Question

我有一个pdb文件，表示文件的轨迹

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我想打印信息

REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t= 400.00000
REMARK    THIS IS A SIMULATION BOX
CRYST1   99.547   99.547   99.547  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   PRO A   1      46.850  67.380  57.030  1.00  0.00
ATOM      2  H1  PRO A   1      46.230  66.770  56.500  1.00  0.00
ATOM      3  H2  PRO A   1      46.420  68.290  56.940  1.00  0.00
ATOM      4  CD  PRO A   1      47.060  66.780  58.360  1.00  0.00
TER
ENDMDL
REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t= 800.00000
REMARK    THIS IS A SIMULATION BOX
MODEL       10
ATOM      1  N   PRO A   1      46.850  67.380  57.030  1.00  0.00
ATOM      2  H1  PRO A   1      46.230  66.770  56.500  1.00  0.00
ATOM      3  H2  PRO A   1      46.420  68.290  56.940  1.00  0.00
ATOM      4  CD  PRO A   1      47.060  66.780  58.360  1.00  0.00
TER
ENDMDL
REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t= 1200.00000
REMARK    THIS IS A SIMULATION BOX
MODEL      100
ATOM      1  N   PRO A   1      46.850  67.380  57.030  1.00  0.00
ATOM      2  H1  PRO A   1      46.230  66.770  56.500  1.00  0.00
ATOM      3  H2  PRO A   1      46.420  68.290  56.940  1.00  0.00
ATOM      4  CD  PRO A   1      47.060  66.780  58.360  1.00  0.00
TER
ENDMDL

适用于所有型号。保留文件的格式。我试过这个

MODEL        1
[all info]
TER
ENDMDL

但是我的文件非常庞大，无法手动完成。我想将每个模型保存为model1，model2等，并将其坐标信息保存到ENDMDL

Answer 1

$ awk '/MODEL/{f="model" $2 ".pdb"} f{print > f} /ENDMDL/ {close(f);f=""}' file
$ cat model1.pdb
MODEL        1
ATOM      1  N   PRO A   1      46.850  67.380  57.030  1.00  0.00
ATOM      2  H1  PRO A   1      46.230  66.770  56.500  1.00  0.00
ATOM      3  H2  PRO A   1      46.420  68.290  56.940  1.00  0.00
ATOM      4  CD  PRO A   1      47.060  66.780  58.360  1.00  0.00
TER
ENDMDL

说明：

/MODEL/ {                 # @ MODEL
    f="model" $2 ".pdb"   # use f as flag and target filename
} 
f {                       # when there is an f
    print > f             # output to file in f
} 
/ENDMDL/ {                # at the ENDMDL
    close(f)              # close the file
    f=""                  # unset f
}

从pdb trajctory中提取每个文件

1 个答案: