--- /dev/null
+package MCview;\r
+import java.util.*;\r
+import java.awt.*;\r
+\r
+public class Atom {\r
+ double x;\r
+ double y;\r
+ double z;\r
+ int number;\r
+ String name;\r
+ String resName;\r
+ int resNumber;\r
+ int type;\r
+ Color color;\r
+ String chain;\r
+\r
+ public Atom(StringTokenizer str) {\r
+ this.number = (new Integer(str.nextToken())).intValue();\r
+ this.name = str.nextToken();\r
+ this.resName = str.nextToken();\r
+\r
+ String tmpstr = new String();\r
+\r
+ try {\r
+ tmpstr = str.nextToken();\r
+\r
+ this.resNumber = (new Integer(tmpstr).intValue());\r
+ this.chain = "A";\r
+ this.color = Color.green;\r
+\r
+ } catch(NumberFormatException e) {\r
+ this.chain = tmpstr;\r
+\r
+ if (tmpstr.equals("A")) {\r
+ this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());\r
+ } else {\r
+ this.color = Color.red;\r
+ }\r
+ this.resNumber = (new Integer(str.nextToken()).intValue());\r
+ }\r
+\r
+ this.x = (double)(new Double(str.nextToken()).floatValue());\r
+ this.y = (double)(new Double(str.nextToken()).floatValue());\r
+ this.z = (double)(new Double(str.nextToken()).floatValue());\r
+\r
+ }\r
+\r
+ public void setColor(Color col) {\r
+ this.color = col;\r
+ }\r
+\r
+}\r
--- /dev/null
+package MCview;\r
+\r
+import java.awt.*;\r
+\r
+public class Bond {\r
+\r
+ float start[];\r
+ float end[];\r
+\r
+ Color startCol;\r
+ Color endCol;\r
+\r
+ public myAtom at1;\r
+ public myAtom at2;\r
+\r
+ public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\r
+ this.start = start;\r
+ this.end = end;\r
+ this.startCol = at1.color;\r
+ this.endCol = at2.color;\r
+ this.at1 = at1;\r
+ this.at2 = at2;\r
+ }\r
+ public Bond(Bond bond) {\r
+ this.start = new float[3];\r
+\r
+ this.start[0] = bond.start[0];\r
+ this.start[1] = bond.start[1];\r
+ this.start[2] = bond.start[2];\r
+\r
+ this.end = new float[3];\r
+\r
+ this.end[0] = bond.end[0];\r
+ this.end[1] = bond.end[1];\r
+ this.end[2] = bond.end[2];\r
+\r
+ this.startCol = bond.startCol;\r
+ this.endCol = bond.endCol;\r
+ }\r
+\r
+ public void print() {\r
+ System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);\r
+ System.out.println("End " + end[0] + " "+ end[1] + " " + end[2]);\r
+ }\r
+\r
+ public float length() {\r
+ float len = (end[0] - start[0])*(end[0] - start[0]) +\r
+ (end[1] - start[1])*(end[1] - start[1]) +\r
+ (end[2] - start[2])*(end[2] - start[2]);\r
+\r
+ len = (float)(Math.sqrt(len));\r
+\r
+ return len;\r
+ }\r
+ public void translate(float x, float y, float z) {\r
+ start[0] = (start[0] + x);\r
+ end[0] = (end[0] + x);\r
+\r
+ start[1] = (start[1] + y);\r
+ end[1] = (end[1] + y);\r
+\r
+ start[2] = (start[2] + z);\r
+ end[2] = (end[2] + z);\r
+ }\r
+}\r
--- /dev/null
+package MCview;\r
+\r
+import java.awt.*;\r
+\r
+public class Bond {\r
+\r
+ float start[];\r
+ float end[];\r
+\r
+ Color startCol;\r
+ Color endCol;\r
+\r
+ public myAtom at1;\r
+ public myAtom at2;\r
+\r
+ public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\r
+ this.start = start;\r
+ this.end = end;\r
+ this.startCol = at1.color;\r
+ this.endCol = at2.color;\r
+ this.at1 = at1;\r
+ this.at2 = at2;\r
+ }\r
+ public Bond(Bond bond) {\r
+ this.start = new float[3];\r
+ this.start[0] = bond.start[0];\r
+ this.start[1] = bond.start[1];\r
+ this.start[2] = bond.start[2];\r
+ this.end = new float[3];\r
+ this.end[0] = bond.end[0];\r
+ this.end[1] = bond.end[1];\r
+ this.end[2] = bond.end[2];\r
+ this.startCol = bond.startCol;\r
+ this.endCol = bond.endCol;\r
+ }\r
+\r
+ public void print() {\r
+ System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);\r
+ System.out.println("End " + end[0] + " "+ end[1] + " " + end[2]);\r
+ }\r
+ \r
+ public float length() {\r
+ float len = (end[0] - start[0])*(end[0] - start[0]) +\r
+ (end[1] - start[1])*(end[1] - start[1]) +\r
+ (end[2] - start[2])*(end[2] - start[2]);\r
+ len = (float)(Math.sqrt(len));\r
+ return len;\r
+ }\r
+ public void translate(float x, float y, float z) {\r
+ start[0] = (start[0] + x);\r
+ end[0] = (end[0] + x);\r
+ start[1] =(start[1] + y);\r
+ end[1] = (end[1] + y);\r
+ start[2] = (start[2] + z);\r
+ end[2] = (end[2] + z);\r
+ }\r
+}\r
--- /dev/null
+package MCview;\r\r
+\r\r
+import java.awt.*;\r\r
+\r\r
+public class Bond {\r\r
+\r\r
+ float start[];\r\r
+ float end[];\r\r
+\r\r
+ Color startCol;\r\r
+ Color endCol;\r\r
+\r\r
+ public myAtom at1;\r\r
+ public myAtom at2;\r\r
+\r\r
+ public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\r\r
+ this.start = start;\r\r
+ this.end = end;\r\r
+ this.startCol = at1.color;\r\r
+ this.endCol = at2.color;\r\r
+ this.at1 = at1;\r\r
+ this.at2 = at2;\r\r
+ }\r\r
+ public Bond(Bond bond) {\r\r
+ this.start = new float[3];\r\r
+ this.start[0] = bond.start[0];\r\r
+ this.start[1] = bond.start[1];\r\r
+ this.start[2] = bond.start[2];\r\r
+ this.end = new float[3];\r\r
+ this.end[0] = bond.end[0];\r\r
+ this.end[1] = bond.end[1];\r\r
+ this.end[2] = bond.end[2];\r\r
+ this.startCol = bond.startCol;\r\r
+ this.endCol = bond.endCol;\r\r
+ }\r\r
+\r\r
+ public void print() {\r\r
+ System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);\r\r
+ System.out.println("End " + end[0] + " "+ end[1] + " " + end[2]);\r\r
+ }\r\r
+ \r\r
+ public float length() {\r\r
+ float len = (end[0] - start[0])*(end[0] - start[0]) +\r\r
+ (end[1] - start[1])*(end[1] - start[1]) +\r\r
+ (end[2] - start[2])*(end[2] - start[2]);\r\r
+ len = (float)(Math.sqrt(len));\r\r
+ return len;\r\r
+ }\r\r
+ public void translate(float x, float y, float z) {\r\r
+ start[0] = (start[0] + x);\r\r
+ end[0] = (end[0] + x);\r\r
+ start[1] =(start[1] + y);\r\r
+ end[1] = (end[1] + y);\r\r
+ start[2] = (start[2] + z);\r\r
+ end[2] = (end[2] + z);\r\r
+ }\r\r
+}\r\r
--- /dev/null
+package MCview;\r
+\r
+public class MCMatrix {\r
+ float matrix[][];\r
+ float tmp[][];\r
+\r
+ float mycos;\r
+ float mysin;\r
+ float myconst = (float)(Math.PI/180);\r
+\r
+ public MCMatrix(int rows, int cols) {\r
+ matrix = new float[rows][cols];\r
+ tmp = new float[rows][cols];\r
+ }\r
+\r
+ public void addElement(int i, int j, float value) {\r
+ matrix[i][j] = value;\r
+ }\r
+\r
+ public void print() {\r
+ System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);\r
+ System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);\r
+ System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);\r
+ }\r
+\r
+ public void rotatex(float degrees) {\r
+ mycos = (float)(Math.cos(degrees*myconst));\r
+ mysin = (float)(Math.sin(degrees*myconst));\r
+\r
+ tmp[0][0] = 1;\r
+ tmp[0][1] = 0;\r
+ tmp[0][2] = 0;\r
+ tmp[1][0] = 0;\r
+ tmp[1][1] = mycos;\r
+ tmp[1][2] = mysin;\r
+ tmp[2][0] = 0;\r
+ tmp[2][1] = -mysin;\r
+ tmp[2][2] = mycos;\r
+ preMultiply(tmp);\r
+ }\r
+\r
+ public void rotatez(float degrees) {\r
+ mycos = (float)(Math.cos(degrees*myconst));\r
+ mysin = (float)(Math.sin(degrees*myconst));\r
+\r
+ tmp[0][0] = mycos;\r
+ tmp[0][1] = -mysin;\r
+ tmp[0][2] = 0;\r
+ tmp[1][0] = mysin;\r
+ tmp[1][1] = mycos;\r
+ tmp[1][2] = 0;\r
+ tmp[2][0] = 0;\r
+ tmp[2][1] = 0;\r
+ tmp[2][2] = 1;\r
+\r
+ preMultiply(tmp);\r
+ }\r
+\r
+ public void rotatey(float degrees) {\r
+ mycos = (float)(Math.cos(degrees*myconst));\r
+ mysin = (float)(Math.sin(degrees*myconst));\r
+\r
+ tmp[0][0] = mycos;\r
+ tmp[0][1] = 0;\r
+ tmp[0][2] = -mysin;\r
+ tmp[1][0] = 0;\r
+ tmp[1][1] = 1;\r
+ tmp[1][2] = 0;\r
+ tmp[2][0] = mysin;\r
+ tmp[2][1] = 0;\r
+ tmp[2][2] = mycos;\r
+\r
+ preMultiply(tmp);\r
+ }\r
+\r
+ public float[] vectorMultiply(float[] vect) {\r
+ float temp[] = new float[3];\r
+\r
+ temp[0] = vect[0];\r
+ temp[1] = vect[1];\r
+ temp[2] = vect[2];\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ temp[i] = (float)matrix[i][0]*vect[0] + (float)matrix[i][1]*vect[1] +(float)matrix[i][2]*vect[2];\r
+ }\r
+\r
+ vect[0] = temp[0];\r
+ vect[1] = temp[1];\r
+ vect[2] = temp[2];\r
+\r
+ return vect;\r
+ }\r
+\r
+ public void preMultiply(float mat[][]) {\r
+ float tmp[][] = new float[3][3];\r
+\r
+ for (int i = 0; i < 3 ; i++) {\r
+ for (int j = 0; j < 3; j++ ) {\r
+ tmp[i][j] = mat[i][0]*matrix[0][j] +\r
+ mat[i][1]*matrix[1][j] +\r
+ mat[i][2]*matrix[2][j];\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3 ; i++) {\r
+ for (int j = 0; j < 3; j++ ) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
+ }\r
+\r
+ public void postMultiply(float mat[][]) {\r
+ float tmp[][] = new float[3][3];\r
+\r
+ for (int i = 0; i < 3 ; i++) {\r
+ for (int j = 0; j < 3; j++ ) {\r
+ tmp[i][j] = matrix[i][0]*mat[0][j] +\r
+ matrix[i][1]*mat[1][j] +\r
+ matrix[i][2]*mat[2][j];\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < 3 ; i++) {\r
+ for (int j = 0; j < 3; j++ ) {\r
+ matrix[i][j] = tmp[i][j];\r
+ }\r
+ }\r
+ }\r
+\r
+ public void setIdentity() {\r
+ matrix[0][0] = 1;\r
+ matrix[1][1] = 1;\r
+ matrix[2][2] = 1;\r
+ matrix[0][1] = 0;\r
+ matrix[0][2] = 0;\r
+ matrix[1][0] = 0;\r
+ matrix[1][2] = 0;\r
+ matrix[2][0] = 0;\r
+ matrix[2][1] = 0;\r
+ }\r
+}\r
+\r
+\r
--- /dev/null
+/* Copyright (C) 1998 Michele Clamp\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
+ */\r
+package MCview;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.gui.*;\r
+\r
+import java.awt.*;\r
+import java.util.*;\r
+\r
+\r
+public class PDBChain {\r
+\r
+ public String id;\r
+ public Vector bonds = new Vector();\r
+ public Vector atoms = new Vector();\r
+ public Vector residues = new Vector();\r
+ public int offset;\r
+\r
+ public Sequence sequence;\r
+ public boolean isVisible = false;\r
+\r
+ //public DrawableSequence ds;\r
+\r
+ public PDBChain(String id) {\r
+ this.id = id;\r
+ }\r
+\r
+\r
+ public String print() {\r
+ String tmp = "";\r
+ for (int i=0; i < bonds.size() ;i++) {\r
+ tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";\r
+ }\r
+ return tmp;\r
+ }\r
+ public void makeCaBondList() {\r
+ for (int i = 0; i < (residues.size() - 1) ; i++) {\r
+ Residue tmpres = (Residue)residues.elementAt(i);\r
+ Residue tmpres2 = (Residue)residues.elementAt(i+1);\r
+ myAtom at1 = tmpres.findAtom("CA");\r
+ myAtom at2 = tmpres2.findAtom("CA");\r
+ if ((at1 != null) && (at2 != null)) {\r
+ if (at1.chain.equals(at2.chain)) {\r
+ makeBond(at1,at2);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public void makeBond(myAtom at1, myAtom at2) {\r
+ float[] start = new float[3];\r
+ float[] end = new float[3];\r
+\r
+ start[0] = at1.x;\r
+ start[1] = at1.y;\r
+ start[2] = at1.z;\r
+\r
+ end[0] = at2.x;\r
+ end[1] = at2.y;\r
+ end[2] = at2.z;\r
+\r
+ bonds.addElement(new Bond(start, end, at1,at2));\r
+ }\r
+\r
+ public void makeResidueList() {\r
+ int count = 0;\r
+ String seq = "";\r
+ for (int i = 0; i < atoms.size(); i++) {\r
+\r
+ myAtom tmp = (myAtom)atoms.elementAt(i);\r
+ String resName = tmp.resName;\r
+ int resNumber = tmp.resNumber;\r
+ int res = resNumber;\r
+\r
+ if (i ==0) {\r
+ offset = resNumber;\r
+ }\r
+ Vector resAtoms = new Vector();\r
+\r
+ resAtoms.addElement((myAtom)atoms.elementAt(i));\r
+ i++;\r
+ resNumber = ((myAtom)atoms.elementAt(i)).resNumber;\r
+\r
+ //Add atoms to a vector while the residue number\r
+ //remains the same\r
+ while ((resNumber == res) && (i < atoms.size())) {\r
+\r
+ resAtoms.addElement((myAtom)atoms.elementAt(i));\r
+ i++;\r
+ if (i < atoms.size()) {\r
+ resNumber = ((myAtom)atoms.elementAt(i)).resNumber;\r
+ } else {\r
+ resNumber++;\r
+ }\r
+ }\r
+\r
+ //We need this to keep in step with the outer for i = loop\r
+ i--;\r
+\r
+ //Make a new Residue object with the new atoms vector\r
+ residues.addElement(new Residue(resAtoms, resNumber - 1,count));\r
+ count++;\r
+ Residue tmpres = (Residue)residues.lastElement();\r
+ myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);\r
+\r
+ // Keep totting up the sequence\r
+ if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
+ System.out.println("Null aa3Hash for " + tmpat.resName);\r
+ } else {\r
+ String tmpres2 =\r
+ ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];\r
+ seq = seq + tmpres2;\r
+ }\r
+ // System.out.println(tmpat.resName + " " + tmpres2);\r
+ }\r
+ sequence = new Sequence("PDB_seq",seq,1,seq.length());\r
+ System.out.println("Sequence = " + seq);\r
+ System.out.println("No of residues = " +residues.size());\r
+ }\r
+\r
+ public void setChargeColours() {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond)bonds.elementAt(i);\r
+\r
+ if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {\r
+ b.startCol = Color.red;\r
+ } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {\r
+ b.startCol = Color.blue;\r
+ } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
+ b.startCol = Color.yellow;\r
+ } else {\r
+ int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\r
+ b.startCol = Color.lightGray;\r
+ }\r
+ if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {\r
+ b.endCol = Color.red;\r
+ } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {\r
+ b.endCol = Color.blue;\r
+ } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
+ b.endCol = Color.yellow;\r
+ } else {\r
+ int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
+ b.endCol = Color.lightGray;\r
+ }\r
+ } catch (Exception e) {\r
+ Bond b = (Bond)bonds.elementAt(i);\r
+ b.startCol = Color.gray;\r
+ b.endCol = Color.gray;\r
+ }\r
+ }\r
+ }\r
+\r
+ public void setHydrophobicityColours() {\r
+ float hydmin = (float)ResidueProperties.getHydmin();\r
+ float hydmax = (float)ResidueProperties.getHydmax();\r
+ double[] hyd = ResidueProperties.getHyd();\r
+\r
+ Hashtable AA3Hash = ResidueProperties.getAA3Hash();\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond)bonds.elementAt(i);\r
+\r
+ int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();\r
+ float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);\r
+\r
+ if (red > (float)1.0) {\r
+ red = (float)1.0;\r
+ }\r
+ if (red < (float)0.0) {\r
+ red = (float)0.0;\r
+ }\r
+\r
+ b.startCol = new Color(red,(float)0.0,(float)1.0-red);\r
+ atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();\r
+\r
+ red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);\r
+\r
+ if (red > (float)1.0) {\r
+ red = (float)1.0;\r
+ }\r
+ if (red < (float)0.0) {\r
+ red = (float)0.0;\r
+ }\r
+\r
+ b.endCol = new Color(red,(float)0.2,(float)1.0-red);\r
+ } catch (Exception e) {\r
+ Bond b = (Bond)bonds.elementAt(i);\r
+ b.startCol = Color.gray;\r
+ b.endCol = Color.gray;\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ public void colourBySequence(DrawableSequence seq) {\r
+\r
+// for (int i = 0; i < bonds.size(); i++) {\r
+// Bond tmp = (Bond)bonds.elementAt(i);\r
+// try {\r
+//\r
+// if (tmp.at1.resNumber >= (offset + seq.pdbstart - 1) && tmp.at1.resNumber <= (offset + seq.pdbend - 1)) {\r
+//\r
+// int pos = seq.seqtart() + (tmp.at1.resNumber - seq.pdbstart - offset) ;\r
+// int index = seq.findIndex(pos);\r
+//\r
+// tmp.startCol = (Color)seq.getResidueBoxColour(index);\r
+//\r
+// } else {\r
+// tmp.startCol = Color.gray;\r
+// }\r
+//\r
+// if (tmp.at2.resNumber >= (offset + seq.pdbstart -1) && tmp.at2.resNumber <= (seq.pdbend+offset-1)) {\r
+//\r
+// int pos = seq.seqstart + (tmp.at2.resNumber - seq.pdbstart-offset);\r
+// int index = seq.findIndex(pos);\r
+//\r
+// tmp.endCol = (Color)seq.getResidueBoxColour(index);\r
+//\r
+// } else {\r
+// tmp.endCol = Color.gray;\r
+// }\r
+// } catch (Exception e) {\r
+// tmp.startCol = Color.lightGray;\r
+// tmp.endCol = Color.lightGray;\r
+// }\r
+// }\r
+ }\r
+\r
+ public void setChainColours() {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond)bonds.elementAt(i);\r
+ try {\r
+ tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);\r
+ tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);\r
+ } catch (Exception e) {\r
+ tmp.startCol = Color.lightGray;\r
+ tmp.endCol = Color.lightGray;\r
+ }\r
+ }\r
+ }\r
+}\r
+\r
+\r
--- /dev/null
+package MCview;\r
+\r
+import jalview.gui.*;\r
+import java.io.*;\r
+import java.net.*;\r
+import java.util.*;\r
+\r
+\r
+public class PDBfile extends jalview.io.FileParse {\r
+\r
+ public Vector chains = new Vector();\r
+\r
+ Vector lineArray = new Vector();\r
+\r
+ public PDBfile(String inFile, String inType) throws IOException {\r
+\r
+ super(inFile,inType);\r
+\r
+ String line;\r
+ this.lineArray = new Vector();\r
+ BufferedReader dataIn;\r
+\r
+ if (inType.equals("File"))\r
+ dataIn = new BufferedReader(new FileReader( inFile ));\r
+\r
+ else\r
+ {\r
+ URL url = new URL(inFile);\r
+ this.fileSize = 0;\r
+ dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ }\r
+\r
+ while ((line = dataIn.readLine()) != null) {\r
+ lineArray.addElement(line);\r
+ }\r
+ noLines = lineArray.size();\r
+\r
+ parse();\r
+\r
+}\r
+\r
+\r
+ public void parse() {\r
+\r
+ System.out.println("Parsing");\r
+\r
+ for (int i = 0; i < lineArray.size(); i++) {\r
+ StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());\r
+ if (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ if (inStr.indexOf("ATOM") != -1) {\r
+ try {\r
+ myAtom tmpatom = new myAtom(str);\r
+ if (findChain(tmpatom.chain) != null) {\r
+ System.out.println("Adding to chain " + tmpatom.chain);\r
+ findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
+ } else {\r
+ System.out.println("Making chain " + tmpatom.chain);\r
+ PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
+ chains.addElement(tmpchain);\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ } catch(NumberFormatException e) {\r
+ System.out.println("Caught" + e);\r
+ System.out.println("Atom not added");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ makeResidueList();\r
+ makeCaBondList();\r
+ // for (int i=0; i < chains.size() ; i++) {\r
+ // String pog = ((PDBChain)chains.elementAt(i)).print();\r
+ // System.out.println(pog);\r
+ // }\r
+ }\r
+\r
+ public void makeResidueList() {\r
+ for (int i=0; i < chains.size() ; i++) {\r
+ ((PDBChain)chains.elementAt(i)).makeResidueList();\r
+ }\r
+ }\r
+ public void makeCaBondList() {\r
+ for (int i=0; i < chains.size() ; i++) {\r
+ ((PDBChain)chains.elementAt(i)).makeCaBondList();\r
+ }\r
+ }\r
+\r
+ public PDBChain findChain(String id) {\r
+ for (int i=0; i < chains.size(); i++) {\r
+ // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);\r
+ if (((PDBChain)chains.elementAt(i)).id.equals(id)) {\r
+ return (PDBChain)chains.elementAt(i);\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+\r
+ public void setChargeColours() {\r
+ for (int i=0; i < chains.size(); i++) {\r
+ ((PDBChain)chains.elementAt(i)).setChargeColours();\r
+ }\r
+ }\r
+\r
+ public void setHydrophobicityColours() {\r
+ for (int i=0; i < chains.size(); i++) {\r
+ ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();\r
+ }\r
+ }\r
+\r
+ public void colourBySequence(DrawableSequence seq) {\r
+//SMJS TODO\r
+// int max = seq.maxchain;\r
+// if (seq.maxchain != -1) {\r
+// ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
+// }\r
+ }\r
+\r
+ public void setChainColours() {\r
+ for (int i=0; i < chains.size(); i++) {\r
+ ((PDBChain)chains.elementAt(i)).setChainColours();\r
+ }\r
+ }\r
+ public static void main(String[] args) {\r
+ try {\r
+ PDBfile pdb = new PDBfile("enkp1.pdb","File");\r
+ } catch(IOException e) {\r
+ System.out.println(e);\r
+ System.exit(0);\r
+ }\r
+ }\r
+}\r
+\r
+\r
+\r
--- /dev/null
+package MCview;\r
+\r
+import java.util.*;\r
+\r
+\r
+public class Residue {\r
+ Vector atoms = new Vector();\r
+\r
+ int number;\r
+ int count;\r
+ int seqnumber;\r
+\r
+ public Residue(Vector atoms, int number, int count) {\r
+ this.atoms = atoms;\r
+ this.number = number;\r
+ this.count = count;\r
+ }\r
+\r
+ public myAtom findAtom(String name) {\r
+\r
+ for (int i = 0; i < atoms.size(); i++) {\r
+ if (((myAtom)atoms.elementAt(i)).name.equals(name)) {\r
+ return (myAtom)atoms.elementAt(i);\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+}\r
--- /dev/null
+package MCview;\r
+\r
+import java.util.*;\r
+\r
+public class Zsort {\r
+\r
+ public static void Zsort(Vector bonds) {\r
+\r
+ sort(bonds,0,bonds.size()-1);\r
+ }\r
+\r
+\r
+\r
+ public static void sort(Vector bonds,int p, int r) {\r
+ int q;\r
+\r
+ if (p < r) {\r
+ q = partition(bonds,p,r);\r
+ sort(bonds,p,q);\r
+ sort(bonds,q+1,r);\r
+ }\r
+ }\r
+\r
+ private static int partition(Vector bonds, int p, int r) {\r
+ float x = ((Bond)bonds.elementAt(p)).start[2];\r
+ int i = p-1;\r
+ int j = r+1;\r
+\r
+ while(true) {\r
+ do {\r
+ j = j-1;\r
+ } while (j >= 0 && ((Bond)bonds.elementAt(j)).start[2] > x);\r
+\r
+ do {\r
+ i = i+1;\r
+ } while (i < bonds.size() && ((Bond)bonds.elementAt(i)).start[2] < x);\r
+\r
+ if ( i < j) {\r
+ Bond tmp = (Bond)bonds.elementAt(i);\r
+ bonds.setElementAt(bonds.elementAt(j),i);\r
+ bonds.setElementAt(tmp,j);\r
+ } else {\r
+ return j;\r
+ }\r
+ }\r
+ }\r
+}\r
+\r
+\r
+\r
--- /dev/null
+package MCview;\r
+\r
+import java.util.*;\r
+import java.awt.*;\r
+\r
+public class myAtom {\r
+ float x;\r
+ float y;\r
+ float z;\r
+\r
+ public int number;\r
+ public String name;\r
+ public String resName;\r
+ public int resNumber;\r
+ public int type;\r
+ public Color color;\r
+ public String chain;\r
+ public boolean isSelected = false;\r
+\r
+ public myAtom(StringTokenizer str) {\r
+\r
+ this.number = (new Integer(str.nextToken())).intValue();\r
+ this.name = str.nextToken();\r
+ this.resName = str.nextToken();\r
+\r
+ String tmpstr = new String();\r
+\r
+ try {\r
+ tmpstr = str.nextToken();\r
+ this.resNumber = (new Integer(tmpstr).intValue());\r
+ this.chain = "A";\r
+ this.color = Color.lightGray;\r
+\r
+ } catch(NumberFormatException e) {\r
+ this.chain = tmpstr;\r
+\r
+ if (tmpstr.equals("A")) {\r
+ this.color = Color.lightGray;\r
+\r
+ } else {\r
+ this.color = Color.red;\r
+ }\r
+\r
+ this.resNumber = (new Integer(str.nextToken()).intValue());\r
+ }\r
+\r
+ this.x = (float)(new Float(str.nextToken()).floatValue());\r
+ this.y = (float)(new Float(str.nextToken()).floatValue());\r
+ this.z = (float)(new Float(str.nextToken()).floatValue());\r
+ }\r
+\r
+ public void setColor(Color col) {\r
+ this.color = col;\r
+ }\r
+}\r
--- /dev/null
+package MCview;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+import java.io.*;\r
+import javax.swing.*;\r
+\r
+public class rotCanvas extends JPanel implements KeyListener,\r
+ MouseListener,\r
+ MouseMotionListener {\r
+ MCMatrix idmat = new MCMatrix(3,3);\r
+ MCMatrix objmat = new MCMatrix(3,3);\r
+\r
+ boolean redrawneeded =true;\r
+\r
+ int omx = 0;\r
+ int mx = 0;\r
+ int omy = 0;\r
+ int my = 0;\r
+\r
+ public PDBfile pdb;\r
+\r
+ int bsize;\r
+\r
+ Image img;\r
+ Graphics ig;\r
+\r
+ Dimension prefsize;\r
+\r
+ float centre[] = new float[3];\r
+ float width[] = new float[3];\r
+\r
+ float maxwidth;\r
+ float scale;\r
+\r
+ String inStr;\r
+ String inType;\r
+\r
+ boolean depthcue = true;\r
+ boolean wire = false;\r
+ boolean bymolecule = false;\r
+ boolean zbuffer = true;\r
+\r
+ boolean dragging;\r
+\r
+ int xstart;\r
+ int xend;\r
+ int ystart;\r
+ int yend;\r
+ int xmid;\r
+ int ymid;\r
+\r
+ Font font = new Font("Helvetica",Font.PLAIN,10);\r
+\r
+ public rotCanvas(PDBfile pdb) throws IOException {\r
+\r
+ this.pdb = pdb;\r
+ this.prefsize = new Dimension( getWidth(), getHeight());\r
+\r
+ //Initialize the matrices to identity\r
+\r
+ for (int i = 0; i < 3; i++) {\r
+ for (int j = 0; j < 3 ; j++) {\r
+ if (i != j) {\r
+ idmat.addElement(i,j,0);\r
+ objmat.addElement(i,j,0);\r
+ } else {\r
+ idmat.addElement(i,j,1);\r
+ objmat.addElement(i,j,1);\r
+ }\r
+ }\r
+ }\r
+\r
+ addMouseMotionListener(this);\r
+ addMouseListener(this);\r
+ addKeyListener(this);\r
+\r
+ addPDBfile();\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+\r
+ }\r
+\r
+ public void addPDBfile() {\r
+ findCentre();\r
+ findWidth();\r
+\r
+ scale = findScale();\r
+\r
+ System.out.println("Scale factor = " + scale);\r
+ }\r
+\r
+ public void deleteBonds() {\r
+ scale = 0;\r
+ maxwidth = 0;\r
+\r
+ width[0] = 0;\r
+ width[1] = 0;\r
+ width[2] = 0;\r
+\r
+ centre[0] = 0;\r
+ centre[1] = 0;\r
+ centre[2] = 0;\r
+\r
+ for (int i=0; i < pdb.chains.size(); i++) {\r
+ ((PDBChain)pdb.chains.elementAt(i)).bonds = null;\r
+ }\r
+ }\r
+\r
+ public void findWidth() {\r
+ float max[] = new float[3];\r
+ float min[] = new float[3];\r
+\r
+ max[0] = (float)-1e30;\r
+ max[1] = (float)-1e30;\r
+ max[2] = (float)-1e30;\r
+\r
+ min[0] = (float)1e30;\r
+ min[1] = (float)1e30;\r
+ min[2] = (float)1e30;\r
+\r
+ for (int ii=0; ii < pdb.chains.size(); ii++) {\r
+ if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+\r
+ Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmp = (Bond)bonds.elementAt(i);\r
+\r
+ if (tmp.start[0] >= max[0])\r
+ max[0] = tmp.start[0];\r
+ if (tmp.start[1] >= max[1])\r
+ max[1] = tmp.start[1];\r
+ if (tmp.start[2] >= max[2])\r
+ max[2] = tmp.start[2];\r
+ if (tmp.start[0] <= min[0])\r
+ min[0] = tmp.start[0];\r
+ if (tmp.start[1] <= min[1])\r
+ min[1] = tmp.start[1];\r
+ if (tmp.start[2] <= min[2])\r
+ min[2] = tmp.start[2];\r
+\r
+ if (tmp.end[0] >= max[0])\r
+ max[0] = tmp.end[0];\r
+ if (tmp.end[1] >= max[1])\r
+ max[1] = tmp.end[1];\r
+ if (tmp.end[2] >= max[2])\r
+ max[2] = tmp.end[2];\r
+ if (tmp.end[0] <= min[0])\r
+ min[0] = tmp.end[0];\r
+ if (tmp.end[1] <= min[1])\r
+ min[1] = tmp.end[1];\r
+ if (tmp.end[2] <= min[2])\r
+ min[2] = tmp.end[2];\r
+ }\r
+ }\r
+ }\r
+\r
+ System.out.println("xmax " + max[0] + " min " + min[0]);\r
+ System.out.println("ymax " + max[1] + " min " + min[1]);\r
+ System.out.println("zmax " + max[2] + " min " + min[2]);\r
+\r
+ width[0] = (float)Math.abs(max[0] - min[0]);\r
+ width[1] = (float)Math.abs(max[1] - min[1]);\r
+ width[2] = (float)Math.abs(max[2] - min[2]);\r
+\r
+ maxwidth = width[0];\r
+\r
+ if (width[1] > width[0])\r
+ maxwidth = width[1];\r
+ if (width[2] > width[1])\r
+ maxwidth = width[2];\r
+\r
+ System.out.println("Maxwidth = " + maxwidth);\r
+ }\r
+\r
+ public float findScale() {\r
+ int dim, width, height;\r
+\r
+ if ( getWidth() != 0) {\r
+ width = getWidth();\r
+ height = getHeight();\r
+\r
+ } else {\r
+ width = prefsize.width;\r
+ height = prefsize.height;\r
+ }\r
+\r
+ if (width < height) {\r
+ dim = width;\r
+ } else {\r
+ dim = height;\r
+ }\r
+\r
+ return (float)(dim/(1.5d*maxwidth));\r
+ }\r
+\r
+\r
+\r
+ public void findCentre() {\r
+ float xtot = 0;\r
+ float ytot = 0;\r
+ float ztot = 0;\r
+\r
+ int bsize = 0;\r
+ //Find centre coordinate\r
+\r
+ for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+ if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+\r
+ Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ bsize += bonds.size();\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+\r
+ xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +\r
+ ((Bond)bonds.elementAt(i)).end[0];\r
+\r
+ ytot = ytot + ((Bond)bonds.elementAt(i)).start[1] +\r
+ ((Bond)bonds.elementAt(i)).end[1];\r
+\r
+ ztot = ztot + ((Bond)bonds.elementAt(i)).start[2] +\r
+ ((Bond)bonds.elementAt(i)).end[2];\r
+ }\r
+ }\r
+ }\r
+\r
+ centre[0] = xtot / (2 * (float)bsize);\r
+ centre[1] = ytot / (2 * (float)bsize);\r
+ centre[2] = ztot / (2 * (float)bsize);\r
+ }\r
+\r
+ public void paintComponent(Graphics g) {\r
+ //Only create the image at the beginning -\r
+ //this saves much memory usage\r
+ if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {\r
+ prefsize.width = getWidth();\r
+ prefsize.height = getHeight();\r
+\r
+ scale = findScale();\r
+ img = createImage(prefsize.width,prefsize.height);\r
+ ig = img.getGraphics();\r
+\r
+ redrawneeded = true;\r
+ }\r
+\r
+ if (redrawneeded == true) {\r
+ drawBackground(ig,Color.black);\r
+ drawScene(ig);\r
+ redrawneeded = false;\r
+ } else {\r
+ ig = img.getGraphics();\r
+ }\r
+\r
+ g.drawImage(img,0,0,this);\r
+ }\r
+\r
+ public void drawBackground(Graphics g, Color col) {\r
+ g.setColor(col);\r
+ g.fillRect(0,0,prefsize.width,prefsize.height);\r
+ }\r
+\r
+\r
+ public void drawScene(Graphics g) {\r
+ // Sort the bonds by z coord\r
+\r
+ Vector bonds = new Vector();\r
+\r
+\r
+ for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+ if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {\r
+\r
+ Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i=0; i < tmp.size(); i++) {\r
+ bonds.addElement(tmp.elementAt(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (zbuffer) {\r
+ Zsort.Zsort(bonds);\r
+ }\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond)bonds.elementAt(i);\r
+\r
+ xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);\r
+ ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);\r
+\r
+ xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);\r
+ yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);\r
+\r
+ xmid = (xend+xstart)/2;\r
+ ymid = (yend+ystart)/2;\r
+\r
+\r
+ if (depthcue && !bymolecule) {\r
+\r
+ if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {\r
+ g.setColor(tmpBond.startCol.darker().darker());\r
+ drawLine(g,xstart,ystart,xmid,ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker().darker());\r
+ drawLine(g,xmid,ymid,xend,yend);\r
+ } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {\r
+ g.setColor(tmpBond.startCol.darker());\r
+ drawLine(g,xstart,ystart,xmid,ymid);\r
+\r
+ g.setColor(tmpBond.endCol.darker());\r
+ drawLine(g,xmid,ymid,xend,yend);\r
+ } else {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g,xstart,ystart,xmid,ymid);\r
+\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g,xmid,ymid,xend,yend);\r
+ }\r
+ } else if (depthcue && bymolecule) {\r
+ if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {\r
+ g.setColor(Color.green.darker().darker());\r
+ drawLine(g,xstart,ystart,xend,yend);\r
+\r
+ } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {\r
+ g.setColor(Color.green.darker());\r
+ drawLine(g,xstart,ystart,xend,yend);\r
+\r
+ } else {\r
+ g.setColor(Color.green);\r
+ drawLine(g,xstart,ystart,xend,yend);\r
+\r
+ }\r
+ } else if (!depthcue && !bymolecule) {\r
+ g.setColor(tmpBond.startCol);\r
+ drawLine(g,xstart,ystart,xmid,ymid);\r
+ g.setColor(tmpBond.endCol);\r
+ drawLine(g,xmid,ymid,xend,yend);\r
+\r
+ } else {\r
+ drawLine(g,xstart,ystart,xend,yend);\r
+ }\r
+ }\r
+ }\r
+\r
+ public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {\r
+ if (!wire) {\r
+\r
+ if (((float)Math.abs(y2-y1)/(float)Math.abs(x2-x1)) < 0.5) {\r
+\r
+ g.drawLine(x1,y1,x2,y2);\r
+ g.drawLine(x1+1,y1+1,x2+1,y2+1);\r
+ g.drawLine(x1,y1-1,x2,y2-1);\r
+ } else {\r
+ g.setColor(g.getColor().brighter());\r
+ g.drawLine(x1,y1,x2,y2);\r
+ g.drawLine(x1+1,y1,x2+1,y2);\r
+ g.drawLine(x1-1,y1,x2-1,y2);\r
+\r
+ }\r
+ } else {\r
+ g.drawLine(x1,y1,x2,y2);\r
+ }\r
+ }\r
+\r
+ public Dimension minimumsize() {\r
+ return prefsize;\r
+ }\r
+ public Dimension preferredsize() {\r
+ return prefsize;\r
+ }\r
+\r
+ public void keyTyped(KeyEvent evt) { }\r
+ public void keyReleased(KeyEvent evt) { }\r
+ public void keyPressed(KeyEvent evt) {\r
+ int key = evt.getKeyChar();\r
+\r
+ if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
+ scale = (float)(scale * 1.1);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
+ scale = (float)(scale * 0.9);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'w') {\r
+\r
+ wire = !wire;\r
+ System.out.println("wireframe " + wire);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'd') {\r
+ depthcue = !depthcue;\r
+ System.out.println("Depth cueing is " + depthcue);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'm') {\r
+ bymolecule = !bymolecule;\r
+ System.out.println("Bymolecule is " + bymolecule);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'z') {\r
+ zbuffer = !zbuffer;\r
+ System.out.println("Z buffering is " + zbuffer);\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'c') {\r
+ bymolecule = false;\r
+ pdb.setChainColours();\r
+ System.out.println("Colouring by chain");\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'h') {\r
+ bymolecule = false;\r
+ pdb.setHydrophobicityColours();\r
+ System.out.println("Colouring by hydrophobicity");\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ } else if (key == 'q') {\r
+ bymolecule = false;\r
+ pdb.setChargeColours();\r
+ System.out.println("Colouring charges and cysteines");\r
+ redrawneeded = true;\r
+ repaint();\r
+\r
+ }\r
+ return;\r
+ }\r
+\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+\r
+ mx = e.getX();\r
+ my = e.getY();\r
+ omx = mx;\r
+ omy = my;\r
+ dragging = false;\r
+}\r
+\r
+ public void mouseMoved(MouseEvent e)\r
+ {\r
+ myAtom fatom = null;\r
+ for (int ii = 0; ii < pdb.chains.size(); ii++)\r
+ {\r
+\r
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
+ if (chain.isVisible)\r
+ {\r
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
+ for (int i = 0; i < bonds.size(); i++)\r
+ {\r
+ Bond tmpBond = (Bond) bonds.elementAt(i);\r
+ int truex = (int) ( (tmpBond.start[0] - centre[0]) * scale +\r
+ getWidth() / 2);\r
+ if (Math.abs(truex - e.getX()) <= 2)\r
+ {\r
+ int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +\r
+ getHeight() / 2);\r
+ if (Math.abs(truey - e.getY()) <= 2)\r
+ fatom = tmpBond.at1;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if(fatom!=null)\r
+ this.setToolTipText(fatom.resName);\r
+ else\r
+ this.setToolTipText(null);\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent e) { }\r
+ public void mouseEntered(MouseEvent e) { }\r
+ public void mouseExited(MouseEvent e) { }\r
+\r
+ public void mouseDragged(MouseEvent evt) {\r
+ int x = evt.getX();\r
+ int y = evt.getY();\r
+ mx = x;\r
+ my = y;\r
+\r
+ MCMatrix objmat = new MCMatrix(3,3);\r
+ objmat.setIdentity();\r
+\r
+ if ((evt.getModifiers() & Event.META_MASK) != 0) {\r
+ objmat.rotatez((float)((mx-omx)));\r
+ } else {\r
+ objmat.rotatex((float)((my-omy)));\r
+ objmat.rotatey((float)((omx-mx)));\r
+ }\r
+\r
+ //Alter the bonds\r
+ for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+ Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+\r
+ Bond tmpBond = (Bond)bonds.elementAt(i);\r
+\r
+ //Translate the bond so the centre is 0,0,0\r
+ tmpBond.translate(-centre[0],-centre[1],-centre[2]);\r
+\r
+ //Now apply the rotation matrix\r
+ tmpBond.start = objmat.vectorMultiply(tmpBond.start);\r
+ tmpBond.end = objmat.vectorMultiply(tmpBond.end);\r
+\r
+ //Now translate back again\r
+ tmpBond.translate(centre[0],centre[1],centre[2]);\r
+ }\r
+ }\r
+\r
+ objmat = null;\r
+\r
+ omx = mx;\r
+ omy = my;\r
+\r
+ redrawneeded = true;\r
+\r
+ paint(this.getGraphics());\r
+\r
+ dragging = true;\r
+ return;\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt) {\r
+ int x = evt.getX();\r
+ int y = evt.getY();\r
+\r
+ if (!dragging) {\r
+ myAtom tmp = findAtom(x,y);\r
+ }\r
+ drawLabels();\r
+ return;\r
+ }\r
+\r
+ public void drawLabels() {\r
+ redrawneeded = true;\r
+ paint(this.getGraphics());\r
+\r
+ for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+\r
+ PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);\r
+\r
+ if (chain.isVisible) {\r
+\r
+ Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond)bonds.elementAt(i);\r
+\r
+ if (tmpBond.at1.isSelected) {\r
+ labelAtom(img.getGraphics(),tmpBond,1);\r
+ }\r
+\r
+ if (tmpBond.at2.isSelected) {\r
+ labelAtom(img.getGraphics(),tmpBond,2);\r
+ }\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ this.getGraphics().drawImage(img,0,0,this);\r
+\r
+ dragging = false;\r
+\r
+ }\r
+\r
+ public void labelAtom(Graphics g,Bond b, int n) {\r
+\r
+ g.setFont(font);\r
+\r
+ if (n ==1) {\r
+\r
+ int xstart = (int)((b.start[0] - centre[0])*scale + getWidth()/2);\r
+ int ystart = (int)((b.start[1] - centre[1])*scale + getHeight()/2);\r
+\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at1.resName + "-" + b.at1.resNumber,xstart,ystart);\r
+ }\r
+\r
+ if (n ==2) {\r
+\r
+ int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);\r
+ int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);\r
+\r
+ g.setColor(Color.red);\r
+ g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);\r
+ }\r
+ }\r
+\r
+\r
+ public myAtom findAtom(int x, int y) {\r
+ myAtom fatom = null;\r
+\r
+ int foundchain = -1;\r
+\r
+ for (int ii = 0; ii < pdb.chains.size() ; ii++) {\r
+\r
+ PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);\r
+\r
+ if (chain.isVisible) {\r
+\r
+ Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;\r
+\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ Bond tmpBond = (Bond)bonds.elementAt(i);\r
+\r
+ int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);\r
+\r
+ if (Math.abs(truex - x) <= 2) {\r
+\r
+ int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);\r
+\r
+ if (Math.abs(truey - y) <= 2) {\r
+\r
+ System.out.println("Found match");\r
+ System.out.println(x + " " + y);\r
+ System.out.println(truex + " " + truey);\r
+ System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);\r
+ System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +\r
+ tmpBond.at1.resNumber + " " + tmpBond.at1.chain);\r
+ fatom = tmpBond.at1;\r
+ fatom.isSelected = !fatom.isSelected;\r
+ foundchain = ii;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (fatom != null) //)&& chain.ds != null)\r
+ {\r
+ chain = (PDBChain)pdb.chains.elementAt(foundchain);\r
+ // SMJS TODO\r
+ // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;\r
+ // int pos = chain.ds.findIndex(tmp);\r
+ // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);\r
+ }\r
+\r
+ }\r
+ return fatom;\r
+ }\r
+\r
+ public void update(Graphics g) {\r
+ paint(g);\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / commitdiff