Comments (7)
kkanekal
commented on July 21, 2024
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
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Rong0802
commented on July 21, 2024
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?
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kkanekal
commented on July 21, 2024
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
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Rong0802
commented on July 21, 2024
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?
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kkanekal
commented on July 21, 2024
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
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Rong0802
commented on July 21, 2024
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?
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kkanekal
commented on July 21, 2024
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?
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Related Issues (20)
- package rdkit and smile format HOT 8
- Bead division problem HOT 7
- Mismatch between dev branch and refactor branch result HOT 5
- Error run auto_martini HOT 2
- how validate auto_martini itp HOT 1
- Vcclabs website down - is it OK to use rdkit.Chem.Crippen module for ALOGP calculation? HOT 2
- No output file HOT 8
- "Missing parentheses in call to 'print'." HOT 15
- Max. number of attempts: 54517 HOT 1
- VisibleDeprecationWarning
- Improving molecule sanitization HOT 1
- auto_martini as an interoperable component HOT 2
- auto_martini fails 4 tests
- auto_martini doesn't work for silica coarse graining HOT 1
- setup.py
- The CG model for ethanol is different from the original paper HOT 1
- martini3 HOT 3
- ALOGPS can't predict fragment HOT 2
- Installation instructions are incomplete HOT 5
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