Revision: 20147
http://sourceforge.net/p/jmol/code/20147
Author: hansonr
Date: 2014-11-28 21:19:35 +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, NWChem,
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
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacArchiveReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/adapter/readers/simple/InputReader.java
Removed Paths:
-------------
trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
Copied: trunk/Jmol/src/org/jmol/adapter/readers/simple/InputReader.java (from
rev 20146, trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java)
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/InputReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/InputReader.java
2014-11-28 21:19:35 UTC (rev 20147)
@@ -0,0 +1,617 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2006-09-28 23:13:00 -0500 (Thu, 28 Sep 2006) $
+ * $Revision: 5772 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.jmol.adapter.readers.simple;
+
+import javajs.util.Lst;
+import java.util.Hashtable;
+
+import java.util.Map;
+
+import org.jmol.adapter.smarter.AtomSetCollectionReader;
+import org.jmol.adapter.smarter.Bond;
+import org.jmol.adapter.smarter.Atom;
+
+import org.jmol.api.JmolAdapter;
+import org.jmol.util.Logger;
+
+import javajs.util.Measure;
+import javajs.util.P3;
+import javajs.util.P4;
+import javajs.util.PT;
+import javajs.util.Quat;
+import javajs.util.V3;
+
+public class InputReader extends AtomSetCollectionReader {
+ /*
+ * A simple Z-matrix reader, also serves as simple input file reader for
+ * CFILE, VFILE, PQS, Orca, NWChem, GAMESS, Gaussian, MOPAC, Q-Chem, Jaguar,
MolPro,
+ * and ADF, as produced by NBO6Pro
+ *
+ * Can be invoked using ZMATRIX:: or with file starting with #ZMATRIX
+ *
+ * MOPAC, CFILE ,and VFILE require MND::, CFI:: (or C::), and VFI:: (or
V::) respectively
+ *
+ * Other invocations include: ADF::, GAU::(or G::), GMS::, JAG::, MP::,
ORC::, NW::, PQS::, QC::,
+ * but those are optional.
+ *
+ * # are comments; can include jmolscript: xxxx
+ *
+ *
+ * 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
+ */
+
+ // 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:
+ //
+ // #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>();
+ private String[] tokens;
+ private boolean isJmolZformat;
+ private Lst<String[]> lineBuffer = new Lst<String[]>();
+ 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("#") || line.startsWith("*") || isMopac && isHeader) {
+ if (line.startsWith("#ZMATRIX"))
+ isJmolZformat = line.toUpperCase().indexOf("GAUSSIAN") < 0
+ && !(isMopac = (line.toUpperCase().indexOf("MOPAC") >= 0));
+ checkCurrentLineForScript();
+ return true;
+ }
+ if (line.indexOf("#") >= 0)
+ line = line.substring(0, line.indexOf("#"));
+ if (line.indexOf(":") >= 0)
+ return true; // Variables: or Constants:
+ if (line.contains("$molecule")) {
+ // Q-Chem input
+ rd(); // spin
+ return readBlock("$end");
+ }
+ if (line.startsWith("$"))
+ return true; // $NBO
+
+ if (line.contains("%mem")) {
+ // Gaussian
+ discardLinesUntilBlank();
+ discardLinesUntilBlank();
+ rd(); // spin
+ return readBlock(null);
+ }
+
+ if (line.contains("ATOMS cartesian")) {
+ // ADF input
+ return readBlock("END");
+ }
+
+ if (line.contains("geometry units angstroms")) {
+ // NWChem input
+ return readBlock("end");
+ }
+
+ if (line.contains("&zmat")) {
+ // 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 > 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
+ && (strEnd == null ? line.length() > 0 : line.indexOf(strEnd) < 0))
+ lineBuffer.addLast(getTokens());
+ return (continuing = false);
+ }
+
+ private String cleanLine() {
+ // 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)
+ line = line.substring(0, pt1) + " " + line.substring(pt2 + 1);
+ return (line = line.trim());
+ }
+
+ @Override
+ protected void finalizeSubclassReader() throws Exception {
+ int firstLine = 0;
+ for (int i = firstLine; i < lineBuffer.size(); i++)
+ if ((tokens = lineBuffer.get(i)).length > 0)
+ getAtom();
+ finalizeReaderASCR();
+ }
+
+ private void getSymbolic() {
+ if (symbolicMap.containsKey(tokens[0]))
+ return;
+ float f = parseFloatStr(tokens[1]);
+ symbolicMap.put(tokens[0], Float.valueOf(f));
+ Logger.info("symbolic " + tokens[0] + " = " + f);
+ }
+
+ private Atom getAtom() throws Exception {
+ Atom atom = new Atom();
+ String element = tokens[0];
+ int i = element.length();
+ while (--i >= 0 && PT.isDigit(element.charAt(i))) {
+ //continue;
+ }
+ if (++i == 0)
+ element = JmolAdapter.getElementSymbol(parseIntStr(element));
+ if (i == 0 || i == element.length()) {
+ // no number -- append ac
+ atom.atomName = element + (ac + 1);
+ } else {
+ // has a number -- pull out element
+ atom.atomName = element;
+ element = element.substring(0, i);
+ }
+ 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 > 5 && 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:
+ // 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:
+ // distance + angle + bond order
+ // O 1 1.3000 2 180 2
+ atom = getAtomGeneral(atom, ia,
+ bondOrder = (int) getValue(tokens.length - 1));
+ break;
+ case 5:
+ if (tokens[1].equals("0")) {
+ // Gaussian Sym 0 x y z
+ atom.set(getValue(2), getValue(3), getValue(4));
+ break;
+ }
+ // distance + angle
+ // H 1 1.089000 2 109.4710
+ //$FALL-THROUGH$
+ case 7:
+ // 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:
+ 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:
+ // distance only
+ // H 1 1.089000
+ if (ac != 1 || (ia = getAtomIndex(1)) != 0) {
+ atom = null;
+ } else {
+ atom.set(getValue(2), 0, 0);
+ }
+ break;
+ case 1:
+ if (ac != 0)
+ atom = null;
+ else
+ atom.set(0, 0, 0);
+ break;
+ default:
+ atom = null;
+ }
+ if (atom == null)
+ throw new Exception("bad Z-Matrix line");
+ vAtoms.addLast(atom);
+ atomMap.put(atom.atomName, Integer.valueOf(ac++));
+ if (element.startsWith("X") && JmolAdapter.getElementNumber(element) < 1) {
+ 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 (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);
+ if (F == null)
+ return Float.NaN;
+ float f = F.floatValue();
+ return (isNeg ? -f : f);
+ }
+
+ private float getValue(int i) throws Exception {
+ float f = getSymbolic(tokens[i]);
+ if (Float.isNaN(f)) {
+ f = parseFloatStr(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
+ || !PT.isLetterOrDigit(name.charAt(0)))
+ return -1;
+ int ia = parseIntStr(name);
+ if (ia <= 0 || name.length() != ("" + ia).length()) {
+ // check for clean integer, not "13C1"
+ Integer I = atomMap.get(name);
+ 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;) {
+ Atom atom = vAtoms.get(i);
+ 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
+ ia = I.intValue();
+ } else {
+ ia--;
+ }
+ return ia;
+ }
+
+ private final P3 pt0 = new P3();
+ private final V3 v1 = new V3();
+ 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) {
+ if (Float.isNaN(theta1) || Float.isNaN(theta2))
+ return null;
+ pt0.setT(vAtoms.get(ia));
+ v1.sub2(vAtoms.get(ib), pt0);
+ v1.normalize();
+ if (theta2 == Float.MAX_VALUE) {
+ // just the first angle being set
+ v2.set(0, 0, 1);
+ (Quat.newVA(v2, theta1)).transformP2(v1, v2);
+ } else if (d >= 0) {
+ // theta2 is a dihedral angle
+ // just do two quaternion rotations
+ v2.sub2(vAtoms.get(ic), pt0);
+ v2.cross(v1, v2);
+ (Quat.newVA(v2, theta1)).transformP2(v1, v2);
+ (Quat.newVA(v1, -theta2)).transformP2(v2, v2);
+ } else {
+ // d < 0
+ // theta1 and theta2 are simple angles atom-ia-ib and atom-ia-ic
+ // get vector that is intersection of two planes and go from there
+ Measure.getPlaneThroughPoint(setAtom(atom, ia, ib, ic, -d, theta1, 0),
+ v1, plane1);
+ Measure.getPlaneThroughPoint(setAtom(atom, ia, ic, ib, -d, theta2, 0),
+ v1, plane2);
+ Lst<Object> list = Measure.getIntersectionPP(plane1, plane2);
+ if (list.size() == 0)
+ return null;
+ pt0.setT((P3) list.get(0));
+ d = (float) Math.sqrt(d * d - pt0.distanceSquared(vAtoms.get(ia)))
+ * Math.signum(theta1) * Math.signum(theta2);
+ v2.setT((V3) list.get(1));
+ }
+ atom.scaleAdd2(d, v2, pt0);
+ return atom;
+ }
+}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacArchiveReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacArchiveReader.java
2014-11-28 20:29:45 UTC (rev 20146)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacArchiveReader.java
2014-11-28 21:19:35 UTC (rev 20147)
@@ -41,7 +41,7 @@
*
*/
-public class MopacArchiveReader extends ZMatrixReader {
+public class MopacArchiveReader extends InputReader {
@Override
Deleted: trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-28 20:29:45 UTC (rev 20146)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-28 21:19:35 UTC (rev 20147)
@@ -1,608 +0,0 @@
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2006-09-28 23:13:00 -0500 (Thu, 28 Sep 2006) $
- * $Revision: 5772 $
- *
- * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: jmol-develop...@lists.sf.net
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-
-package org.jmol.adapter.readers.simple;
-
-import javajs.util.Lst;
-import java.util.Hashtable;
-
-import java.util.Map;
-
-import org.jmol.adapter.smarter.AtomSetCollectionReader;
-import org.jmol.adapter.smarter.Bond;
-import org.jmol.adapter.smarter.Atom;
-
-import org.jmol.api.JmolAdapter;
-import org.jmol.util.Logger;
-
-import javajs.util.Measure;
-import javajs.util.P3;
-import javajs.util.P4;
-import javajs.util.PT;
-import javajs.util.Quat;
-import javajs.util.V3;
-
-public class ZMatrixReader extends AtomSetCollectionReader {
- /*
- * 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
- *
- *
- * 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
- */
-
- // 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:
- //
- // #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>();
- private String[] tokens;
- private boolean isJmolZformat;
- private Lst<String[]> lineBuffer = new Lst<String[]>();
- 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("#") || line.startsWith("*") || isMopac && isHeader) {
- if (line.startsWith("#ZMATRIX"))
- isJmolZformat = line.toUpperCase().indexOf("GAUSSIAN") < 0
- && !(isMopac = (line.toUpperCase().indexOf("MOPAC") >= 0));
- checkCurrentLineForScript();
- return true;
- }
- if (line.indexOf("#") >= 0)
- line = line.substring(0, line.indexOf("#"));
- if (line.indexOf(":") >= 0)
- return true; // Variables: or Constants:
- if (line.contains("$molecule")) {
- // Q-Chem input
- rd(); // spin
- return readBlock("$end");
- }
- if (line.startsWith("$"))
- return true; // $NBO
- if (line.contains("%mem")) {
- // Gaussian
- discardLinesUntilBlank();
- discardLinesUntilBlank();
- rd(); // spin
- return readBlock(null);
- }
- if (line.contains("ATOMS cartesian")) {
- // ADF input
- return readBlock("END");
- }
- if (line.contains("&zmat")) {
- // 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 > 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
- && (strEnd == null ? line.length() > 0 : line.indexOf(strEnd) < 0))
- lineBuffer.addLast(getTokens());
- return (continuing = false);
- }
-
- private String cleanLine() {
- // 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)
- line = line.substring(0, pt1) + " " + line.substring(pt2 + 1);
- return (line = line.trim());
- }
-
- @Override
- protected void finalizeSubclassReader() throws Exception {
- int firstLine = 0;
- for (int i = firstLine; i < lineBuffer.size(); i++)
- if ((tokens = lineBuffer.get(i)).length > 0)
- getAtom();
- finalizeReaderASCR();
- }
-
- private void getSymbolic() {
- if (symbolicMap.containsKey(tokens[0]))
- return;
- float f = parseFloatStr(tokens[1]);
- symbolicMap.put(tokens[0], Float.valueOf(f));
- Logger.info("symbolic " + tokens[0] + " = " + f);
- }
-
- private Atom getAtom() throws Exception {
- Atom atom = new Atom();
- String element = tokens[0];
- int i = element.length();
- while (--i >= 0 && PT.isDigit(element.charAt(i))) {
- //continue;
- }
- if (++i == 0)
- element = JmolAdapter.getElementSymbol(parseIntStr(element));
- if (i == 0 || i == element.length()) {
- // no number -- append ac
- atom.atomName = element + (ac + 1);
- } else {
- // has a number -- pull out element
- atom.atomName = element;
- element = element.substring(0, i);
- }
- 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:
- // 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:
- // distance + angle + bond order
- // O 1 1.3000 2 180 2
- atom = getAtomGeneral(atom, ia,
- bondOrder = (int) getValue(tokens.length - 1));
- break;
- case 5:
- if (tokens[1].equals("0")) {
- // Gaussian Sym 0 x y z
- atom.set(getValue(2), getValue(3), getValue(4));
- break;
- }
- // distance + angle
- // H 1 1.089000 2 109.4710
- //$FALL-THROUGH$
- case 7:
- // 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:
- 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:
- // distance only
- // H 1 1.089000
- if (ac != 1 || (ia = getAtomIndex(1)) != 0) {
- atom = null;
- } else {
- atom.set(getValue(2), 0, 0);
- }
- break;
- case 1:
- if (ac != 0)
- atom = null;
- else
- atom.set(0, 0, 0);
- break;
- default:
- atom = null;
- }
- if (atom == null)
- throw new Exception("bad Z-Matrix line");
- vAtoms.addLast(atom);
- atomMap.put(atom.atomName, Integer.valueOf(ac++));
- if (element.startsWith("X") && JmolAdapter.getElementNumber(element) < 1) {
- 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 (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);
- if (F == null)
- return Float.NaN;
- float f = F.floatValue();
- return (isNeg ? -f : f);
- }
-
- private float getValue(int i) throws Exception {
- float f = getSymbolic(tokens[i]);
- if (Float.isNaN(f)) {
- f = parseFloatStr(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
- || !PT.isLetterOrDigit(name.charAt(0)))
- return -1;
- int ia = parseIntStr(name);
- if (ia <= 0 || name.length() != ("" + ia).length()) {
- // check for clean integer, not "13C1"
- Integer I = atomMap.get(name);
- 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;) {
- Atom atom = vAtoms.get(i);
- 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
- ia = I.intValue();
- } else {
- ia--;
- }
- return ia;
- }
-
- private final P3 pt0 = new P3();
- private final V3 v1 = new V3();
- 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) {
- if (Float.isNaN(theta1) || Float.isNaN(theta2))
- return null;
- pt0.setT(vAtoms.get(ia));
- v1.sub2(vAtoms.get(ib), pt0);
- v1.normalize();
- if (theta2 == Float.MAX_VALUE) {
- // just the first angle being set
- v2.set(0, 0, 1);
- (Quat.newVA(v2, theta1)).transformP2(v1, v2);
- } else if (d >= 0) {
- // theta2 is a dihedral angle
- // just do two quaternion rotations
- v2.sub2(vAtoms.get(ic), pt0);
- v2.cross(v1, v2);
- (Quat.newVA(v2, theta1)).transformP2(v1, v2);
- (Quat.newVA(v1, -theta2)).transformP2(v2, v2);
- } else {
- // d < 0
- // theta1 and theta2 are simple angles atom-ia-ib and atom-ia-ic
- // get vector that is intersection of two planes and go from there
- Measure.getPlaneThroughPoint(setAtom(atom, ia, ib, ic, -d, theta1, 0),
- v1, plane1);
- Measure.getPlaneThroughPoint(setAtom(atom, ia, ic, ib, -d, theta2, 0),
- v1, plane2);
- Lst<Object> list = Measure.getIntersectionPP(plane1, plane2);
- if (list.size() == 0)
- return null;
- pt0.setT((P3) list.get(0));
- d = (float) Math.sqrt(d * d - pt0.distanceSquared(vAtoms.get(ia)))
- * Math.signum(theta1) * Math.signum(theta2);
- v2.setT((V3) list.get(1));
- }
- atom.scaleAdd2(d, v2, pt0);
- return atom;
- }
-}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-28
20:29:45 UTC (rev 20146)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-28
21:19:35 UTC (rev 20147)
@@ -52,7 +52,7 @@
"WebMO;",
"pdb.", ";Pdb;Pqr;P2n;",
"pymol.", ";PyMOL;",
- "simple.",
";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;ZMatrix;",
+ "simple.",
";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;Input;",
"xtal.",
";Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;"
+
"VaspPoscar;VaspChgcar;Wien2k;Xcrysden;",
"xml.",
";XmlArgus;XmlCml;XmlChem3d;XmlMolpro;XmlOdyssey;XmlXsd;XmlVasp;XmlQE;",
@@ -156,8 +156,8 @@
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";
+ if
(";zmatrix;cfi;c;vfi;v;mnd;jag;adf;gms;g;gau;mp;nw;orc;pqs;qc;".indexOf(type)
>= 0)
+ return "Input";
String set;
int pt;
@@ -329,8 +329,8 @@
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=", "AM1"};
+ private final static String[] inputFileStartRecords =
+ {"Input", "#ZMATRIX", "%mem=", "AM1"};
private final static String[] magresFileStartRecords =
{"Magres", "#$magres", "# magres"};
@@ -351,7 +351,7 @@
{ sptRecords, m3dStartRecords, cubeFileStartRecords,
mol2Records, webmoFileStartRecords,
moldenFileStartRecords, dcdFileStartRecords, tlsDataOnlyFileStartRecords,
- zMatrixFileStartRecords, magresFileStartRecords, pymolStartRecords,
+ inputFileStartRecords, magresFileStartRecords, pymolStartRecords,
janaStartRecords, jsonStartRecords, jcampdxStartRecords };
////////////////////////////////////////////////////////////////
@@ -788,10 +788,9 @@
private final static String[] gaussianFchkContainsRecords =
{ "GaussianFchk", "Number of point charges in /Mol/" };
- private final static String[] zmatrixContainsRecords =
- { "ZMatrix", " ATOMS cartesian", "$molecule", "&zmat", "geometry={",
"$DATA", "%coords", "GEOM=PQS" };
-
-
+ private final static String[] inputContainsRecords =
+ { "Input", " ATOMS cartesian", "$molecule", "&zmat", "geometry={", "$DATA",
"%coords", "GEOM=PQS", "geometry units angstroms" };
+
private final static String[][] headerContainsRecords =
{ sptRecords, bilbaoContainsRecords, xmlContainsRecords,
gaussianContainsRecords,
ampacContainsRecords, mopacContainsRecords, qchemContainsRecords,
@@ -803,7 +802,7 @@
dmolContainsRecords, gulpContainsRecords,
espressoContainsRecords, siestaContainsRecords, xcrysDenContainsRecords,
mopacArchiveContainsRecords,abinitContainsRecords,gaussianFchkContainsRecords,
- zmatrixContainsRecords
+ inputContainsRecords
};
@@ -871,9 +870,10 @@
}
private static boolean checkVasp(String[] lines, boolean isPoscar) {
- String line = lines[isPoscar ? 7 : 6].toLowerCase();
+ int i = (isPoscar ? (lines[5].length() < 2 ? 8 : 7) : 6);
+ String line = lines[i].toLowerCase();
if (isPoscar && line.contains("selective"))
- line = lines[7].toLowerCase();
+ line = lines[++i].toLowerCase();
return (line.contains("direct") || line.contains("cartesian"));
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-28 20:29:45 UTC
(rev 20146)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-28 21:19:35 UTC
(rev 20147)
@@ -17,7 +17,7 @@
Jmol.___JmolVersion="14.3.11_2014.11.28"
-new feature: readers for ESS input types: CFILE, VFILE, MOPAC, Gaussian,
GAMESS, Orca, PQS
+new feature: readers for ESS input types: CFILE, VFILE, MOPAC, NWChem,
Gaussian, GAMESS, Orca, PQS
-- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
bug fix: dynamicMeasurements deprecated in 14.1.1 but
Modified: trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java
2014-11-28 20:29:45 UTC (rev 20146)
+++ trunk/Jmol/test/org/jmol/adapter/smarter/TestSmarterJmolAdapter.java
2014-11-28 21:19:35 UTC (rev 20147)
@@ -80,7 +80,7 @@
result.addDirectory("dmol", "outmol", "Dmol");
result.addDirectory("folding", "xyz;xyz.gz", "FoldingXyz");
result.addDirectory("../Jmol-FAH/projects", "xyz;xyz.gz", "FoldingXyz");
- result.addDirectory("gamess", "log;out", ";Gamess;GamessUS;GamessUK;");
+ result.addDirectory("gamess", "log;out;txt", ";Gamess;GamessUS;GamessUK;");
result.addDirectory("gaussian", "log;out", "Gaussian");
result.addDirectory("gennbo", "out;36;37", "GenNBO");
result.addDirectory("ghemical", "gpr", "GhemicalMM");
@@ -117,7 +117,7 @@
result.addDirectory("webmo", "mo", "WebMO");
result.addDirectory("xsd", "xsd", "XmlXsd");
result.addDirectory("xyz", "xyz", "Xyz");
- result.addDirectory("zmatrix", "txt;zmat", "ZMatrix");
+ result.addDirectory("zmatrix", "txt;zmat", "Input");
return result;
}
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