From: <eg...@us...> - 2006-08-14 19:36:53
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Revision: 6784 Author: egonw Date: 2006-08-14 12:36:41 -0700 (Mon, 14 Aug 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6784&view=rev Log Message: ----------- Removed IAtom.getFractional[X|Y|Z]2d() Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/Atom.java trunk/cdk/src/org/openscience/cdk/debug/DebugAtom.java trunk/cdk/src/org/openscience/cdk/debug/DebugPseudoAtom.java trunk/cdk/src/org/openscience/cdk/interfaces/IAtom.java trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java trunk/cdk/src/org/openscience/cdk/test/AtomTest.java trunk/cdk/src/org/openscience/cdk/test/io/cml/CMLRoundTripTest.java Modified: trunk/cdk/src/org/openscience/cdk/Atom.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/Atom.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/Atom.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -420,48 +420,6 @@ fractionalPoint3d.z = zFract; notifyChanged(); } - /** - * Returns the x coordinate for of the fractional coordinate of this atom. - * - * @return the x coordinate for of the fractional coordinate of this atom. - * - * @see #setFractX3d - */ - public double getFractX3d() { - if (fractionalPoint3d == null) { - return 0.0; - } else { - return fractionalPoint3d.x; - } - } - /** - * Returns the y coordinate for of the fractional coordinate of this atom. - * - * @return the y coordinate for of the fractional coordinate of this atom. - * - * @see #setFractY3d - */ - public double getFractY3d() { - if (fractionalPoint3d == null) { - return 0.0; - } else { - return fractionalPoint3d.y; - } - } - /** - * Returns the z coordinate for of the fractional coordinate of this atom. - * - * @return the z coordinate for of the fractional coordinate of this atom. - * - * @see #setFractZ3d - */ - public double getFractZ3d() { - if (fractionalPoint3d == null) { - return 0.0; - } else { - return fractionalPoint3d.z; - } - } /** * Sets the x coordinate for of the 2D location of this atom. Modified: trunk/cdk/src/org/openscience/cdk/debug/DebugAtom.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/debug/DebugAtom.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/debug/DebugAtom.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -171,21 +171,6 @@ super.setFractZ3d(zFract); } - public double getFractX3d() { - logger.debug("Getting fractional X3d: ", super.getFractX3d()); - return super.getFractX3d(); - } - - public double getFractY3d() { - logger.debug("Getting fractional Y3d: ", super.getFractY3d()); - return super.getFractY3d(); - } - - public double getFractZ3d() { - logger.debug("Getting fractional Z3d: ", super.getFractZ3d()); - return super.getFractZ3d(); - } - public void setX2d(double xCoord) { logger.debug("Setting X2d: ", xCoord); super.setX2d(xCoord); Modified: trunk/cdk/src/org/openscience/cdk/debug/DebugPseudoAtom.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/debug/DebugPseudoAtom.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/debug/DebugPseudoAtom.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -179,21 +179,6 @@ super.setFractZ3d(zFract); } - public double getFractX3d() { - logger.debug("Getting fractional X3d: ", super.getFractX3d()); - return super.getFractX3d(); - } - - public double getFractY3d() { - logger.debug("Getting fractional Y3d: ", super.getFractY3d()); - return super.getFractY3d(); - } - - public double getFractZ3d() { - logger.debug("Getting fractional Z3d: ", super.getFractZ3d()); - return super.getFractZ3d(); - } - public void setX2d(double xCoord) { logger.debug("Setting X2d: ", xCoord); super.setX2d(xCoord); Modified: trunk/cdk/src/org/openscience/cdk/interfaces/IAtom.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/interfaces/IAtom.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/interfaces/IAtom.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -190,30 +190,6 @@ public void setFractZ3d(double zFract); /** - * Returns the x coordinate for of the fractional coordinate of this atom. - * - * @return the x coordinate for of the fractional coordinate of this atom. - * @see #setFractX3d - */ - public double getFractX3d(); - - /** - * Returns the y coordinate for of the fractional coordinate of this atom. - * - * @return the y coordinate for of the fractional coordinate of this atom. - * @see #setFractY3d - */ - public double getFractY3d(); - - /** - * Returns the z coordinate for of the fractional coordinate of this atom. - * - * @return the z coordinate for of the fractional coordinate of this atom. - * @see #setFractZ3d - */ - public double getFractZ3d(); - - /** * Sets the x coordinate for of the 2D location of this atom. * You should know your context here. There is no guarantee that point2d and point3d * contain consistent information. Both are handled independently. Modified: trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -212,10 +212,7 @@ IAtom[] atoms = crystal.getAtoms(); for (int i=0; i<atoms.length; i++) { IAtom atom = atoms[i]; - Point3d frac = new Point3d(); - frac.x = atom.getFractX3d(); - frac.y = atom.getFractY3d(); - frac.z = atom.getFractZ3d(); + Point3d frac = new Point3d(atom.getFractionalPoint3d()); Point3d cart = CrystalGeometryTools.fractionalToCartesian(a,b,c, frac); atom.setPoint3d(cart); } Modified: trunk/cdk/src/org/openscience/cdk/test/AtomTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/AtomTest.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/test/AtomTest.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -145,24 +145,6 @@ testSetFractionalPoint3d_Point3d(); } - public void testGetFractX3d() { - IAtom a = builder.newAtom("C"); - a.setFractionalPoint3d(new Point3d(0.5, 0.6, 0.7)); - assertEquals(0.5, a.getFractX3d(), 0.001); - } - - public void testGetFractY3d() { - IAtom a = builder.newAtom("C"); - a.setFractionalPoint3d(new Point3d(0.5, 0.6, 0.7)); - assertEquals(0.6, a.getFractY3d(), 0.001); - } - - public void testGetFractZ3d() { - IAtom a = builder.newAtom("C"); - a.setFractionalPoint3d(new Point3d(0.5, 0.6, 0.7)); - assertEquals(0.7, a.getFractZ3d(), 0.001); - } - public void testSetFractX3d_double() { IAtom a = builder.newAtom("C"); a.setFractX3d(0.5); @@ -357,7 +339,7 @@ // test cloning atom.setFractX3d(5); - assertEquals(clone.getFractX3d(), 2.0, 0.001); + assertEquals(clone.getFractionalPoint3d().x, 2.0, 0.001); } /** Modified: trunk/cdk/src/org/openscience/cdk/test/io/cml/CMLRoundTripTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/io/cml/CMLRoundTripTest.java 2006-08-14 19:30:36 UTC (rev 6783) +++ trunk/cdk/src/org/openscience/cdk/test/io/cml/CMLRoundTripTest.java 2006-08-14 19:36:41 UTC (rev 6784) @@ -136,9 +136,7 @@ assertEquals(1, roundTrippedMol.getAtomCount()); org.openscience.cdk.interfaces.IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); - assertEquals(atom.getFractX3d(), roundTrippedAtom.getFractX3d(), 0.00001); - assertEquals(atom.getFractY3d(), roundTrippedAtom.getFractY3d(), 0.00001); - assertEquals(atom.getFractZ3d(), roundTrippedAtom.getFractZ3d(), 0.00001); + assertEquals(atom.getFractionalPoint3d(), roundTrippedAtom.getFractionalPoint3d(), 0.00001); } public void testPseudoAtom() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |