Menu
▾
▴
[Cdk-commits] CVS: cdk/src/org/openscience/cdk Crystal.java,NONE,1.1 ChemModel.java,1.3,1.4
|
From: Egon W. <eg...@us...> - 2002-09-03 15:42:53
|
Update of /cvsroot/cdk/cdk/src/org/openscience/cdk
In directory usw-pr-cvs1:/tmp/cvs-serv30177/src/org/openscience/cdk
Modified Files:
ChemModel.java
Added Files:
Crystal.java
Log Message:
Added Crystal class.
--- NEW FILE: Crystal.java ---
/*
* $RCSfile: Crystal.java,v $
* $Author: egonw $
* $Date: 2002/09/03 15:42:48 $
* $Revision: 1.1 $
*
* Copyright (C) 1997-2002 The Chemistry Development Kit (CDK) project
*
* Contact: ste...@ic..., gez...@ma..., eg...@sc...
*
* This program 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 program 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 program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package org.openscience.cdk;
/**
* Class representing a molecular crystal.
* The crystal is described with molecules in fractional
* coordinates and three cell axes: a,b and c.
*
* @keyword crystal
*/
public class Crystal extends AtomContainer {
/** x,y,z components of a axis */
private double ax,ay,az;
/** x,y,z components of b axis */
private double bx,by,bz;
/** x,y,z components of c axis */
private double cx,cy,cz;
/**
* Number of symmetry related atoms.
*/
private int Z = 1;
/**
* Number of symmetry related atoms.
*/
private String spaceGroup = "P1";
/**
* Constructs a new crystal with zero length cell axis.
*/
public Crystal() {
setZeroAxes();
}
/**
* Constructs a new crystal with zero length cell axis
* and adds the atoms in the AtomContainer as cell content.
*/
public Crystal(AtomContainer ac) {
this();
add(ac);
}
/**
* Sets the A unit cell axes in carthesian coordinates.
*/
public void setA(double x, double y, double z) {
ax = x; ay = y; az = z;
}
/**
* Adds the atoms in the AtomContainer as cell content.
*/
public void add(AtomContainer ac) {
super.add(ac);
}
/**
* Sets the B unit cell axes in carthesian coordinates.
*/
public void setB(double x, double y, double z) {
bx = x; by = y; bz = z;
}
/**
* Sets the C unit cell axes in carthesian coordinates.
*/
public void setC(double x, double y, double z) {
cx = x; cy = y; cz = z;
}
/**
* Gets the space group of this crystal.
*
* @return the space group of this crystal structure
*/
public String getSpaceGroup() {
return spaceGroup;
}
/**
* Sets the space group of this crystal. If not space group
* is not recognized then P1 is assumed.
*
* Recognized space group strings:
* "P1"
* "P 2_1 2_1 2_1"
*
* @param group the space group of this crystal structure
*/
public void setSpaceGroup(String group) {
if ("P1".equals(group)) {
} else if ("P 2_1 2_1 2_1".equals(group)) {
setZ(4);
} else {
return;
}
spaceGroup = group;
}
/**
* Gets the number of asymmetric parts in the unit cell.
*
* @return Z
*/
public int getZ() {
return Z;
}
/**
* Sets the number of asymmetric parts in the unit cell.
* This is used internally only by setSpaceGroup()
*
* @param z Z
* @see setSpaceGroup()
*/
private void setZ(int z) {
Z = z;
}
/**
* Returns a String representation of this crystal.
*/
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append("Crystal:\n");
sb.append(" space group: " + getSpaceGroup() + "\n");
sb.append(" Z: " + getZ() + "\n");
sb.append(" a : " + ax + ", " + ay + ", " + az + "\n");
sb.append(" b : " + bx + ", " + by + ", " + bz + "\n");
sb.append(" c : " + cx + ", " + cy + ", " + cz + "\n");
sb.append(" atoms: " + getAtomCount() + "\n");
sb.append(" assym atoms: " + getAtomCount()/getZ() + "\n");
return sb.toString();
}
/**
* Initializes the unit cell axes to zero length.
*/
private void setZeroAxes() {
ax = 0.0; ay = 0.0; az = 0.0;
bx = 0.0; by = 0.0; bz = 0.0;
cx = 0.0; cy = 0.0; cz = 0.0;
}
}
Index: ChemModel.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/ChemModel.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** ChemModel.java 4 Aug 2002 12:25:46 -0000 1.3
--- ChemModel.java 3 Sep 2002 15:42:47 -0000 1.4
***************
*** 36,44 ****
/**
! * SetOfMolecules
*/
! protected SetOfMolecules setOfMolecules;
! protected RingSet ringSet;
/**
--- 36,52 ----
/**
! * A SetOfMolecules
*/
! protected SetOfMolecules setOfMolecules = null;
!
! /**
! * A RingSet
! */
! protected RingSet ringSet = null;
! /**
! * A Crystal
! */
! protected Crystal crystal = null;
/**
***************
*** 104,108 ****
* Sets the RingSet of this ChemModel
*
! * @param ringSet
*/
public void setRingSet(RingSet ringSet)
--- 112,116 ----
* Sets the RingSet of this ChemModel
*
! * @param ringSet
*/
public void setRingSet(RingSet ringSet)
***************
*** 110,113 ****
this.ringSet = ringSet;
}
}
!
--- 118,139 ----
this.ringSet = ringSet;
}
+
+ /**
+ * Gets the Crystal contained in this ChemModel
+ *
+ * @return The crystal in this model
+ */
+ public Crystal getCrystal() {
+ return this.crystal;
+ }
+
+ /**
+ * Sets the Crystal contained in this ChemModel
+ *
+ * @param c the Crystal to store in this model
+ */
+ public void setCrystal(Crystal c) {
+ this.crystal = c;
+ }
}
!
|