Revision: 20690
http://sourceforge.net/p/jmol/code/20690
Author: hansonr
Date: 2015-08-12 06:12:07 +0000 (Wed, 12 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.08.11"
bug fix: a = {*}.label("%[xxx]") does not work.
bug fix: "".format([a,b]) crashes Jmol
new feature: load <mmCIF file> filter "addBonds"
-- processes _struct_conn records
-- inter-group connections only
-- includes _struct_conn bond types:
covale covalent bond
covale_base covalent modification of a nucleotide base
covale_phosphate covalent modification of a nucleotide phosphate
covale_sugar covalent modification of a nucleotide sugar
disulf disulfide bridge
metalc metal coordination
-- ignores _struct_conn bond types:
hydrog hydrogen bond
mismat mismatched base pairs
modres covalent residue modification
saltbr ionic interaction
new feature: load *1crn*
-- loads PDBe "updated" CIF files to allow CONECT-like bond creation
-- for example, http://www.ebi.ac.uk/pdbe/static/entry/1h68_updated.cif
-- suitable replacement for PDB CONECT
-- processes _chem_comp_bond and _struct_conn categories
-- presence of _chem_comp_bond will process _struct_conn as well, regardless
of filter "addbonds"
(because _chem_comp bonds are only intra-group, and for full CONECT-like
behavior, we need all bonds)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-08-11 21:13:26 UTC (rev 20689)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-08-12 06:12:07 UTC (rev 20690)
@@ -1002,6 +1002,7 @@
String key2 = vwr.getChainID(getField(STRUCT_CONN_ASYM2), true) +
getField(STRUCT_CONN_COMP2)
+ parseFloatStr(getField(STRUCT_CONN_SEQ2))
+ getField(STRUCT_CONN_ATOM2) + getField(STRUCT_CONN_ALT2);
+ System.out.println(type + "\t" + key1 + " " + key2);
int order = getBondOrder(getField(STRUCT_CONN_ORDER));
if (structConnMap == null)
structConnMap = new Lst<Object[]>();
@@ -1035,8 +1036,6 @@
private boolean processCompBondLoopBlock() throws Exception {
doSetBonds = true;
parseLoopParametersFor(FAMILY_COMPBOND, chemCompBondFields);
- if (!checkAllFieldsPresent(chemCompBondFields, true))
- return false;
while (parser.getData()) {
String comp = getField(CHEM_COMP_BOND_ID);
String atom1 = getField(CHEM_COMP_BOND_ATOM_ID_1);
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-11 21:13:26 UTC
(rev 20689)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-12 06:12:07 UTC
(rev 20690)
@@ -1347,7 +1347,7 @@
// format("array", x)
SV x1 = (args.length < 2 || intValue == T.format ? mp.getX() : null);
String format = (args.length == 0 ? "%U" : args[0].tok == T.varray ? null
: SV.sValue(args[0]));
- if (args.length > 0 && x1 != null && format != null) {
+ if (!isLabel && args.length > 0 && x1 != null && format != null) {
// x1.format(["energy", "pointGroup"]);
// x1.format("%5.3f %5s", ["energy", "pointGroup"])
// but not x1.format()
@@ -1386,7 +1386,7 @@
BS bs = SV.getBitSet(x1, true);
boolean asArray = T.tokAttr(intValue, T.minmaxmask); // "all"
- return mp.addXObj(bs == null ? SV.sprintf(PT.formatCheck(format), x1) : e
+ return mp.addXObj(format == null ? "" : bs == null ?
SV.sprintf(PT.formatCheck(format), x1) : e
.getCmdExt().getBitsetIdent(bs, format, x1.value, true, x1.index,
asArray));
@@ -1394,20 +1394,36 @@
/**
* [ {...},{...}... ] ==> [[...],[...]]
+ *
* @param listIn
* @param formatList
* @return sublist
*/
private Lst<SV> getSublist(Lst<SV> listIn, Lst<SV> formatList) {
Lst<SV> listOut = new Lst<SV>();
+ Map<String, SV> map;
+ SV v;
+ Lst<SV> list;
for (int i = 0, n = listIn.size(); i < n; i++) {
- Lst<SV> list = new Lst<SV>();
- Map<String, SV> map = listIn.get(i).getMap();
- for (int j = 0, n1 = formatList.size(); j < n1; j++) {
- SV v = map.get(SV.sValue(formatList.get(j)));
- list.addLast(v == null ? SV.newS("") : v);
+ SV element = listIn.get(i);
+ switch (element.tok) {
+ case T.hash:
+ map = element.getMap();
+ list = new Lst<SV>();
+ for (int j = 0, n1 = formatList.size(); j < n1; j++) {
+ v = map.get(SV.sValue(formatList.get(j)));
+ list.addLast(v == null ? SV.newS("") : v);
+ }
+ listOut.addLast(SV.getVariableList(list));
+ break;
+ case T.varray:
+ map = new Hashtable<String, SV>();
+ list = element.getList();
+ for (int j = 0, n1 = Math.min(list.size(), formatList.size()); j < n1;
j++) {
+ map.put(SV.sValue(formatList.get(j)), list.get(j));
+ }
+ listOut.addLast(SV.getVariable(map));
}
- listOut.addLast(SV.getVariableList(list));
}
return listOut;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-11 21:13:26 UTC
(rev 20689)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-12 06:12:07 UTC
(rev 20690)
@@ -51,6 +51,9 @@
Jmol.___JmolVersion="14.3.16_2015.08.11"
+bug fix: a = {*}.label("%[xxx]") does not work.
+bug fix: "".format([a,b]) crashes Jmol
+
new feature: load <mmCIF file> filter "addBonds"
-- processes _struct_conn records
-- inter-group connections only
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
