ nH += na;
+ stringInfo = simpleReplace(stringInfo, "%ATOMS%", s
+ .substring(1));
+ stringInfo = simpleReplace(stringInfo, "%S%",
+ (na == 1 ? "" : "s"));
+ stringInfo = simpleReplace(stringInfo, "%NATOMS%", ""
+ + na);
+ }
+ info("Jmol using " + stringInfo);
+ add(peakData, stringInfo);
+ }
+ setSpectrumPeaks(spectrum, peakData, nH);
+ return n;
+ } catch (Exception e) {
+ return 0;
+ }
}
+ private void info(String s) {
+ Logger.info(s);
+ }
+
+ private BS unescapeBitSet(String s) {
+ return Escape.uB(s);
+ }
+
+ private String simpleReplace(String s, String sfrom, String sto) {
+ return TextFormat.simpleReplace(s, sfrom, sto);
+ }
+
+ private String escape(String s) {
+ return Escape.eS(s);
+ }
+
+ private String getQuotedAttribute(String s, String attr) {
+ return Parser.getQuotedAttribute(s, attr);
+ }
+
/**
+ * @param o1
+ * @param o2
+ * @param nH
+ */
+ private void setSpectrumPeaks(Object o1, Object o2,
+ int nH) {
+ // only in JSpecView
+ }
+
+ private void add(JmolList<String> peakData, String info) {
+ peakData.addLast(info);
+ }
+
+ private String getPeakFilePath() {
+ return " file=" + Escape.eS(peakFilePath);
+ }
+
+
+ /**
+ * @param ignored
+ * @param tag
+ * @return line
+ * @throws Exception
+ */
+ private String discardUntil(Object ignored, String tag) throws Exception {
+ return discardLinesUntilContains2("<" + tag, "##");
+ }
+
+ /**
+ * @return index
+ */
+ private int getPeakIndex() {
+ return ++peakIndex[0];
+ }
+
+ /**
* integrate the <PeakAssignment> records into the associated models, and
delete unreferenced n.m models
*/
@SuppressWarnings("unchecked")
@@ -341,10 +493,10 @@
for (int p = 0; p < n; p++) {
line = peakData.get(p);
String type = getAttribute(line, "type");
- modelID = getAttribute(line, "model");
- int i = findModelById(modelID);
+ thisModelID = getAttribute(line, "model");
+ int i = findModelById(thisModelID);
if (i < 0) {
- Logger.warn("cannot find model " + modelID + " required for " + line);
+ Logger.warn("cannot find model " + thisModelID + " required for " +
line);
continue;
}
addType(i, type);
@@ -372,9 +524,9 @@
}
n = atomSetCollection.getAtomSetCount();
for (int i = n; --i >= 0;) {
- modelID = (String) atomSetCollection
+ thisModelID = (String) atomSetCollection
.getAtomSetAuxiliaryInfoValue(i, "modelID");
- if (havePeaks && !bsModels.get(i) && modelID.indexOf(".") >= 0) {
+ if (havePeaks && !bsModels.get(i) && thisModelID.indexOf(".") >= 0) {
atomSetCollection.removeAtomSet(i);
n--;
}
Modified: branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
2013-09-18 23:07:12 UTC (rev 18668)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
2013-09-18 23:09:05 UTC (rev 18669)
@@ -209,7 +209,7 @@
atomSetCollection.addAtom(new Atom());
}
- String[] atomTypes;
+ private String[] atomTypes;
private void getAtomTypes() throws Exception {
atomTypes = getDataBlock();
}
Deleted: branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
2013-09-18 23:07:12 UTC (rev 18668)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
2013-09-18 23:09:05 UTC (rev 18669)
@@ -1,65 +0,0 @@
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2006-10-15 17:34:01 -0500 (Sun, 15 Oct 2006) $
- * $Revision: 5957 $
- *
- * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: jmol-develop...@lists.sf.net
- *
- * 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.more;
-
-import org.jmol.util.JmolList;
-
-
-import org.jmol.adapter.readers.cifpdb.PdbReader;
-import org.jmol.adapter.smarter.Atom;
-
-/**
- * P2N file reader.
- *
- * This format is the input for Resp ESP Charge Derive server
- * http://q4md-forcefieldtools.org/
- *
- */
-
-public class P2nReader extends PdbReader {
-
- private JmolList<String> altNames = new JmolList<String>();
-
- @Override
- protected void setAdditionalAtomParameters(Atom atom) {
- String altName = line.substring(69, 72).trim();
- if (altName.length() == 0)
- altName = atom.atomName;
- if (useAltNames)
- atom.atomName = altName;
- else
- altNames.addLast(altName);
- }
-
- @Override
- protected void finalizeReader() throws Exception {
- finalizeReaderPDB();
- if (!useAltNames)
- atomSetCollection.setAtomSetAuxiliaryInfo("altName", altNames
- .toArray(new String[altNames.size()]));
- }
-
-}
-
Deleted: branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/PqrReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/PqrReader.java
2013-09-18 23:07:12 UTC (rev 18668)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/more/PqrReader.java
2013-09-18 23:09:05 UTC (rev 18669)
@@ -1,72 +0,0 @@
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2006-10-15 17:34:01 -0500 (Sun, 15 Oct 2006) $
- * $Revision: 5957 $
- *
- * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: jmol-develop...@lists.sf.net
- *
- * 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.more;
-
-import org.jmol.adapter.readers.cifpdb.PdbReader;
-
-/**
- * PQR file reader.
- *
-Angel Herraez, 2009 04 19
-
-free form added Bob Hanson hans...@stolaf.edu 2012 06 25
-
-filter "FREE"
-
-PQR format is a format based on pdb, where the occupancy is replaced with the
atomic
-charge and the temperature (or B factor) is replaced with atomic radius
(however,
-the column positions in many pqr files do not match those of pdb files). This
gives
-the acronym: P for pdb, Q for charge, R for radius. Jmol interprets the charge
values
-(property partialcharge) and the radii (property vanderwaals), and can hence
use them
-e.g. in color atoms partialCharge and spacefill.
-
-The PQR format has somewhat uncertain origins, but is used by several
computational biology packages, including MEAD, AutoDock and APBS[1], for which
it is the primary input format.
-
-PQR format description[2] within APBS documentation. Note that APBS reads PQR
loosely, based only on white space delimiters, but Jmol may be more strict
about column positions.
-
-PDB files can be converted to PQR by the PDB2PQR software[3], which adds
missing hydrogen atoms and calculates the charge and radius parameters from a
variety of force fields.
-
-
-1.- http://apbs.sourceforge.net/
-2.- http://apbs.sourceforge.net/doc/user-guide/index.html#pqr-format
-3.- http://pdb2pqr.sourceforge.net/
-4.- http://cardon.wustl.edu/MediaWiki/index.php/PQR_format
-
- *
- */
-
-public class PqrReader extends PdbReader {
-
-
- protected boolean gromacsWideFormat;
-
- @Override
- protected void initializeReader() throws Exception {
- isPQR = true;
- super.initializeReader();
- }
-
-}
-
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
