How to save Jupyter notebook output in a file using python command?

Question

I was trying to save output of my Jupyternotebook 'npsmiles_descriptors.py' into a text file so that it can be used by other applications. Can anyone help me out by pointing out the error in my last command. I am getting syntax error.


    df1 = df['smiles']
    
    print(df['smiles'])
    
    0      O1[C@@H]2C[C@H](O)[C@@]3([C@H]([C@H](OC(=O)c4...
    1      OC[C@H]1N(CCC1)C(=O)[C@@H](NC(=O)[C@H](CCCCC)...
    2      O1[C@@H](C[C@H](O)\C=C/[C@@H]([C@H](O)[C@H](\...
    3      O1[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O...
    4      O1[C@@H]([C@H](C[C@@H](C)[C@]1(O)CO)C)[C@@H]1...
    5      P(O[C@H]1[C@H](O[C@@]2(O[C@@H](C\C=C\c3nc(oc3...
    6      O1[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]1n1c2NC=[N...
    7      O1[C@H]2[C@@H](CC[C@@]3(O[C@]34[C@@H]2C(=CC4)...
    8      O1[C@H](CO)[C@@H](O)[C@@H](O)[C@@H]1n1cnc(C(=...
    9      O1[C@@]2(C)[C@@](O)([C@@]3([C@@H]([C@H](O)[C@...
    10              S(=O)(=O)([O-])N1C[C@](OC)(NC(=O)C)C1=O
    11     S1[C@H]2N(C(C(=O)[O-])=C(C1)COC(=O)N)C(=O)[C@...
    12     O1[C@@H]2C[C@@]3(O[C@H]([C@H](CC)C)[C@H](C=C3...
    13     O1[C@@H](C)[C@@H](O)[C@@H]([NH3+])C[C@@H]1O[C...
    14     O=C1[C@]2(O)[C@@H](C=C1C)[C@]1(O)[C@H]([C@H]3...
    15     S(CC[NH3+])C=1C[C@H]2N(C=1C(=O)[O-])C(=O)[C@@...
    16     O=C1N(C)[C@@H]([C@H](O)[C@@H](C\C=C\C)C)C(=O)...
    17     O1[C@H](/C(=C/[C@H]2C[C@@H](OC)[C@H](O)CC2)/C...
    18     O1C[C@H]1C(=O)CCCCC[C@@H]1NC(=O)[C@@H]2N(CCC2...
    19     O(C)c1cc2N([C@@H]3[C@]4([C@H]5[NH+](CC=C[C@@]...
    20     O(C)C1=CC=C2c3c(cc(OC)c(OC)c3OC)CC[C@H](NC(=O...
    21     O=C([C@@H](\C=C(\C=C\C(=O)N[O-])/C)C)c1ccc(N(...
    22     O1[C@](C)([C@H]2[C@H](OC)[C@H](OC(=O)\C=C\C=C...
    23     O1[C@H]2n3c4c(c5c(CNC5=O)c5c6c(n(c45)[C@]1(C)...
    24     O1[C@H](CC)[C@](O)(C)[C@H](O)[C@@H](C)C(=O)[C...
    25     O1[C@@H](CO)[C@H](O)[C@@H](O)[C@H]([NH2+]C)[C...
    26    S1[C@H]2N([C@@H](C(=O)[O--])C1(C)C)C(=O)[C@H]...
    27     O=C(N[C@@H](O)C(=O)NCCCC[NH2+]CCC[NH3+])C[C@@...
    28     O1[C@@H](CC(=O)[C@@H](\C=C(/C)\[C@@H](O)[C@@H...
    29     Oc1ccc(cc1)[C@H](O)[C@@H](O)[C@@H]1NC(=O)[C@H...
    30     O1[C@@H]2[C@@](O)([C@]34O[C@@H]5OC(=O)[C@H](O...
    31     Clc1c2Oc3cc4[C@@H](NC(=O)[C@@H](NC(=O)[C@H](N...
    32     O1[C@@H](C)[C@H](C)[C@H](O)[C@H](\C=C\C=C\C=C...
    33     Clc1c2c(C(O[C@@H](C[C@H]3O[C@@H]3/C=C\C=C\C(=...
    34     O1[C@H](C[C@@H](O)[C@H](C\C=C\Cc2c(C1=O)c(O)c...
    35     S1C2=N[C@H](c3oc(c(n3)-c3oc(c(n3)-c3occ(n3)-c...
    36     O1c2c3c4c(c(O)c2C)c(O)c(NC(=O)/C(=C\C=C\[C@H]...
    37     O1[C@@H](C[C@H](OC)[C@@H](O)CC\C=C(\C=C\[C@H]...
    38     O1[C@@H](C\C=C\C=C\[C@H](O)[C@@H](C[C@H](CC=O...
    39     O1[C@@]2(C(=O)[O-])[C@](O)(C(O)=O)[C@H](O[C@]...
    40         O1C[C@H](CO)[C@@H](O)C[C@]12OC[C@@H](CC2)CCS
    41     ClC(\C=C\[C@@H](O)CC(C[C@H]1O[C@H]2[C@H](O)[C...
    42     O1[C@@H]2[C@H](O[C@@]3([C@H](O[C@@H]4[C@H](O[...
    43     O(C)c1cc2c(nccc2[C@@H](O)[C@H]2[N@@H+]3C[C@@H...
    44     O1C[C@H](N=C1c1ccccc1O)C(=O)N[C@@H](CCCCN([O-...
    45     O(C)c1c(OC)c2[nH]c(cc2cc1OC)C(=O)N1C=2[C@]3([...
    46     [S+](CCCNC(=O)c1nc(sc1)-c1nc(sc1)CCNC(=O)[C@@...
    47      O1[C@H](CCC\C=C\[C@H]2[C@@H](C[C@@H](O)C2)[C...
    48     O1[C@@]23[C@@H]([C@H](C)C(=C)[C@@H](O)[C@@H]2...
    49     s1cc(nc1C)\C=C(/C)\[C@H]1OC(=O)C[C@H](O)C(C)(...
    50     S(C(=O)[C@@]1(NC(=O)[C@H](C)[C@@H]1O)[C@@H](O...
    51     Ic1c(C)c(C(S[C@@H]2[C@H](O[C@@H](ON[C@H]3[C@H...
    52     O1[C@@H]2O[C@@]3(OO[C@]24[C@@H](CC[C@H]([C@@H...
    53     O1[C@@H](C[C@@H](O)CC1=O)CC[C@@H]1[C@@H]2C(C=...
    54     O1[C@@H](C[C@@H](OC(=O)[C@@H](NC=O)CC(C)C)C\C...
    55     O1[C@@H](C[C@H]2CO[C@@H](C\C(=C\C(OCCCCCCCCC(...
    56     O1[C@H](C)[C@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=...
    57     O=C(N[C@@H](CC(C)C)C(=O)[O-])[C@@H](O)[C@H]([...
    58       OC/C(=C\CC\C(=C\CO)\C)/CC\C=C(\CC\C=C(\C)/C)/C
    59     O(C)C1=C2C[C@H](C[C@H](OC)[C@H](O)[C@H](\C=C(...
    Name: smiles, dtype: object
    
    python npsmiles_descriptors.py > out.txt  
    
      File "<ipython-input-35-e13d177d9791>", line 1
        python npsmiles_descriptors.py > out.txt
                                  ^
    SyntaxError: invalid syntax

redirection `>` is used in Linux/Window shell (like Bash, cmd.exr) but error shows that you try to run in Python shell. Maybe runs `python npsmiles_descriptors.py > out.txt` without `Juputer` but directly in console/terminal/cmd.exe — furas, Sep 09 '20 at 02:42
you can run python program in notebook using `!python npsmiles_descriptors.py > out.txt`, — Srinivas, Sep 09 '20 at 03:00

score 0 · Answer 1 · answered Sep 09 '20 at 03:56

0

Use !python npsmiles_descriptors.py > out.txt instead. !<command line command> is shorthand for

import os
os.system("<command line command>")

in a Jupyter Notebook.

Credit: https://stackoverflow.com/a/47952494/14212394

answered Sep 09 '20 at 03:56

Seth

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How to save Jupyter notebook output in a file using python command?

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