计算原子坐标之间的距离(Calculating the distance between atomi

2019-07-04 07:10发布

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我有一个文本文件，如下图所示

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碳原子间的距离，即计算的第一和第二原子之间，然后和之间的第二和第三原子等的距离.....两个原子之间的距离可以被表示为： distance = sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2) .

列7,8和9表示在x，y和z坐标respectively.I需要打印的距离和相应的残余物对（第4栏），如下所示。（距离的值不是真实）

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

我怎样才能做到这一点的计算与Perl或Python？

Answer 1:

如果你的数据是由空格隔开，简单的split可以做的工作。缓冲线将它们相互比较顺序。

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（与样品数据）：

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

如果您的数据是制表符分隔，可以拆分上/\t/ ，而不是' ' 。

Answer 2:

请在空格不拆

这里给出其他答案做一个有缺陷的假设 - 即坐标将是空间分隔的。每的PDB规范ATOM ，这不是 necessarilly的情况下：记录PDB值由列索引指定，并且可以流入彼此。例如，你的第一个ATOM记录上写着：

ATOM    920  CA  GLN A 203      39.292 -13.354  17.416  1.00 55.76           C

但是，这是完全合法的，以及：

ATOM    920  CA  GLN A 203      39.292-13.3540  17.416  1.00 55.76           C

更好的办法

由于指定的列项指数，以及可能发生在PDB文件中的其他问题的数量，你不应该写自己的解析器。在PDB格式是凌乱的，并且有很多的特殊情况和错误格式的文件来处理。相反，使用已经为你写一个解析器。

我喜欢Biopython的PDB.PDBParser 。它将分析结构为你为Python对象，完成与方便的功能。如果你喜欢Perl中，检查出的BioPerl 。

PDB.Residue对象允许通过名称原子键访问，并PDB.Atom对象重载-操作员两个原子之间的距离返回。我们可以用它来写干净，简洁的代码：

码

from Bio import PDB
parser = PDB.PDBParser()

# Parse the structure into a PDB.Structure object
pdb_code = "1exm"
pdb_path = "pdb1exm.ent"
struct = parser.get_structure(pdb_code, pdb_path)

# Grab the first two residues from the structure
residues = struct.get_residues()
res_one = residues.next()
res_two = residues.next()

try:
    alpha_dist = res_one['CA'] - res_two['CA']
except KeyError:
    print "Alpha carbon missing, computing distance impossible!"

Answer 3:

假设你的数据在“atoms.txt”，这由线读取它的线并拆分项目分成列表：

import csv

with open("atoms.txt") as f:
  reader = csv.reader(f)
  for line, in reader:
      entries = line.split()
      print entries

现在，每个列表提取所需的列，并计算距离等（记住，Python中的列表是从零开始）。

Answer 4:

理论上，应该使用MDAnalysis包的“切片”原子和细分，并计算它们之间的距离测量的Python的方式。事实上，MDAnalysis支持多种MD模拟和化学结构格式。

对于一个小更详细的例子，也看到了上Biostars.org以下条目。

Answer 5:

如果你有兴趣在短短的一对，bash的工作就好了。这是一个脚本，我使用，我有它设置为在年底重新启动（如果你想关闭这个功能）。它会提示你哪些原子。 PDB文件可以有不同的列设置，因此对于AWK线确保列匹配。用新的PDB文件在使用前做手工测试用例。这是微不足道的，但在我的剧本PDB文件更改为你的。

#!/usr/bin/env bash

echo " "
echo "Use one letter abbreviations. Case doesn't matter." 
echo "Example: A 17 CA or n 162 cg"

echo " - - - - - - - - - - - - - - - - - -"
#------------First Selection------------

read -e -p "What first atom? " sel1

# echo $sel1
sel1caps=${sel1^^}
# echo "sel1caps="$sel1caps

arr1=($sel1caps)
# echo "arr1[0]= "${arr1[0]}
# echo "arr1[1]= "${arr1[1]}
# echo "arr1[2]= "${arr1[2]}

#To convert one to three letters

if [ ${arr1[0]} = A ] ; then
    SF1=ALA
elif [ ${arr1[0]} = H ] ; then
    SF1=HIS
elif [ ${arr1[0]} = R ] ; then
    SF1=ARG
elif [ ${arr1[0]} = K ] ; then
    SF1=LYS
elif [ ${arr1[0]} = I ] ; then
    SF1=ILE
elif [ ${arr1[0]} = F ] ; then
    SF1=PHE 
elif [ ${arr1[0]} = L ] ; then
    SF1=LEU
elif [ ${arr1[0]} = W ] ; then
    SF1=TRP
elif [ ${arr1[0]} = M ] ; then
    SF1=MET
elif [ ${arr1[0]} = P ] ; then
    SF1=PRO 
elif [ ${arr1[0]} = C ] ; then
    SF1=CYS 
elif [ ${arr1[0]} = N ] ; then
    SF1=ASN
elif [ ${arr1[0]} = V ] ; then
    SF1=VAL
elif [ ${arr1[0]} = G ] ; then
    SF1=GLY 
elif [ ${arr1[0]} = S ] ; then
    SF1=SER 
elif [ ${arr1[0]} = Q ] ; then
    SF1=GLN 
elif [ ${arr1[0]} = Y ] ; then
    SF1=TYR 
elif [ ${arr1[0]} = D ] ; then
    SF1=ASP
elif [ ${arr1[0]} = E ] ; then
    SF1=GLU 
elif [ ${arr1[0]} = T ] ; then
    SF1=THR 
else
    echo "use one letter codes"
    echo "exiting"
    exit
fi

# echo "SF1 ="$SF1

#If there is nothing printing for line 1, check the expression for your pdb file. The spaces may need adjustment at the end.
line1=$(grep -E "${arr1[2]} *?${SF1}(.*?) ${arr1[1]}     " 1A23.pdb)
# echo $line1

ar_l1=($line1)
# echo "ar_l1[1]="${ar_l1[1]}

echo " - - - - - - - - - - - - - - - - - -"
#------------Second Selection------------

read -e -p "What second atom? " sel2

# echo $sel2

sel2caps=${sel2^^}
# echo "sel2caps="$sel2caps

arr2=($sel2caps)
# echo "arr2[0]= "${arr2[0]}
# echo "arr2[1]= "${arr2[1]}
# echo "arr2[2]= "${arr2[2]}

#To convert one to three letters

if [ ${arr2[0]} = A ] ; then
    SF2=ALA
elif [ ${arr2[0]} = H ] ; then
    SF2=HIS
elif [ ${arr2[0]} = R ] ; then
    SF2=ARG
elif [ ${arr2[0]} = K ] ; then
    SF2=LYS
elif [ ${arr2[0]} = I ] ; then
    SF2=ILE
elif [ ${arr2[0]} = F ] ; then
    SF2=PHE 
elif [ ${arr2[0]} = L ] ; then
    SF2=LEU
elif [ ${arr2[0]} = W ] ; then
    SF2=TRP
elif [ ${arr2[0]} = M ] ; then
    SF2=MET
elif [ ${arr2[0]} = P ] ; then
    SF2=PRO 
elif [ ${arr2[0]} = C ] ; then
    SF2=CYS 
elif [ ${arr2[0]} = N ] ; then
    SF2=ASN
elif [ ${arr2[0]} = V ] ; then
    SF2=VAL
elif [ ${arr2[0]} = G ] ; then
    SF2=GLY 
elif [ ${arr2[0]} = S ] ; then
    SF2=SER 
elif [ ${arr2[0]} = Q ] ; then
    SF2=GLN 
elif [ ${arr2[0]} = Y ] ; then
    SF2=TYR 
elif [ ${arr2[0]} = D ] ; then
    SF2=ASP
elif [ ${arr2[0]} = E ] ; then
    SF2=GLU 
elif [ ${arr2[0]} = T ] ; then
    SF2=THR 
else
    echo "use one letter codes"
    echo "exiting"
    exit
fi

# echo "SF2 ="$SF2


line2=$(grep -E "${arr2[2]} *?${SF2}(.*?) ${arr2[1]}     " 1A23.pdb)
# echo $line2

ar_l2=($line2)
# echo "ar_l2[1]="${ar_l2[1]}
# echo "ar_l2[1]="${ar_l2[1]}

atom1=${ar_l1[1]}
atom2=${ar_l2[1]}
echo "==========================="
echo ${arr1[0]}${arr1[1]}${arr1[2]}" to "${arr2[0]}${arr2[1]}${arr2[2]}":"
# 6, 7, 8 are column numbers in the pdb file. 
# If there are multiple molecules it should be 7, 8, 9.
awk '$2=='$atom1'{x1=$7;y1=$8;z1=$9}                                 # get the ATOM 1
     $2=='$atom2'{x2=$7;y2=$8;z2=$9}                               # get the ATOM 2
     END{print sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2) + (z1-z2)*(z1-z2))}' 1A23.pdb    # calculate the distance.

echo "Angstroms"
echo "==========================="
echo " "
echo "-_-_-_-_Running Script Again_-_-_-_-"
./distance_soln.sh

Answer 6:

一个简单的Python代码可以做的工作。我假设你所有的内容都在文件“input.txt中”。

def process(line1, line2):
    content1 = line1.split()
    content2 = line2.split()
    x1, y1, z1 = float(content1[6]), float(content1[7]), float(content1[8])
    x2, y2, z2 = float(content2[6]), float(content2[7]), float(content2[8])
    distance = math.sqrt(math.pow(x1-x2, 2) + math.pow(y1-y2, 2) + math.pow(z1-z2, 2))
    return content1[3]+"-"+content2[3]+" "+ "{0:.2f}".format(distance)

with open("input.txt") as f:
    line1 = f.readline()
    for line in f:
        line2 = line
        print(process(line1, line2))
        line1 = line2

请不要让我知道如果你发现在使用该脚本任何差异或问题。

文章来源: Calculating the distance between atomic coordinates