Revision: 20266
http://sourceforge.net/p/jmol/code/20266
Author: hansonr
Date: 2015-02-04 12:47:46 +0000 (Wed, 04 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.04"
new feature: print data({*},"xyz")
-- (lower case) writes only atom data lines
new feature: print data({*},"XYZ", true)
-- third parameter TRUE writes all trajectories
bug fix: show mouse fails in JavaScript
-- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
-- because of a Java2Script compiler creates standard array [...]
-- from new int[] {....} whereas it should create Clazz.newArray() and fill it
bug fix: writing of file formats was inconsistent between WRITE and data()
(not fixed in 14.2)
bug fix: Jmol writing of PDB file data did not include TER records (not fixed
in 14.2)
bug fix: label %r should print "1" for non-PDB file atoms
bug fix: 01.30 mutate {xxx} ~... skips first-listed replacement group identifier
bug fix: 01.29 breaks loading non-trajectory file after a trajectory is loaded
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/binding/Binding.java
Modified: trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -56,8 +56,6 @@
public short getGroupID(String g3);
- public boolean mutate(BS bs, String fileName, String[] sequence);
-
public String toStdAmino3(String sValue);
}
Modified: trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -95,4 +95,6 @@
public void resetRasmolBonds(BS bs);
+ boolean mutate(BS bs, String group, String[] sequence);
+
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -836,7 +836,133 @@
ms.haveStraightness = true;
}
+ @Override
+ public boolean mutate(BS bs, String group, String[] sequence) {
+
+ int i0 = bs.nextSetBit(0);
+ if (sequence == null)
+ return mutateAtom(i0, group);
+ boolean isFile = (group == null);
+ if (isFile)
+ group = sequence[0];
+ Group lastGroup = null;
+ boolean isOK = true;
+ for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1)) {
+ Group g = ms.at[i].group;
+ if (g == lastGroup)
+ continue;
+ lastGroup = g;
+ if (!isFile) {
+ group = sequence[pt++ % sequence.length];
+ if (group.equals("UNK"))
+ continue;
+ group = "==" + group;
+ }
+ mutateAtom(i, group);
+ }
+ return isOK;
+ }
+
+ private boolean mutateAtom(int iatom, String fileName) {
+ // no mutating a trajectory. What would that mean???
+ int iModel = ms.at[iatom].mi;
+ if (ms.isTrajectory(iModel))
+ return false;
+
+ String[] info = vwr.fm.getFileInfo();
+ boolean b = vwr.getBoolean(T.appendnew);
+ Group g = ms.at[iatom].group;
+ //try {
+ // get the initial group -- protein for now
+ if (!(g instanceof AminoMonomer))
+ return false;
+ ((BioModel) ms.am[iModel]).isMutated = true;
+ AminoMonomer res0 = (AminoMonomer) g;
+ int ac = ms.ac;
+ BS bsRes0 = new BS();
+ res0.setAtomBits(bsRes0);
+ int r = g.getResno();
+
+ // just use a script -- it is much easier!
+
+ fileName = PT.esc(fileName);
+ String script = "" +
+ "try{\n"
+ + " var atoms0 = {*}\n"
+ + " var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
+ + " set appendNew false\n"
+ + " load append "+fileName+"\n"
+ + " set appendNew " + b + "\n"
+ + " var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
+ + " if ({r1 & within(group, r0)}){\n"
+ + " var haveHs = ({_H & connected(res0)} != 0)\n"
+ + " if (!haveHs) {delete _H & res1}\n"
+ + " var sm = '[*.N][*.CA][*.C][*.O]'\n"
+ + " var keyatoms = res1.find(sm)\n"
+ + " var x = compare(res1,res0,sm,'BONDS')\n"
+ + " if(x){\n"
+ + " print 'mutating ' + res0[1].label('%n%r') + ' to ' +
"+fileName+".trim('=')\n"
+ + " rotate branch @x\n"
+ + " compare res1 res0 SMARTS @sm rotate translate 0\n"
+ + " var c = {!res0 & connected(res0)}\n"
+ + " var N2 = {*.N & c}\n"
+ + " var C0 = {*.C & c}\n"
+ + " delete res0\n"
+ + " if (N2) {\n"
+ + " delete *.OXT and res1\n"
+ + " connect {N2} {keyatoms & *.C}\n"
+ + " }\n"
+ + " if (C0) {\n"
+ + " connect {C0} {keyatoms & *.N}\n"
+ + " }\n"
+ + " }\n"
+ + " }\n"
+ + "}catch(e){print e}\n";
+ try {
+ if (Logger.debugging)
+ Logger.debug(script);
+ vwr.eval.runScript(script);
+ } catch (Exception e) {
+ // TODO
+ }
+ if (ms.ac == ac)
+ return false;
+ // check for protein monomer
+ g = ms.at[ms.ac - 1].group;
+ if (g != ms.at[ac + 1].group || !(g instanceof AminoMonomer)) {
+ BS bsAtoms = new BS();
+ g.setAtomBits(bsAtoms);
+ vwr.deleteAtoms(bsAtoms, false);
+ return false;
+ }
+ AminoMonomer res1 = (AminoMonomer) g;
+
+ // must get new group into old chain
+
+ Group[] groups = res0.chain.groups;
+ for (int i = groups.length; --i >= 0;)
+ if (groups[i] == res0) {
+ groups[i] = res1;
+ break;
+ }
+ res1.setResno(r);
+ res1.chain.groupCount = 0;
+ res1.chain = res0.chain;
+ BS bsExclude = BSUtil.newBitSet2(0, ms.mc);
+ bsExclude.clear(res1.chain.model.modelIndex);
+ res1.chain.model.groupCount = -1;
+ res1.chain.model.freeze();
+ ms.recalculatePolymers(bsExclude);
+ //} catch (Exception e) {
+ // System.out.println("" + e);
+ // }
+ vwr.setBooleanProperty("appendNew", b);
+ vwr.fm.setFileInfo(info);
+ return true;
+ }
+
+
/////////////////////////////////////////////////////////////////////////
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -41,7 +41,6 @@
import org.jmol.modelset.ModelLoader;
import org.jmol.modelset.ModelSet;
import org.jmol.script.SV;
-import org.jmol.script.ScriptException;
import org.jmol.script.T;
import org.jmol.util.BSUtil;
import org.jmol.util.Edge;
@@ -1768,132 +1767,6 @@
return (groupID == -1 ? addGroup3Name(group3) : groupID);
}
- @Override
- public boolean mutate(BS bs, String group, String[] sequence) {
-
- int i0 = bs.nextSetBit(0);
- if (sequence == null)
- return mutateAtom(i0, group);
- boolean isFile = (group == null);
- if (isFile)
- group = sequence[0];
- Group lastGroup = null;
- boolean isOK = true;
- for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1)) {
- Group g = vwr.ms.at[i].group;
- if (g == lastGroup)
- continue;
- lastGroup = g;
- if (!isFile) {
- group = sequence[pt++ % sequence.length];
- if (group.equals("UNK"))
- continue;
- group = "==" + group;
- }
- mutateAtom(i, group);
- }
- return isOK;
- }
-
- private boolean mutateAtom(int iatom, String fileName) {
- // no mutating a trajectory. What would that mean???
- int iModel = vwr.ms.at[iatom].mi;
- if (vwr.ms.isTrajectory(iModel))
- return false;
-
- String[] info = vwr.fm.getFileInfo();
- boolean b = vwr.getBoolean(T.appendnew);
- Group g = vwr.ms.at[iatom].group;
- //try {
- // get the initial group -- protein for now
- if (!(g instanceof AminoMonomer))
- return false;
- ((BioModel) vwr.ms.am[iModel]).isMutated = true;
- AminoMonomer res0 = (AminoMonomer) g;
- int ac = vwr.ms.ac;
- BS bsRes0 = new BS();
- res0.setAtomBits(bsRes0);
- int r = g.getResno();
-
- // just use a script -- it is much easier!
-
- fileName = PT.esc(fileName);
- String script = "" +
- "try{\n"
- + " var atoms0 = {*}\n"
- + " var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
- + " set appendNew false\n"
- + " load append "+fileName+"\n"
- + " set appendNew " + b + "\n"
- + " var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
- + " if ({r1 & within(group, r0)}){\n"
- + " var haveHs = ({_H & connected(res0)} != 0)\n"
- + " if (!haveHs) {delete _H & res1}\n"
- + " var sm = '[*.N][*.CA][*.C][*.O]'\n"
- + " var keyatoms = res1.find(sm)\n"
- + " var x = compare(res1,res0,sm,'BONDS')\n"
- + " if(x){\n"
- + " print 'mutating ' + res0[1].label('%n%r') + ' to ' +
"+fileName+".trim('=')\n"
- + " rotate branch @x\n"
- + " compare res1 res0 SMARTS @sm rotate translate 0\n"
- + " var c = {!res0 & connected(res0)}\n"
- + " var N2 = {*.N & c}\n"
- + " var C0 = {*.C & c}\n"
- + " delete res0\n"
- + " if (N2) {\n"
- + " delete *.OXT and res1\n"
- + " connect {N2} {keyatoms & *.C}\n"
- + " }\n"
- + " if (C0) {\n"
- + " connect {C0} {keyatoms & *.N}\n"
- + " }\n"
- + " }\n"
- + " }\n"
- + "}catch(e){print e}\n";
- try {
- if (Logger.debugging)
- Logger.debug(script);
- vwr.eval.runScript(script);
- } catch (ScriptException e) {
- // TODO
- }
- if (vwr.ms.ac == ac)
- return false;
- // check for protein monomer
- g = vwr.ms.at[vwr.ms.ac - 1].group;
- if (g != vwr.ms.at[ac + 1].group || !(g instanceof AminoMonomer)) {
- BS bsAtoms = new BS();
- g.setAtomBits(bsAtoms);
- vwr.deleteAtoms(bsAtoms, false);
- return false;
- }
- AminoMonomer res1 = (AminoMonomer) g;
-
- // must get new group into old chain
-
- Group[] groups = res0.chain.groups;
- for (int i = groups.length; --i >= 0;)
- if (groups[i] == res0) {
- groups[i] = res1;
- break;
- }
- res1.setResno(r);
- res1.chain.groupCount = 0;
- res1.chain = res0.chain;
- BS bsExclude = BSUtil.newBitSet2(0, vwr.ms.mc);
- bsExclude.clear(res1.chain.model.modelIndex);
- res1.chain.model.groupCount = -1;
- res1.chain.model.freeze();
- vwr.ms.recalculatePolymers(bsExclude);
- //} catch (Exception e) {
- // System.out.println("" + e);
- // }
- vwr.setBooleanProperty("appendNew", b);
- vwr.fm.setFileInfo(info);
- return true;
-
- }
-
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -2213,7 +2213,7 @@
return;
String group = e.optParameterAsString(i);
e.checkLast(i);
- if (chk)
+ if (chk || !vwr.ms.am[vwr.ms.mc - 1].isBioModel)
return;
boolean isFile = (tokAt(i) == T.string && !group.startsWith("~"));
String[] list = null;
@@ -2223,14 +2223,14 @@
} else {
group = PT.replaceAllCharacters(group, ",; \t\n", " ").trim()
.toUpperCase();
- if (group.startsWith("~") || group.length() != 3
+ boolean isOneLetter = group.startsWith("~");
+ if (isOneLetter || group.length() != 3
|| !vwr.getJBR().isKnownPDBGroup(group, 20))
- group = vwr.getJBR().toStdAmino3(group);
+ group = vwr.getJBR().toStdAmino3(isOneLetter ? group.substring(1) :
group);
}
list = PT.getTokens(group);
- if (list.length == 0)
- return;
- vwr.getJBR().mutate(bs, group, list);
+ if (list.length > 0)
+ vwr.ms.bioModel.mutate(bs, group, list);
}
private void navigate() throws ScriptException {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -15,7 +15,7 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.01.31"
+Jmol.___JmolVersion="14.3.12_2015.02.04"
new feature: print data({*},"xyz")
-- (lower case) writes only atom data lines
@@ -23,9 +23,15 @@
new feature: print data({*},"XYZ", true)
-- third parameter TRUE writes all trajectories
-bug fix: writing formats was inconsistent
-bug fix: Jmol writing of PDB file data did not include TER records
+bug fix: show mouse fails in JavaScript
+ -- we cannot test using PT.isAI() in org.jmol.viewer.binding.Binding
+ -- because of a Java2Script compiler creates standard array [...]
+ -- from new int[] {....} whereas it should create Clazz.newArray() and fill
it
+bug fix: writing of file formats was inconsistent between WRITE and data()
(not fixed in 14.2)
+bug fix: Jmol writing of PDB file data did not include TER records (not fixed
in 14.2)
bug fix: label %r should print "1" for non-PDB file atoms
+bug fix: 01.30 mutate {xxx} ~... skips first-listed replacement group
identifier
+bug fix: 01.29 breaks loading non-trajectory file after a trajectory is loaded
JmolVersion="14.3.12_2015.01.30b"
Modified: trunk/Jmol/src/org/jmol/viewer/binding/Binding.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/binding/Binding.java 2015-02-03 23:27:55 UTC
(rev 20265)
+++ trunk/Jmol/src/org/jmol/viewer/binding/Binding.java 2015-02-04 12:47:46 UTC
(rev 20266)
@@ -307,7 +307,16 @@
Lst<String>[] names = new Lst[actionInfo.length];
Lst<String[]> user = new Lst<String[]>();
for (Object obj : bindings.values()) {
- if (PT.isAI(obj)) {
+ if (PT.isAS(obj)) {
+ String action = ((String[]) obj)[0];
+ String script = ((String[]) obj)[1];
+ if (qlow == null || qlow.indexOf("user") >= 0 || action.indexOf(qlow)
>= 0 || script.indexOf(qlow) >= 0)
+ user.addLast((String[]) obj);
+ } else {
+
+ // we cannot test using PT.isAI() here because of a Java2Script
compiler error
+ // in relation to new int[] {.....} BH 2015.02.03
+
int[] info = (int[]) obj;
int i = info[1];
if (names[i] == null)
@@ -316,11 +325,6 @@
if (qlow == null
|| (actionNames[i] + ";" + actionInfo[i] + ";" +
name).toLowerCase().indexOf(qlow) >= 0)
names[i].addLast(name);
- } else if (PT.isAS(obj)) {
- String action = ((String[]) obj)[0];
- String script = ((String[]) obj)[1];
- if (qlow == null || qlow.indexOf("user") >= 0 || action.indexOf(qlow)
>= 0 || script.indexOf(qlow) >= 0)
- user.addLast((String[]) obj);
}
}
for (int i = 0; i < actionInfo.length; i++) {
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