Open Rong0802 opened 5 years ago
kkanekal
commented
5 years ago 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
commented
5 years ago 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
commented
5 years ago 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
commented
5 years ago 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
How can I solve this problem?
kkanekal
commented
5 years ago 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
commented
5 years ago 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
commented
5 years ago 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?
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?