计算原子坐标之间的距离 [英] Calculating the distance between atomic coordinates

问题描述

我有一个如下所示的文本文件

I have a text file as shown below

ATOM    920  CA  GLN A 203      39.292 -13.354  17.416  1.00 55.76           C 
ATOM    929  CA  HIS A 204      38.546 -15.963  14.792  1.00 29.53           C
ATOM    939  CA  ASN A 205      39.443 -17.018  11.206  1.00 54.49           C  
ATOM    947  CA  GLU A 206      41.454 -13.901  10.155  1.00 26.32           C
ATOM    956  CA  VAL A 207      43.664 -14.041  13.279  1.00 40.65           C 
.
.
.

ATOM    963  CA  GLU A 208      45.403 -17.443  13.188  1.00 40.25           C  

我想计算两个α碳原子之间的距离，即计算第一个和第二个原子之间的距离，然后计算第二个和第三个原子之间的距离，依此类推.....两个原子之间的距离可以表示为: c0>

I would like to calculate the distance between two alpha carbon atoms i.e calculate the distance between first and second atom and then between second and third atom and so on..... The distance between two atoms can be expressed as:distance = sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2) .

第7、8和9列分别代表x，y和z坐标.我需要打印距离和对应的残基对(第4列)，如下所示(距离的值不是实数)

The columns 7,8 and 9 represents x,y and z co-ordinates respectively.I need to print the distance and the corresponding residue pairs(column 4) as shown below.(the values of distance are not real)

GLN-HIS   4.5
HIS-ASN   3.2
ASN-GLU   2.5

如何使用perl或python进行此计算?

How can I do this calculation with perl or python?

推荐答案

如果您的数据用空格分隔，则简单的split即可完成工作.缓冲线以顺序比较它们.

If your data is separated by whitespace, a simple split can do the job. Buffering the lines to compare them to each other sequentially.

use strict;
use warnings;

my @line;
while (<>) {
    push @line, $_;            # add line to buffer
    next if @line < 2;         # skip unless buffer is full
    print proc(@line), "\n";   # process and print 
    shift @line;               # remove used line 
}

sub proc {
    my @a = split ' ', shift;   # line 1
    my @b = split ' ', shift;   # line 2
    my $x = ($a[6]-$b[6]);      # calculate the diffs
    my $y = ($a[7]-$b[7]);
    my $z = ($a[8]-$b[8]);
    my $dist = sprintf "%.1f",                # format the number
                   sqrt($x**2+$y**2+$z**2);   # do the calculation
    return "$a[3]-$b[3]\t$dist"; # return the string for printing
}

输出(带有示例数据):

GLN-HIS 3.8
HIS-ASN 3.8
ASN-GLU 3.9
GLU-VAL 3.8

如果数据用制表符分隔，则可以在/\t/而不是' '上拆分.

If your data is tab separated, you can split on /\t/ instead of ' '.

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