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Published 20 hours ago • verified publisher icon tbereau

No module named 'sanifix4'

Open Rong0802 opened this issue 5 years ago • 7 comments

hello, someone can help me please. I am still new in the use of python I was unable to find the sanifix4 module when I installed auto-martini. Then I use pip install sanifix4 to install sanifix4, the error is as follows： ERROR: Could not find a version that satisfies the requirement sanifix4 (from versions: none) ERROR: No matching distribution found for sanifix4

How can I solve this problem?

Rong0802 avatar Sep 16 '19 02:09 Rong0802

Hi,

Thanks for bringing this to my attention. I forgot to add the sanifix4.py file when I updated the master branch. The problem should be fixed now. You can either just update your existing branch by typing "git pull" in the auto_martini folder, or you can just checkout or re-download the code again.

-Kiran

kkanekal avatar Sep 16 '19 08:09 kkanekal

Thank you for your replay I re-download the code. But the new problem has appeared again. When I run auto_martini, I get the following error:

(my-rdkit-env) PS D:\work_software\auto-martini\auto_martini-master> python .\auto_martini Traceback (most recent call last): File ".\auto_martini", line 38, in from sanifix4 import AdjustAromaticNs File "D:\work_software\auto-martini\auto_martini-master\sanifix4.py", line 277 print '#---------------------' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print('#---------------------')?

How can I solve this problem?

Rong0802 avatar Sep 17 '19 09:09 Rong0802

Hi,

I suspect that this error is due to the fact that you are using Python 3, whereas the code is meant to run on Python 2.7.X.

-Kiran

kkanekal avatar Sep 17 '19 09:09 kkanekal

Hello, the sanifix problem has been solved. When I tried "auto-martini --smi "N1=C(N)NN=C1N" --mol GUA", the program reported the following error:

(my-rdkit-env) PS D:\work_software\auto-martini\auto_martini-master> python .\auto_martini --smi "N1=C(N)NN=C1N" --mol G UA Traceback (most recent call last): File ".\auto_martini", line 1389, in cg_molecule(mol, args.molname, args.aa, args.cg, args.forcepred) File ".\auto_martini", line 1270, in cg_molecule ring_atoms_flat) File ".\auto_martini", line 498, in find_bead_pos acceptable_trial = check_beads(list_heavy_atoms, heavyatom_coords, trial_comb, ring_atoms, list_bonds) File ".\auto_martini", line 408, in check_beads for bi in xrange(len(trial_comb)): NameError: name 'xrange' is not defined

How can I solve this problem?

Rong0802 avatar Sep 17 '19 09:09 Rong0802

Hi,

Again, this is a Python 3 issue. As far as I can understand the xrange function was renamed to range in Python 3. If you intend to convert the code to be compatible with Python 3 and not run it in Python 2.7.x, I highly recommend you google the errors you are getting before commenting here, as I am still unfamiliar with the specific differences between the two versions of Python and will only be of limited help.

-Kiran

kkanekal avatar Sep 17 '19 09:09 kkanekal

Hi I have successfully installed auto-martini, but there is a new problem when I run the program. usage: auto_martini [-h] (--sdf SDF | --smi SMI) --mol MOLNAME [--aa AA] [--cg CG] [-v] [--fpred] auto_martini: error: argument --mol is required (my-rdkit-env) sun@sun-QiTianM620-N000:~/桌面/auto-martini/auto_martini-master$ python auto_martini --sdf peg400.sdf --mol PEG WARNING:main:Error with BeautifulSoup constructor How can I solve this problem?

Rong0802 avatar Sep 19 '19 09:09 Rong0802

Hi,

Try running the following python code:

from bs4 import BeautifulSoup import lxml import requests session = requests.session() req = session.get('http://vcclab.org/web/alogps/calc?SMILES=CCCC') doc = BeautifulSoup(req.content, "lxml") soup = doc.prettify() print soup

you should get this output:

<html> <body> mol_N logP logS SMILES <br/> mol_1 2.81 -1.91 CCCC <br/> </body> </html>

Is this the case?

kkanekal avatar Sep 19 '19 15:09 kkanekal