Revision: 20957
http://sourceforge.net/p/jmol/code/20957
Author: hansonr
Date: 2016-02-10 02:22:20 +0000 (Wed, 10 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.5.2_2016.02.09"
new feature: invertselected ATOMS {ring atoms to invert}
-- inverts ring stereochemistry
-- requires prior selection of all atoms to be involved in the inversion
bug fix: SMARTS pattern [ALA.*] not working without biological polymer type
indication
bug fix: SMARTS pattern [r500] not working outside of MINIMIZE
Revision Links:
--------------
http://sourceforge.net/p/jmol/code/500
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-06
21:26:19 UTC (rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-10
02:22:20 UTC (rev 20957)
@@ -4078,6 +4078,7 @@
// invertSelected PLANE
// invertSelected HKL
// invertSelected STEREO {sp3Atom} {one or two groups)
+ // invertSelected ATOM {ring atom sets}
P3 pt = null;
P4 plane = null;
BS bs = null;
@@ -4104,6 +4105,14 @@
case T.hkl:
plane = hklParameter(2);
break;
+ case T.atoms:
+ bs = atomExpressionAt(2);
+ if (!chk) {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ vwr.invertRingAt(i, false);
+ }
+ }
+ return;
}
checkLengthErrorPt(iToken + 1, 1);
if (plane == null && pt == null && iAtom == Integer.MIN_VALUE)
Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-02-06
21:26:19 UTC (rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-02-10
02:22:20 UTC (rev 20957)
@@ -206,7 +206,7 @@
boolean aromaticStrict = ((flags & Edge.FLAG_AROMATIC_STRICT) != 0);
boolean aromaticDefined = ((flags & Edge.FLAG_AROMATIC_DEFINED) != 0);
if (aromaticStrict && vRings == null)
- vRings = AU.createArrayOfArrayList(4);
+ vRings = AU.createArrayOfArrayList(4);
if (aromaticDefined && needAromatic) {
// predefined aromatic bonds
bsAromatic = SmilesAromatic.checkAromaticDefined(jmolAtoms, bsSelected);
@@ -235,10 +235,10 @@
SmilesSearch search = SmilesParser.getMolecule(smarts, true);
Lst<Object> vR = (Lst<Object>) subsearch(search, false, true);
if (vRings != null && i <= 5) {
- Lst<BS> v = new Lst<BS>();
- for (int j = vR.size(); --j >= 0; )
+ Lst<BS> v = new Lst<BS>();
+ for (int j = vR.size(); --j >= 0;)
v.addLast((BS) vR.get(j));
- vRings[i-3] = v;
+ vRings[i - 3] = v;
}
if (needAromatic) {
if (!aromaticDefined && (!aromaticStrict || i == 5 || i == 6))
@@ -246,8 +246,18 @@
BS bs = (BS) vR.get(r);
if (aromaticDefined
|| SmilesAromatic.isFlatSp2Ring(jmolAtoms, bsSelected, bs,
- (aromaticStrict ? 0.1f : 0.01f)))
+ (aromaticStrict ? 0.1f : 0.01f))) {
bsAromatic.or(bs);
+ if (!aromaticStrict)
+ switch (i) {
+ case 5:
+ bsAromatic5.or(bs);
+ break;
+ case 6:
+ bsAromatic6.or(bs);
+ break;
+ }
+ }
}
if (aromaticStrict) {
switch (i) {
@@ -260,7 +270,7 @@
bsAromatic);
else
SmilesAromatic.checkAromaticStrict(jmolAtoms, bsAromatic, v5,
vR);
- vRings[3] = new Lst<BS>();
+ vRings[3] = new Lst<BS>();
setAromatic56(v5, bsAromatic5, 5, vRings[3]);
setAromatic56(vR, bsAromatic6, 6, vRings[3]);
break;
@@ -859,11 +869,10 @@
if (patternAtom.residueChar != null || patternAtom.elementNumber ==
-2) {
char atype = a.getBioSmilesType();
char ptype = patternAtom.getBioSmilesType();
- char resChar = (patternAtom.residueChar == null ? '*'
- : patternAtom.residueChar.charAt(0));
boolean ok = true;
boolean isNucleic = false;
switch (ptype) {
+ case '\0':
case '*':
ok = true;
break;
@@ -882,6 +891,8 @@
if (!ok)
break;
String s = a.getGroup1('\0').toUpperCase();
+ char resChar = (patternAtom.residueChar == null ? '*'
+ : patternAtom.residueChar.charAt(0));
boolean isOK = (resChar == s.charAt(0));
switch (resChar) {
case '*':
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-06
21:26:19 UTC (rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10
02:22:20 UTC (rev 20957)
@@ -1823,44 +1823,8 @@
}
return;
case PICKING_INVERT_STEREO:
- if (bnd(clickAction, ACTION_assignNew)) {
- bs = vwr.getAtomBitSet("connected(atomIndex=" + atomIndex
- + ") and !within(SMARTS,'[r50,R]')");
- int nb = bs.cardinality();
- switch (nb) {
- case 0:
- case 1:
- // not enough non-ring atoms
- return;
- case 2:
- break;
- case 3:
- case 4:
- // three or four are not in a ring. So let's find the shortest two
- // branches and invert them.
- int[] lengths = new int[nb];
- int[] points = new int[nb];
- int ni = 0;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
ni++) {
- lengths[ni] = vwr.getBranchBitSet(i, atomIndex, true)
- .cardinality();
- points[ni] = i;
- }
- for (int j = 0; j < nb - 2; j++) {
- int max = Integer.MIN_VALUE;
- int imax = 0;
- for (int i = 0; i < nb; i++)
- if (lengths[i] >= max && bs.get(points[i])) {
- imax = points[i];
- max = lengths[i];
- }
- bs.clear(imax);
- }
- }
- vwr.undoMoveActionClear(atomIndex, AtomCollection.TAINT_COORD, true);
- vwr.invertSelected(null, null, atomIndex, bs);
- vwr.setStatusAtomPicked(atomIndex, "inverted: " + Escape.eBS(bs),
null);
- }
+ if (bnd(clickAction, ACTION_assignNew))
+ vwr.invertRingAt(atomIndex), true);
return;
case PICKING_DELETE_ATOM:
if (bnd(clickAction, ACTION_deleteAtom)) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-02-06 21:26:19 UTC
(rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -60,7 +60,7 @@
"cod",
"http://www.crystallography.net/cod/cif/%c1/%c2%c3/%c4%c5/%FILE.cif";,
"nmr", "http://www.nmrdb.org/new_predictor?POST?molfile=";,
"nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=";,
- "pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";,
// new Jmol 14.5.0 10/28/2015
+ "pdb",
"http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/%c2%c3/pdb%file.ent.gz";,
// new Jmol 14.5.0 10/28/2015 -- not enabled for JavaScript
"pdb0", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
"pdbe", "http://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif";,
"pdbe2", "http://www.ebi.ac.uk/pdbe/static/entry/%FILE_updated.cif";,
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06
21:26:19 UTC (rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-10
02:22:20 UTC (rev 20957)
@@ -7,8 +7,13 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.2_2016.02.06"
+Jmol.___JmolVersion="14.4.2_2016.02.09"
+bug fix: SMARTS pattern [ALA.*] not working without biological polymer type
indication
+bug fix: SMARTS pattern [r500] not working outside of MINIMIZE
+
+JmolVersion="14.4.2_2016.02.06"
+
bug fix: isosurface "==xxxx" not setting default omap cutoff and sigma 3.0
bug fix: small MRC map files mistaken for DELPHI files, which start with the
4-byte integer 20.
bug fix: MRC/CCP4 surface/map files still sometimes inside out.
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-06 21:26:19 UTC
(rev 20956)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -3926,17 +3926,17 @@
return name;
}
} else {
- format = (
- // following is temporary, until issues are resolved for AJAX asych
- isJS && g.loadFormat.equals(g.pdbLoadFormat) ? g.pdbLoadFormat0
- : g.loadFormat);
+ format = (
+ // following is temporary, until issues are resolved for AJAX asych
+ isJS && g.loadFormat.equals(g.pdbLoadFormat) ? g.pdbLoadFormat0
+ : g.loadFormat);
}
//$FALL-THROUGH$
case '#': // ligand
if (format == null)
format = g.pdbLoadLigandFormat;
if (id.indexOf(".") >= 0 && format.equals(g.pdbLoadFormat))
- format = g.pdbLoadFormat0; // older version for =1crn.cif or
=1crn.pdb
+ format = g.pdbLoadFormat0; // older version for =1crn.cif or =1crn.pdb
return g.resolveDataBase(null, id, format);
case '*':
// European Bioinformatics Institute
@@ -7435,6 +7435,46 @@
sm.setStatusAtomMoved(bs);
}
+ public void invertRingAt(int atomIndex, boolean isClick) {
+ // [r50 here just sets the max ring size to 50
+ BS bs = getAtomBitSet("connected(atomIndex=" + atomIndex + ") and
!within(SMARTS,'[r50,R]')");
+ int nb = bs.cardinality();
+ switch (nb) {
+ case 0:
+ case 1:
+ // not enough non-ring atoms
+ return;
+ case 2:
+ break;
+ case 3:
+ case 4:
+ // three or four are not in a ring. So let's find the shortest two
+ // branches and invert them.
+ int[] lengths = new int[nb];
+ int[] points = new int[nb];
+ int ni = 0;
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1), ni++) {
+ lengths[ni] = getBranchBitSet(i, atomIndex, true).cardinality();
+ points[ni] = i;
+ }
+ for (int j = 0; j < nb - 2; j++) {
+ int max = Integer.MIN_VALUE;
+ int imax = 0;
+ for (int i = 0; i < nb; i++)
+ if (lengths[i] >= max && bs.get(points[i])) {
+ imax = points[i];
+ max = lengths[i];
+ }
+ bs.clear(imax);
+ }
+ }
+ if (isClick)
+ undoMoveActionClear(atomIndex, AtomCollection.TAINT_COORD, true);
+ invertSelected(null, null, atomIndex, bs);
+ if (isClick)
+ setStatusAtomPicked(atomIndex, "inverted: " + Escape.eBS(bs), null);
+ }
+
public void invertSelected(P3 pt, P4 plane, int iAtom, BS invAtoms) {
// Eval
BS bs = bsA();
@@ -9363,4 +9403,5 @@
jsonParser = ((JSJSONParser)
Interface.getInterface("javajs.util.JSJSONParser", this, "script"));
return jsonParser.parseMap(ann, true);
}
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-06 21:26:19 UTC
(rev 20956)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -4078,6 +4078,7 @@
// invertSelected PLANE
// invertSelected HKL
// invertSelected STEREO {sp3Atom} {one or two groups)
+ // invertSelected ATOM {ring atom sets}
P3 pt = null;
P4 plane = null;
BS bs = null;
@@ -4104,6 +4105,14 @@
case T.hkl:
plane = hklParameter(2);
break;
+ case T.atoms:
+ bs = atomExpressionAt(2);
+ if (!chk) {
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ vwr.invertRingAt(i, false);
+ }
+ }
+ return;
}
checkLengthErrorPt(iToken + 1, 1);
if (plane == null && pt == null && iAtom == Integer.MIN_VALUE)
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-02-06 21:26:19 UTC
(rev 20956)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -206,7 +206,7 @@
boolean aromaticStrict = ((flags & Edge.FLAG_AROMATIC_STRICT) != 0);
boolean aromaticDefined = ((flags & Edge.FLAG_AROMATIC_DEFINED) != 0);
if (aromaticStrict && vRings == null)
- vRings = AU.createArrayOfArrayList(4);
+ vRings = AU.createArrayOfArrayList(4);
if (aromaticDefined && needAromatic) {
// predefined aromatic bonds
bsAromatic = SmilesAromatic.checkAromaticDefined(jmolAtoms, bsSelected);
@@ -235,10 +235,10 @@
SmilesSearch search = SmilesParser.getMolecule(smarts, true);
Lst<Object> vR = (Lst<Object>) subsearch(search, false, true);
if (vRings != null && i <= 5) {
- Lst<BS> v = new Lst<BS>();
- for (int j = vR.size(); --j >= 0; )
+ Lst<BS> v = new Lst<BS>();
+ for (int j = vR.size(); --j >= 0;)
v.addLast((BS) vR.get(j));
- vRings[i-3] = v;
+ vRings[i - 3] = v;
}
if (needAromatic) {
if (!aromaticDefined && (!aromaticStrict || i == 5 || i == 6))
@@ -246,8 +246,18 @@
BS bs = (BS) vR.get(r);
if (aromaticDefined
|| SmilesAromatic.isFlatSp2Ring(jmolAtoms, bsSelected, bs,
- (aromaticStrict ? 0.1f : 0.01f)))
+ (aromaticStrict ? 0.1f : 0.01f))) {
bsAromatic.or(bs);
+ if (!aromaticStrict)
+ switch (i) {
+ case 5:
+ bsAromatic5.or(bs);
+ break;
+ case 6:
+ bsAromatic6.or(bs);
+ break;
+ }
+ }
}
if (aromaticStrict) {
switch (i) {
@@ -260,7 +270,7 @@
bsAromatic);
else
SmilesAromatic.checkAromaticStrict(jmolAtoms, bsAromatic, v5,
vR);
- vRings[3] = new Lst<BS>();
+ vRings[3] = new Lst<BS>();
setAromatic56(v5, bsAromatic5, 5, vRings[3]);
setAromatic56(vR, bsAromatic6, 6, vRings[3]);
break;
@@ -859,11 +869,10 @@
if (patternAtom.residueChar != null || patternAtom.elementNumber ==
-2) {
char atype = a.getBioSmilesType();
char ptype = patternAtom.getBioSmilesType();
- char resChar = (patternAtom.residueChar == null ? '*'
- : patternAtom.residueChar.charAt(0));
boolean ok = true;
boolean isNucleic = false;
switch (ptype) {
+ case '\0':
case '*':
ok = true;
break;
@@ -882,6 +891,8 @@
if (!ok)
break;
String s = a.getGroup1('\0').toUpperCase();
+ char resChar = (patternAtom.residueChar == null ? '*'
+ : patternAtom.residueChar.charAt(0));
boolean isOK = (resChar == s.charAt(0));
switch (resChar) {
case '*':
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-06 21:26:19 UTC
(rev 20956)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -1823,44 +1823,8 @@
}
return;
case PICKING_INVERT_STEREO:
- if (bnd(clickAction, ACTION_assignNew)) {
- bs = vwr.getAtomBitSet("connected(atomIndex=" + atomIndex
- + ") and !within(SMARTS,'[r50,R]')");
- int nb = bs.cardinality();
- switch (nb) {
- case 0:
- case 1:
- // not enough non-ring atoms
- return;
- case 2:
- break;
- case 3:
- case 4:
- // three or four are not in a ring. So let's find the shortest two
- // branches and invert them.
- int[] lengths = new int[nb];
- int[] points = new int[nb];
- int ni = 0;
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
ni++) {
- lengths[ni] = vwr.getBranchBitSet(i, atomIndex, true)
- .cardinality();
- points[ni] = i;
- }
- for (int j = 0; j < nb - 2; j++) {
- int max = Integer.MIN_VALUE;
- int imax = 0;
- for (int i = 0; i < nb; i++)
- if (lengths[i] >= max && bs.get(points[i])) {
- imax = points[i];
- max = lengths[i];
- }
- bs.clear(imax);
- }
- }
- vwr.undoMoveActionClear(atomIndex, AtomCollection.TAINT_COORD, true);
- vwr.invertSelected(null, null, atomIndex, bs);
- vwr.setStatusAtomPicked(atomIndex, "inverted: " + Escape.eBS(bs),
null);
- }
+ if (bnd(clickAction, ACTION_assignNew))
+ vwr.invertRingAt(atomIndex), true);
return;
case PICKING_DELETE_ATOM:
if (bnd(clickAction, ACTION_deleteAtom)) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-06 21:26:19 UTC
(rev 20956)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-10 02:22:20 UTC
(rev 20957)
@@ -64,8 +64,18 @@
TODO: isosurface molecular has an issue with 2gb1
-Jmol.___JmolVersion="14.5.2_2016.02.06"
+Jmol.___JmolVersion="14.5.2_2016.02.09"
+new feature: invertselected ATOMS {ring atoms to invert}
+ -- inverts ring stereochemistry
+ -- requires prior selection of all atoms to be involved in the inversion
+
+bug fix: SMARTS pattern [ALA.*] not working without biological polymer type
indication
+bug fix: SMARTS pattern [r500] not working outside of MINIMIZE
+
+
+JmolVersion="14.5.2_2016.02.06"
+
new feature: isosurface BACKSHELL
-- displays just the back side of an isosurface
-- works by reversing the normals, then showing front only
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-06 21:26:19 UTC (rev
20956)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-02-10 02:22:20 UTC (rev
20957)
@@ -7435,6 +7435,46 @@
sm.setStatusAtomMoved(bs);
}
+ public void invertRingAt(int atomIndex, boolean isClick) {
+ // [r50 here just sets the max ring size to 50
+ BS bs = getAtomBitSet("connected(atomIndex=" + atomIndex + ") and
!within(SMARTS,'[r50,R]')");
+ int nb = bs.cardinality();
+ switch (nb) {
+ case 0:
+ case 1:
+ // not enough non-ring atoms
+ return;
+ case 2:
+ break;
+ case 3:
+ case 4:
+ // three or four are not in a ring. So let's find the shortest two
+ // branches and invert them.
+ int[] lengths = new int[nb];
+ int[] points = new int[nb];
+ int ni = 0;
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1), ni++) {
+ lengths[ni] = getBranchBitSet(i, atomIndex, true).cardinality();
+ points[ni] = i;
+ }
+ for (int j = 0; j < nb - 2; j++) {
+ int max = Integer.MIN_VALUE;
+ int imax = 0;
+ for (int i = 0; i < nb; i++)
+ if (lengths[i] >= max && bs.get(points[i])) {
+ imax = points[i];
+ max = lengths[i];
+ }
+ bs.clear(imax);
+ }
+ }
+ if (isClick)
+ undoMoveActionClear(atomIndex, AtomCollection.TAINT_COORD, true);
+ invertSelected(null, null, atomIndex, bs);
+ if (isClick)
+ setStatusAtomPicked(atomIndex, "inverted: " + Escape.eBS(bs), null);
+ }
+
public void invertSelected(P3 pt, P4 plane, int iAtom, BS invAtoms) {
// Eval
BS bs = bsA();
@@ -9363,4 +9403,5 @@
jsonParser = ((JSJSONParser)
Interface.getInterface("javajs.util.JSJSONParser", this, "script"));
return jsonParser.parseMap(ann, true);
}
+
}
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