我有一个pdb文件，如下所示。
ATOM 76 N ARG 6 -6.350 -3.503 0.748 -0.3479 1.5500
ATOM 77 H ARG 6 -6.002 -3.513 1.699 0.2747 1.3000
ATOM 78 CA ARG 6 -7.756 -3.896 0.534 -0.2637 1.7000
ATOM 79 HA ARG 6 -8.024 -4.587 1.334 0.1560 1.3000
ATOM 80 CB ARG 6 -8.589 -2.608 0.737 -0.0007 1.7000
ATOM 81 HB2 ARG 6 -8.208 -2.089 1.620 0.0327 1.3000
ATOM 82 HB3 ARG 6 -8.439 -1.940 -0.114 0.0327 1.3000
ATOM 83 CG ARG 6 -10.086 -2.834 0.970 0.0390 1.7000
ATOM 84 HG2 ARG 6 -10.274 -3.897 1.124 0.0285 1.3000
ATOM 85 HG3 ARG 6 -10.378 -2.310 1.876 0.0285 1.3000
ATOM 86 CD ARG 6 -10.953 -2.295 -0.177 0.0486 1.7000
ATOM 87 HD2 ARG 6 -10.985 -1.204 -0.114 0.0687 1.3000
ATOM 88 HD3 ARG 6 -10.524 -2.559 -1.143 0.0687 1.3000
ATOM 89 NE ARG 6 -12.315 -2.833 -0.075 -0.5295 1.5500
ATOM 90 HE ARG 6 -13.010 -2.260 0.390 0.3456 1.3000
ATOM 91 CZ ARG 6 -12.694 -4.065 -0.346 0.8076 1.7000
ATOM 92 NH1 ARG 6 -13.877 -4.453 0.009 -0.8627 1.5500
ATOM 93 1HH1 ARG 6 -14.040 -5.443 0.120 0.4478 1.3000
ATOM 94 2HH1 ARG 6 -14.432 -3.807 0.560 0.4478 1.3000
ATOM 95 NH2 ARG 6 -11.920 -4.944 -0.916 -0.8627 1.5500
ATOM 96 1HH2 ARG 6 -12.283 -5.850 -1.134 0.4478 1.3000
ATOM 97 2HH2 ARG 6 -10.979 -4.672 -1.190 0.4478 1.3000
ATOM 98 C ARG 6 -8.062 -4.673 -0.777 0.7341 1.7000
ATOM 99 O ARG 6 -9.133 -4.539 -1.331 -0.5894 1.5000
......
ATOM 172 N S1P 12 -14.038 -6.148 4.609 -0.4157 1.5500
ATOM 173 H S1P 12 -13.159 -6.030 4.131 0.2719 1.3000
ATOM 174 CA S1P 12 -14.531 -4.998 5.067 1.8687 1.7000
ATOM 175 HA S1P 12 -15.438 -5.137 5.650 -0.3423 1.3000
ATOM 176 CB S1P 12 -13.509 -4.203 5.988 -0.2136 1.7000
ATOM 177 2HB S1P 12 -14.138 -4.223 6.879 0.0612 1.3000
ATOM 178 3HB S1P 12 -12.848 -5.033 6.243 0.0612 1.3000
ATOM 179 OG S1P 12 -12.482 -3.545 5.746 -0.5829 1.5000
ATOM 180 P S1P 12 -11.815 -3.403 4.409 1.4551 1.8500
ATOM 181 O3P S1P 12 -10.346 -3.231 4.357 -0.8194 1.5000
ATOM 182 O1P S1P 12 -11.897 -4.712 3.815 -0.9362 1.5000
ATOM 183 H1P S1P 12 -10.980 -4.847 3.540 0.5898 0.8000
ATOM 184 O2P S1P 12 -12.533 -2.620 3.418 -0.7440 1.5000
ATOM 185 H2P S1P 12 -13.423 -2.977 3.402 0.5973 0.8000
ATOM 186 C S1P 12 -14.940 -4.030 3.844 -0.6568 1.7000
ATOM 187 O S1P 12 -14.809 -4.386 2.691 -0.1942 1.5000
我想做的是想找到文件中两个原子之间的距离。
我感兴趣的两个原子是
ATOM 91 CZ ARG 6 -12.694 -4.065 -0.346 0.8076 1.7000
和
ATOM 180 P S1P 12 -11.815 -3.403 4.409 1.4551 1.8500
例如，行中的x y z坐标为-11.815 -3.403 4.409
我环顾四周，但只有我能找到的脚本是计算所有原子的距离或两个不同文件之间的距离。
先谢谢你。
答案 0 :(得分：2)
你可以从这里开始：
awk '$2=="91"{x1=$6;y1=$7;z1=$8} # get the ATOM 1
$2=="180" {x2=$6;y2=$7;z2=$8} # get the ATOM 2
END{print sqrt((x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2)}' file # calculate the distance.
4.88067
不确定为什么^在GAWK 3.1.5中不受支持，这个怎么样？
awk '$2=="91"{x1=$6;y1=$7;z1=$8} # get the ATOM 1
$2=="180" {x2=$6;y2=$7;z2=$8} # get the ATOM 2
END{print sqrt((x1-x2)*(x1-x2) + (y1-y2)*(y1-y2) + (z1-z2)*(z1-z2))}' file # calculate the distance.
答案 1 :(得分：0)
这是一个包含建议的awk命令的完整脚本。将pdb文件更改为您的下面，并将其放在与pdb文件相同的目录中。
#!/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 " "
# 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 " "
# 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 "==========================="
# 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=$6;y1=$7;z1=$8} # get the ATOM 1
$2=='$atom2'{x2=$6;y2=$7;z2=$8} # 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 "==========================="