Help With My Application (WPF)

Dec 12 2009 2:59 AM
I am currently developing a wpf application to extract a sequence from a file contained within a rich textbox. What I have been able to do is load the file (a pdb file, which is basically a text file and can be opened in wordpad) into the rich text box on my form. What I am having difficulty with is extracting the information I want from this rich text box. I have enclosed my application and the raw data above (2B0F), and would be very grateful if you could review it and see how to get this particular aspect working. A PDB file is a Protein Data Bank used in Mass Spectromatry, and is big because the data it contains is extensive. (PLEASE CONTACT ME IF YOU WANT THE DATA AND CAN HELP ME) Basically, what I intend is to load the .pdb file into the rich text box, and then extract the sequence data. This data looks like: MODEL 1 ATOM 1 N GLY A 1 296.995 21.768 -6.913 1.00 0.00 N ATOM 2 CA GLY A 1 296.814 21.433 -8.356 1.00 0.00 C ATOM 3 C GLY B 1 295.982 20.178 -8.579 1.00 0.00 C ATOM 4 O GLY B 1 295.381 19.654 -7.643 1.00 0.00 O ATOM 5 HA2 GLY B 1 296.321 22.263 -8.844 1.00 0.00 H ATOM 6 HA3 GLY B 1 297.784 21.294 -8.810 1.00 0.00 H ATOM 7 H1 GLY A 1 297.491 22.677 -6.814 1.00 0.00 H etc, with a whole lot of data that I do not need at the moment at the top above this as you can see (you will need to scroll to see the data I am meaning in my application once you have loaded the pdb file. I would like to extract the sequence from this data above, and put it into a rich text box, so it looks like this (this is all the data from the sequence I have enclosed): As you can see, all I need is the atom number and the chemical code from the centre, as well as divide this up into two chains (for example chain A represents all those that have an A, and chain B represents all those that have a B in it. >Chain_A 1 - GLY 2 - PRO 3 - ASN 4 - THR 5 - GLU 6 - PHE 7 - ALA 8 - LEU 9 - SER 10 - LEU 11 - LEU 12 - ARG 13 - LYS 14 - ASN 15 - ILE 16 - MET 17 - THR 18 - ILE 19 - THR 20 - THR 21 - SER 22 - LYS 23 - GLY 24 - GLU 25 - PHE 26 - THR 27 - GLY 28 - LEU 29 - GLY 30 - ILE 31 - HIS 32 - ASP 33 - ARG 34 - VAL 35 - CYS 36 - VAL 37 - ILE 38 - PRO 39 - THR 40 - HIS 41 - ALA 42 - GLN 43 - PRO 44 - GLY 45 - ASP 46 - ASP 47 - VAL 48 - LEU 49 - VAL 50 - ASN 51 - GLY 52 - GLN 53 - LYS 54 - ILE 55 - ARG 56 - VAL 57 - LYS 58 - ASP 59 - LYS 60 - TYR 61 - LYS 62 - LEU 63 - VAL 64 - ASP 65 - PRO 66 - GLU 67 - ASN 68 - ILE 69 - ASN 70 - LEU 71 - GLU 72 - LEU 73 - THR 74 - VAL 75 - LEU 76 - THR 77 - LEU 78 - ASP 79 - ARG 80 - ASN 81 - GLU 82 - LYS 83 - PHE 84 - ARG 85 - ASP 86 - ILE 87 - ARG 88 - GLY 89 - PHE 90 - ILE 91 - SER 92 - GLU 93 - ASP 94 - LEU 95 - GLU 96 - GLY 97 - VAL 98 - ASP 99 - ALA 100 - THR 101 - LEU 102 - VAL 103 - VAL 104 - HIS 105 - SER 106 - ASN 107 - ASN 108 - PHE 109 - THR 110 - ASN 111 - THR 112 - ILE 113 - LEU 114 - GLU 115 - VAL 116 - GLY 117 - PRO 118 - VAL 119 - THR 120 - MET 121 - ALA 122 - GLY 123 - LEU 124 - ILE 125 - ASN 126 - LEU 127 - SER 128 - SER 129 - THR 130 - PRO 131 - THR 132 - ASN 133 - ARG 134 - MET 135 - ILE 136 - ARG 137 - TYR 138 - ASP 139 - TYR 140 - ALA 141 - THR 142 - LYS 143 - THR 144 - GLY 145 - GLN 146 - CYS 147 - GLY 148 - GLY 149 - VAL 150 - LEU 151 - CYS 152 - ALA 153 - THR 154 - GLY 155 - LYS 156 - ILE 157 - PHE 158 - GLY 159 - ILE 160 - HIS 161 - VAL 162 - GLY 163 - GLY 164 - ASN 165 - GLY 166 - ARG 167 - GLN 168 - GLY 169 - PHE 170 - SER 171 - ALA 172 - GLN 173 - LEU 174 - LYS 175 - LYS 176 - GLN 177 - TYR 178 - PHE 179 - VAL 180 - GLU 181 - LYS 182 - GLN >Chain_B 1 - LEU 2 - GLU 3 - ALA 4 - LEU 5 - PHE 6 - GLN I would be very grateful if you were able to help me, as I am somewhat new in programming WPF. Thank-you once again, Timothy Johansen.