• Home
• net.sourceforge.jmol
• jmol
• 14.12.1
• source code
• IsoExt.java

×

Project download

Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance.
Project price only 1 $

You can buy this project and download/modify it how often you want.

org.jmol.scriptext.IsoExt Maven / Gradle / Ivy

/* $RCSfile$
 * $Author: hansonr $
 * $Date: 2006-03-05 12:22:08 -0600 (Sun, 05 Mar 2006) $
 * $Revision: 4545 $
 *
 * Copyright (C) 2002-2005  The Jmol Development Team
 *
 * Contact: [email protected]
 *
 *  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.scriptext;

import java.util.Hashtable;
import java.util.Map;

import org.jmol.api.Interface;
import org.jmol.api.JmolDataManager;
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
import org.jmol.c.VDW;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.quantum.MepCalculation;
import org.jmol.quantum.QS;
import org.jmol.script.SV;
import org.jmol.script.ScriptError;
import org.jmol.script.ScriptEval;
import org.jmol.script.ScriptException;
import org.jmol.script.ScriptInterruption;
import org.jmol.script.T;
import org.jmol.shape.MeshCollection;
import org.jmol.util.BSUtil;
import org.jmol.util.BoxInfo;
import org.jmol.util.C;
import org.jmol.util.ColorEncoder;
import org.jmol.util.Escape;
import org.jmol.util.MeshCapper;
import org.jmol.util.Parser;
import org.jmol.util.Triangulator;

import javajs.J2SIgnoreImport;
import javajs.util.AU;
import javajs.util.Lst;
import javajs.util.SB;

import org.jmol.util.Logger;

import javajs.util.M4;
import javajs.util.P3;
import javajs.util.P4;
import javajs.util.PT;
import javajs.util.Quat;
import javajs.util.T3;
import javajs.util.V3;

import org.jmol.util.SimpleUnitCell;
import org.jmol.util.TempArray;
import org.jmol.viewer.JC;
import org.jmol.viewer.JmolAsyncException;

@J2SIgnoreImport(org.jmol.quantum.QS.class)
public class IsoExt extends ScriptExt {

  public IsoExt() {
    // used by Reflection
  }
  
  @Override
  public String dispatch(int iTok, boolean b, T[] st) throws ScriptException {
    chk = e.chk; 
    slen = e.slen;
    this.st = st;

    switch (iTok) {
    case JC.SHAPE_CGO:
      cgo();
      break;
    case JC.SHAPE_CONTACT:
      contact();
      break;
    case JC.SHAPE_DIPOLES:
      dipole();
      break;
    case JC.SHAPE_DRAW:
      draw();
      break;
    case JC.SHAPE_ISOSURFACE:
    case JC.SHAPE_PLOT3D:
    case JC.SHAPE_PMESH:
      isosurface(iTok);
      break;
    case JC.SHAPE_LCAOCARTOON:
      lcaoCartoon();
      break;
    case JC.SHAPE_MO:
    case JC.SHAPE_NBO:
      mo(b, iTok);
      break;
    }
    return null;
  }

  private void dipole() throws ScriptException {
    ScriptEval eval = e;
    // dipole intWidth floatMagnitude OFFSET floatOffset {atom1} {atom2}
    String propertyName = null;
    Object propertyValue = null;
    boolean iHaveAtoms = false;
    boolean iHaveCoord = false;
    boolean idSeen = false;
    boolean getCharges = false;
    BS bsSelected = null;

    eval.sm.loadShape(JC.SHAPE_DIPOLES);
    if (tokAt(1) == T.list && listIsosurface(JC.SHAPE_DIPOLES))
      return;
    setShapeProperty(JC.SHAPE_DIPOLES, "init", null);
    if (slen == 1) {
      setShapeProperty(JC.SHAPE_DIPOLES, "thisID", null);
      return;
    }
    for (int i = 1; i < slen; ++i) {
      propertyName = null;
      propertyValue = null;
      switch (getToken(i).tok) {
      case T.all:
        propertyName = "all";
        getCharges = true;
        break;
      case T.on:
        propertyName = "on";
        break;
      case T.off:
        propertyName = "off";
        break;
      case T.delete:
        propertyName = "delete";
        break;
      case T.integer:
      case T.decimal:
        propertyName = "value";
        propertyValue = Float.valueOf(floatParameter(i));
        break;
      case T.bitset:
        if (tokAt(i + 1) == T.bitset) {
          // fix for atomno2 < atomno1
          setShapeProperty(JC.SHAPE_DIPOLES, "startSet", atomExpressionAt(i++));
        } else {
          // early Jmol
          propertyName = "atomBitset";
        }
        //$FALL-THROUGH$
      case T.expressionBegin:
        if (propertyName == null)
          propertyName = (iHaveAtoms || iHaveCoord ? "endSet" : "startSet");
        propertyValue = bsSelected = atomExpressionAt(i);
        i = eval.iToken;
        if (tokAt(i + 1) == T.nada && propertyName == "startSet")
          propertyName = "atomBitset";
        iHaveAtoms = true;
        getCharges = true;
        break;
      case T.leftbrace:
      case T.point3f:
        // {X, Y, Z}
        P3 pt = getPoint3f(i, true);
        i = eval.iToken;
        propertyName = (iHaveAtoms || iHaveCoord ? "endCoord" : "startCoord");
        propertyValue = pt;
        iHaveCoord = true;
        break;
      case T.bonds:
        propertyName = "bonds";
        getCharges = true;
        break;
      case T.calculate:
        getCharges = true;
        propertyName = "calculate";
        if (tokAt(i+1) == T.bitset || tokAt(i + 1) == T.expressionBegin) {
          propertyValue = bsSelected = atomExpressionAt(++i);
          i = eval.iToken;
        }
        break;
      case T.id:
        setShapeId(JC.SHAPE_DIPOLES, ++i, idSeen);
        i = eval.iToken;
        break;
      case T.cross:
        propertyName = "cross";
        propertyValue = Boolean.TRUE;
        break;
      case T.nocross:
        propertyName = "cross";
        propertyValue = Boolean.FALSE;
        break;
      case T.offset:
        if (isFloatParameter(i + 1)) {
        float v = floatParameter(++i);
        if (eval.theTok == T.integer) {
          propertyName = "offsetPercent";
          propertyValue = Integer.valueOf((int) v);
        } else {
          propertyName = "offset";
          propertyValue = Float.valueOf(v);
        }
        } else {
          propertyName = "offsetPt";
          propertyValue = centerParameter(++i);
          i = eval.iToken;
        }
        break;
      case T.offsetside:
        propertyName = "offsetSide";
        propertyValue = Float.valueOf(floatParameter(++i));
        break;
      case T.val:
        propertyName = "value";
        propertyValue = Float.valueOf(floatParameter(++i));
        break;
      case T.width:
        propertyName = "width";
        propertyValue = Float.valueOf(floatParameter(++i));
        break;
      default:
        if (eval.theTok == T.times || T.tokAttr(eval.theTok, T.identifier)) {
          setShapeId(JC.SHAPE_DIPOLES, i, idSeen);
          i = eval.iToken;
          break;
        }
        invArg();
      }
      idSeen = (eval.theTok != T.delete && eval.theTok != T.calculate);
      if (getCharges) {
        // ensures that we do have charges and catch the Script interruption if asynchronous
        if (!chk)
          eval.getPartialCharges(bsSelected);
        getCharges = false;
      }
      if (propertyName != null)
        setShapeProperty(JC.SHAPE_DIPOLES, propertyName, propertyValue);
    }
    if (iHaveCoord || iHaveAtoms)
      setShapeProperty(JC.SHAPE_DIPOLES, "set", null);
  }

  private void draw() throws ScriptException {
    ScriptEval eval = e;
    eval.sm.loadShape(JC.SHAPE_DRAW);
    switch (tokAt(1)) {
    case T.list:
      if (listIsosurface(JC.SHAPE_DRAW))
        return;
      break;
    case T.helix:
    case T.quaternion:
    case T.ramachandran:
      e.getCmdExt().dispatch(T.plot, false, st);
      return;
    }
    boolean havePoints = false;
    boolean isInitialized = false;
    boolean isSavedState = false;
    boolean isIntersect = false;
    boolean isFrame = false;
    P4 plane;
    int tokIntersect = 0;
    float translucentLevel = Float.MAX_VALUE;
    int[] colorArgb = new int[] { Integer.MIN_VALUE };
    int intScale = 0;
    String swidth = "";
    int iptDisplayProperty = 0;
    P3 center = null;
    String thisId = initIsosurface(JC.SHAPE_DRAW);
    boolean idSeen = (thisId != null);
    boolean isWild = (idSeen && getShapeProperty(JC.SHAPE_DRAW, "ID") == null);
    int[] connections = null;
    int iConnect = 0;
    int iArray = -1;
    for (int i = eval.iToken; i < slen; ++i) {
      String propertyName = null;
      Object propertyValue = null;
      int tok = getToken(i).tok;
      switch (tok) {
      case T.pointgroup:
        // draw pointgroup [array  of points] CENTER xx
        // draw pointgroup SPACEGROUP
        // draw pointgroup [C2|C3|Cs|Ci|etc.] [n] [scale x]
        P3[] pts = (eval.isArrayParameter(++i) ? eval.getPointArray(i, -1,
            false) : null);
        if (pts != null) {
          i = eval.iToken + 1;
          if (tokAt(i) == T.center) {
            center = eval.centerParameter(++i, null);
            i = eval.iToken + 1;
          }
        }
        String type;
        switch (tokAt(i)) {
        case T.scale:
          type = "";
          break;
        case T.chemicalshift:
          type = "Cs";
          break;
        case T.dollarsign:
          Object[] data = new Object[] { eval.objectNameParameter(++i), null };
          if (chk)
            return;
          vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "points", data);
          pts = (P3[]) data[1];
          if (pts == null)
            invArg();
          type = "";
          break;
        case T.polyhedra:
          type = ":poly";
          break;
        case T.spacegroup:
          if (center == null)
            center = new P3();
          Lst crpts = vwr.ms.generateCrystalClass(vwr.bsA().nextSetBit(0),
              P3.new3(Float.NaN, Float.NaN, Float.NaN));
          if (pts != null)
            invArg();
          pts = new P3[crpts.size()];
          for (int j = crpts.size(); --j >= 0;)
            pts[j] = crpts.get(j);
          i++;
          type = "";
          break;
        default:
          type = eval.optParameterAsString(i);
          break;
        }
        float scale = 1;
        int index = 0;
        if (type.length() > 0) {
          ++i;
          if (isFloatParameter(i + 1))
            index = intParameter(i++);
        }
        if (tokAt(i) == T.scale)
          scale = floatParameter(++i);
        if (!chk)
          eval.runScript(vwr.ms.getPointGroupAsString(vwr.bsA(), type, index,
              scale, pts, center, thisId == null ? "" : thisId));
        return;
      case T.unitcell:
      case T.boundbox:
        if (chk)
          break;
        SymmetryInterface uc = null;
        if (tok == T.unitcell) {
          if (eval.isArrayParameter(i + 1)) {
            P3[] points = eval.getPointArray(i + 1, -1, false);
            uc = vwr.getSymTemp().getUnitCell(points, false, null);
            i = eval.iToken;
          } else {
            uc = vwr.getCurrentUnitCell();
          }
          if (uc == null)
            invArg();
        }
        Lst