MATLAB-如何将具有另一个文本文件中ID的SDF文件中的分子提取到新的SDF文件中？

ehxuflar  于 2022-11-15  发布在  Matlab
关注(0)|答案(1)|浏览(246)

我有一个包含数千个分子的SDF文件和几个按某些特征分组在一起的ID文本文件。现在，我有一个脚本，它加载到带有分子特征的CSV数据库中，并通过基于这些特征进行分类来生成ID文本文件。我想使用这些文本文件来解析SDF文件，以获得带有相应分子的新SDF文件。此外，我还想在MatLab中实现这一点。
例如，以下是原始SDF文件中的一些分子：

NCGC00178831-03
  Marvin  07111412562D          

 34 37  0  0  0  0            999 V2000
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    2.8647   -2.4751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8647   -1.6501    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.5808   -1.2318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2970   -1.6501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0017   -1.2318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7179   -1.6501    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0017   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2970    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5808   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8647    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1485   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7293   -3.5407    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0132   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1599   -3.9590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4438   -3.5407    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0115   -3.5407    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7276   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4438   -5.1908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3 13  1  0  0  0  0
  4  5  1  0  0  0  0
  4 10  1  0  0  0  0
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 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
M  CHG  2   1  -1   3   1
M  END
>  <Formula>
C27H25ClN6

>  <FW>
468.9806 (35.4535+224.2805+209.2465)

>  <DSSTox_CID>
25848

>  <SR-HSE>
0

$$$$
NCGC00166114-03
  Marvin  07111412562D          

 31 32  0  0  0  0            999 V2000
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M  CHG  4   7  -1  21  -1  30   1  31   1
M  END
>  <Formula>
C20H6Br4Na2O5

>  <FW>
691.8542 (645.8757+22.9892+22.9892)

>  <DSSTox_CID>
5234

>  <SR-HSE>
0

$$$$
NCGC00263563-01
  Marvin  07111412562D          

 71 76  0  0  1  0            999 V2000
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 33 44  1  0  0  0  0
 33 67  1  6  0  0  0
 35 38  1  0  0  0  0
 35 59  1  1  0  0  0
 36 40  1  0  0  0  0
 36 45  2  0  0  0  0
 37 38  1  0  0  0  0
 37 60  1  1  0  0  0
 39 44  1  0  0  0  0
 41 43  1  0  0  0  0
 47 61  1  0  0  0  0
 48 62  1  0  0  0  0
 50 63  1  0  0  0  0
 51 64  1  0  0  0  0
M  CHG  2  40  -1  71   1
M  END
>  <Formula>
C47H83NO17

>  <FW>
934.1584 (916.1205+18.0379)

>  <DSSTox_CID>
28909

>  <SR-HSE>
0

$$$$

以下是文本文件中的一些ID：

NCGC00015959-03
NCGC00168261-01
NCGC00257010-01
NCGC00254654-01
NCGC00254471-01

生成的SDF文件应该如下所示：

NCGC00015959-03
  Marvin  07111412562D          

 25 30  0  0  0  0            999 V2000
    3.4098   -1.3130    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    4.8329   -1.3130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4098   -2.1380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1248   -2.5436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6948   -2.5436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8329   -2.1380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1248   -0.8937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5547   -0.8937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9799   -2.1380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6948   -3.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2718   -2.5436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2718   -3.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1248   -3.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9799   -3.7741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5547   -2.5436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2765   -1.3130    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7128   -0.0894    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881   -2.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881   -3.6160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8746   -0.7562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5378    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.9423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4098   -3.7741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2765   -2.1380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6948   -0.8937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  2  0  0  0  0
  1 25  1  0  0  0  0
  2  7  1  0  0  0  0
  2  6  2  0  0  0  0
  2  8  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  4 13  1  0  0  0  0
  4  6  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 15  1  0  0  0  0
  8 16  2  0  0  0  0
  8 17  1  0  0  0  0
  9 11  2  0  0  0  0
 10 14  1  0  0  0  0
 10 23  1  0  0  0  0
 11 18  1  0  0  0  0
 11 12  1  0  0  0  0
 12 14  2  0  0  0  0
 12 19  1  0  0  0  0
 13 23  2  0  0  0  0
 15 24  2  0  0  0  0
 16 20  1  0  0  0  0
 16 24  1  0  0  0  0
 17 21  1  0  0  0  0
 18 22  1  0  0  0  0
 19 22  1  0  0  0  0
 20 21  1  0  0  0  0
M  CHG  1   1   1
M  END
>  <Formula>
C20H14NO4

>  <FW>
332.3289

>  <DSSTox_CID>
25204

>  <NR-AR>
0

>  <NR-ER-LBD>
1

>  <NR-AhR>
1

$$$$
NCGC00168261-01
  Marvin  07111412562D          

 23 25  0  0  0  0            999 V2000
    2.1236   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4205   -2.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1236   -3.3074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4205   -3.7235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7174   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7174   -3.3074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8554   -2.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4205   -1.2412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8554   -3.7235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5656   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5656   -3.3074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8554   -1.2412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7174   -0.8251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.2412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0430   -2.8984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7174   -4.1324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2902   -3.7378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7174    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0292   -3.3145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4569   -3.3360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7538   -3.7378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1743   -3.7378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  7  1  0  0  0  0
  2  5  2  0  0  0  0
  2  9  1  0  0  0  0
  3  4  1  0  0  0  0
  3 10  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6 16  1  0  0  0  0
  6 17  1  0  0  0  0
  7 11  2  0  0  0  0
  7 13  1  0  0  0  0
  8 15  2  0  0  0  0
  9 14  2  0  0  0  0
 10 12  2  0  0  0  0
 11 12  1  0  0  0  0
 12 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 22  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
M  END
>  <Formula>
C21H26O2

>  <FW>
310.4299

>  <DSSTox_CID>
28922

>  <NR-AR>
0

>  <NR-AhR>
1

>  <SR-MMP>
1

$$$$
NCGC00257010-01
  Marvin  07111412562D          

 35 37  0  0  0  0            999 V2000
    2.0286   -3.5779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0019   -7.8578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0019   -0.7019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8589   -3.5779    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6092   -2.8589    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6092   -4.2799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2784   -4.2799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5825   -7.1217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5825   -1.4381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3681   -3.5779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5024   -3.5779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5024   -4.9989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0915   -4.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3412   -3.5779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3412   -4.9989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7704   -4.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7704   -2.8589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7294   -1.1385    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    6.2829   -0.2996    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.7294   -7.4213    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.4384   -8.5597    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    6.2829   -8.2601    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.4384    0.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.0019   -2.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0019   -6.4112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7607   -1.4381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7607   -7.1217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7607   -5.7008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7607   -2.8589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5825   -5.7008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5825   -2.8589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3412   -6.4112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3412   -2.1485    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.9103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0086   -4.2542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  2  8  1  0  0  0  0
  2 20  1  0  0  0  0
  2 21  1  0  0  0  0
  2 22  1  0  0  0  0
  3  9  1  0  0  0  0
  3 18  1  0  0  0  0
  3 19  1  0  0  0  0
  3 23  1  0  0  0  0
  4  7  1  0  0  0  0
  5 17  1  0  0  0  0
  6 16  1  0  0  0  0
  7 13  2  0  0  0  0
  8 27  1  0  0  0  0
  8 25  2  0  0  0  0
  9 26  2  0  0  0  0
  9 24  1  0  0  0  0
 10 16  1  0  0  0  0
 10 34  1  0  0  0  0
 10 35  1  0  0  0  0
 10 17  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
 12 13  1  0  0  0  0
 12 15  2  0  0  0  0
 14 29  1  0  0  0  0
 15 28  1  0  0  0  0
 24 31  2  0  0  0  0
 25 30  1  0  0  0  0
 26 33  1  0  0  0  0
 27 32  2  0  0  0  0
 28 30  2  0  0  0  0
 28 32  1  0  0  0  0
 29 31  1  0  0  0  0
 29 33  2  0  0  0  0
M  END
>  <Formula>
C25H24F6N4

>  <FW>
494.4753

>  <DSSTox_CID>
3868

>  <NR-AR>
0

>  <NR-ER>
1

>  <NR-AhR>
1

$$$$

我看过这个帖子：Extract molecules in order from SDF file according to IDs given in another file，它在Unix中提供了解决这个问题的解决方案。我在命令行中使用了这个变通方法：awk 'BEGIN{ORS="$$$$"}NR==FNR{a[$1]=$0;next}$1 in a' ids.txt RS="$" molecules.sdf > molecules_by_ids.sdf，并且能够获得我想要的大部分内容。然而，即使我使用这个命令行选项，我也不能100%地从SDF文件中提取分子。例如，有981个分子对其中一个特征是阳性的，文本文件得到981个ID，这个命令给出了SDF文件中的950个分子。
我真正想要的是一个不会遗漏生成文件中任何分子的MatLab解决方案。我感谢任何为解决问题所做的努力。谢谢!

matlab

1条答案

按热度按时间
3zwtqj6y

3zwtqj6y1#

我在MatLab中找到的一个解决办法是以下函数，其中“id”是ID TXT文件的名称，“sdfs”是SDF数据库，而“SDF_NAME”是新SDF文件的名称，分子由ID提取：

function write_sdf(id, sdfs, sdf_name)
% Open the text file of ids.
fid = fopen(id);

% Convert the sdf file to a character array.
data = fileread(sdfs);

% For each id, get the portion of the sdf file corresponding
% to the molecule id.
while true
    mol_id = fgetl(fid);
    mol_full = '';

    % When we're at the end of the file, leave the loop.
    if mol_id == -1
        % We're done with the id file.
        fclose(fid);
        break;
    else
        mol_after = extractAfter(data, mol_id);
        mol_between = extractBefore(mol_after, '$$$$');
        mol_full = [char(mol_id) char(mol_between) '$$$$'];

        % Write the molecule to the sdf file.
        writelines(mol_full, sdf_name, WriteMode='append');
    end
 end

end

这个解决方案的问题是它非常慢。如果有人知道更快的方法，请让我知道！现在，我将使用这个。

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