patrickfuller/blender-chemicals

Draws chemicals in Blender using common input formats (smiles, molfiles, cif files, etc.)

blender-chemicals's Issues

It can`t open blender

when i input this “blender-chemicals c1ccccc1” ，get a mistake:blender-chemicals : 无法将“blender-chemicals”项识别为 cmdlet、函数、脚本文件或可运行程序的名称。请检查名称的拼写，如
果包括路径，请确保路径正确，然后再试一次。
所在位置 行:1 字符: 1

• blender-chemicals c1ccccc1

•   + CategoryInfo          : ObjectNotFound: (blender-chemicals:String) [], CommandNotFoundException
    + FullyQualifiedErrorId : CommandNotFoundException
  

what should i do? thank you!

blender didn't work

when i input blender-chemicals c1ccccc1, conda shows me:

——————————————————————————————————
(blender) PS C:\Users\Administrator> blender-chemicals c1ccccc1
==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot open aromatic.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot open atomtyp.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot open element.txt defaulting to compiled data.
==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot open phmodel.txt defaulting to compiled data.
==============================
*** Open Babel Error  in OpenBabel::OBBuilder::LoadFragments
  Cannot open fragments.txt
==============================
*** Open Babel Error  in OpenBabel::OBForceFieldMMFF94::ParseParamFile
  Cannot open parameter file
==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot open element.txt defaulting to compiled data.
Could not find installed copy of Blender. Either make sure it's on your path or copy the contents of `drawer.py` into a running blender instance.
————————————————————————————

Blender 2.80 wrong output

Hi,

i just wanted to try out your script with blender 2.80 on a Linux machine. The benzene example just creates a cylinder and a sphere in the middle of the viewport and nothing else.

Maybe something changed in the last 2 years, which version did you use?

Or do you have another idea?

forcefaction

Traceback (most recent call last): File "C:\..b\site-packages\openbabel.py", line 22, in swig_import_helper return importlib.import_module(mname)

C:\Users\15020>python -m blender_chemicals.run c1ccccc1
Traceback (most recent call last):
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\site-packages\openbabel.py", line 22, in swig_import_helper
return importlib.import_module(mname)
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\importlib_init_.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 658, in _load_unlocked
File "", line 571, in module_from_spec
File "", line 922, in create_module
File "", line 219, in _call_with_frames_removed
ImportError: DLL load failed: 找不到指定的程序。

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\site-packages\blender_chemicals\run.py", line 10, in
import pybel
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\site-packages\pybel.py", line 53, in
import openbabel as ob
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\site-packages\openbabel.py", line 25, in
_openbabel = swig_import_helper()
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\site-packages\openbabel.py", line 24, in swig_import_helper
return importlib.import_module('openbabel')
File "C:\Users\15020\AppData\Local\Programs\Python\Python36\lib\importlib_init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
ImportError: DLL load failed: 找不到指定的程序。

C:\Users\15020>

Ich möchte chemicalische sachen kaufen Können Sie mir dabei helfen

Windows Issues

Leaving this here for future reference.

I received some comments about running this on windows, and I wanted to address common issues.

First, the conversion command json_formatter.py file type json > molecule.json. This may fail due to an improper open babel install, or due to string encoding (more on this later). For open babel, attempt to reinstall.

Next, the blender command-line command: & 'C:\path\to\blender.exe' -P molecule_to_blender.py. If there is a json encoding issue, it's due to the above problem. The computer is probably not in UTF-8 (generally latin-1). Modernize the encoding, and this goes away. The other issue is around paths. You need to run this command in the blender-chemicals directory for the paths to work.

Proof it works.

can not run from anoconda

blender-chemicals c1ccccc1

Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot open aromatic.txt defaulting to compiled data.

Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot open atomtyp.txt defaulting to compiled data.

Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot open element.txt defaulting to compiled data.

Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot open phmodel.txt defaulting to compiled data.

Open Babel Error in OpenBabel::OBBuilder::LoadFragments
Cannot open fragments.txt

Open Babel Error in OpenBabel::OBForceFieldMMFF94::ParseParamFile
Cannot open parameter file

Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot open element.txt defaulting to compiled data.

HI!
I followed the instruction to install the software mentioned in the ReadMe, but when I try to run this program, it will show this on my computer, how can I solve this problem?

os : win10
blender Version: 2.81

Hitting a problem at line with the line: args = sys.argv[sys.argv.index('--') + 1:]

Hello,

I've pasted "draw.py" in the scripting panel and hard-coded the path...everything seems to run well until it gets to the line I put in the title (and below).
Using Blender 2.9

Obviously, I don't get outputs!
To check my hardcoded PATH, I went into Anaconda and ran the lines and asked it to PRINT the JSON in the console. It performed perfectly, so I'm fairly confident of this part.

I wish I could give you the output in the console, but I have none, I'm using Blender portable 2.9...seems to be more stable on my laptop than the installed one.

Thanks in advance!

Bit of code so it gets clearer:

#Hard-coding my location:
PATH = 'C:/Users/UserName/Documents/Molecules_jsons/' #Obviously /UserName/ has the right name, but I removed it here
with open(os.path.join(PATH, 'caffeine.json')) as in_file: #Testing "draw.py" using caffeine.
atom_data = json.load(in_file)

#The part that's giving me headaches

if name == 'main':
"""Uses Blender's limited argv interface to pass args from main script."""
args = sys.argv[sys.argv.index('--') + 1:] #This line stops script in Blender, I've not changed anything from "draw.py"
show_bonds, join = True, True
if '--space-filling' in args:
show_bonds = False
args.remove('--space-filling')
if '--no-join' in args:
join = False
args.remove('--no-join')

try:
    with open(args[0]) as in_file:
        molecule = json.load(in_file)
except IOError:
    molecule = json.loads(args[0])

draw_molecule(molecule, show_bonds=show_bonds, join=join)

UPDATE:
I got Blender to show me the console (Finally, why a separate window!):
Traceback (most recent call last):
File "\draw_molecules.py", line 159, in
ValueError: '--' is not in list
Error: Python script failed, check the message in the system console

Can´t get Blender-chemicals to find blender

Hello,
I´ve been at this for the last couple of days but I can´t get rid of this paticular problem.
I´m not completly certain if I have openbabel properly installed but I really hope so because I followed the instructions as discribed and I can import pybel. I don´t wont to bother you with wrongly installing openbabel as some people already have.

Looking forward to your help and hope as soon as blender-chemicals knows where my blender is it will work and I´ll be happy.

> (python) PS C:\WINDOWS\system32> blender-chemicals c1ccccc1
> ==============================
> *** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
>   Cannot open aromatic.txt defaulting to compiled data.
> ==============================
> *** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
>   Cannot open element.txt defaulting to compiled data.
> ==============================
> *** Open Babel Error  in OpenBabel::OBBuilder::LoadFragments
>   Cannot open fragments.txt
> ==============================
> *** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
>   Cannot open element.txt defaulting to compiled data.
> Could not find installed copy of Blender. Either make sure it's on your path or copy the contents of `drawer.py` into a running blender instance.

OS: Win10
Blender: 2.82
Openbabel: 3.0.12
Blender-chemicals: 0.3.0

Dead links to github.io

I just clicked on your blog link in README.md, and got a 404 error page.