/// <summary> Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
/// The first Atom end up in the origin, the second on on the x axis, and the third
/// one in the XY plane. The rest is added by applying the Zmatrix distances, angles
/// and dihedrals.
///
/// </summary>
/// <param name="distances"> Array of distance variables of the Z matrix
/// </param>
/// <param name="angles"> Array of angle variables of the Z matrix
/// </param>
/// <param name="dihedrals"> Array of distance variables of the Z matrix
/// </param>
/// <param name="first_atoms"> Array of atom ids of the first involed atom in distance, angle and dihedral
/// </param>
/// <param name="second_atoms"> Array of atom ids of the second involed atom in angle and dihedral
/// </param>
/// <param name="third_atoms"> Array of atom ids of the third involed atom in dihedral
///
/// </param>
/// <cdk.dictref> blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates </cdk.dictref>
public static Point3d[] zmatrixToCartesian(double[] distances, int[] first_atoms, double[] angles, int[] second_atoms, double[] dihedrals, int[] third_atoms)
{
Point3d[] cartesianCoords = new Point3d[distances.Length];
for (int index = 0; index < distances.Length; index++)
{
if (index == 0)
{
cartesianCoords[index] = new Point3d(0d, 0d, 0d);
}
else if (index == 1)
{
cartesianCoords[index] = new Point3d(distances[1], 0d, 0d);
}
else if (index == 2)
{
cartesianCoords[index] = new Point3d((-System.Math.Cos((angles[2] / 180) * System.Math.PI)) * distances[2] + distances[1], System.Math.Sin((angles[2] / 180) * System.Math.PI) * distances[2], 0d);
}
else
{
Vector3d cd = new Vector3d();
cd.sub(cartesianCoords[third_atoms[index]], cartesianCoords[second_atoms[index]]);
Vector3d bc = new Vector3d();
bc.sub(cartesianCoords[second_atoms[index]], cartesianCoords[first_atoms[index]]);
Vector3d n1 = new Vector3d();
n1.cross(cd, bc);
n1.normalize();
Vector3d n2 = rotate(n1, bc, dihedrals[index]);
n2.normalize();
Vector3d ba = rotate(bc, n2, -angles[index]);
ba.normalize();
Vector3d ban = new Vector3d(ba);
ban.scale(distances[index]);
Point3d result = new Point3d();
result.add(cartesianCoords[first_atoms[index]], ba);
cartesianCoords[index] = result;
}
}
return cartesianCoords;
}
/// <summary> Inverts three cell axes.
///
/// </summary>
/// <returns> a 3x3 matrix with the three cartesian vectors representing
/// the unit cell axes. The a axis is the first row.
/// </returns>
public static Vector3d[] calcInvertedAxes(Vector3d aAxis, Vector3d bAxis, Vector3d cAxis)
{
double det = aAxis.x * bAxis.y * cAxis.z - aAxis.x * bAxis.z * cAxis.y - aAxis.y * bAxis.x * cAxis.z + aAxis.y * bAxis.z * cAxis.x + aAxis.z * bAxis.x * cAxis.y - aAxis.z * bAxis.y * cAxis.x;
Vector3d[] invaxes = new Vector3d[3];
invaxes[0] = new Vector3d();
invaxes[0].x = (bAxis.y * cAxis.z - bAxis.z * cAxis.y) / det;
invaxes[0].y = (bAxis.z * cAxis.x - bAxis.x * cAxis.z) / det;
invaxes[0].z = (bAxis.x * cAxis.y - bAxis.y * cAxis.x) / det;
invaxes[1] = new Vector3d();
invaxes[1].x = (aAxis.z * cAxis.y - aAxis.y * cAxis.z) / det;
invaxes[1].y = (aAxis.x * cAxis.z - aAxis.z * cAxis.x) / det;
invaxes[1].z = (aAxis.y * cAxis.x - aAxis.x * cAxis.y) / det;
invaxes[2] = new Vector3d();
invaxes[2].x = (aAxis.y * bAxis.z - aAxis.z * bAxis.y) / det;
invaxes[2].y = (aAxis.z * bAxis.x - aAxis.x * bAxis.z) / det;
invaxes[2].z = (aAxis.x * bAxis.y - aAxis.y * bAxis.x) / det;
return invaxes;
}
public virtual void endElement(CMLStack xpath, System.String uri, System.String name, System.String raw)
{
////logger.debug("EndElement: ", name);
System.String cData = currentChars;
if ("bond".Equals(name))
{
if (!stereoGiven)
bondStereo.Add("");
if (bondStereo.Count > bondDictRefs.Count)
bondDictRefs.Add(null);
}
else if ("atom".Equals(name))
{
if (atomCounter > eltitles.Count)
{
eltitles.Add(null);
}
if (atomCounter > hCounts.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
hCounts.Add("0");
}
if (atomCounter > atomDictRefs.Count)
{
atomDictRefs.Add(null);
}
if (atomCounter > isotope.Count)
{
isotope.Add(null);
}
if (atomCounter > spinMultiplicities.Count)
{
spinMultiplicities.Add(null);
}
if (atomCounter > formalCharges.Count)
{
/* while strictly undefined, assume zero
implicit hydrogens when no number is given */
formalCharges.Add("0");
}
/* It may happen that not all atoms have
associated 2D or 3D coordinates. accept that */
if (atomCounter > x2.Count && x2.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x2.Add(null);
y2.Add(null);
}
if (atomCounter > x3.Count && x3.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
x3.Add(null);
y3.Add(null);
z3.Add(null);
}
if (atomCounter > xfract.Count && xfract.Count != 0)
{
/* apparently, the previous atoms had atomic
coordinates, add 'null' for this atom */
xfract.Add(null);
yfract.Add(null);
zfract.Add(null);
}
}
else if ("molecule".Equals(name))
{
storeData();
cdo.endObject("Molecule");
}
else if ("crystal".Equals(name))
{
if (crystalScalar > 0)
{
// convert unit cell parameters to cartesians
Vector3d[] axes = CrystalGeometryTools.notionalToCartesian(unitcellparams[0], unitcellparams[1], unitcellparams[2], unitcellparams[3], unitcellparams[4], unitcellparams[5]);
aAxis = axes[0];
bAxis = axes[1];
cAxis = axes[2];
cartesianAxesSet = true;
cdo.startObject("a-axis");
cdo.setObjectProperty("a-axis", "x", aAxis.x.ToString());
cdo.setObjectProperty("a-axis", "y", aAxis.y.ToString());
cdo.setObjectProperty("a-axis", "z", aAxis.z.ToString());
cdo.endObject("a-axis");
cdo.startObject("b-axis");
cdo.setObjectProperty("b-axis", "x", bAxis.x.ToString());
cdo.setObjectProperty("b-axis", "y", bAxis.y.ToString());
cdo.setObjectProperty("b-axis", "z", bAxis.z.ToString());
cdo.endObject("b-axis");
cdo.startObject("c-axis");
cdo.setObjectProperty("c-axis", "x", cAxis.x.ToString());
cdo.setObjectProperty("c-axis", "y", cAxis.y.ToString());
cdo.setObjectProperty("c-axis", "z", cAxis.z.ToString());
cdo.endObject("c-axis");
}
else
{
////logger.error("Could not find crystal unit cell parameters");
}
cdo.endObject("Crystal");
}
else if ("list".Equals(name))
{
cdo.endObject("SetOfMolecules");
}
else if ("coordinate3".Equals(name))
{
if (BUILTIN.Equals("xyz3"))
{
////logger.debug("New coord3 xyz3 found: ", currentChars);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(currentChars);
x3.Add(st.NextToken());
y3.Add(st.NextToken());
z3.Add(st.NextToken());
////logger.debug("coord3 x3.length: ", x3.Count);
////logger.debug("coord3 y3.length: ", y3.Count);
////logger.debug("coord3 z3.length: ", z3.Count);
}
catch (System.Exception exception)
{
////logger.error("CMLParsing error while setting coordinate3!");
////logger.debug(exception);
}
}
else
{
////logger.warn("Unknown coordinate3 BUILTIN: " + BUILTIN);
}
}
else if ("string".Equals(name))
{
if (BUILTIN.Equals("elementType"))
{
////logger.debug("Element: ", cData.Trim());
elsym.Add(cData);
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("Bond: ref #", curRef);
if (curRef == 1)
{
bondARef1.Add(cData.Trim());
}
else if (curRef == 2)
{
bondARef2.Add(cData.Trim());
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("Bond: order ", cData.Trim());
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("formalCharge"))
{
// NOTE: this combination is in violation of the CML DTD!!!
////logger.warn("formalCharge BUILTIN accepted but violating CML DTD");
////logger.debug("Charge: ", cData.Trim());
System.String charge = cData.Trim();
if (charge.StartsWith("+") && charge.Length > 1)
{
charge = charge.Substring(1);
}
formalCharges.Add(charge);
}
}
else if ("float".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
x3.Add(cData.Trim());
}
else if (BUILTIN.Equals("y3"))
{
y3.Add(cData.Trim());
}
else if (BUILTIN.Equals("z3"))
{
z3.Add(cData.Trim());
}
else if (BUILTIN.Equals("x2"))
{
x2.Add(cData.Trim());
}
else if (BUILTIN.Equals("y2"))
{
y2.Add(cData.Trim());
}
else if (BUILTIN.Equals("order"))
{
// NOTE: this combination is in violation of the CML DTD!!!
order.Add(cData.Trim());
}
else if (BUILTIN.Equals("charge") || BUILTIN.Equals("partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else if ("integer".Equals(name))
{
if (BUILTIN.Equals("formalCharge"))
{
formalCharges.Add(cData.Trim());
}
}
else if ("coordinate2".Equals(name))
{
if (BUILTIN.Equals("xy2"))
{
////logger.debug("New coord2 xy2 found.", cData);
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
x2.Add(st.NextToken());
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 175, 1);
}
}
}
else if ("stringArray".Equals(name))
{
if (BUILTIN.Equals("id") || BUILTIN.Equals("atomId") || BUILTIN.Equals("atomID"))
{
// invalid according to CML1 DTD but found in OpenBabel 1.x output
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
System.String token = st.NextToken();
////logger.debug("StringArray (Token): ", token);
elid.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 186, 1);
}
}
else if (BUILTIN.Equals("elementType"))
{
try
{
bool countAtoms = (atomCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countAtoms)
{
atomCounter++;
}
elsym.Add(st.NextToken());
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRefs"))
{
curRef++;
////logger.debug("New atomRefs found: ", curRef);
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("atomRef"))
{
curRef++;
////logger.debug("New atomRef found: ", curRef); // this is CML1 stuff, we get things like:
/*
<bondArray>
<stringArray builtin="atomRef">a2 a2 a2 a2 a3 a3 a4 a4 a5 a6 a7 a9</stringArray>
<stringArray builtin="atomRef">a9 a11 a12 a13 a5 a4 a6 a9 a7 a8 a8 a10</stringArray>
<stringArray builtin="order">1 1 1 1 2 1 2 1 1 1 2 2</stringArray>
</bondArray>
*/
try
{
bool countBonds = (bondCounter == 0) ? true : false;
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
if (countBonds)
{
bondCounter++;
}
System.String token = st.NextToken();
////logger.debug("Token: ", token);
if (curRef == 1)
{
bondARef1.Add(token);
}
else if (curRef == 2)
{
bondARef2.Add(token);
}
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
else if (BUILTIN.Equals("order"))
{
////logger.debug("New bond order found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Token: ", token);
order.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 194, 1);
}
}
}
else if ("integerArray".Equals(name))
{
////logger.debug("IntegerArray: builtin = ", BUILTIN);
if (BUILTIN.Equals("formalCharge"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
{
System.String token = st.NextToken();
////logger.debug("Charge added: ", token);
formalCharges.Add(token);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
}
else if ("scalar".Equals(name))
{
if (xpath.ToString().EndsWith("crystal/scalar/"))
{
////logger.debug("Going to set a crystal parameter: " + crystalScalar, " to ", cData);
try
{
unitcellparams[crystalScalar - 1] = System.Double.Parse(cData.Trim());
}
catch (System.FormatException exception)
{
////logger.error("Content must a float: " + cData);
}
}
else
{
if (xpath.ToString().EndsWith("bond/scalar/"))
{
if (DICTREF.Equals("mdl:stereo"))
{
bondStereo.Add(cData.Trim());
stereoGiven = true;
}
}
else
{
if (xpath.ToString().EndsWith("atom/scalar/"))
{
if (DICTREF.Equals("cdk:partialCharge"))
{
partialCharges.Add(cData.Trim());
}
}
else
{
if (xpath.ToString().EndsWith("molecule/scalar/"))
{
if (DICTREF.Equals("pdb:id"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Ignoring scalar: " + xpath);
}
}
}
}
}
else if ("floatArray".Equals(name))
{
if (BUILTIN.Equals("x3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 213, 1);
}
}
else if (BUILTIN.Equals("z3"))
{
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
z3.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 221, 1);
}
}
else if (BUILTIN.Equals("x2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
x2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 205, 1);
}
}
else if (BUILTIN.Equals("y2"))
{
////logger.debug("New floatArray found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
y2.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 454, 1);
}
}
else if (BUILTIN.Equals("partialCharge"))
{
////logger.debug("New floatArray with partial charges found.");
try
{
SupportClass.Tokenizer st = new SupportClass.Tokenizer(cData);
while (st.HasMoreTokens())
partialCharges.Add(st.NextToken());
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
notify("CMLParsing error: " + e, SYSTEMID, 462, 1);
}
}
}
else if ("basic".Equals(name))
{
// assuming this is the child element of <identifier>
this.inchi = cData;
}
else if ("name".Equals(name))
{
if (xpath.ToString().EndsWith("molecule/name/"))
{
cdo.setObjectProperty("Molecule", DICTREF, cData);
}
}
else
{
////logger.warn("Skipping element: " + name);
}
currentChars = "";
BUILTIN = "";
elementTitle = "";
}
/// <summary> Sets the value of this matrix to a scale and translation matrix;
/// the translation is scaled by the scale factor and all of the
/// matrix values are modified.
/// </summary>
/// <param name="v1">the translation amount
/// </param>
/// <param name="scale">the scale factor for the matrix
/// </param>
public void set_Renamed(Vector3d v1, double scale)
{
m00 = scale; m01 = 0.0; m02 = 0.0; m03 = scale * v1.x;
m10 = 0.0; m11 = scale; m12 = 0.0; m13 = scale * v1.y;
m20 = 0.0; m21 = 0.0; m22 = scale; m23 = scale * v1.z;
m30 = 0.0; m31 = 0.0; m32 = 0.0; m33 = 1.0;
}
/// <summary> Clean all data about read bonds.</summary>
protected internal virtual void newCrystalData()
{
unitcellparams = new double[6];
cartesianAxesSet = false;
crystalScalar = 0;
aAxis = new Vector3d();
bAxis = new Vector3d();
cAxis = new Vector3d();
}
/// <summary> Copies the matrix values in the specified row into the vector parameter.</summary>
/// <param name="row"> the matrix row
/// </param>
/// <param name="v"> the vector into which the matrix row values will be copied
/// </param>
public void getRow(int row, Vector3d v)
{
if (row == 0)
{
v.x = m00;
v.y = m01;
v.z = m02;
}
else if (row == 1)
{
v.x = m10;
v.y = m11;
v.z = m12;
}
else if (row == 2)
{
v.x = m20;
v.y = m21;
v.z = m22;
}
else
{
throw new Exception();//ArrayIndexOutOfBoundsException(VecMathI18N.getString("Matrix3d2"));
}
}
/// <summary> Sets the specified column of this matrix3d to the vector provided.</summary>
/// <param name="column">the column number to be modified (zero indexed)
/// </param>
/// <param name="v">the replacement column
/// </param>
public void setColumn(int column, Vector3d v)
{
switch (column)
{
case 0:
this.m00 = v.x;
this.m10 = v.y;
this.m20 = v.z;
break;
case 1:
this.m01 = v.x;
this.m11 = v.y;
this.m21 = v.z;
break;
case 2:
this.m02 = v.x;
this.m12 = v.y;
this.m22 = v.z;
break;
default:
throw new Exception();//ArrayIndexOutOfBoundsException(VecMathI18N.getString("Matrix3d9"));
}
}
/// <cdk.dictref> blue-obelisk:convertCartesianIntoNotionalCoordinates </cdk.dictref>
public static double[] cartesianToNotional(Vector3d aAxis, Vector3d bAxis, Vector3d cAxis)
{
double[] notionalCoords = new double[6];
notionalCoords[0] = aAxis.length();
notionalCoords[1] = bAxis.length();
notionalCoords[2] = cAxis.length();
notionalCoords[3] = bAxis.angle(cAxis) * 180.0 / System.Math.PI;
notionalCoords[4] = aAxis.angle(cAxis) * 180.0 / System.Math.PI;
notionalCoords[5] = aAxis.angle(bAxis) * 180.0 / System.Math.PI;
return notionalCoords;
}
/// <summary> Modifies the translational components of this matrix to the values of
/// the Vector3d argument; the other values of this matrix are not modified.
/// </summary>
/// <param name="trans">the translational component
/// </param>
public void setTranslation(Vector3d trans)
{
m03 = trans.x;
m13 = trans.y;
m23 = trans.z;
}
/// <summary> Performs an SVD normalization of this matrix to calculate the rotation
/// as a 3x3 matrix, the translation, and the scale. None of the matrix values are modified.
/// </summary>
/// <param name="m1">The normalized matrix representing the rotation
/// </param>
/// <param name="t1">The translation component
/// </param>
/// <returns> The scale component of this transform
/// </returns>
public double get_Renamed(Matrix3f m1, Vector3d t1)
{
get_Renamed(t1);
return SVD(m1);
}
/// <summary> Retrieves the translational components of this matrix.</summary>
/// <param name="trans">the vector that will receive the translational component
/// </param>
public void get_Renamed(Vector3d trans)
{
trans.x = m03;
trans.y = m13;
trans.z = m23;
}
/// <summary> Constructs and initializes a Matrix4d from the rotation matrix,
/// translation, and scale values; the scale is applied only to the
/// rotational components of the matrix (upper 3x3) and not to the
/// translational components.
/// </summary>
/// <param name="m1"> The rotation matrix representing the rotational components
/// </param>
/// <param name="t1"> The translational components of the matrix
/// </param>
/// <param name="s"> The scale value applied to the rotational components
/// </param>
public Matrix4d(Matrix3f m1, Vector3d t1, double s)
{
// why no set(Matrix3f, Vector3d, double) ?
// set(Matrix3f, Vector3f, float) is there.
// feel inconsistent.
set_Renamed(m1);
mulRotationScale(s);
setTranslation(t1);
m33 = 1.0;
}
/// <summary> Constructs and initializes a Matrix4d from the rotation matrix,
/// translation, and scale values; the scale is applied only to the
/// rotational components of the matrix (upper 3x3) and not to the
/// translational components.
/// </summary>
/// <param name="m1"> The rotation matrix representing the rotational components
/// </param>
/// <param name="t1"> The translational components of the matrix
/// </param>
/// <param name="s"> The scale value applied to the rotational components
/// </param>
public Matrix4d(Matrix3d m1, Vector3d t1, double s)
{
set_Renamed(m1, t1, s);
}
/// <summary> Constructs and initializes a Matrix4d from the quaternion,
/// translation, and scale values; the scale is applied only to the
/// rotational components of the matrix (upper 3x3) and not to the
/// translational components.
/// </summary>
/// <param name="q1"> The quaternion value representing the rotational component
/// </param>
/// <param name="t1"> The translational component of the matrix
/// </param>
/// <param name="s"> The scale value applied to the rotational components
/// </param>
public Matrix4d(Quat4f q1, Vector3d t1, double s)
{
set_Renamed(q1, t1, s);
}
/// <summary> Transforms the normal parameter by this transform and places the value
/// back into normal. The fourth element of the normal is assumed to be zero.
/// </summary>
/// <param name="normal">the input normal to be transformed.
/// </param>
public void transform(Vector3d normal)
{
transform(normal, normal);
}
/// <summary> Transforms the normal parameter by this Matrix4d and places the value
/// into normalOut. The fourth element of the normal is assumed to be zero.
/// </summary>
/// <param name="normal">the input normal to be transformed.
/// </param>
/// <param name="normalOut">the transformed normal
/// </param>
public void transform(Vector3d normal, Vector3d normalOut)
{
normalOut.set_Renamed(m00 * normal.x + m01 * normal.y + m02 * normal.z, m10 * normal.x + m11 * normal.y + m12 * normal.z, m20 * normal.x + m21 * normal.y + m22 * normal.z);
}
/// <cdk.dictref> blue-obelisk:convertFractionIntoCartesianCoordinates </cdk.dictref>
public static Point3d fractionalToCartesian(Vector3d aAxis, Vector3d bAxis, Vector3d cAxis, Point3d frac)
{
Point3d cart = new Point3d();
cart.x = frac.x * aAxis.x + frac.y * bAxis.x + frac.z * cAxis.x;
cart.y = frac.x * aAxis.y + frac.y * bAxis.y + frac.z * cAxis.y;
cart.z = frac.x * aAxis.z + frac.y * bAxis.z + frac.z * cAxis.z;
return cart;
}
/// <cdk.dictref> blue-obelisk:convertCartesianIntoFractionalCoordinates </cdk.dictref>
public static Point3d cartesianToFractional(Vector3d aAxis, Vector3d bAxis, Vector3d cAxis, Point3d cartPoint)
{
Vector3d[] invaxis = calcInvertedAxes(aAxis, bAxis, cAxis);
Point3d frac = new Point3d();
frac.x = invaxis[0].x * cartPoint.x + invaxis[0].y * cartPoint.y + invaxis[0].z * cartPoint.z;
frac.y = invaxis[1].x * cartPoint.x + invaxis[1].y * cartPoint.y + invaxis[1].z * cartPoint.z;
frac.z = invaxis[2].x * cartPoint.x + invaxis[2].y * cartPoint.y + invaxis[2].z * cartPoint.z;
return frac;
}
/// <summary> Calculates cartesian vectors for unit cell axes from axes lengths and angles
/// between axes.
///
/// <p>To calculate cartesian coordinates, it places the a axis on the x axes,
/// the b axis in the xy plane, making an angle gamma with the a axis, and places
/// the c axis to fullfil the remaining constraints. (See also
/// <a href="http://server.ccl.net/cca/documents/molecular-modeling/node4.html">the
/// CCL archive</a>.)
///
/// </summary>
/// <param name="alength"> length of the a axis
/// </param>
/// <param name="blength"> length of the b axis
/// </param>
/// <param name="clength"> length of the c axis
/// </param>
/// <param name="alpha"> angle between b and c axes in degrees
/// </param>
/// <param name="beta"> angle between a and c axes in degrees
/// </param>
/// <param name="gamma"> angle between a and b axes in degrees
/// </param>
/// <returns> an array of Vector3d objects with the three cartesian vectors representing
/// the unit cell axes.
///
/// </returns>
/// <cdk.keyword> notional coordinates </cdk.keyword>
/// <cdk.dictref> blue-obelisk:convertNotionalIntoCartesianCoordinates </cdk.dictref>
public static Vector3d[] notionalToCartesian(double alength, double blength, double clength, double alpha, double beta, double gamma)
{
Vector3d[] axes = new Vector3d[3];
/* 1. align the a axis with x axis */
axes[0] = new Vector3d();
axes[0].x = alength;
axes[0].y = 0.0;
axes[0].z = 0.0;
double toRadians = System.Math.PI / 180.0;
/* some intermediate variables */
double cosalpha = System.Math.Cos(toRadians * alpha);
double cosbeta = System.Math.Cos(toRadians * beta);
double cosgamma = System.Math.Cos(toRadians * gamma);
double singamma = System.Math.Sin(toRadians * gamma);
/* 2. place the b is in xy plane making a angle gamma with a */
axes[1] = new Vector3d();
axes[1].x = blength * cosgamma;
axes[1].y = blength * singamma;
axes[1].z = 0.0;
/* 3. now the c axis, with more complex maths */
axes[2] = new Vector3d();
double volume = alength * blength * clength * System.Math.Sqrt(1.0 - cosalpha * cosalpha - cosbeta * cosbeta - cosgamma * cosgamma + 2.0 * cosalpha * cosbeta * cosgamma);
axes[2].x = clength * cosbeta;
axes[2].y = clength * (cosalpha - cosbeta * cosgamma) / singamma;
axes[2].z = volume / (alength * blength * singamma);
return axes;
}
/// <summary> Constructs and initializes a Vector3f from the specified Vector3d.</summary>
/// <param name="v1">the Vector3d containing the initialization x y z data
/// </param>
public Vector3f(Vector3d v1):base(v1)
{
}
/// <summary> Constructs and initializes an AxisAngle4d from the specified
/// axis and angle.
/// </summary>
/// <param name="axis">the axis
/// </param>
/// <param name="angle">the angle of rotation in radian
///
/// </param>
/// <since> Java 3D 1.2
/// </since>
public AxisAngle4d(Vector3d axis, double angle)
{
this.x = axis.x;
this.y = axis.y;
this.z = axis.z;
this.angle = angle;
}
/// <summary> Sets the value of this matrix from the rotation expressed by the
/// rotation matrix m1, the translation t1, and the scale s. The translation
/// is not modified by the scale.
/// </summary>
/// <param name="m1">The rotation component
/// </param>
/// <param name="t1">The translation component
/// </param>
/// <param name="scale">The scale component
/// </param>
public void set_Renamed(Matrix3d m1, Vector3d t1, double scale)
{
setRotationScale(m1);
mulRotationScale(scale);
setTranslation(t1);
m33 = 1.0;
}
/// <summary> Initializes the unit cell axes to zero length.</summary>
private void setZeroAxes()
{
aAxis = new Vector3d(0.0, 0.0, 0.0);
bAxis = new Vector3d(0.0, 0.0, 0.0);
cAxis = new Vector3d(0.0, 0.0, 0.0);
}
/// <summary> Sets the value of this AxisAngle4d to the specified
/// axis and angle.
/// </summary>
/// <param name="axis">the axis
/// </param>
/// <param name="angle">the angle of rotation in radians
///
/// </param>
/// <since> Java 3D 1.2
/// </since>
public void set_Renamed(Vector3d axis, double angle)
{
this.x = axis.x;
this.y = axis.y;
this.z = axis.z;
this.angle = angle;
}
private IChemFile readChemFile(IChemFile file)
{
IChemSequence seq = file.Builder.newChemSequence();
IChemModel model = file.Builder.newChemModel();
ICrystal crystal = null;
int lineNumber = 0;
Vector3d a, b, c;
try
{
System.String line = input.ReadLine();
while (input.Peek() != -1 && line != null)
{
//logger.debug((lineNumber++) + ": ", line);
if (line.StartsWith("frame:"))
{
//logger.debug("found new frame");
model = file.Builder.newChemModel();
crystal = file.Builder.newCrystal();
// assume the file format is correct
//logger.debug("reading spacegroup");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
crystal.SpaceGroup = line;
//logger.debug("reading unit cell axes");
Vector3d axis = new Vector3d();
//logger.debug("parsing A: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.A = axis;
axis = new Vector3d();
//logger.debug("parsing B: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.B = axis;
axis = new Vector3d();
//logger.debug("parsing C: ");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.x = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.y = FortranFormat.atof(line);
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
axis.z = FortranFormat.atof(line);
crystal.C = axis;
//logger.debug("Crystal: ", crystal);
a = crystal.A;
b = crystal.B;
c = crystal.C;
//logger.debug("Reading number of atoms");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int atomsToRead = System.Int32.Parse(line);
//logger.debug("Reading no molecules in assym unit cell");
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
int Z = System.Int32.Parse(line);
crystal.Z = Z;
System.String symbol;
double charge;
Point3d cart;
for (int i = 1; i <= atomsToRead; i++)
{
cart = new Point3d();
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
symbol = line.Substring(0, (line.IndexOf(":")) - (0));
charge = System.Double.Parse(line.Substring(line.IndexOf(":") + 1));
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.x = System.Double.Parse(line); // x
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.y = System.Double.Parse(line); // y
line = input.ReadLine();
//logger.debug((lineNumber++) + ": ", line);
cart.z = System.Double.Parse(line); // z
IAtom atom = file.Builder.newAtom(symbol);
atom.setCharge(charge);
// convert cartesian coords to fractional
Point3d frac = CrystalGeometryTools.cartesianToFractional(a, b, c, cart);
atom.setFractionalPoint3d(frac);
crystal.addAtom(atom);
//logger.debug("Added atom: ", atom);
}
model.Crystal = crystal;
seq.addChemModel(model);
}
else
{
//logger.debug("Format seems broken. Skipping these lines:");
while (!line.StartsWith("frame:") && input.Peek() != -1 && line != null)
{
line = input.ReadLine();
//logger.debug(lineNumber++ + ": ", line);
}
//logger.debug("Ok, resynched: found new frame");
}
}
file.addChemSequence(seq);
}
catch (System.Exception exception)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.String message = "Error while parsing CrystClust file: " + exception.Message;
//logger.error(message);
//logger.debug(exception);
throw new CDKException(message, exception);
}
return file;
}
/// <summary> Sets the value of this matrix from the rotation expressed by the
/// quaternion q1, the translation t1, and the scale s.
/// </summary>
/// <param name="q1"> the rotation expressed as a quaternion
/// </param>
/// <param name="t1"> the translation
/// </param>
/// <param name="s"> the scale value
/// </param>
public void set_Renamed(Quat4d q1, Vector3d t1, double s)
{
set_Renamed(q1);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
mulRotationScale((float) s);
m03 = (float) t1.x;
m13 = (float) t1.y;
m23 = (float) t1.z;
}
/// <summary> Copies the matrix values in the specified column into the vector
/// parameter.
/// </summary>
/// <param name="column"> the matrix column
/// </param>
/// <param name="v"> the vector into which the matrix row values will be copied
/// </param>
public void getColumn(int column, Vector3d v)
{
if (column == 0)
{
v.x = m00;
v.y = m10;
v.z = m20;
}
else if (column == 1)
{
v.x = m01;
v.y = m11;
v.z = m21;
}
else if (column == 2)
{
v.x = m02;
v.y = m12;
v.z = m22;
}
else
{
throw new Exception();//ArrayIndexOutOfBoundsException(VecMathI18N.getString("Matrix3d4"));
}
}
/// <summary> Sets the value of this matrix from the rotation expressed by the
/// rotation matrix m1, the translation t1, and the scale s. The translation
/// is not modified by the scale.
/// </summary>
/// <param name="m1">The rotation component
/// </param>
/// <param name="t1">The translation component
/// </param>
/// <param name="scale">The scale component
/// </param>
public void set_Renamed(Matrix3d m1, Vector3d t1, double scale)
{
setRotationScale(m1);
//UPGRADE_WARNING: Data types in Visual C# might be different. Verify the accuracy of narrowing conversions. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1042'"
mulRotationScale((float) scale);
setTranslation(t1);
m33 = 1.0f;
}
private static double getAngle(IAtom atom1, IAtom atom2, IAtom atom3)
{
Vector3d centerAtom = new Vector3d();
centerAtom.x = atom1.X3d;
centerAtom.y = atom1.Y3d;
centerAtom.z = atom1.Z3d;
Vector3d firstAtom = new Vector3d();
Vector3d secondAtom = new Vector3d();
firstAtom.x = atom2.X3d;
firstAtom.y = atom2.Y3d;
firstAtom.z = atom2.Z3d;
secondAtom.x = atom3.X3d;
secondAtom.y = atom3.Y3d;
secondAtom.z = atom3.Z3d;
firstAtom.sub(centerAtom);
secondAtom.sub(centerAtom);
return firstAtom.angle(secondAtom);
}
/// <summary> Modifies the translational components of this matrix to the values of
/// the Vector3d argument; the other values of this matrix are not modified.
/// </summary>
/// <param name="trans">the translational component
/// </param>
private void setTranslation(Vector3d trans)
{
m03 = (float) trans.x;
m13 = (float) trans.y;
m23 = (float) trans.z;
}
