woolfson-group / isambard

Intelligent System for Analysis, Model Building And Rational Design.

ISAMBARD HAS MOVED!

With the impending release of v2.0.0, the ISAMBARD repository has moved into it's own organisation. All future issues and pull requests should be made there.

isambard's Issues

Make an installer or package through pip/conda.

The installation process is pretty complex at the moment, this needs to be addressed.

AttributeError: 'WindowsPath' object has no attribute 'expanduser'

I did

import isembard

and pasted the path to scwrl4

r"C:\bin\Scwrl\Scwrl4.exe"

pathlib.Path does not have exapnduser, while os.path does have this attribute.

I'm using Python 3.4.3 :: Continuum Analytics, Inc. win-32bit

No configuration file ('.isambard_settings') found in 'c:/Users/ajasjal'.                                                    
Running configure.py...                                                                                                      
                                                                                                                             
Generating configuration files for ISAMBARD.                                                                                 
All required input can use tab completion for paths.                                                                         
Setting up SCWRL 4.0 (Recommended)                                                                                           
Please provide a path to your SCWRL executable Tab completion enabled:                                                       
r"C:\bin\Scwrl\Scwrl4.exe"                                                                                                   
Traceback (most recent call last):                                                                                           
  File "c:\gits\isambard\isambard\configure.py", line 200, in <module>                                                       
    main(arguments)                                                                                                          
  File "c:\gits\isambard\isambard\configure.py", line 41, in main                                                            
    install(settings_path, basic=args.basic)                                                                                 
  File "c:\gits\isambard\isambard\configure.py", line 51, in install                                                         
    base_install()                                                                                                           
  File "c:\gits\isambard\isambard\configure.py", line 67, in base_install                                                    
    scwrl_path = get_user_path('Please provide a path to your SCWRL executable', required=False)                             
  File "c:\gits\isambard\isambard\configure.py", line 155, in get_user_path                                                  
    path = pathlib.Path(ui_path).expanduser().resolve()  # Convert relative paths to absolute                                
AttributeError: 'WindowsPath' object has no attribute 'expanduser'                                                           
---------------------------------------------------------------------------                                                  
FileNotFoundError                         Traceback (most recent call last)                                                  
<ipython-input-1-ecf256aec169> in <module>()                                                                                 
----> 1 import isambard                                                                                                      
                                                                                                                             
c:\gits\isambard\isambard\__init__.py in <module>()                                                                          
     10                                                                                                                      
     11 try:                                                                                                                 
---> 12     from settings import global_settings                                                                             
     13     import settings                                                                                                  
     14     import ampal                                                                                                     
                                                                                                                             
c:\gits\isambard\isambard\settings.py in <module>()                                                                          
     46 if not os.path.isfile(settings_path):                                                                                
     47     print("No configuration file ('.isambard_settings') found in '{}'.\nRunning configure.py...\n".format(home_dir)) 
---> 48     configure()                                                                                                      
     49 else:                                                                                                                
     50     load_global_settings()                                                                                           
                                                                                                                             
c:\gits\isambard\isambard\settings.py in configure()                                                                         
     23                      os.path.join(package_dir, 'configure.py'),                                                      
     24                      '-o'])                                                                                          
---> 25     load_global_settings()                                                                                           
     26     return                                                                                                           
     27                                                                                                                      
                                                                                                                             
c:\gits\isambard\isambard\settings.py in load_global_settings()                                                              
     29 def load_global_settings():                                                                                          
     30     """Loads settings file containing paths to dependencies and other optional configuration elements."""            
---> 31     with open(settings_path, 'r') as settings_f:                                                                     
     32         global global_settings                                                                                       
     33         settings_json = json.loads(settings_f.read())                                                                
                                                                                                                             
FileNotFoundError: [Errno 2] No such file or directory: 'c:/Users/ajasjal\\.isambard_settings'                               

Write Installation Documentation

Write installation documentation based on the new pip install method.

DSSP waits for key to be pressed

On windows DSSP waits for a key to be pressed if called without arguments.

when importing isambard in ipython the whole program is blocked.

Adding --version when calling DSSP should fix this.

I can do a pull request.

import isambard error

import isambard
ValueError Traceback (most recent call last)
in ()
----> 1 import isambard

/home/python/lib/python2.7/site-packages/isambard/init.py in ()
10
11 try:
---> 12 from settings import global_settings
13 import settings
14 import ampal

/home/python/lib/python2.7/site-packages/isambard/settings.py in ()
46 configure()
47 else:
---> 48 load_global_settings()
49
50

/home/python/lib/python2.7/site-packages/isambard/settings.py in load_global_settings()
31 with open(settings_path, 'r') as settings_f:
32 global global_settings
---> 33 settings_json = json.loads(settings_f.read())
34 if global_settings is None:
35 global_settings = settings_json

/usr/lib/python2.7/json/init.pyc in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
336 parse_int is None and parse_float is None and
337 parse_constant is None and object_pairs_hook is None and not kw):
--> 338 return _default_decoder.decode(s)
339 if cls is None:
340 cls = JSONDecoder

/usr/lib/python2.7/json/decoder.pyc in decode(self, s, _w)
364
365 """
--> 366 obj, end = self.raw_decode(s, idx=_w(s, 0).end())
367 end = _w(s, end).end()
368 if end != len(s):

/usr/lib/python2.7/json/decoder.pyc in raw_decode(self, s, idx)
382 obj, end = self.scan_once(s, idx)
383 except StopIteration:
--> 384 raise ValueError("No JSON object could be decoded")
385 return obj, end

ValueError: No JSON object could be decoded

AMPALTagging Tutorial

When runing the tutorial I get the error

ImportError: No module named 'isambard.add_ons'

I also can not find convert_pdb_to_assembly and tag_socket in the code.