Revision: 21609
http://sourceforge.net/p/jmol/code/21609
Author: hansonr
Date: 2017-05-19 17:09:25 +0000 (Fri, 19 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.16.1" // 2017.05.19
new feature: load =chebi/nnnnnn chEBI 2D molecule load, with minimal
100-step minimization
bug fix: CML reader does not read 2D wedge/hash information
bug fix: CIP fix for missing branch descriptors; 984 lines
bug fix: CIP adds helicene M/P chirality
- validated using CCDC structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
- http://pubs.rsc.org/en/content/articlehtml/2017/CP/C6CP07552E
code: CIP: additional simplification;
code: CIP status: implementation complete, including:
All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
R/S, E/Z, M/P (odd-cumulene and helicene), r/s, seqCis/seqTrans (as
Z/E)
fused benzenoid aromatic Mancude ring "Kekule weighted" atom number
adjustments
* Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
* atom is its own sphere, not the sphere of its duplicated atom.
*
* Stated more precisely:
*
* Proposed amended Sequence Rule 1:
*
* (1a) higher atomic number precedes lower;
*
* (1b) in comparing two duplicate nodes, lower root distance precedes higher
* root distance, where "root distance" is defined:
*
* (i) in the case of a duplicate atom for which the atomic number is averaged
* over two or more atoms in applying Rule 1a, the distance from the duplicate
* node itself to the root node; and
*
* (ii) in all other cases, the distance of its corresponding nonduplicated atom
* node to the root node.
*
IUPAC Blue Book 2013 errors of note:
,"147":"r,,,R,,,,r,,,S" // chiral phosphine ignored in BB P-93.5.1.1.2 for S vs
R
{
"id" : "148"
"name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane"
"ref_pname_pin" : "P-93.5.1.1.2"
"stereo" : ",r,,,R,,,,r,,,R,,,"
}
,"148":"r,,,S,,,,r,,,R,,,,s,,,s" // r,,,S,,,,r,,,S,,,,s,,,S Jmol disagrees
with BB P-93.5.1.1.2 or R and S p. 1243
{
"id" : "149"
"name_pname_pin" :
"bis[(1r,4r)-4-methylcyclohexyl]-(1s,4s)-4-methylcyclohexylphosphane"
"ref_pname_pin" : "P-93.5.1.1.2"
"stereo" : ",r,,,S,,,,r,,,S,,,,s,,,S,,,"
}
,"202":"RR" // // p. 1265 disagrees with BB P-93.5.3.5 for RR vs. SS
{
"id" : "203"
"name_pname_pin" :
"(5S,8R,11S)-1,12-dioxatrispiro[4.2.2.4^{11}.2^{8}.2^{5}]nonadecane"
"ref_pname_pin" : "P-93 5.3.5"
}
,"227":"SrSEErS" // disagrees with BB P-93.5.7.2 for S vs. r
{
"id" : "228"
"name_pname_pin" :
"(1E)-1-{(1'S,1r,4s)-[1,1'-bi(cyclohexan)]-3'-en-4-yl}-N-[(1r,4r)-4-phenylcyclohexyl]methan-1-imine"
"ref_pname_pin" : "P-93.5.7.2"
"stereo" : "S,,,,,,,r,S,,,,,,,E,,r,r,,,,,,,,,,,,"
}
,"230":"@3D RrRsR" // p 1282 disagrees with BB P-93.6
{
"id" : "231"
"name_pname_pin" :
"(2R)-1-[(1r,4R)-4-methylcyclohexyl]-3-[(1s,4S)-4-methylcyclohexyl]propan-2-ol"
"ref_pname_pin" : "P-93.6"
"stereo" : ",,,,r,,,R,,,,s,,,R,,,"
}
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/util/CommandHistory.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2017-05-18 04:50:52 UTC (rev 21608)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2017-05-19 17:09:25 UTC (rev 21609)
@@ -125,7 +125,7 @@
protected String moleculeID;
protected Map<String, Object> htModelAtomMap;
- private boolean is2d;
+ private boolean optimize2d;
/**
* state constants
@@ -142,14 +142,14 @@
MOLECULE_ATOM_SCALAR = 9,
MOLECULE_BOND_ARRAY = 10,
MOLECULE_BOND = 11,
- MOLECULE_FORMULA = 12,
- MOLECULE_ATOM_BUILTIN = 13,
- MOLECULE_BOND_BUILTIN = 14,
- MODULE = 15,
+ MOLECULE_BOND_STEREO = 12,
+ MOLECULE_FORMULA = 13,
+ MOLECULE_ATOM_BUILTIN = 14,
+ MOLECULE_BOND_BUILTIN = 15,
+ MODULE = 16,
SYMMETRY = 17,
LATTICE_VECTOR = 18,
ASSOCIATION = 19;
-
/**
* the current state
*/
@@ -169,8 +169,10 @@
@Override
protected void processXml(XmlReader parent,
Object saxReader) throws Exception {
- is2d = parent.checkFilterKey("2D");
+ optimize2d = parent.checkFilterKey("2D");
processXml2(parent, saxReader);
+ if (optimize2d)
+ set2D();
}
@Override
@@ -306,7 +308,7 @@
for (int i = tokenCount; --i >= 0;)
atomArray[i].atomName = tokens[i];
}
- boolean is3d = (!is2d && (val = atts.get("x3")) != null);
+ boolean is3d = (!optimize2d && (val = atts.get("x3")) != null);
if (is3d) {
is3d = true;
coords3D = true;
@@ -418,8 +420,14 @@
setKeepChars(true);
state = MOLECULE_BOND_BUILTIN;
scalarDictValue = val;
+ } else if (name.equals("bondstereo")) {
+ state = MOLECULE_BOND_STEREO;
}
break;
+ case MOLECULE_BOND_STEREO:
+ setKeepChars(true);
+ state = MOLECULE_BOND_STEREO;
+ break;
case MOLECULE_ATOM:
if (name.equals("scalar")) {
state = MOLECULE_ATOM_SCALAR;
@@ -622,6 +630,13 @@
atom.elementSymbol = chars.toString();
setKeepChars(false);
break;
+ case MOLECULE_BOND_STEREO:
+ String stereo = chars.toString();
+ if (bond.order == 1)
+ bond.order = (stereo.equals("H") ? JmolAdapter.ORDER_STEREO_FAR :
JmolAdapter.ORDER_STEREO_NEAR);
+ setKeepChars(false);
+ state = MOLECULE_BOND;
+ break;
case MOLECULE_BOND_BUILTIN: // ACD Labs
state = MOLECULE_BOND;
if (scalarDictValue.equals("atomRef")) {
@@ -690,8 +705,10 @@
parent.applySymmetryToBonds = true;
a1 = fixSerialName(a1);
a2 = fixSerialName(a2);
- if (joinList == null || !checkBondToR(a1, a2))
+ if (joinList == null || !checkBondToR(a1, a2)) {
asc.addNewBondFromNames(a1, a2, order);
+ bond = asc.bonds[asc.bondCount - 1];
+ }
}
private String fixSerialName(String a) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2017-05-18
04:50:52 UTC (rev 21608)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2017-05-19
17:09:25 UTC (rev 21609)
@@ -33,6 +33,7 @@
import org.jmol.adapter.smarter.Atom;
import org.jmol.adapter.smarter.AtomSetCollection;
import org.jmol.adapter.smarter.AtomSetCollectionReader;
+import org.jmol.adapter.smarter.Bond;
import org.jmol.adapter.smarter.Resolver;
import org.jmol.api.Interface;
import org.jmol.util.Logger;
@@ -92,6 +93,7 @@
public class XmlReader extends AtomSetCollectionReader {
protected Atom atom;
+ protected Bond bond;
//protected String[] domAttributes;
protected XmlReader parent; // XmlReader itself; to be assigned by the
subReader
public Map<String, String> atts;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -2964,6 +2964,8 @@
vwr.shm.setShapeSizeBs(JC.SHAPE_BALLS, 0, vwr.rd,
BSUtil.newAndSetBit(atomIndex));
setAtomName(atomIndex, type + atom.getAtomNumber(), false);
+ if (vwr.getBoolean(T.modelkitmode))
+ am[atom.mi].isModelKit = true;
if (!am[atom.mi].isModelKit)
taintAtom(atomIndex, TAINT_ATOMNAME);
} else if (type.equals("Pl")) {
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -5108,6 +5108,7 @@
P3 pt = (++e.iToken < slen ? centerParameter(e.iToken) : null);
if (chk)
return;
+ vwr.pushState();
switch (atomsOrBonds) {
case T.atoms:
e.clearDefinedVariableAtomSets();
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -197,7 +197,14 @@
// 4. Rule 3 requires the concept of "auxiliary" (temporary,
digraph-specific) descriptors.
// This concept of auxiliary descriptors is the key to not having
an analysis
// blow up or somehow require complex, impossible iteration.
- // 5. Rule 4a needs to be addressed exhaustively prior to Rules 4b and 4c.
+ // 5. Rule 4a needs to be addressed exhaustively prior to Rules 4b and 4c.
This involves the
+ // the initial generation of all auxiliary descriptors, including
r/s and R/S at
+ // branching points. In the course of doing this, all rules, 1-5,
must be employed
+ // at these auxiliary centers using the already-created digraph.
This rule serves to
+ // avoid the need for Rule 4b for all except the most unusual
cases, where, for example,
+ // there are two otherwise identical branches, but one can be
identified as S and the
+ // other only r or no-stereo, but not R. Thus, only branches that
end up as R/R, R/S, S/S,
+ // r/r, r/s, s/s, or nst/nst need be investigated by Rule 4b.
// 6. Rule 4b Somehow missed in the discussion is that the reference
descriptor is determined
// once and only once for each branch from the center under
scrutiny. All Rules
// preceding Rule 4 can be applied to iterated subsections of a
digraph. Not this one,
@@ -204,7 +211,7 @@
// nor Rule 5, though. The key is to determine one single "Mata
sequence" of R and S descriptors
// for each pair of branches being considered. This same
reference carries through all
// future iterations of the algorithm for that branch.
- // 7. Rule 4c Again, this rule must be invoked only after Rule 4b is
completely set, and again
+ // 7. Rule 4c Again, this subrule must be invoked only after Rule 4b is
completed, and again
// it is only for the root branches, not anywhere else.
// 8. Rule 5 Final setting pseudoasymmetry (r/s, m/p) can be done along the
same line as Rule 4b,
// but with slightly different sorting criteria.
@@ -217,6 +224,7 @@
// prefilterAtoms()
// checkForAlkenes()
// checkForSmallRings()
+ // checkForHelicenes()
// checkForBridgeheadNitrogens()
// checkForKekuleIssues()
// checkForAtropisomerism()
@@ -224,6 +232,7 @@
// if (haveAlkenes) {
// for(all double bonds) getBondChirality(a1, a2)
// removeUnnecessaryEZDesignations()
+ // indicateHeliceneChirality()
// }
// }
//
@@ -307,10 +316,11 @@
static final int RULE_2 = 3;
static final int RULE_3 = 4;
static final int RULE_4a = 5;
- static final int RULE_4bc = 6; // can be done together; no need for a
separate loop
- static final int RULE_5 = 7;
+ static final int RULE_4b = 6;
+ static final int RULE_4c = 7;
+ static final int RULE_5 = 8;
- static final String[] ruleNames = {"","1a", "1b", "2", "3", "4a", "4bc",
"5"};
+ static final String[] ruleNames = {"","1a", "1b", "2", "3", "4a", "4b",
"4c", "5"};
public String getRuleName() {
return ruleNames[currentRule];
@@ -325,7 +335,7 @@
/**
* maximum path to display for debugging only
*/
- public static final int MAX_PATH = 30;
+ public static final int MAX_PATH = 50;
/**
* maximum ring size that can have a double bond with no E/Z designation;
@@ -436,32 +446,33 @@
int c = getAtomChiralityLimited(a, null, null, RULE_5);
a.setCIPChirality(c == 0 ? JC.CIP_CHIRALITY_NONE : c);
}
+ if (haveAlkenes) {
- // set bond chiralities
-
- if (haveAlkenes) {
+ // set bond chiralities E/Z and M/P
+
Lst<int[]> lstEZ = new Lst<int[]>();
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
getAtomBondChirality(atoms[i], lstEZ, bsToDo);
if (lstSmallRings.size() > 0 && lstEZ.size() > 0)
clearSmallRingEZ(atoms, lstEZ);
- }
-
- // add helical chiralities
+
+ // Add helicene chiralities -- predetermined using a Jmol SMARTS
conformational search.
+ //
+ // M: A{a}(.t:-10,-40)a(.t:-10,-40)aaa
+ // P: A{a}(.t:10,40)a(.t:10,40)aaa
+ //
+ // Note that indicators are on the first and last aromatic atoms {a}.
- if (bsHelixM != null)
- for (int i = bsHelixM.nextSetBit(0); i >= 0; i = bsHelixM.nextSetBit(i +
1))
- atoms[i].setCIPChirality(STEREO_M);
+ if (bsHelixM != null)
+ for (int i = bsHelixM.nextSetBit(0); i >= 0; i = bsHelixM.nextSetBit(i
+ 1))
+ atoms[i].setCIPChirality(STEREO_M);
- if (bsHelixM != null)
- for (int i = bsHelixM.nextSetBit(0); i >= 0; i = bsHelixM.nextSetBit(i +
1))
- atoms[i].setCIPChirality(STEREO_M);
+ if (bsHelixP != null)
+ for (int i = bsHelixP.nextSetBit(0); i >= 0; i = bsHelixP.nextSetBit(i
+ 1))
+ atoms[i].setCIPChirality(STEREO_P);
+ }
- if (bsHelixP != null)
- for (int i = bsHelixP.nextSetBit(0); i >= 0; i = bsHelixP.nextSetBit(i +
1))
- atoms[i].setCIPChirality(STEREO_P);
-
if (Logger.debugging) {
Logger.info("sp2-aromatic = " + bsKekuleAmbiguous);
Logger.info("smallRings = " + PT.toJSON(null,lstSmallRings));
@@ -1391,13 +1402,6 @@
isTrigonalPyramidal = (bondCount == 3 && !isAlkene && (elemNo > 10 ||
bsAzacyclic != null
&& bsAzacyclic.get(atomIndex)));
canBePseudo = (bondCount == 4 || isTrigonalPyramidal);
- //String c = atom.getCIPChirality(false);
- // What we are doing here is creating a lexigraphically sortable string
- // R < S < r < s < ~ and C < T < ~ // actually, C and T are not used
- // we ignore r and s here.
- //if (c.equals("") || c.equals("r") || c.equals("s"))
- //c = "~"; // none
- //knownAtomChirality = c;
if (parent != null)
sphere = parent.sphere + 1;
if (sphere == 1) {
@@ -1577,10 +1581,6 @@
Arrays.sort(atoms);
return true;
- // pretty sure this next test cannot be true
-// if (isTerminal)
-// System.out.println("????");
-// return !isTerminal;
}
/**
@@ -1638,7 +1638,7 @@
}
// if this is Rule 4 or 5, then we do a check of the forward-based
stereochemical path
- boolean checkRule4List = (rule4List != null && (currentRule == RULE_4bc
|| currentRule == RULE_5));
+ boolean checkRule4List = (rule4List != null && currentRule > RULE_4a);
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
for (int j = i + 1; j < 4; j++) {
@@ -1989,7 +1989,8 @@
return checkRule3(b); // can be IGNORE
case RULE_4a:
return checkRules4a(b, " sr SR PM");
- case RULE_4bc:
+ case RULE_4b:
+ case RULE_4c:
case RULE_5:
return TIED; // not carried out here because these need access to a
full list of ligands
// case RULE_4c: // taken care of by RULE_4bc
@@ -2217,7 +2218,6 @@
* (IGNORE)
*/
private int compareMataPair(int ia, int ib) {
- boolean isRule5 = (currentRule == RULE_5);
// note that opposites will need to generate "R" or "S" keys, which will
be
// resolved as "r" or "s"
// but generally we will want to process this as "R" and "S"
@@ -2224,54 +2224,60 @@
// note that this analysis cannot be done ahead of time
String aStr = rule4List[ia].substring(1);
String bStr = rule4List[ib].substring(1);
- boolean haveRS = false;
- if (atoms[ia].nextChiralBranch != null) {
- String s = atoms[ia].getMataList(getFirstRef(aStr), isRule5);
- haveRS = (s.indexOf("|") >= 0);
- aStr = (haveRS ? s : aStr + s);
- }
- if (atoms[ib].nextChiralBranch != null) {
- String s = atoms[ib].getMataList(getFirstRef(bStr), isRule5);
- haveRS |= (s.indexOf("|") >= 0);
- bStr = (s.indexOf("|") < 0 ? bStr + s : s);
- }
- if (Logger.debugging)
- Logger.info(dots() + this + " comparing " + atoms[ia] + " " + aStr + "
to "
- + atoms[ib] + " " + bStr);
- if (isRule5 || !haveRS && aStr.length() != bStr.length()) {
- // note that these two strings can be different lengths
- // if we have sXX and ~
- return sign(aStr.compareTo(bStr));
- }
- if (haveRS) {
- // Mata(2005) Figure 9
- // We are trying to ascertain that
- // R lull R luuu
- // S luuu is the same as S lull
- //
- // Solution is to SUM all winners. If that is 0, then they are the same
- String[] aList = PT.split(aStr, "|");
- String[] bList = PT.split(bStr, "|");
- int minScore = Integer.MAX_VALUE;
- int sumScore = 0;
- aStr = aList[0];
- bStr = bList[0];
- for (int i = aList.length; --i >= 0;) {
- for (int j = bList.length; --j >= 0;) {
- int score = compareRule4PairStr(aList[i], bList[j], true);
- sumScore += score;
- if (score != TIED && Math.abs(score) <= minScore) {
- minScore = Math.abs(score);
- aStr = aList[i];
- bStr = bList[j];
+ if (currentRule == RULE_4c) {
+ aStr = PT.rep(aStr, "~", "");
+ bStr = PT.rep(bStr, "~", "");
+ } else {
+ boolean haveRS = false;
+ boolean isRule5 = (currentRule == RULE_5);
+ if (atoms[ia].nextChiralBranch != null) {
+ String s = atoms[ia].getMataList(getFirstRef(aStr), isRule5);
+ haveRS = (s.indexOf("|") >= 0);
+ aStr = (haveRS ? s : aStr + s);
+ }
+ if (atoms[ib].nextChiralBranch != null) {
+ String s = atoms[ib].getMataList(getFirstRef(bStr), isRule5);
+ haveRS |= (s.indexOf("|") >= 0);
+ bStr = (s.indexOf("|") < 0 ? bStr + s : s);
+ }
+ if (Logger.debugging)
+ Logger.info(dots() + this + " comparing " + atoms[ia] + " " + aStr
+ + " to " + atoms[ib] + " " + bStr);
+ if (isRule5 || !haveRS && aStr.length() != bStr.length()) {
+ // note that these two strings can be different lengths
+ // if we have sXX and ~
+ return sign(aStr.compareTo(bStr));
+ }
+ aStr = cleanRule4Str(aStr);
+ bStr = cleanRule4Str(bStr);
+ if (haveRS) {
+ // Mata(2005) Figure 9
+ // We are trying to ascertain that
+ // R lull R luuu
+ // S luuu is the same as S lull
+ //
+ // Solution is to SUM all winners. If that is 0, then they are the
same
+ String[] aList = PT.split(aStr, "|");
+ String[] bList = PT.split(bStr, "|");
+ int minScore = Integer.MAX_VALUE;
+ int sumScore = 0;
+ aStr = aList[0];
+ bStr = bList[0];
+ for (int i = aList.length; --i >= 0;) {
+ for (int j = bList.length; --j >= 0;) {
+ int score = compareRule4PairStr(aList[i], bList[j], true);
+ sumScore += score;
+ if (score != TIED && Math.abs(score) <= minScore) {
+ minScore = Math.abs(score);
+ aStr = aList[i];
+ bStr = bList[j];
+ }
}
}
+ if (sumScore == TIED)
+ return TIED;
}
- if (sumScore == TIED)
- return TIED;
}
- aStr = PT.rep(aStr, "~", "");
- bStr = PT.rep(bStr, "~", "");
if (aStr.length() == 1 && "RS".indexOf(aStr) < 0) {
int score = checkEnantiomer(aStr, bStr, 0, aStr.length(), " rs");
switch (score) {
@@ -2285,6 +2291,11 @@
return compareRule4PairStr(aStr, bStr, false);
}
+ private String cleanRule4Str(String aStr) {
+ return (aStr.length() > 1 ?
+ PT.replaceAllCharacters(aStr, "sr~", "") : aStr);
+ }
+
/**
* Just get the first R- or S-equivalent in "~~~~xxxxx"
* @param aStr
@@ -2412,7 +2423,7 @@
*/
private int compareRule4PairStr(String aStr, String bStr, boolean
isRSTest) {
if (Logger.debugging)
- Logger.info(dots() + this + " Rule 4b comparing " + aStr + " " + bStr);
+ Logger.info(dots() + this.myPath + " Rule 4b comparing " + aStr + " "
+ bStr);
doCheckPseudo = false;
int n = aStr.length();
if (n == 0 || n != bStr.length())
@@ -2655,17 +2666,18 @@
s = s.toUpperCase(); // Rule 4c or diasteriomers // AY-236.148
auxChirality = s;
subRS = "";
- if (ret != null)
- ret[0] = null;
+ //if (ret != null)
+ //ret[0] = null;
} else {
// if here, adj is TIED (0)
CIPAtom atom1 = (CIPAtom) clone();
if (atom1.set()) {
atom1.addReturnPath(null, this);
+ //System.out.println("determining " + s + " for " +
atom1.myPath);
atom1.sortByRule(RULE_1a);
rs = atom1.checkHandedness();
s = (rs == STEREO_R ? "R" : rs == STEREO_S ? "S" : "~");
- System.out.println("determining " + s + " for " + root + "->"
+ atom1);
+ //System.out.println("determining " + s + " for " +
atom1.myPath);
node1.addMataRef(sphere, priority, rs);
}
}
@@ -2738,8 +2750,13 @@
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
if (rs1.equals(rs2))
- return TIED;
- String rs = (rs1.indexOf("R") < 0 && rs1.indexOf("S") < 0 ? "~rs" :
"~RS");
+ return TIED;
+ boolean haveRS = (rs1.indexOf("R") >= 0 || rs1.indexOf("S") >= 0);
+ String rs = (haveRS ? "~RS" : "~rs");
+ if (haveRS) {
+ rs1 = PT.replaceAllCharacters(rs1, "rs", "~");
+ rs2 = PT.replaceAllCharacters(rs2, "rs", "~");
+ }
int score = checkEnantiomer(rs1, rs2, 1, n, rs);
if (score == DIASTEREOMERIC) {
switch (compareMataPair(i1, i2)) {
@@ -2910,6 +2927,7 @@
a.atoms = new CIPAtom[4];
a.priorities = new int[4];
a.htPathPoints = htPathPoints;
+ a.doCheckPseudo = false;
for (int i = 0; i < 4; i++) {
// a.priorities[i] = priorities[i];
if (atoms[i] != null) {
@@ -2916,6 +2934,7 @@
a.atoms[i] = atoms[i];
}
}
+ a.ties = null;
if (Logger.debugging)
Logger.info("cloning " + this + " as " + a);
return a;
Modified: trunk/Jmol/src/org/jmol/util/CommandHistory.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/CommandHistory.java 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/util/CommandHistory.java 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -255,4 +255,19 @@
//System.out.println("HISTORY:" + i+" "+commandList.get(i));
}
+ private Lst<String> lstStates;
+
+ public void pushState(String stateInfo) {
+ if (lstStates == null)
+ lstStates = new Lst<String>();
+ lstStates.addLast(stateInfo);
+ }
+
+ public String popState() {
+ if (lstStates == null || lstStates.size() == 0)
+ return null;
+ String s = lstStates.removeItemAt(lstStates.size() - 1);
+ return s;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -210,6 +210,12 @@
&& Viewer.hasDatabasePrefix(name0)) {
htParams.put("dbName", name0);
}
+ if (name.endsWith("%2D%")) {
+ String filter = (String) htParams.get("filter");
+ htParams.put("filter", (filter == null ? "" : filter) + "2D");
+ name = name.substring(0, name.length() - 4);
+ }
+
int pt = name.indexOf("::");
String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
String fileType = (pt >= 0 ? name.substring(0, pt) : null);
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-05-18 04:50:52 UTC (rev
21608)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-05-19 17:09:25 UTC (rev
21609)
@@ -129,6 +129,7 @@
// note list of RCSB access points:
http://www.rcsb.org/pdb/static.do?p=download/http/index.html
public static String[] databases = {
+ "chebi",
"http://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=%file%2D%";,
"aflowbin",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
// _#DOCACHE_ flag indicates that the loaded file should be saved in any
state in full
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-18 04:50:52 UTC
(rev 21608)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-19 17:09:25 UTC
(rev 21609)
@@ -54,9 +54,12 @@
# command, and then write a PDB file, all the occupancies are listed as 1.00
# instead of the occupancies I tried to assign in jmol.
+# TODO: fix UNDO
-Jmol.___JmolVersion="14.15.5"
+Jmol.___JmolVersion="14.16.1" // 2017.05.19
+new feature: load =chebi/nnnnnn chEBI 2D molecule load, with minimal
100-step minimization
+
bug fix: CML reader does not read 2D wedge/hash information
bug fix: CIP fix for missing branch descriptors; 984 lines
@@ -69,7 +72,7 @@
code: CIP status: implementation complete, including:
All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
R/S, E/Z, M/P (odd-cumulene and helicene), r/s, seqCis/seqTrans (as
Z/E)
- benzenoid (including fused benzenoid heteroaromatic) Mancude ring
"Kekule weighted" atom number adjustments
+ fused benzenoid aromatic Mancude ring "Kekule weighted" atom number
adjustments
* Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
* atom is its own sphere, not the sphere of its duplicated atom.
@@ -93,7 +96,7 @@
IUPAC Blue Book 2013 errors of note:
-,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2
for S vs R
+,"147":"r,,,R,,,,r,,,S" // chiral phosphine ignored in BB P-93.5.1.1.2 for S
vs R
{
"id" : "148"
"name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane"
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-05-18 04:50:52 UTC (rev
21608)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2017-05-19 17:09:25 UTC (rev
21609)
@@ -7944,6 +7944,20 @@
commandHistory.addCommand(PT.replaceAllCharacters(command, "\r\n\t", " "));
}
+ public void pushState() {
+ if (autoExit || !haveDisplay || !getPreserveState())
+ return;
+ commandHistory.pushState(getStateInfo());
+ }
+
+ public void popState() {
+ if (autoExit || !haveDisplay || !getPreserveState())
+ return;
+ String state = commandHistory.popState();
+ if (state != null)
+ evalStringQuiet(state);
+ }
+
/**
* Removes one command from the command history
*
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