Revision: 21636
http://sourceforge.net/p/jmol/code/21636
Author: hansonr
Date: 2017-06-17 12:04:50 +0000 (Sat, 17 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.19.1"
new feature: WRITE "SDF" implements atom value V nnn ... information
-- requires assigning the data property name "atom_values" in the model's
molData property
-- for example:
$ load $2,3-dichlorobutane
$ molData = {"atom_values":"chirality"}
$ model properties "molData" molData
$ write diol.sdf
-- note that if the model already has a molData property, then use the
following to append to it:
$ molData = (_M.molData ? _M.molData : {})
$ molData.atom_values = "chirality"
$ model properties "molData" molData
new feature: x = load("filename","JSON")
-- loads JSON data into variable
bug fix: CIP gives wrong alkene root distance for cyclopropene
bug fix: WRITE of structure file does not report number of atoms and warn if
selected is different from this molecule
bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates
bug fix: MOL/SDF files should truncate lines at 80 characters.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-06-14 18:41:46 UTC (rev 21635)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-06-17 12:04:50 UTC (rev 21636)
@@ -83,6 +83,8 @@
protected boolean allow2D = true;
private int iatom0;
private V3000Rdr vr;
+ private int atomCount;
+ private String[] atomData;
@Override
public void initializeReader() throws Exception {
@@ -100,8 +102,9 @@
continuing = false;
return false;
}
- } else if (line.equals("M END"))
+ } else if (line.equals("M END")) {
return true;
+ }
if (doGetModel(++modelNumber, null)) {
iatom0 = asc.ac;
processMolSdHeader();
@@ -200,6 +203,7 @@
// xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
private void readAtomsAndBonds(int ac, int bc) throws Exception {
+ atomCount = ac;
for (int i = 0; i < ac; ++i) {
rd();
int len = line.length();
@@ -247,10 +251,16 @@
addMolAtom(iAtom, isotope, elementSymbol, charge, x, y, z);
}
+ rd();
+ if (line.startsWith("V ")) {
+ readAtomValues();
+ }
+
// read bonds
for (int i = 0; i < bc; ++i) {
- rd();
+ if (i > 0)
+ rd();
String iAtom1, iAtom2;
int stereo = 0;
iAtom1 = line.substring(0, 3).trim();
@@ -268,7 +278,7 @@
// read V2000 user data
- Map<String, String> molData = new Hashtable<String, String>();
+ Map<String, Object> molData = new Hashtable<String, Object>();
rd();
while (line != null && line.indexOf("$$$$") != 0) {
if (line.indexOf(">") == 0) {
@@ -281,10 +291,40 @@
}
rd();
}
+ if (atomData != null) {
+ Object atomValueName = molData.get("atom_value_name");
+ molData.put(atomValueName == null ? "atom_values" :
atomValueName.toString(), atomData);
+ }
if (!molData.isEmpty())
asc.setModelInfoForSet("molData", molData, asc.iSet);
}
+ /**
+ * Read all V nnn lines as string data; user can adapt as needed.
+ *
+ * @throws Exception
+ */
+ private void readAtomValues() throws Exception {
+ atomData = new String[atomCount];
+ for (int i = atomData.length; --i >= 0;)
+ atomData[i] = "";
+ while (line.indexOf("V ") == 0) {
+ int iAtom = parseIntAt(line, 3);
+ if (iAtom < 1 || iAtom > atomCount) {
+ Logger.error("V nnn does not evalute to a valid atom number: " +
iAtom);
+ return;
+ }
+ String s = line.substring(6).trim();
+ atomData[iAtom - 1] = s;
+ rd();
+ }
+ }
+
+ /**
+ * Read all M ISO lines. These are absolute isotope numbers.
+ *
+ * @throws Exception
+ */
private void readIsotopes() throws Exception {
int n = parseIntAt(line, 6);
try {
@@ -308,7 +348,7 @@
* @param molData
* @throws Exception
*/
- private void readMolData(Map<String, String> molData) throws Exception {
+ private void readMolData(Map<String, Object> molData) throws Exception {
Atom[] atoms = asc.atoms;
// "> <xxx>" becomes "xxx"
// "> yyy <xxx> zzz" becomes "yyy <xxx> zzz"
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-06-14 18:41:46 UTC (rev
21635)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-06-17 12:04:50 UTC (rev
21636)
@@ -497,7 +497,8 @@
int getTargetValence() {
switch (getElementNumber()) {
case 6: //C
- case 14: //Si
+ case 14: //Si
+ case 32: // Ge
return 4;
case 5: // B
case 7: // N
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -3967,7 +3967,11 @@
} else if (data == "CIF" || data == "SDF" || data == "MOL" || data ==
"MOL67" || data == "V2000"
|| data == "V3000" || data == "CD" || data == "JSON" || data == "XYZ"
|| data == "XYZRN" || data == "XYZVIB" || data == "CML") {
- data = vwr.getModelExtract("selected", isCoord, false, data);
+ BS selected = vwr.bsA(), bsModel;
+ msg = " (" + selected.cardinality() + " atoms)";
+ if (vwr.am.cmi >= 0 && !selected.equals(bsModel =
vwr.getModelUndeletedAtomsBitSet(vwr.am.cmi)))
+ msg += "\nNote! Selected atom set " + selected + " is not the same
as the current model " + bsModel;
+ data = vwr.getModelExtract(selected, isCoord, false, data);
if (data.startsWith("ERROR:"))
bytes = data;
} else if (data == "CFI") {
@@ -4113,14 +4117,14 @@
params.put("width", Integer.valueOf(width));
params.put("height", Integer.valueOf(height));
params.put("nVibes", Integer.valueOf(nVibes));
- msg = vwr.processWriteOrCapture(params);
- if (msg == null)
- msg = "canceled";
- if (isImage && msg.startsWith("OK"))
- msg += "; width=" + width + "; height=" + height;
+ String ret = vwr.processWriteOrCapture(params);
+ if (ret == null)
+ ret = "canceled";
+ if (isImage && ret.startsWith("OK"))
+ ret += "; width=" + width + "; height=" + height;
if (timeMsg)
showString(Logger.getTimerMsg("write", 0));
- return writeMsg(msg);
+ return writeMsg(ret + (msg == null ? "" : msg));
}
public Lst<Object> prepareBinaryOutput(SV tvar) {
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -2114,26 +2114,17 @@
// file("myfile.xyz")
// load("myfile.png",true)
// load("myfile.txt",1000)
- // load("myfil.xyz",0,true)
+ // load("myfile.xyz",0,true)
+ // load("myfile.json","JSON")
+ // load("myfile.json","JSON", true)
- String file;
- int nBytesMax = -1;
- boolean asBytes = false;
- boolean async = vwr.async;
- switch (args.length) {
- case 3:
- async = SV.bValue(args[2]);
- //$FALL-THROUGH$
- case 2:
- nBytesMax = (args[1].tok == T.integer ? args[1].asInt() : -1);
- asBytes = args[1].tok == T.on;
- //$FALL-THROUGH$
- case 1:
- file = FileManager.fixDOSName(SV.sValue(args[0]));
- break;
- default:
+ if (args.length < 1 || args.length > 3)
return false;
- }
+ String file = FileManager.fixDOSName(SV.sValue(args[0]));
+ boolean asBytes = (args.length > 1 && args[1].tok == T.on);
+ boolean async = (vwr.async || args.length > 2 && args[args.length - 1].tok
== T.on);
+ int nBytesMax = (args.length > 1 && args[1].tok == T.integer ?
args[1].asInt() : -1);
+ boolean asJSON = (args.length > 1 &&
args[1].asString().equalsIgnoreCase("JSON"));
if (asBytes)
return mp.addXMap(vwr.fm.getFileAsMap(file));
boolean isQues = file.startsWith("?");
@@ -2148,8 +2139,9 @@
// The evaluation will be repeated up to this point, so for example,
// x = (i++) + load("?") would increment i twice.
}
- return mp.addXStr(isFile ? vwr.fm.getFilePath(file, false, false) : vwr
- .getFileAsString4(file, nBytesMax, false, false, true, "script"));
+ String str = isFile ? vwr.fm.getFilePath(file, false, false) : vwr
+ .getFileAsString4(file, nBytesMax, false, false, true, "script");
+ return (asJSON ? mp.addXObj(vwr.parseJSON(str)) : mp.addXStr(str));
}
private boolean evaluateMath(ScriptMathProcessor mp, SV[] args, int tok) {
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -467,7 +467,9 @@
SimpleNode atomA = atom12[j];
Edge[] bb = ((Node) atomA).getEdges();
for (int b = 0; b < bb.length; b++) {
- if (bb[b].getCovalentOrder() != 1 ||
bb[b].getOtherNode(atomA).getElementNumber() == 1)
+ SimpleNode other;
+ if (bb[b].getCovalentOrder() != 1 || (other =
bb[b].getOtherNode(atomA)).getElementNumber() == 1
+ && other.getIsotopeNumber() == 1)
continue;
edges[j][edgeCount++] = bb[b];
if (getBondStereochemistry(bb[b], atomA) != '\0') {
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -108,6 +108,8 @@
*
* code history:
*
+ * 6/12/2017 Jmo 14.18.2 tested for Rule 1b sphere (AY236.53, 163, 173, 192);
957 lines
+ *
* 6/8/2017 Jmol 14.18.2 removed unnecessary presort for Rule 1b
*
* 5/27/17 Jmol 14.17.2 fully interfaced using SimpleNode and SimpleEdge
@@ -320,6 +322,14 @@
// }
//
// Of course, the actual code is a bit more complex than that.
+ //
+ // approximate line count calculated using MSDOS batch script:
+ //
+ // type CIPChirality.java | find /V "}"|find /V "//" |find /V "import" |
find /V "*" |find ";"|find /V "Logger"|find /V "System.out" > t
+ // type CIPChirality.java | find /V "}"|find /V "//" |find /V "import" |
find /V "*" |find "if"|find /V "Logger"|find /V "System.out" >> t
+ // type CIPChirality.java | find "COUNT_LINE" >> t
+ // type t |find " " /C
+
static final int NO_CHIRALITY = 0;
static final int TIED = NO_CHIRALITY;
@@ -427,6 +437,7 @@
// for reflection
//System.out.println("TESTING ALLOWRULE1B");
//allowRule1bAlkenes = false;
+ System.out.println("TESTING SPHERE+1");
}
/**
@@ -470,7 +481,7 @@
BS bs = BSUtil.copy(bsAtoms);
lstSmallRings = new Lst<BS>();
- while (!bs.isEmpty())
+ while (!bs.isEmpty()) // COUNT_LINE
getSmallRings(atoms[bs.nextSetBit(0)], bs);
bsKekuleAmbiguous = getKekule(atoms);
bsAzacyclic = getAzacyclic(atoms, bsAtoms);
@@ -918,7 +929,7 @@
if (nSP2 != null)
nSP2[0] = 2;
int ppt = 0;
- while (true) {
+ while (true) { // COUNT_LINE
if (atom2.getCovalentBondCount() != 2)
return atom2;
SimpleEdge[] edges = atom2.getEdges();
@@ -968,7 +979,7 @@
boolean isChiral = false, isAlkene = false;
try {
if (cipAtom == null) {
- cipAtom = new CIPAtom().create(atom, null, false, isAlkene, false);
+ cipAtom = new CIPAtom().create(atom, null, isAlkene, false, false);
int nSubs = atom.getCovalentBondCount(), elemNo =
atom.getElementNumber();
isAlkene = (nSubs == 3 && elemNo <= 10 &&
!cipAtom.isTrigonalPyramidal); // (IUPAC 2013.P-93.2.4)
if (nSubs != (parent == null ? 4 : 3)
@@ -1014,7 +1025,7 @@
}
if (Logger.debugging)
Logger.info(atom + " " + JC.getCIPChiralityName(rs) + " by Rule "
- + getRuleName() + "\n----------------------------------");
+ + getRuleName() + "\n----------------------------------");
// Logger
break;
}
}
@@ -1071,10 +1082,10 @@
*/
private int setBondChirality(SimpleNode a, SimpleNode pa, SimpleNode pb,
SimpleNode b,
boolean isAxial, int ruleMax) {
- CIPAtom a1 = new CIPAtom().create(a, null, false, true, false);
+ CIPAtom a1 = new CIPAtom().create(a, null, true, false, false);
int atop = getAlkeneEndTopPriority(a1, pa, isAxial, ruleMax);
int ruleA = currentRule;
- CIPAtom b2 = new CIPAtom().create(b, null, false, true, false);
+ CIPAtom b2 = new CIPAtom().create(b, null, true, false, false);
int btop = getAlkeneEndTopPriority(b2, pb, isAxial, ruleMax);
int ruleB = currentRule;
int c = (atop >= 0 && btop >= 0 ? getEneChirality(b2.atoms[btop], b2, a1,
@@ -1127,7 +1138,7 @@
int ruleMax) {
a.canBePseudo = a.isAxialRoot = isAxial;
return getAtomChiralityLimited(a.atom, a,
- new CIPAtom().create(pa, null, false, true, false), ruleMax) - 1;
+ new CIPAtom().create(pa, null, true, false, false), ruleMax) - 1;
}
/**
@@ -1427,13 +1438,13 @@
* @param atom
* or null to indicate a null placeholder
* @param parent
+ * @param isAlkene
* @param isDuplicate
- * @param isAlkene
* @param isParentBond TODO
* @return this
*/
- CIPAtom create(SimpleNode atom, CIPAtom parent, boolean isDuplicate,
- boolean isAlkene, boolean isParentBond) {
+ CIPAtom create(SimpleNode atom, CIPAtom parent, boolean isAlkene,
+ boolean isDuplicate, boolean isParentBond) {
this.id = ++ptID;
this.parent = parent;
if (atom == null)
@@ -1532,7 +1543,7 @@
BS bsRing = BSUtil.newAndSetBit(atomIndex);
CIPAtom p = this;
int index = -1;
- while ((p = p.parent) != null && index != atomIndex)
+ while ((p = p.parent) != null && index != atomIndex) // COUNT_LINE
bsRing.set(index = p.atomIndex);
if (bsRing.cardinality() <= SMALL_RING_MAX) {
for (int i = lstSmallRings.size(); --i >= 0;)
@@ -1549,12 +1560,9 @@
*
*/
boolean setNode() {
- if (isSet)
+ // notice we are setting isSet TRUE here, not just testing it.
+ if (isSet || (isSet = true) && isDuplicate)
return true;
- isSet = true;
- if (isDuplicate)
- return true;
-
SimpleEdge[] bonds = atom.getEdges();
int nBonds = bonds.length;
if (Logger.debuggingHigh)
@@ -1576,34 +1584,25 @@
setEne();
}
}
- if (nBonds == 1 && order == 1 && isParentBond) {
- isTerminal = true;
- return true;
- }
+ if (nBonds == 1 && order == 1 && isParentBond)
+ return isTerminal = true;
// from here on, isTerminal indicates an error condition
switch (order) {
case 3:
- if (addAtom(pt++, other, isParentBond, false, isParentBond) == null)
{
- isTerminal = true;
- return false;
- }
+ if (addAtom(pt++, other, isParentBond, false, isParentBond) == null)
+ return !(isTerminal = true);
//$FALL-THROUGH$
case 2:
- if (addAtom(pt++, other, order != 2 || isParentBond, order == 2,
isParentBond) == null) {
- isTerminal = true;
- return false;
- }
+ if (addAtom(pt++, other, order != 2 || isParentBond, order == 2,
isParentBond) == null)
+ return !(isTerminal = true);
//$FALL-THROUGH$
case 1:
- if (!isParentBond
- && addAtom(pt++, other, order != 1 && elemNo <= 10, false,
false) == null) {
- isTerminal = true;
- return false;
- }
- break;
+ if (isParentBond
+ || addAtom(pt++, other, order != 1 && elemNo <= 10, false,
false) != null)
+ break;
+ //$FALL-THROUGH$
default:
- isTerminal = true;
- return false;
+ return !(isTerminal = true);
}
}
// don't think this can happen
@@ -1610,7 +1609,7 @@
isTerminal = (pt == 0);
nAtoms = pt;
for (; pt < atoms.length; pt++)
- atoms[pt] = new CIPAtom().create(null, this, true, false, false);
+ atoms[pt] = new CIPAtom().create(null, this, false, true, false);
// Do an initial very shallow atom-only Rule 1 sort using a.compareTo(b)
@@ -1644,6 +1643,7 @@
* @param other
* @param isDuplicate
* @param isAlkene
+ * @param isParentBond
* @return new atom or null
*/
CIPAtom addAtom(int i, SimpleNode other, boolean isDuplicate, boolean
isAlkene, boolean isParentBond) {
@@ -1654,8 +1654,7 @@
}
if (parent == null) {
// For top level, we do not allow two 1H atoms.
- int atomIsotope = other.getIsotopeNumber();
- if (atomIsotope == 1) {
+ if (other.getIsotopeNumber() == 1) {
if (++h1Count > 1) {
if (Logger.debuggingHigh)
Logger.info(" second H atom found on " + atom);
@@ -1664,7 +1663,7 @@
}
}
return atoms[i] = new CIPAtom()
- .create(other, this, isDuplicate, isAlkene, isParentBond);
+ .create(other, this, isAlkene, isDuplicate, isParentBond);
}
/**
@@ -1679,8 +1678,7 @@
*/
boolean sortSubstituents(int sphere) {
- int[] indices = new int[4];
- int[] prevPrior = new int[4];
+ int[] indices = new int[4], prevPrior = new int[4];
ties = null;
int nTies = 0;
for (int i = 0; i < 4; i++) {
@@ -1703,8 +1701,7 @@
CIPAtom a = atoms[i];
for (int j = i + 1; j < 4; j++) {
CIPAtom b = atoms[j];
- boolean logger_debugHigh = Logger.debuggingHigh && b.isHeavy()
- && a.isHeavy();
+ boolean logger_debugHigh = Logger.debuggingHigh && b.isHeavy() &&
a.isHeavy();
int score = (a.atom == null ? B_WINS : b.atom == null ? A_WINS
: prevPrior[i] == prevPrior[j] ? TIED
: prevPrior[j] < prevPrior[i] ? B_WINS : A_WINS);
@@ -1854,25 +1851,22 @@
* @return [0 (TIED), -1 (A_WINS), or 1 (B_WINS)] * sphere where broken
*/
private int breakTie(CIPAtom b, int sphere) {
- if (atomIndex == 1 && b.atomIndex == 3)
- if (Logger.debugging && isHeavy() && b.isHeavy())
+ if (Logger.debugging && isHeavy() && b.isHeavy())
Logger.info(dots() + "tie for " + this + " and " + b + " at sphere "
+ sphere);
- // Two duplicates of the same atom are always tied.
- if (isDuplicate && b.isDuplicate && atom == b.atom
- && rootDistance == b.rootDistance)
+ // Two duplicates of the same atom are always tied, if they have the
same root distance.
+ if (isDuplicate && b.isDuplicate && atom == b.atom && rootDistance ==
b.rootDistance)
return TIED;
// Do a duplicate check -- if that is not a TIE we do not have to go any
further.
// NOTE THAT THIS IS NOT EXPLICIT IN THE RULES
// BECAUSE DUPLICATES LOSE IN THE NEXT SPHERE, NOT THIS.
-
- // THE NEED FOR (sphere+1) HERE SHOWS THAT
+ // THE NEED FOR (sphere+1) in AY236.53, 163, 173, 192 SHOWS THAT
// SUBRULE 1a MUST BE COMPLETED EXHAUSTIVELY PRIOR TO SUBRULE 1b.
int score = checkIsDuplicate(b);
if (score != TIED)
- return score * (sphere + 1);
+ return score * (sphere + 1); // COUNT_LINE
// return NO_CHIRALITY/TIED if:
// a) one or the other can't be set (because it has too many
connections)
@@ -1885,26 +1879,8 @@
// We are done -- again, for the next sphere, actually -- if one of these
// is terminal.
if (isTerminal != b.isTerminal)
- return (isTerminal ? B_WINS : A_WINS) * (sphere + 1);
+ return (isTerminal ? B_WINS : A_WINS) * (sphere + 1); // COUNT_LINE
- // Rule 1b requires a special presort to ensure that all duplicate atoms
- // are in the right order -- first by element number and then by root
distance.
- // Otherwise we are liable to have an a-b alignment such as the following
- // when we have SMARTS C1...C=C1
- //
- // a b
- // C C
- // (C-alk) (C-ring)
- // (C-ring) (C-alk)
- // H H
- //
- // see bh64.65
-
- if (currentRule == RULE_1b) {
- preSortRule1b();
- b.preSortRule1b();
- }
-
// Phase I -- shallow check only
//
// Check to see if any of the three connections to a and b are different.
@@ -1931,30 +1907,6 @@
}
/**
- * Sort duplicate nodes of the same element by root distance, from closest
- * to root to furthest.
- *
- */
- private void preSortRule1b() {
- CIPAtom a1, a2;
- for (int i = 0; i < 3; i++) {
- if (!(a1 = atoms[i]).isDuplicate)
- continue;
- if (Logger.debuggingHigh)
- Logger.info("presort1b: " + i + " " + a1.myPath);
- for (int j = i + 1; j < 4; j++) {
- if (!(a2 = atoms[j]).isDuplicate || a1.elemNo != a2.elemNo
- || a1.rootDistance <= a2.rootDistance)
- continue;
- atoms[i] = a2;
- atoms[j] = a1;
- j = 4;
- i = -1;
- }
- }
- }
-
- /**
* Just checking for hydrogen.
*
* @return true if not hydrogen.
@@ -1985,7 +1937,7 @@
if (Logger.debugging && ai.isHeavy() && bi.isHeavy())
Logger.info(ai.dots() + "compareShallow " + i + " " + this + "."
+ ai + "/" + b + "." + bi + ": " + score * (sphere + 1)); //
Logger
- return score * (sphere + 1);
+ return score * (sphere + 1); // COUNT_LINE
}
}
return TIED;
@@ -2036,7 +1988,8 @@
return (b == null ? A_WINS
: (atom == null) != (b.atom == null) ? (atom == null ? B_WINS
: A_WINS) : (score = checkRule1a(b)) != TIED ? score
- : checkIsDuplicate(b));
+ : (score = checkIsDuplicate(b)) != TIED ? score :
+ !isDuplicate ? TIED : checkRule1b(b));
}
/**
@@ -2064,8 +2017,7 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
private int checkIsDuplicate(CIPAtom b) {
- return b.isDuplicate == isDuplicate ? TIED : b.isDuplicate ? A_WINS
- : B_WINS;
+ return b.isDuplicate == isDuplicate ? TIED : b.isDuplicate ? A_WINS :
B_WINS;
}
/**
@@ -2246,7 +2198,7 @@
Lst<CIPAtom> path = new Lst<CIPAtom>();
CIPAtom thisAtom = this, newSub, oldParent = fromAtom, oldSub =
newParent;
// create path back to root
- while (oldParent.parent != null && oldParent.parent.atoms[0] != null) {
+ while (oldParent.parent != null && oldParent.parent.atoms[0] != null) {
// COUNT_LINE
if (Logger.debuggingHigh)
Logger.info("path:" + oldParent.parent + "->" + oldParent);
path.addLast(oldParent = oldParent.parent);
@@ -2254,8 +2206,8 @@
path.addLast(null);
for (int i = 0, n = path.size(); i < n; i++) {
oldParent = path.get(i);
- newSub = (oldParent == null ? new CIPAtom().create(null, this, true,
- isAlkene, false) : (CIPAtom) oldParent.clone());
+ newSub = (oldParent == null ? new CIPAtom().create(null, this,
isAlkene,
+ true, false) : (CIPAtom) oldParent.clone());
newSub.sphere = thisAtom.sphere + 1;
thisAtom.replaceParentSubstituent(oldSub, newParent, newSub);
if (i > 0 && thisAtom.isAlkene && !thisAtom.isAlkeneAtom2) {
@@ -2532,7 +2484,7 @@
for (int c = 1; c < n; c++) {
boolean alike = (aref == aStr.charAt(c));
if (alike != (bref == bStr.charAt(c)))
- return (isRSTest ? c : 1) * (alike ? A_WINS : B_WINS);
+ return (isRSTest ? c : 1) * (alike ? A_WINS : B_WINS); // COUNT_LINE
}
if (isRSTest)
return TIED;
@@ -2563,8 +2515,7 @@
for (int i = 0; i < n; i++)
sorted[i] = PT.rep(sorted[i], "A", aref);
if (Logger.debuggingHigh)
- for (int i = 0; i < n; i++)
- // Logger
+ for (int i = 0; i < n; i++) // Logger
Logger.info("Sorted Mata list " + i + " " + aref + ": " + sorted[i]);
return sorted;
}
@@ -2826,10 +2777,9 @@
* @param rs
*/
private void addMataRef(int sphere, int priority, int rs) {
- if (rule4Count == null) {
+ if (rule4Count == null)
rule4Count = new int[] { Integer.MAX_VALUE, 0, 0 };
- }
- int n = sphere * 10 + priority;
+ int n = sphere * 10 + priority; // COUNT_LINE
if (n <= rule4Count[0]) {
if (n < rule4Count[0]) {
rule4Count[0] = n;
@@ -2859,7 +2809,7 @@
return NOT_RELEVANT;
int n = rs1.length();
if (n != rs2.length())
- return NOT_RELEVANT; // TODO: ?? this may not be true -- paths with
and without O, N, C for example, that still have stereochemistry
+ return NOT_RELEVANT;
if (rs1.equals(rs2))
return TIED;
boolean haveRS = (rs1.indexOf("R") >= 0 || rs1.indexOf("S") >= 0);
@@ -2903,9 +2853,8 @@
int score = i1 + rs.indexOf(rs2.charAt(i));
if (score == 0)
continue;
- if (score != STEREO_BOTH_RS) {
+ if (score != STEREO_BOTH_RS)
return DIASTEREOMERIC;
- }
if (finalScore == TIED)
finalScore = (i1 == STEREO_R ? A_WINS : B_WINS);
}
@@ -2939,7 +2888,7 @@
atom1.atoms[bondCount - 1] = atoms[Math.max(ia, ib)];
int rs = atom1.checkHandedness();
if (Logger.debugging) {
- for (int i = 0; i < 4; i++)
+ for (int i = 0; i < 4; i++) // Logger
Logger.info("pseudo " + rs + " " + priorities[i] + " " +
atoms[i].myPath);
}
return rs;
@@ -3018,19 +2967,11 @@
a.htPathPoints = htPathPoints;
a.doCheckPseudo = false;
a.alkeneParent = null;
- //a.rule4Count = null;
- //a.rule4List = null;
- for (int i = 0; i < 4; i++) {
- // a.priorities[i] = priorities[i];
- if (atoms[i] != null) {
+ for (int i = 0; i < 4; i++)
+ if (atoms[i] != null)
a.atoms[i] = atoms[i];
- }
- }
a.ties = null;
-// if (Logger.debugging)
-// Logger.info("cloning " + this + " as " + a);
return a;
-
}
@Override
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -56,9 +56,31 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.18.2"
+Jmol.___JmolVersion="14.19.1"
+new feature: WRITE "SDF" implements atom value V nnn ... information
+ -- requires assigning the data property name "atom_values" in the model's
molData property
+ -- for example:
+
+ $ load $2,3-dichlorobutane
+ $ molData = {"atom_values":"chirality"}
+ $ model properties "molData" molData
+ $ write diol.sdf
+
+ -- note that if the model already has a molData property, then use the
following to append to it:
+
+ $ molData = (_M.molData ? _M.molData : {})
+ $ molData.atom_values = "chirality"
+ $ model properties "molData" molData
+
+
+
+new feature: x = load("filename","JSON")
+ -- loads JSON data into variable
bug fix: CIP gives wrong alkene root distance for cyclopropene
+bug fix: WRITE of structure file does not report number of atoms and warn if
selected is different from this molecule
+bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates
+bug fix: MOL/SDF files should truncate lines at 80 characters.
JmolVersion="14.18.1" // 2017.06.06
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-06-14 18:41:46 UTC
(rev 21635)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-06-17 12:04:50 UTC
(rev 21636)
@@ -23,8 +23,16 @@
*/
package org.jmol.viewer;
+import java.util.Arrays;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Properties;
+
import javajs.J2SIgnoreImport;
-
import javajs.util.AU;
import javajs.util.BArray;
import javajs.util.Base64;
@@ -39,15 +47,6 @@
import javajs.util.V3;
import javajs.util.XmlUtil;
-import java.util.Arrays;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Properties;
-
import org.jmol.api.Interface;
import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolPropertyManager;
@@ -58,18 +57,18 @@
import org.jmol.modelset.BondSet;
import org.jmol.modelset.Chain;
import org.jmol.modelset.Group;
-import org.jmol.modelsetbio.BioModel;
import org.jmol.modelset.LabelToken;
import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
+import org.jmol.modelsetbio.BioModel;
import org.jmol.script.SV;
import org.jmol.script.T;
import org.jmol.shape.Shape;
import org.jmol.util.BSUtil;
import org.jmol.util.C;
+import org.jmol.util.Edge;
import org.jmol.util.Elements;
import org.jmol.util.Escape;
-import org.jmol.util.Edge;
import org.jmol.util.JmolMolecule;
import org.jmol.util.Logger;
import org.jmol.viewer.binding.Binding;
@@ -1148,10 +1147,8 @@
return getModelCif(bs);
if (type.equalsIgnoreCase("CML"))
return getModelCml(bs, Integer.MAX_VALUE, true, doTransform,
allTrajectories);
-
if (type.equals("PDB") || type.equals("PQR"))
return getPdbAtomData(bs, null, type.equals("PQR"), doTransform,
allTrajectories);
-
boolean asV3000 = type.equalsIgnoreCase("V3000");
boolean asSDF = type.equalsIgnoreCase("SDF");
boolean noAromatic = type.equalsIgnoreCase("MOL");
@@ -1165,7 +1162,10 @@
BS bsModels = vwr.ms.getModelBS(bsAtoms, true);
if (!isXYZ && !asJSON) {
String title = vwr.ms.getFrameTitle(bsModels.nextSetBit(0));
- mol.append(title != null ? title.replace('\n',' ') : isModelKit ? "Jmol
Model Kit" : FileManager.fixDOSName(vwr.fm.getFullPathName(false)));
+ title = (title != null ? title.replace('\n',' ') : isModelKit ? "Jmol
Model Kit" : FileManager.fixDOSName(vwr.fm.getFullPathName(false)));
+ if (title.length() > 80)
+ title = title.substring(0, 77) + "...";
+ mol.append(title);
String version = Viewer.getJmolVersion();
mol.append("\n__Jmol-").append(version.substring(0, 2));
int cMM, cDD, cYYYY, cHH, cmm;
@@ -1308,12 +1308,16 @@
}
private boolean addMolFile(int iModel, SB mol, BS bsAtoms, BS bsBonds,
- boolean asV3000, boolean asJSON, boolean
noAromatic, Quat q) {
+ boolean asV3000, boolean asJSON,
+ boolean noAromatic, Quat q) {
int nAtoms = bsAtoms.cardinality();
int nBonds = bsBonds.cardinality();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999))
return false;
boolean asSDF = (iModel >= 0);
+ @SuppressWarnings("unchecked")
+ Map<String, Object> molData = (asSDF ? (Map<String, Object>) vwr.ms
+ .getInfo(iModel, "molData") : null);
ModelSet ms = vwr.ms;
int[] atomMap = new int[ms.ac];
P3 pTemp = new P3();
@@ -1320,7 +1324,8 @@
if (asV3000) {
mol.append(" 0 0 0 0 0 0 999 V3000");
} else if (asJSON) {
- mol.append("{\"mol\":{\"createdBy\":\"Jmol "+ Viewer.getJmolVersion() +
"\",\"a\":[");
+ mol.append("{\"mol\":{\"createdBy\":\"Jmol " + Viewer.getJmolVersion()
+ + "\",\"a\":[");
} else {
PT.rightJustify(mol, " ", "" + nAtoms);
PT.rightJustify(mol, " ", "" + nBonds);
@@ -1330,22 +1335,26 @@
mol.append("\n");
if (asV3000) {
mol.append("M V30 BEGIN CTAB\nM V30 COUNTS ").appendI(nAtoms)
- .append(" ").appendI(nBonds).append(" 0 0 0\n").append(
- "M V30 BEGIN ATOM\n");
+ .append(" ").appendI(nBonds).append(" 0 0 0\n")
+ .append("M V30 BEGIN ATOM\n");
}
+ Object o = (molData == null ? null : molData.get("atom_value_name"));
+ if (o instanceof SV)
+ o = ((SV) o).asString();
+ int valueType = (o == null ? T.nada : T.getTokFromName("" + o));
+ SB atomValues = (valueType == T.nada ? null : new SB());
for (int i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms
.nextSetBit(i + 1))
- getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp,
asV3000,
- asJSON);
+ getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp,
+ asV3000, asJSON, atomValues, valueType);
if (asV3000) {
mol.append("M V30 END ATOM\nM V30 BEGIN BOND\n");
} else if (asJSON) {
mol.append("],\"b\":[");
- }
+ }
for (int i = bsBonds.nextSetBit(0), n = 0; i >= 0; i = bsBonds
.nextSetBit(i + 1))
getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON,
noAromatic);
- // 21 21 0 0 0
if (asV3000) {
mol.append("M V30 END BOND\nM V30 END CTAB\n");
}
@@ -1352,29 +1361,31 @@
if (asJSON)
mol.append("]}}");
else {
+ if (atomValues != null && atomValues.length() > 0)
+ mol.append(atomValues.toString());
mol.append("M END\n");
}
if (asSDF) {
try {
- @SuppressWarnings("unchecked")
- Map<String, Object> molData = (Map<String, Object>)
vwr.ms.getInfo(iModel, "molData");
- float[] pc = ms.getPartialCharges();
- if (pc != null) {
- if (molData == null)
- molData = new Hashtable<String, Object>();
- SB sb = new SB();
- sb.appendI(nAtoms).appendC('\n');
- for (int i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms
- .nextSetBit(i + 1))
- sb.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');
- molData.put("jmol_partial_charges", sb.toString());
- }
- for (String key: molData.keySet()) {
- Object o = molData.get(key);
- if (o instanceof SV)
- o = ((SV)o).asString();
- mol.append("> <" + key.toUpperCase() +
">\n").append(PT.trim(o.toString(), "\n")).append("\n\n");
- }
+ float[] pc = ms.getPartialCharges();
+ if (pc != null) {
+ if (molData == null)
+ molData = new Hashtable<String, Object>();
+ SB sb = new SB();
+ sb.appendI(nAtoms).appendC('\n');
+ for (int i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms
+ .nextSetBit(i + 1))
+ sb.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');
+ molData.put("jmol_partial_charges", sb.toString());
+ }
+ for (String key : molData.keySet()) {
+ o = molData.get(key);
+ if (o instanceof SV)
+ o = ((SV) o).asString();
+ mol.append("> <" + key.toUpperCase() + ">\n");
+ output80CharWrap(mol, o.toString(), 80);
+ mol.append("\n\n");
+ }
} catch (Throwable e) {
// ignore
}
@@ -1383,6 +1394,33 @@
return true;
}
+ /**
+ *
+ * @param mol
+ * @param data
+ * @param maxN 80 for multi-line wrap; something smaller for single line
output
+ */
+ private void output80CharWrap(SB mol, String data, int maxN) {
+ if (maxN < 80)
+ data = PT.rep(data, "\n", "|");
+ String[] lines = PT.split(PT.trim(PT.rep(data, "\n\n", "\n"), "\n"), "\n");
+ for (int i = 0; i < lines.length; i++)
+ outputLines(mol, lines[i], maxN);
+ }
+
+ private void outputLines(SB mol, String data, int maxN) {
+ boolean done = false;
+ for (int i = 0, n = data.length(); i < n && !done; i += 80) {
+ mol.append(data.substring(i, Math.min(i + maxN, n)));
+ if (!(done = (maxN != 80)) && i + 80 < n)
+ mol.append("+");
+ mol.append("\n");
+ }
+
+ // TODO
+
+ }
+
private static BS getCovalentBondsForAtoms(Bond[] bonds, int bondCount, BS
bsAtoms) {
BS bsBonds = new BS();
for (int i = 0; i < bondCount; i++) {
@@ -1421,9 +1459,15 @@
*/
private void getAtomRecordMOL(int iModel, ModelSet ms, SB mol, int n, Atom
a, Quat q,
- P3 pTemp, boolean asV3000, boolean asJSON) {
- // -0.9920 3.2030 9.1570 Cl 0 0 0 0 0
- // 3.4920 4.0920 5.8700 Cl 0 0 0 0 0
+ P3 pTemp, boolean asV3000, boolean asJSON, SB
atomValues, int tokValue) {
+
//https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true
+ //__Jmol-14_06161707413D 1 1.00000 0.00000 0
+ //Jmol version 14.19.1 2017-06-12 00:33 EXTRACT: ({0:23})
+ // 24 25 0 0 0 0 1 V2000
+ // 1.3120 -1.0479 0.0025 N 0 0 0 0 0 0
+ // 2.2465 -2.1762 0.0031 C 0 0 0 0 0 0
+ // 1.7906 0.2081 0.0011 C 0 0 0 0 0 0
+ //xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
//012345678901234567890123456789012
getPointTransf(iModel, ms, a, q, pTemp);
int elemNo = a.getElementNumber();
@@ -1453,7 +1497,7 @@
mol.append("\"x\":").appendF(a.x).append(",\"y\":").appendF(a.y)
.append(",\"z\":").appendF(a.z).append("}");
} else {
- mol.append(PT.sprintf("%10.5p%10.5p%10.5p", "p", o));
+ mol.append(PT.sprintf("%10.4p%10.4p%10.4p", "p", o));
mol.append(" ").append(sym);
if (sym.length() == 1)
mol.append(" ");
@@ -1463,9 +1507,36 @@
PT.rightJustify(mol, " ", "" + iso);
PT.rightJustify(mol, " ", "" + (charge == 0 ? 0 : 4 - charge));
mol.append(" 0 0 0 0\n");
+
+ String label = (atomValues == null || asV3000 ? null :
+ getAtomPropertyAsString(a, tokValue));
+ if (label != null && (label = label.trim()).length() > 0) {
+ String sn = " " + n + " ";
+ atomValues.append("V ").append(sn.substring(sn.length() - 4));
+ output80CharWrap(atomValues, label, 73);
+ }
}
}
+ private P3 ptTemp;
+ private String getAtomPropertyAsString(Atom a, int tok) {
+ switch (tok & T.PROPERTYFLAGS) {
+ case T.intproperty:
+ int i = a.atomPropertyInt(tok);
+ return (tok == T.color ?
PT.trim(Escape.escapeColor(i),"[x]").toUpperCase() : "" + i);
+ case T.strproperty:
+ return a.atomPropertyString(vwr, tok);
+ case T.floatproperty:
+ float f = a.atomPropertyFloat(vwr, tok, null);
+ return (Float.isNaN(f) ? null : "" + f);
+ default: // point property
+ if (ptTemp == null)
+ ptTemp = new P3();
+ a.atomPropertyTuple(vwr, tok, ptTemp);
+ return (ptTemp == null ? null : ptTemp.toString());
+ }
+ }
+
/**
* pick up the appropriate value for this atom
* @param i
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
