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No module named 'sanifix4' #17

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Rong0802 opened this issue Sep 16, 2019 · 7 comments
Open

No module named 'sanifix4' #17

Rong0802 opened this issue Sep 16, 2019 · 7 comments

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@Rong0802
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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?
@kkanekal
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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

@Rong0802
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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?

@kkanekal
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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

@Rong0802
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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?

@kkanekal
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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

@Rong0802
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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?

@kkanekal
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kkanekal commented Sep 19, 2019 •
edited
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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?

@tbereau tbereau mentioned this issue Oct 26, 2020
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@kkanekal @Rong0802