Help With My Application (WPF)
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.