Revision: 20146
http://sourceforge.net/p/jmol/code/20146
Author: hansonr
Date: 2014-11-28 20:29:45 +0000 (Fri, 28 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.11.28"
new feature: readers for ESS input types: CFILE, VFILE, MOPAC, Gaussian,
GAMESS, Orca, PQS
-- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/io/JmolUtil.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-27 05:38:51 UTC (rev 20145)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-28 20:29:45 UTC (rev 20146)
@@ -29,7 +29,6 @@
import java.util.Map;
-
import org.jmol.adapter.smarter.AtomSetCollectionReader;
import org.jmol.adapter.smarter.Bond;
import org.jmol.adapter.smarter.Atom;
@@ -46,151 +45,156 @@
public class ZMatrixReader extends AtomSetCollectionReader {
/*
- * a simple Z-matrix reader, also serves as simple
- * input file reader for Q-Chem, Jaguar, MolPro, and ADF, as produced by
NBO6Pro
+ * A simple Z-matrix reader, also serves as simple input file reader for
+ * CFILE, VFILE, PQS, Orca, GAMESS, Gaussian, MOPAC, Q-Chem, Jaguar, MolPro,
+ * and ADF, as produced by NBO6Pro
*
* Can be invoked using ZMATRIX:: or with file starting with #ZMATRIX
+ *
+ * CFILE and VFILE require CFI:: and VFI::, respectively, or just C:: and
V::
+ *
+ * Other invocations include: ADF::, G::, GMS::, JAG::, MND::, MP::, ORC::,
PQS::, QC::,
+ * but those are optional.
+ *
* # are comments; can include jmolscript: xxxx
*
- * a positive dihedral is defined as being
- *
- * (back)
- * +120 /
- * (front)---O
*
* Any invalid element symbol such as X or XX indicates a dummy
* atom that will not be included in the model but is needed
* to create the structure
*
+ *
* Bob Hanson hans...@stolaf.edu 11/19/2011
*/
- /* SYNTAX
+ // a positive dihedral is defined as being
+ //
+ // (back)
+ // +120 /
+ // (front)---O
-Anything after # on a line is considered a comment.
-A first line starting with #ZMATRIX defines the file type:
- Jmol z-format type (just #ZMATRIX)
- Gaussian (#ZMATRIX GAUSSIAN)
- Mopac (#ZMATRIX MOPAC)
-Lines starting with # may contain jmolscript
-Blank lines are ignored:
+ // Anything after # on a line is considered a comment.
+ // A first line starting with #ZMATRIX defines the file type:
+ // Jmol z-format type (just #ZMATRIX)
+ // Gaussian (#ZMATRIX GAUSSIAN)
+ // Mopac (#ZMATRIX MOPAC)
+ // Lines starting with # may contain jmolscript
+ // Blank lines are ignored:
+ //
+ // #ZMATRIX -- methane
+ // #jmolscript: spin on
+ //
+ // C
+ // H 1 1.089000
+ // H 1 1.089000 2 109.4710
+ // H 1 1.089000 2 109.4710 3 120.0000
+ // H 1 1.089000 2 109.4710 3 -120.0000
+ //
+ // Bonds will not generally be added, leaving Jmol to do its autoBonding.
+ // To add bond orders, just add them as one more integer on any line
+ // other than the first-atom line:
+ //
+ // #ZMATRIX -- CO2
+ // C
+ // O 1 1.3000 2
+ // O 1 1.3000 2 180 2
+ //
+ // Any position number may be replaced by a unique atom name, with number:
+ //
+ // #ZMATRIX -- CO2
+ // C1
+ // O1 C1 1.3000 2
+ // O2 C1 1.3000 O1 180 2
+ //
+ // Ignored dummy atoms are any atoms starting with "X" and a number,
+ // allowing for positioning:
+ //
+ // #ZMATRIX -- CO2
+ // X1
+ // X2 X1 1.0
+ // C1 X1 1.0 X2 90
+ // O1 C1 1.3000 X2 90 X1 0 2
+ // O2 C1 1.3000 O1 180 X2 0 2
+ //
+ // Negative distance indicates that the second angle is a normal angle, not
a dihedral:
+ //
+ // #ZMATRIX -- NH3 (using simple angles only)
+ // N1
+ // H1 N1 1.0
+ // H2 N1 1.0 H1 107
+ // H3 N1 -1.0 H1 107 H2 107
+ //
+ // Negative distance and one negative angle reverses the chirality:
+ //
+ // #ZMATRIX -- NH3 (using simple angles only; reversed chirality):
+ // N1
+ // H1 N1 1.0
+ // H2 N1 1.0 H1 107
+ // H3 N1 -1.0 H1 -107 H2 107
+ //
+ // Symbolics may be used -- they may be listed first or last:
+ //
+ // #ZMATRIX
+ //
+ // dist 1.0
+ // angle 107
+ //
+ // N1
+ // H1 N1 dist
+ // H2 N1 dist H1 angle
+ // H3 N1 -dist H1 angle H2 angle
+ //
+ // All atoms will end up with numbers in their names,
+ // but you do not need to include those in the z-matrix file
+ // if atoms have unique elements or you are referring
+ // to the last atom of that type. Still, numbering is recommended.
+ //
+ // #ZMATRIX
+ //
+ // dist 1.0
+ // angle 107
+ //
+ // N # will be N1
+ // H N dist # will be H2
+ // H N dist H angle # will be H3
+ // H N -dist H2 angle H angle # H here refers to H3
+ //
+ // MOPAC format will have an initial comment section. Isotopes are in the
form of "C13".
+ // If isotopes are used, the file type MUST be identified as #ZMATRIX
MOPAC.
+ // Lines prior to the first line with less than 2 characters will be
considered to be comments and ignored.
+ //
+ // AM1
+ // Ethane
+ //
+ // C
+ // C 1 r21
+ // H 2 r32 1 a321
+ // H 2 r32 1 a321 3 d4213
+ // H 2 r32 1 a321 3 -d4213
+ // H 1 r32 2 a321 3 60.
+ // H 1 r32 2 a321 3 180.
+ // H 1 r32 2 a321 3 d300
+ //
+ // r21 1.5
+ // r32 1.1
+ // a321 109.5
+ // d4213 120.0
+ // d300 300.0
+ //
+ // Gaussian will not have the third line blank and has a slightly
+ // different format for showing the alternative two-angle format
+ // involving the eighth field having the flag 1
+ // (see http://www.gaussian.com/g_tech/g_ur/c_zmat.htm):
+ //
+ // C5 O1 1.0 C2 110.4 C4 105.4 1
+ // C6 O1 R C2 A1 C3 A2 1
+ //
+ // Note that Gaussian cartesian format is allowed -- simply
+ // set the first atom index to be 0.
+ //
+ //
+ // No distinction between "Variable:" and "Constant:" is made by Jmol.
-#ZMATRIX -- methane
-#jmolscript: spin on
-
-C
-H 1 1.089000
-H 1 1.089000 2 109.4710
-H 1 1.089000 2 109.4710 3 120.0000
-H 1 1.089000 2 109.4710 3 -120.0000
-
-Bonds will not generally be added, leaving Jmol to do its autoBonding.
-To add bond orders, just add them as one more integer on any line
-other than the first-atom line:
-
-#ZMATRIX -- CO2
-C
-O 1 1.3000 2
-O 1 1.3000 2 180 2
-
-Any position number may be replaced by a unique atom name, with number:
-
-#ZMATRIX -- CO2
-C1
-O1 C1 1.3000 2
-O2 C1 1.3000 O1 180 2
-
-Ignored dummy atoms are any atoms starting with "X" and a number,
-allowing for positioning:
-
-#ZMATRIX -- CO2
-X1
-X2 X1 1.0
-C1 X1 1.0 X2 90
-O1 C1 1.3000 X2 90 X1 0 2
-O2 C1 1.3000 O1 180 X2 0 2
-
-Negative distance indicates that the second angle is a normal angle, not a
dihedral:
-
-#ZMATRIX -- NH3 (using simple angles only)
-N1
-H1 N1 1.0
-H2 N1 1.0 H1 107
-H3 N1 -1.0 H1 107 H2 107
-
-Negative distance and one negative angle reverses the chirality:
-
-#ZMATRIX -- NH3 (using simple angles only; reversed chirality):
-N1
-H1 N1 1.0
-H2 N1 1.0 H1 107
-H3 N1 -1.0 H1 -107 H2 107
-
-Symbolics may be used -- they may be listed first or last:
-
-#ZMATRIX
-
-dist 1.0
-angle 107
-
-N1
-H1 N1 dist
-H2 N1 dist H1 angle
-H3 N1 -dist H1 angle H2 angle
-
-All atoms will end up with numbers in their names,
-but you do not need to include those in the z-matrix file
-if atoms have unique elements or you are referring
-to the last atom of that type. Still, numbering is recommended.
-
-#ZMATRIX
-
-dist 1.0
-angle 107
-
-N # will be N1
-H N dist # will be H2
-H N dist H angle # will be H3
-H N -dist H2 angle H angle # H here refers to H3
-
-MOPAC format will have an initial comment section. Isotopes are in the form of
"C13".
-If isotopes are used, the file type MUST be identified as #ZMATRIX MOPAC.
-Lines prior to the first line with less than 2 characters will be considered
to be comments and ignored.
-
- AM1
-Ethane
-
-C
-C 1 r21
-H 2 r32 1 a321
-H 2 r32 1 a321 3 d4213
-H 2 r32 1 a321 3 -d4213
-H 1 r32 2 a321 3 60.
-H 1 r32 2 a321 3 180.
-H 1 r32 2 a321 3 d300
-
-r21 1.5
-r32 1.1
-a321 109.5
-d4213 120.0
-d300 300.0
-
-Gaussian will not have the third line blank and has a slightly
-different format for showing the alternative two-angle format
-involving the eighth field having the flag 1
-(see http://www.gaussian.com/g_tech/g_ur/c_zmat.htm):
-
-C5 O1 1.0 C2 110.4 C4 105.4 1
-C6 O1 R C2 A1 C3 A2 1
-
-Note that Gaussian cartesian format is allowed -- simply
-set the first atom index to be 0:
-
-
-No distinction between "Variable:" and "Constant:" is made by Jmol.
-
- */
-
protected int ac;
protected Lst<Atom> vAtoms = new Lst<Atom>();
private Map<String, Integer> atomMap = new Hashtable<String, Integer>();
@@ -200,14 +204,14 @@
private Map<String, Float> symbolicMap = new Hashtable<String, Float>();
private boolean isMopac;
private boolean isHeader = true;
-
+
@Override
protected boolean checkLine() throws Exception {
// easiest just to grab all lines that are comments or symbolic first,
then do the processing of atoms.
cleanLine();
if (line.length() <= 2) // for Mopac, could be blank or an atom symbol,
but not an atom name
isHeader = false;
- if (line.startsWith("#") || isMopac && isHeader) {
+ if (line.startsWith("#") || line.startsWith("*") || isMopac && isHeader) {
if (line.startsWith("#ZMATRIX"))
isJmolZformat = line.toUpperCase().indexOf("GAUSSIAN") < 0
&& !(isMopac = (line.toUpperCase().indexOf("MOPAC") >= 0));
@@ -222,7 +226,7 @@
// Q-Chem input
rd(); // spin
return readBlock("$end");
- }
+ }
if (line.startsWith("$"))
return true; // $NBO
if (line.contains("%mem")) {
@@ -240,25 +244,111 @@
// Jaguar input
return readBlock("&");
}
-
+ if (line.contains("%coords")) {
+ // ORCA input
+ discardLinesUntilContains("coords");
+ return readBlock("end");
+ }
+ if (line.contains("GEOM=PQS")) {
+ // PQS input
+ return readBlock("BASIS");
+ }
if (line.contains("geometry={")) {
// MolPRO via NBO6
readLines(2);
return readBlock("}");
}
-
+
tokens = getTokensStr(line);
- if (tokens.length == 2) {
+
+ if (tokens.length > 10)
+ return readVFI();
+
+ switch (tokens.length) {
+ case 1:
+ lineBuffer.clear();
+ break;
+ case 2:
+ if (parseIntStr(line) > 0 && parseInt() >= 0) {
+ // int int --> Gaussian CFILE (via NBO)
+ readCFI();
+ return (continuing = false);
+ }
getSymbolic();
return true;
+ case 10:
+ // MOPAC archive format
+ if (tokens[0].equals("0"))
+ return (continuing = false);
+ if (tokens[1].indexOf(".") < 0)
+ return true;
+ if (lineBuffer.size() > 0
+ && lineBuffer.get(lineBuffer.size() - 1).length < 8)
+ lineBuffer.clear();
+ break;
}
lineBuffer.addLast(tokens);
return true;
}
+ private void readCFI() throws Exception {
+ // from NBO
+ tokens = getTokens();
+ int nAtoms = (int) getValue(0);
+ int nBonds = (int) getValue(1);
+ Map<String, Atom> map = new Hashtable<String, Atom>();
+ for (int i = 0; i < nAtoms; i++) {
+ tokens = getTokensStr(rd());
+ if (tokens[1].equals("0"))
+ continue;
+ Atom a = addAtomXYZSymName(tokens, 2, null, null);
+ a.elementNumber = (short) getValue(1);
+ map.put(tokens[0], a);
+ }
+ float[] bonds = fillFloatArray(null, 0, new float[nBonds * 2]);
+ float[] orders = fillFloatArray(null, 0, new float[nBonds]);
+ for (int i = 0, pt = 0; i < nBonds; i++)
+ asc.addBond(new Bond(map.get("" + (int) bonds[pt++]).index, map.get(""
+ + (int) bonds[pt++]).index, (int) orders[i]));
+ }
+
+ private boolean readVFI() throws Exception {
+ // VFI format -- more than 10 tokens
+ // 0 0 0 1 1 0.0000 0 0.00 0 0.00 0 2
+ // 0 0 1 2 74 1.6040 1 0.00 0 0.00 0 1 3 4
5 6 7
+ // 0 1 2 3 1 1.6040 2 116.57 3 0.00 0 2
+ // 3 1 2 4 1 1.6040 4 116.57 5 216.00 6 2
+ // 3 1 2 5 1 1.6040 7 63.43 8 108.00 9 2
+ // 1 4 2 7 1 1.6040 10 63.43 11 108.00 12 2
+ // 4 3 2 6 1 1.6040 13 63.43 14 108.00 15 2
+ // 6 2 3 8 0 1.0000 16 120.00 17 72.00 18
+
+ Map<String, Atom> map = new Hashtable<String, Atom>();
+ Lst<String[]> bonds = new Lst<String[]>();
+ while (tokens != null && tokens.length > 0) {
+ for (int i = tokens.length; --i >= 11;)
+ bonds.addLast(new String[] { tokens[3], tokens[i] });
+ String id = tokens[3];
+ tokens = (tokens[2].equals("0") ? new String[] { tokens[4] } : tokens[1]
+ .equals("0") ? new String[] { tokens[4], tokens[2], tokens[5] }
+ : tokens[0].equals("0") ? new String[] { tokens[4], tokens[2],
+ tokens[5], tokens[1], tokens[7] }
+ : new String[] { tokens[4], tokens[2], tokens[5], tokens[1],
+ tokens[7], tokens[0], tokens[9] });
+ Atom atom = getAtom();
+ map.put(id, atom);
+ tokens = getTokensStr(rd());
+ }
+ for (int i = bonds.size(); --i >= 0;) {
+ String[] b = bonds.get(i);
+ asc.addBond(new Bond(map.get(b[0]).index, map.get(b[1]).index, 1));
+ }
+ return (continuing = false);
+ }
+
private boolean readBlock(String strEnd) throws Exception {
lineBuffer.clear();
- while (rd() != null && cleanLine() != null
+ while (rd() != null && cleanLine() != null
&& (strEnd == null ? line.length() > 0 : line.indexOf(strEnd) < 0))
lineBuffer.addLast(getTokens());
return (continuing = false);
@@ -268,7 +358,8 @@
// remove commas for Gaussian and parenthetical expressions for MOPAC
line = line.replace(',', ' ');
int pt1, pt2;
- while ((pt1 = line.indexOf('(')) >= 0 && (pt2 = line.indexOf('(', pt1)) >=
0)
+ while ((pt1 = line.indexOf('(')) >= 0
+ && (pt2 = line.indexOf('(', pt1)) >= 0)
line = line.substring(0, pt1) + " " + line.substring(pt2 + 1);
return (line = line.trim());
}
@@ -290,8 +381,7 @@
Logger.info("symbolic " + tokens[0] + " = " + f);
}
- private void getAtom() throws Exception {
- float f;
+ private Atom getAtom() throws Exception {
Atom atom = new Atom();
String element = tokens[0];
int i = element.length();
@@ -299,8 +389,8 @@
//continue;
}
if (++i == 0)
- throw new Exception("Bad Z-matrix atom name");
- if (i == element.length()) {
+ element = JmolAdapter.getElementSymbol(parseIntStr(element));
+ if (i == 0 || i == element.length()) {
// no number -- append ac
atom.atomName = element + (ac + 1);
} else {
@@ -308,64 +398,76 @@
atom.atomName = element;
element = element.substring(0, i);
}
- if (isMopac && i != tokens[0].length()) // C13 == 13C
+ if (isMopac && i != tokens[0].length()) // C13 == 13C
element = tokens[0].substring(i) + element;
+ parseAtomTokens(atom, element);
+ return atom;
+ }
+
+ private void parseAtomTokens(Atom atom, String element) throws Exception {
setElementAndIsotope(atom, element);
-
+
+ if (tokens.length > 1 && tokens[1].indexOf(".") >= 0) {
+ // C
+ // O 1.200000 1 1 0 0
+ // H 1.080000 1 120.000000 1 1 2 0
+ // H 1.080000 0 120.000000 0 180.000000 0 1 2 3
+ // 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
+ String[] t = tokens;
+ int l = t.length;
+ tokens = (t[l - 3].equals("0") ? new String[] { t[0] }
+ : t[l - 2].equals("0") ? new String[] { t[0], t[l - 3], t[1] }
+ : t[l - 1].equals("0") ? new String[] { t[0], t[l - 3], t[1], t[l -
2], t[3] }
+ : new String[] { t[0], t[l - 3], t[1], t[l - 2], t[3], t[l - 1],
t[5] });
+ }
int ia = getAtomIndex(1);
int bondOrder = 0;
switch (tokens.length) {
case 8:
- // angle + dihedral + bond order
- // angle + angle + bond order
+ // distance + angle + dihedral + bond order (not 1)
+ // O2 C1 1.3000 O1 180 X2 0 2
+ // distance + angle + angle + "1"
+ // O2 C1 1.3000 O1 180 X2 120 1
case 6:
- // angle + bond order
- bondOrder = (int) getValue(tokens.length - 1);
- //$FALL-THROUGH$
+ // distance + angle + bond order
+ // O 1 1.3000 2 180 2
+ atom = getAtomGeneral(atom, ia,
+ bondOrder = (int) getValue(tokens.length - 1));
+ break;
case 5:
- // angle
- // Gaussian Sym 0 x y z
- if (tokens.length == 5 && tokens[1].equals("0")) {
+ if (tokens[1].equals("0")) {
+ // Gaussian Sym 0 x y z
atom.set(getValue(2), getValue(3), getValue(4));
- bondOrder = 0;
break;
}
+ // distance + angle
+ // H 1 1.089000 2 109.4710
//$FALL-THROUGH$
case 7:
- // angle + dihedral or angle + angle
- int ib, ic;
- if (tokens.length < 7 && ac != 2
- || (ib = getAtomIndex(3)) < 0
- || (ic = (tokens.length < 7 ? -2 : getAtomIndex(5))) == -1
- ) {
- atom = null;
- } else {
- float d = getValue(2);
- float theta1 = getValue(4);
- float theta2 = (tokens.length < 7 ? Float.MAX_VALUE : getValue(6));
- if (tokens.length == 8 && !isJmolZformat && !isMopac && bondOrder == 1)
- // Gaussian indicator of alternative angle representation
- d = -Math.abs(d);
- atom = setAtom(atom, ia, ib, ic, d, theta1, theta2);
- }
+ // distance + angle + dihedral
+ // H 1 1.089000 2 109.4710 3 120.0000
+ // distance + two angles
+ // H3 N1 1.0 H1 107 H2 107 1
+ atom = getAtomGeneral(atom, ia, 0);
break;
case 4:
- // angle + bond order
- // Gaussian cartesian
if (getAtomIndex(1) < 0) {
+ // Gaussian cartesian
+ // N1 0.0 0.0 0.0
atom.set(getValue(1), getValue(2), getValue(3));
break;
}
+ // distance + bond order
+ // O 1 1.3000 2
bondOrder = (int) getValue(3);
//$FALL-THROUGH$
case 3:
- // angle
- f = getValue(2);
- if (ac != 1
- || (ia = getAtomIndex(1)) != 0) {
+ // distance only
+ // H 1 1.089000
+ if (ac != 1 || (ia = getAtomIndex(1)) != 0) {
atom = null;
} else {
- atom.set(f, 0, 0);
+ atom.set(getValue(2), 0, 0);
}
break;
case 1:
@@ -380,21 +482,35 @@
if (atom == null)
throw new Exception("bad Z-Matrix line");
vAtoms.addLast(atom);
- atomMap.put(atom.atomName, Integer.valueOf(ac));
- ac++;
+ atomMap.put(atom.atomName, Integer.valueOf(ac++));
if (element.startsWith("X") && JmolAdapter.getElementNumber(element) < 1) {
- Logger.info("#dummy atom ignored: atom " + ac + " - "
- + atom.atomName);
+ Logger.info("#dummy atom ignored: atom " + ac + " - " + atom.atomName);
} else {
asc.addAtom(atom);
setAtomCoord(atom);
Logger.info(atom.atomName + " " + atom.x + " " + atom.y + " " + atom.z);
- if (isJmolZformat && bondOrder > 0)
- asc.addBond(new Bond(atom.index,
- vAtoms.get(ia).index, bondOrder));
+ if (bondOrder < 0 || isJmolZformat && bondOrder > 0)
+ asc.addBond(new Bond(atom.index, vAtoms.get(ia).index, Math
+ .abs(bondOrder)));
}
}
+ private Atom getAtomGeneral(Atom atom, int ia, int bondOrder)
+ throws Exception {
+ int ib, ic;
+ if (tokens.length < 7 && ac != 2 || (ib = getAtomIndex(3)) < 0
+ || (ic = (tokens.length < 7 ? -2 : getAtomIndex(5))) == -1) {
+ return null;
+ }
+ float d = getValue(2);
+ float theta1 = getValue(4);
+ float theta2 = (tokens.length < 7 ? Float.MAX_VALUE : getValue(6));
+ if (tokens.length == 8 && !isJmolZformat && !isMopac && bondOrder == 1)
+ // Gaussian indicator of alternative angle representation
+ d = -Math.abs(d);
+ return atom = setAtom(atom, ia, ib, ic, d, theta1, theta2);
+ }
+
private float getSymbolic(String key) {
boolean isNeg = key.startsWith("-");
Float F = symbolicMap.get(isNeg ? key.substring(1) : key);
@@ -403,20 +519,20 @@
float f = F.floatValue();
return (isNeg ? -f : f);
}
-
+
private float getValue(int i) throws Exception {
float f = getSymbolic(tokens[i]);
- if (Float.isNaN(f))
+ if (Float.isNaN(f)) {
f = parseFloatStr(tokens[i]);
- if (Float.isNaN(f))
- throw new Exception("Bad Z-matrix value: " + tokens[i]);
+ if (Float.isNaN(f))
+ throw new Exception("Bad Z-matrix value: " + tokens[i]);
+ }
return f;
}
private int getAtomIndex(int i) {
String name;
- if (i >= tokens.length
- || (name = tokens[i]).indexOf(".") >= 0
+ if (i >= tokens.length || (name = tokens[i]).indexOf(".") >= 0
|| !PT.isLetterOrDigit(name.charAt(0)))
return -1;
int ia = parseIntStr(name);
@@ -426,16 +542,16 @@
if (I == null) {
// We allow just an element name without a number if it is unique.
// The most recent atom match will be used
- for (i = vAtoms.size(); --i >= 0; ) {
+ for (i = vAtoms.size(); --i >= 0;) {
Atom atom = vAtoms.get(i);
- if (atom.atomName.startsWith(name)
+ if (atom.atomName.startsWith(name)
&& atom.atomName.length() > name.length()
&& PT.isDigit(atom.atomName.charAt(name.length()))) {
I = atomMap.get(atom.atomName);
break;
- }
+ }
}
- }
+ }
if (I == null)
ia = -1;
else
@@ -451,9 +567,9 @@
private final V3 v2 = new V3();
private final P4 plane1 = new P4();
private final P4 plane2 = new P4();
-
+
protected Atom setAtom(Atom atom, int ia, int ib, int ic, float d,
- float theta1, float theta2) {
+ float theta1, float theta2) {
if (Float.isNaN(theta1) || Float.isNaN(theta2))
return null;
pt0.setT(vAtoms.get(ia));
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-27
05:38:51 UTC (rev 20145)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-28
20:29:45 UTC (rev 20146)
@@ -156,6 +156,9 @@
private final static String getReaderFromType(String type) {
type = ";" + type.toLowerCase() + ";";
+ if (";cfi;vfi;mnd;jag;adf;gms;g;c;mp;nw;orc;pqs;qc;v;".indexOf(type) >= 0)
+ return "ZMatrix";
+
String set;
int pt;
for (int i = readerSets.length; --i >= 0;)
@@ -212,8 +215,6 @@
* This is only necessary for a few file types, where only numbers are
involved --
* molecular dynamics coordinate files, for instance (mdcrd).
*
- * We must do this in a very specific order. DON'T MESS WITH THIS!
- *
* @param readerOrDocument
* @param returnLines
* @return readerName or a few lines, if requested, or null
@@ -221,24 +222,22 @@
*/
private static String determineAtomSetCollectionReader(Object
readerOrDocument, boolean returnLines)
throws Exception {
+
+
+ // We must do this in a very specific order. DON'T MESS WITH THIS!
+
if (readerOrDocument instanceof GenericBinaryDocument) {
// only binary type to date;
return "PyMOL";
}
+
+ String readerName;
+
LimitedLineReader llr = new LimitedLineReader((BufferedReader)
readerOrDocument, 16384);
- // first check just the first 64 bytes
-
String leader = llr.getHeader(LEADER_CHAR_MAX).trim();
- for (int i = 0; i < fileStartsWithRecords.length; ++i) {
- String[] recordTags = fileStartsWithRecords[i];
- for (int j = 1; j < recordTags.length; ++j) {
- String recordTag = recordTags[j];
- if (leader.startsWith(recordTag))
- return recordTags[0];
- }
- }
+ // Test 1. check magic number for embedded Jmol script or PNGJ
// PNG or BCD-encoded JPG or JPEG
if (leader.indexOf("PNG") == 1 && leader.indexOf("PNGJ") >= 0)
@@ -246,9 +245,12 @@
if (leader.indexOf("PNG") == 1 || leader.indexOf("JPG") == 1
|| leader.indexOf("JFIF") == 6)
return "spt"; // presume embedded script --- allows dragging into Jmol
- if (leader.startsWith("##TITLE"))
- return "Jcampdx";
+ // Test 2. check starting 64 bytes of file
+
+ if ((readerName = checkFileStart(leader)) != null)
+ return readerName;
+
// now allow identification in first 16 lines
// excluding those starting with "#"
@@ -260,149 +262,137 @@
nLines++;
}
- String readerName;
- if ((readerName = checkSpecial(nLines, lines, false)) != null)
+ // Test 3. check special file formats (pass 1)
+
+ if ((readerName = checkSpecial1(nLines, lines)) != null)
return readerName;
+ // Test 4. check line starts
+
if ((readerName = checkLineStarts(lines)) != null)
return readerName;
+ // Test 5. check content of initial 16K bytes of file
+
if ((readerName = checkHeaderContains(llr.getHeader(0))) != null)
return readerName;
- if ((readerName = checkSpecial(nLines, lines, true)) != null)
+ // Test 6. check special file formats (pass 2)
+
+ if ((readerName = checkSpecial2(lines)) != null)
return readerName;
+ // Failed to identify file type
+
return (returnLines ? "\n" + lines[0] + "\n" + lines[1] + "\n" + lines[2]
+ "\n" : null);
}
- private static String checkHeaderContains(String header) throws Exception {
- for (int i = 0; i < headerContainsRecords.length; ++i) {
- String[] recordTags = headerContainsRecords[i];
- for (int j = 1; j < recordTags.length; ++j) {
- String recordTag = recordTags[j];
- if (header.indexOf(recordTag) < 0)
- continue;
- String type = recordTags[0];
- // for XML check for an error message from a server -- certainly not
XML
- // but new CML format includes
xmlns:xhtml="http://www.w3.org/1999/xhtml"; in <cml> tag.
- return (!type.equals("Xml") ? type
- : header.indexOf("<!DOCTYPE HTML PUBLIC") < 0
- && header.indexOf("XHTML") < 0
- && (header.indexOf("xhtml") < 0 || header.indexOf("<cml") >= 0)
- ? getXmlType(header)
- : null);
- }
- }
- return null;
- }
+ ////////////////////////////////////////////////////////////////
+ // Test 2. check to see if first few bytes (trimmed) start with any of these
strings
+ ////////////////////////////////////////////////////////////////
- private static String checkLineStarts(String[] lines) {
- for (int i = 0; i < lineStartsWithRecords.length; ++i) {
- String[] recordTags = lineStartsWithRecords[i];
+ private static String checkFileStart(String leader) {
+ for (int i = 0; i < fileStartsWithRecords.length; ++i) {
+ String[] recordTags = fileStartsWithRecords[i];
for (int j = 1; j < recordTags.length; ++j) {
String recordTag = recordTags[j];
- for (int k = 0; k < lines.length; k++) {
- if (lines[k].startsWith(recordTag))
- return recordTags[0];
- }
+ if (leader.startsWith(recordTag))
+ return recordTags[0];
}
}
return null;
}
- private static String getXmlType(String header) throws Exception {
- if (header.indexOf("http://www.molpro.net/";) >= 0) {
- return "XmlMolpro";
- }
- if (header.indexOf("odyssey") >= 0) {
- return "XmlOdyssey";
- }
- if (header.indexOf("C3XML") >= 0) {
- return "XmlChem3d";
- }
- if (header.indexOf("arguslab") >= 0) {
- return "XmlArgus";
- }
- if (header.indexOf("jvxl") >= 0
- || header.indexOf(CML_NAMESPACE_URI) >= 0
- || header.indexOf("cml:") >= 0) {
- return "XmlCml";
- }
- if (header.indexOf("XSD") >= 0) {
- return "XmlXsd";
- }
- if (header.indexOf(">vasp") >= 0) {
- return "XmlVasp";
- }
- if (header.indexOf("<GEOMETRY_INFO>") >= 0) {
- return "XmlQE";
- }
-
- return "XmlCml(unidentified)";
- }
+ private final static int LEADER_CHAR_MAX = 64;
+
+ private final static String[] sptRecords =
+ { "spt", "# Jmol state", "# Jmol script", "JmolManifest" };
+
+ private final static String[] m3dStartRecords =
+ { "Alchemy", "STRUCTURE 1.00 1" }; // M3D reader is very similar to
Alchemy
+
+ private final static String[] cubeFileStartRecords =
+ {"Cube", "JVXL", "#JVXL"};
+ private final static String[] mol2Records =
+ {"Mol2", "mol2", "@<TRIPOS>"};
-//
-// private final static String checkType(String[][] typeTags, String type) {
-// for (int i = 0; i < typeTags.length; ++i)
-// if (typeTags[i][0].toLowerCase().equals(type))
-// return typeTags[i][0];
-// return null;
-// }
-//
+ private final static String[] webmoFileStartRecords =
+ {"WebMO", "[HEADER]"};
+ private final static String[] moldenFileStartRecords =
+ {"Molden", "[Molden"};
+
+ private final static String[] dcdFileStartRecords =
+ {"BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"};
+
+ private final static String[] tlsDataOnlyFileStartRecords =
+ {"TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"};
- private final static String checkSpecial(int nLines, String[] lines,
- boolean isEnd) {
+ private final static String[] zMatrixFileStartRecords =
+ {"ZMatrix", "#ZMATRIX", "%mem=", "AM1"};
+
+ private final static String[] magresFileStartRecords =
+ {"Magres", "#$magres", "# magres"};
+
+ private final static String[] pymolStartRecords =
+ {"PyMOL", "}q" };
+
+ private final static String[] janaStartRecords =
+ { "Jana", "Version Jana" };
+
+ private final static String[] jsonStartRecords =
+ { "JSON", "{\"mol\":" };
+
+ private final static String[] jcampdxStartRecords =
+ { "Jcampdx", "##TITLE" };
+
+ private final static String[][] fileStartsWithRecords =
+ { sptRecords, m3dStartRecords, cubeFileStartRecords,
+ mol2Records, webmoFileStartRecords,
+ moldenFileStartRecords, dcdFileStartRecords, tlsDataOnlyFileStartRecords,
+ zMatrixFileStartRecords, magresFileStartRecords, pymolStartRecords,
+ janaStartRecords, jsonStartRecords, jcampdxStartRecords };
+
+ ////////////////////////////////////////////////////////////////
+ // Test 3. check first time for special file types
+ ////////////////////////////////////////////////////////////////
+
+ private final static String checkSpecial1(int nLines, String[] lines) {
// the order here is CRITICAL
-
- if (isEnd) {
- if (checkGromacs(lines))
- return "Gromacs";
- if (checkCrystal(lines))
- return "Crystal";
- if (checkCastep(lines))
- return "Castep";
- if (checkVasp(lines, true))
- return "VaspPoscar";
- if (checkVasp(lines, false))
- return "VaspChgcar";
- } else {
- if (nLines == 1 && lines[0].length() > 0
- && PT.isDigit(lines[0].charAt(0)))
- return "Jme"; //only one line, and that line starts with a number
-
- if (checkMopacGraphf(lines))
- return "MopacGraphf"; //must be prior to checkFoldingXyz and checkMol
- if (checkOdyssey(lines))
- return "Odyssey";
- switch (checkMol(lines)) {
- case 1:
- case 3:
- case 2000:
- case 3000:
- return "Mol";
- }
- switch(checkXyz(lines)) {
- case 1:
- return "Xyz";
- case 2:
- return "Bilbao";
- }
- if (checkAlchemy(lines[0]))
- return "Alchemy";
- if (checkFoldingXyz(lines))
- return "FoldingXyz";
- if (checkCube(lines))
- return "Cube";
- if (checkWien2k(lines))
- return "Wien2k";
- if (checkAims(lines))
- return "Aims";
- if (checkGenNBO(lines))
- return "GenNBO";
+
+ if (nLines == 1 && lines[0].length() > 0 && PT.isDigit(lines[0].charAt(0)))
+ return "Jme"; //only one line, and that line starts with a number
+
+ if (checkMopacGraphf(lines))
+ return "MopacGraphf"; //must be prior to checkFoldingXyz and checkMol
+ if (checkOdyssey(lines))
+ return "Odyssey";
+ switch (checkMol(lines)) {
+ case 1:
+ case 3:
+ case 2000:
+ case 3000:
+ return "Mol";
}
+ switch (checkXyz(lines)) {
+ case 1:
+ return "Xyz";
+ case 2:
+ return "Bilbao";
+ }
+ if (checkAlchemy(lines[0]))
+ return "Alchemy";
+ if (checkFoldingXyz(lines))
+ return "FoldingXyz";
+ if (checkCube(lines))
+ return "Cube";
+ if (checkWien2k(lines))
+ return "Wien2k";
+ if (checkAims(lines))
+ return "Aims";
+ if (checkGenNBO(lines))
+ return "GenNBO";
return null;
}
@@ -445,47 +435,6 @@
return false;
}
- private static boolean checkCastep(String[] lines) {
- for ( int i = 0; i<lines.length; i++ ) {
- if (lines[i].indexOf("Frequencies in cm-1") == 1
- || lines[i].contains("CASTEP")
- || lines[i].toUpperCase().startsWith("%BLOCK LATTICE_ABC")
- || lines[i].toUpperCase().startsWith("%BLOCK LATTICE_CART")
- || lines[i].toUpperCase().startsWith("%BLOCK POSITIONS_FRAC")
- || lines[i].toUpperCase().startsWith("%BLOCK POSITIONS_ABS")
- || lines[i].contains("<-- E")) return true;
- }
- return false;
- }
-
- private static boolean checkVasp(String[] lines, boolean isPoscar) {
- String line = lines[isPoscar ? 7 : 6].toLowerCase();
- if (isPoscar && line.contains("selective"))
- line = lines[7].toLowerCase();
- return (line.contains("direct") || line.contains("cartesian"));
- }
-
- private static boolean checkCrystal(String[] lines) {
- String s = lines[1].trim();
- if (s.equals("SLAB") ||s.equals("MOLECULE")
- || s.equals("CRYSTAL")
- || s.equals("POLYMER") || (s = lines[3]).equals("SLAB")
- || s.equals("MOLECULE") || s.equals("POLYMER"))
- return true;
- for (int i = 0; i < lines.length; i++) {
- if (lines[i].trim().equals("OPTGEOM") ||
lines[i].trim().equals("FREQCALC") ||
- lines[i].contains("DOVESI")
- || lines[i].contains("TORINO")
- || lines[i].contains("http://www.crystal.unito.it";)
- //new lenghty scripts for CRYSTAL14
- || lines[i].contains("Pcrystal")
- || lines[i].contains("MPPcrystal")
- || lines[i].contains("crystal executable"))
- return true;
- }
- return false;
- }
-
private static boolean checkCube(String[] lines) {
try {
for (int j = 2; j <= 5; j++) {
@@ -543,16 +492,6 @@
|| lines[2].indexOf(" N A T U R A L A T O M I C O R B I T A L") >=
0);
}
- private static boolean checkGromacs(String[] lines) {
- if (PT.parseInt(lines[1]) == Integer.MIN_VALUE)
- return false;
- int len = -1;
- for (int i = 2; i < 16 && len != 0; i++)
- if ((len = lines[i].length()) != 69 && len != 45 && len != 0)
- return false;
- return true;
- }
-
private static int checkMol(String[] lines) {
String line4trimmed = ("X" + lines[3]).trim().toUpperCase();
if (line4trimmed.length() < 7 || line4trimmed.indexOf(".") >= 0)
@@ -609,11 +548,11 @@
return false;
}
- private static boolean checkWien2k(String[] lines) {
- return (lines[2].startsWith("MODE OF CALC=")
- || lines[2].startsWith(" RELA")
- || lines[2].startsWith(" NREL"));
- }
+ private static boolean checkWien2k(String[] lines) {
+ return (lines[2].startsWith("MODE OF CALC=")
+ || lines[2].startsWith(" RELA") || lines[2]
+ .startsWith(" NREL"));
+ }
private static int checkXyz(String[] lines) {
// first and third lines numerical --> Bilbao format
@@ -631,76 +570,25 @@
}
return 0;
}
-
-
-/*
- private void dumpLines(String[] lines) {
- for (int i = 0; i < lines.length; i++) {
- Logger.info("\nLine "+i + " len " + lines[i].length());
- for (int j = 0; j < lines[i].length(); j++)
- Logger.info("\t"+(int)lines[i].charAt(j));
- }
- Logger.info("");
- }
-
-*/
////////////////////////////////////////////////////////////////
- // these test files that startWith one of these strings
+ // Test 4. One of the first 16 lines starts with one of these strings
////////////////////////////////////////////////////////////////
- private final static int LEADER_CHAR_MAX = 64;
-
- private final static String[] sptRecords =
- { "spt", "# Jmol state", "# Jmol script", "JmolManifest" };
-
- private final static String[] m3dStartRecords =
- { "Alchemy", "STRUCTURE 1.00 1" }; // M3D reader is very similar to
Alchemy
-
- private final static String[] cubeFileStartRecords =
- {"Cube", "JVXL", "#JVXL"};
+ private static String checkLineStarts(String[] lines) {
+ for (int i = 0; i < lineStartsWithRecords.length; ++i) {
+ String[] recordTags = lineStartsWithRecords[i];
+ for (int j = 1; j < recordTags.length; ++j) {
+ String recordTag = recordTags[j];
+ for (int k = 0; k < lines.length; k++) {
+ if (lines[k].startsWith(recordTag))
+ return recordTags[0];
+ }
+ }
+ }
+ return null;
+ }
- private final static String[] mol2Records =
- {"Mol2", "mol2", "@<TRIPOS>"};
-
- private final static String[] webmoFileStartRecords =
- {"WebMO", "[HEADER]"};
-
- private final static String[] moldenFileStartRecords =
- {"Molden", "[Molden"};
-
- private final static String[] dcdFileStartRecords =
- {"BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"};
-
- private final static String[] tlsDataOnlyFileStartRecords =
- {"TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"};
-
- private final static String[] zMatrixFileStartRecords =
- {"ZMatrix", "#ZMATRIX", "%mem="};
-
- private final static String[] magresFileStartRecords =
- {"Magres", "#$magres", "# magres"};
-
- private final static String[] pymolStartRecords =
- {"PyMOL", "}q" };
-
- private final static String[] janaStartRecords =
- { "Jana", "Version Jana" };
-
- private final static String[] jsonStartRecords =
- { "JSON", "{\"mol\":" };
-
- private final static String[][] fileStartsWithRecords =
- { sptRecords, m3dStartRecords, cubeFileStartRecords,
- mol2Records, webmoFileStartRecords,
- moldenFileStartRecords, dcdFileStartRecords, tlsDataOnlyFileStartRecords,
- zMatrixFileStartRecords, magresFileStartRecords, pymolStartRecords,
- janaStartRecords, jsonStartRecords };
-
- ////////////////////////////////////////////////////////////////
- // these test if one of the first 16 lines starts with one of these strings
- ////////////////////////////////////////////////////////////////
-
private final static String[] mmcifLineStartRecords =
{ "MMCif", "_entry.id", "_database_PDB_", "_pdbx_", "_chem_comp.pdbx_type",
"_audit_author.name" };
@@ -763,9 +651,61 @@
////////////////////////////////////////////////////////////////
- // contains formats
+ // Test 5. contents of first 16384 bytes
////////////////////////////////////////////////////////////////
+ private static String checkHeaderContains(String header) throws Exception {
+ for (int i = 0; i < headerContainsRecords.length; ++i) {
+ String[] recordTags = headerContainsRecords[i];
+ for (int j = 1; j < recordTags.length; ++j) {
+ String recordTag = recordTags[j];
+ if (header.indexOf(recordTag) < 0)
+ continue;
+ String type = recordTags[0];
+ // for XML check for an error message from a server -- certainly not
XML
+ // but new CML format includes
xmlns:xhtml="http://www.w3.org/1999/xhtml"; in <cml> tag.
+ return (!type.equals("Xml") ? type
+ : header.indexOf("<!DOCTYPE HTML PUBLIC") < 0
+ && header.indexOf("XHTML") < 0
+ && (header.indexOf("xhtml") < 0 || header.indexOf("<cml") >= 0)
+ ? getXmlType(header)
+ : null);
+ }
+ }
+ return null;
+ }
+
+ private static String getXmlType(String header) throws Exception {
+ if (header.indexOf("http://www.molpro.net/";) >= 0) {
+ return "XmlMolpro";
+ }
+ if (header.indexOf("odyssey") >= 0) {
+ return "XmlOdyssey";
+ }
+ if (header.indexOf("C3XML") >= 0) {
+ return "XmlChem3d";
+ }
+ if (header.indexOf("arguslab") >= 0) {
+ return "XmlArgus";
+ }
+ if (header.indexOf("jvxl") >= 0
+ || header.indexOf(CML_NAMESPACE_URI) >= 0
+ || header.indexOf("cml:") >= 0) {
+ return "XmlCml";
+ }
+ if (header.indexOf("XSD") >= 0) {
+ return "XmlXsd";
+ }
+ if (header.indexOf(">vasp") >= 0) {
+ return "XmlVasp";
+ }
+ if (header.indexOf("<GEOMETRY_INFO>") >= 0) {
+ return "XmlQE";
+ }
+
+ return "XmlCml(unidentified)";
+ }
+
private final static String[] bilbaoContainsRecords =
{ "Bilbao", ">Bilbao Crystallographic Server<" };
@@ -849,7 +789,7 @@
{ "GaussianFchk", "Number of point charges in /Mol/" };
private final static String[] zmatrixContainsRecords =
- { "ZMatrix", " ATOMS cartesian", "$molecule", "&zmat", "geometry={", "$DATA"
};
+ { "ZMatrix", " ATOMS cartesian", "$molecule", "&zmat", "geometry={",
"$DATA", "%coords", "GEOM=PQS" };
private final static String[][] headerContainsRecords =
@@ -866,5 +806,77 @@
zmatrixContainsRecords
};
+
+ ////////////////////////////////////////////////////////////////
+ // Test 6. check second time for special file types
+ ////////////////////////////////////////////////////////////////
+
+ private final static String checkSpecial2(String[] lines) {
+ // the order here is CRITICAL
+ if (checkGromacs(lines))
+ return "Gromacs";
+ if (checkCrystal(lines))
+ return "Crystal";
+ if (checkCastep(lines))
+ return "Castep";
+ if (checkVasp(lines, true))
+ return "VaspPoscar";
+ if (checkVasp(lines, false))
+ return "VaspChgcar";
+ return null;
+ }
+
+ private static boolean checkCrystal(String[] lines) {
+ String s = lines[1].trim();
+ if (s.equals("SLAB") ||s.equals("MOLECULE")
+ || s.equals("CRYSTAL")
+ || s.equals("POLYMER") || (s = lines[3]).equals("SLAB")
+ || s.equals("MOLECULE") || s.equals("POLYMER"))
+ return true;
+ for (int i = 0; i < lines.length; i++) {
+ if (lines[i].trim().equals("OPTGEOM") ||
lines[i].trim().equals("FREQCALC") ||
+ lines[i].contains("DOVESI")
+ || lines[i].contains("TORINO")
+ || lines[i].contains("http://www.crystal.unito.it";)
+ //new lenghty scripts for CRYSTAL14
+ || lines[i].contains("Pcrystal")
+ || lines[i].contains("MPPcrystal")
+ || lines[i].contains("crystal executable"))
+ return true;
+ }
+ return false;
+ }
+
+ private static boolean checkGromacs(String[] lines) {
+ if (PT.parseInt(lines[1]) == Integer.MIN_VALUE)
+ return false;
+ int len = -1;
+ for (int i = 2; i < 16 && len != 0; i++)
+ if ((len = lines[i].length()) != 69 && len != 45 && len != 0)
+ return false;
+ return true;
+ }
+
+ private static boolean checkCastep(String[] lines) {
+ for ( int i = 0; i<lines.length; i++ ) {
+ if (lines[i].indexOf("Frequencies in cm-1") == 1
+ || lines[i].contains("CASTEP")
+ || lines[i].toUpperCase().startsWith("%BLOCK LATTICE_ABC")
+ || lines[i].toUpperCase().startsWith("%BLOCK LATTICE_CART")
+ || lines[i].toUpperCase().startsWith("%BLOCK POSITIONS_FRAC")
+ || lines[i].toUpperCase().startsWith("%BLOCK POSITIONS_ABS")
+ || lines[i].contains("<-- E")) return true;
+ }
+ return false;
+ }
+
+ private static boolean checkVasp(String[] lines, boolean isPoscar) {
+ String line = lines[isPoscar ? 7 : 6].toLowerCase();
+ if (isPoscar && line.contains("selective"))
+ line = lines[7].toLowerCase();
+ return (line.contains("direct") || line.contains("cartesian"));
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/io/JmolUtil.java
===================================================================
--- trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-27 05:38:51 UTC (rev
20145)
+++ trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-28 20:29:45 UTC (rev
20146)
@@ -370,7 +370,7 @@
if (tokens[0].indexOf(".") > 0)
return (line3.length() >= 60 || tokens.length != 3 ? null :
"VaspChgcar"); // M40 files are > 60 char
if (nAtoms >= 0)
- return "Cube"; //Can't be a Jvxl file;
+ return (tokens.length == 4 ? "Cube" : null); //Can't be a Jvxl file;
nAtoms = -nAtoms;
for (int i = 4 + nAtoms; --i >= 0;)
if ((line = br.readLineWithNewline()) == null)
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2014-11-27 05:38:51 UTC (rev
20145)
+++ trunk/Jmol/src/org/jmol/script/T.java 2014-11-28 20:29:45 UTC (rev
20146)
@@ -1000,6 +1000,7 @@
public final static int drawhover = booleanparam | 56;
public final static int drawpicking = booleanparam | 57;
public final static int dsspcalchydrogen = booleanparam | 58;
+ public final static int dynamicmeasurements = booleanparam | 59;
//DEPRECATED; not implemented; leave here to avoid SET error
public final static int ellipsoidarcs = booleanparam | 60;
public final static int ellipsoidarrows = booleanparam | 61;
public final static int ellipsoidaxes = booleanparam | 62;
@@ -1176,7 +1177,7 @@
public final static int dotted = misc | 102;
public final static int downsample = misc | 104;
public final static int drawing = misc | 105;
- public final static int eccentricity = misc | 106;
+ public final static int eccentricity = misc | 107;
public final static int ed = misc | 108 | expression;
public final static int edges = misc | 109;
public final static int energy = misc | 110;
@@ -2195,6 +2196,7 @@
"distanceFactor",
"downsample",
"drawing",
+ "dynamicMeasurements",
"eccentricity",
"ed",
"edges",
@@ -3216,6 +3218,7 @@
distancefactor, // "distanceFactor"
downsample, // "downsample"
drawing, // "drawing"
+ dynamicmeasurements, // "dynamicMeasurements"
eccentricity, // "eccentricity"
ed, // "ed"
edges, // "edges"
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-27 05:38:51 UTC
(rev 20145)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-28 20:29:45 UTC
(rev 20146)
@@ -15,8 +15,16 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.11_2014.11.27"
+Jmol.___JmolVersion="14.3.11_2014.11.28"
+new feature: readers for ESS input types: CFILE, VFILE, MOPAC, Gaussian,
GAMESS, Orca, PQS
+ -- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
+
+bug fix: dynamicMeasurements deprecated in 14.1.1 but
+ not left in as a valid token to allow use
+
+JmolVersion="14.3.11_2014.11.27"
+
new feature: GAMESS input reader
new feature: NBO .37 archive file coordinate reader (not MOs)
new feature: ZMatrixReader also serves as simple input file reader
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