Help with my WPF Application
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Thread: Help with my WPF Application

  1. #1
    Join Date
    Dec 2009
    Posts
    7

    Help with my WPF Application

    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.

    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.


    Timothy Johansen
    W e b D e s i g n e r / P r o g r a m m e r

    Ph: (06) 3592292
    Mob: (027) 7262096
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  2. #2
    Arjay's Avatar
    Arjay is offline Moderator / MS MVP Power Poster
    Join Date
    Aug 2004
    Posts
    11,442

    Re: Help with my WPF Application

    Why do you want to load the file into a rich text box and then extract the data? Why not just extract the data from the file directly?

  3. #3
    Join Date
    Sep 2006
    Posts
    31

    Re: Help with my WPF Application

    Here you go..
    I used 2 textBoxes just replace it with richttextbox.text and your set tested and works

    Code:
            private List<string> Chains = new List<string>();
            private List<List<string>> ContentChains = new List<List<string>>();
            private void button1_Click(object sender, EventArgs e)
            {
                
                string[] linesArray = textBox1.Text.Split('\n');
                int chainNr;
                foreach (string s in linesArray)
                {
                    String[] array = s.Split(' ');
                    if (!Chains.Contains(array[4]))
                    {
                        Chains.Add(array[4]);
                        ContentChains.Add(new List<string>());
                    }
                        chainNr = Chains.IndexOf(array[4]);
    
                        List<string> list = ContentChains.ElementAt(chainNr);
                        list.Add(array[3]);
                }
    
            }
    
    
            //Used to show values in another textbox
            private void button2_Click(object sender, EventArgs e)
            {
                    int i = 0;
                    foreach (String s in Chains)
                    {
    
                        textBox2.Text += "Chain " + s + Environment.NewLine;
                        List<string> list = ContentChains.ElementAt(i);
                        int j=0;
                        foreach (String st in list)
                        {
                            
                            textBox2.Text += j + " " + st + Environment.NewLine;
                            j++;
                        }
    
                        i++;
                    }
                
    
                
            }
    Here is an preview of the output
    Chain A
    0 GLY
    1 GLY
    2 GLY
    Chain B
    0 GLY
    1 GLY
    2 GLY
    3 GLY


    greetz kristof

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