org.jmol.shapebio.BioShapeCollection Maven / Gradle / Ivy
/* $RCSfile$
* $Author: hansonr $
* $Date: 2015-12-23 09:23:37 +0100 (Wed, 23 Dec 2015) $
* $Revision: 20903 $
*
* Copyright (C) 2003-2005 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 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.shapebio;
import java.util.Hashtable;
import java.util.Map;
import javajs.util.AU;
import org.jmol.atomdata.RadiusData;
import org.jmol.c.PAL;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.modelset.Group;
import org.jmol.modelset.Model;
import org.jmol.modelsetbio.BioModel;
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.modelsetbio.Monomer;
import org.jmol.shape.Shape;
import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.viewer.JC;
/****************************************************************
* Mps stands for Model-Polymer-Shape
*
* When a Cartoon is instantiated with a call to setSize(),
* it creates an MpsShape for each BioPolymer in the model set.
*
* It is these shapes that are the real "shapes". Unlike other
* shapes, which are indexed by atom and throughout the entire
* model set, these shapes are indexed by residue and are
* restricted to a given BioPolymer within a given Model.
*
* Model
*
****************************************************************/
public abstract class BioShapeCollection extends Shape {
Atom[] atoms;
short madOn = -2;
short madHelixSheet = 3000;
short madTurnRandom = 800;
short madDnaRna = 5000;
boolean isActive = false;
public BioShape[] bioShapes;
@Override
public final void initModelSet() {
isBioShape = true;
atoms = ms.at;
initialize();
}
@Override
public void initShape() {
// nothing to do
}
@Override
public int getSizeG(Group group) {
Monomer m = (Monomer) group;
int groupIndex = m.groupIndex;
int leadAtomIndex = m.getLeadAtom().i;
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
for (int j = 0; j < bioShape.monomerCount; j++) {
if (bioShape.monomers[j].groupIndex == groupIndex
&& bioShape.monomers[j].getLeadAtom().i == leadAtomIndex)
return bioShape.mads[j];
}
}
return 0;
}
@Override
public void replaceGroup(Group g0, Group g1) {
//BioShapeCollection only; after MUTATE
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
for (int j = 0; j < bioShape.monomerCount; j++)
if (bioShape.monomers[j] == g0) {
bioShape.monomers[j] = (Monomer) g1;
break;
}
}
}
@Override
public void setShapeSizeRD(int size, RadiusData rd, BS bsSelected) {
short mad = (short) size;
initialize();
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0)
bioShape.setMad(mad, bsSelected, (rd == null ? null : rd.values));
}
}
@Override
public void setProperty(String propertyName, Object value, BS bsSelected) {
setPropBSC(propertyName, value, bsSelected);
}
protected void setPropBSC(String propertyName, Object value, BS bsSelected) {
if (propertyName == "refreshTrajectories") {
int modelIndex = ((Integer) ((Object[]) value)[0]).intValue();
for (int i = bioShapes.length; --i >= 0;) {
BioShape b = bioShapes[i];
if (b.modelIndex == modelIndex)
b.falsifyMesh();
}
return;
}
if (propertyName == "deleteModelAtoms") {
atoms = (Atom[]) ((Object[]) value)[1];
int modelIndex = ((int[]) ((Object[]) value)[2])[0];
for (int i = bioShapes.length; --i >= 0;) {
BioShape b = bioShapes[i];
if (b.modelIndex > modelIndex) {
b.modelIndex--;
b.leadAtomIndices = b.bioPolymer.getLeadAtomIndices();
} else if (b.modelIndex == modelIndex) {
bioShapes = (BioShape[]) AU.deleteElements(bioShapes, i, 1);
}
}
return;
}
initialize();
if ("color" == propertyName) {
byte pid = PAL.pidOf(value);
short colix = C.getColixO(value);
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0)
bioShape.setColixBS(colix, pid, bsSelected);
}
return;
}
if ("params" == propertyName) {
int n = bsSelected.length();
int[] atomMap = new int[n];
for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1), pt++)
atomMap[i] = pt;
for (int i = bioShapes.length; --i >= 0;)
bioShapes[i].setParams((Object[]) value, atomMap, bsSelected);
return;
}
if ("colorPhase" == propertyName) {
// cartoons and ribbons only
Object[] twoColors = (Object[]) value;
short colixBack = C.getColixO(twoColors[0]);
short colix = C.getColixO(twoColors[1]);
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0) {
bioShape.setColixBS(colix, PAL.PALETTE_VOLATILE, bsSelected);
bioShape.setColixBack(colixBack, bsSelected);
}
}
return;
}
if ("translucency" == propertyName) {
boolean isTranslucent = ("translucent".equals(value));
for (int i = bioShapes.length; --i >= 0;) {
BioShape bioShape = bioShapes[i];
if (bioShape.monomerCount > 0)
bioShape.setTranslucent(isTranslucent, bsSelected, translucentLevel);
}
return;
}
setPropS(propertyName, value, bsSelected);
}
@Override
public String getShapeState() {
// leaving this here because it is so specialized
Map temp = new Hashtable();
Map temp2 = new Hashtable();
String type = JC.shapeClassBases[shapeID];
for (int iShape = bioShapes.length; --iShape >= 0;)
bioShapes[iShape].getBioShapeState(type, translucentAllowed, temp, temp2);
String s = "\n"
+ vwr.getCommands(temp, temp2,
shapeID == JC.SHAPE_BACKBONE ? "Backbone" : "select");
return s;
}
void initialize() {
int modelCount = ms.mc;
Model[] models = ms.am;
int n = ms.getBioPolymerCountInModel(-1);
BioShape[] shapes = new BioShape[n--];
for (int i = modelCount; --i >= 0;)
for (int j = ms.getBioPolymerCountInModel(i); --j >= 0; n--) {
BioPolymer bp = ((BioModel) models[i]).bioPolymers[j];
shapes[n] = (bioShapes == null || bioShapes.length <= n
|| bioShapes[n] == null || bioShapes[n].bioPolymer != bp ? new BioShape(
this, i, bp)
: bioShapes[n]);
}
bioShapes = shapes;
}
@Override
public void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BS bsNot) {
for (int i = bioShapes.length; --i >= 0; )
bioShapes[i].findNearestAtomIndex(xMouse, yMouse, closest, bsNot);
}
@Override
public void setModelVisibilityFlags(BS bsModels) {
if (bioShapes == null)
return;
bsModels = BSUtil.copy(bsModels);
if (ms.trajectory != null)
ms.trajectory.setBaseModels(bsModels);
for (int i = bioShapes.length; --i >= 0;) {
BioShape b = bioShapes[i];
b.modelVisibilityFlags = (bsModels.get(b.modelIndex) ? vf : 0);
}
}
@Override
public void setAtomClickability() {
if (bioShapes == null)
return;
for (int i = bioShapes.length; --i >= 0; )
bioShapes[i].setAtomClickability();
}
int getMpsShapeCount() {
return bioShapes.length;
}
public BioShape getBioShape(int i) {
return bioShapes[i];
}
}
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