Graphical interface for AutoDock Vina #107
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Loosely based on the original AutoDock plugin.
speleo3
approved these changes
Nov 18, 2019
plugins/vina.py
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| DEFAULT_PREFS = { | ||
| 'DOCKING_VINA': '/usr/bin/vina', | ||
| 'DOCKING_OBABEL': '/usr/bin/obabel', | ||
| 'DOCKING_ADT_PYTHON': '/usr/bin/python2.7', | ||
| 'DOCKING_PREPARE_RECEPTOR': '/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_receptor4.py', | ||
| 'DOCKING_PREPARE_FLEXRECEPTOR': '/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_flexreceptor4.py', | ||
| } |
There was a problem hiding this comment.
You could try something like this:
try:
from AutoDockTools import Utilities24
utilities24_dir = os.path.dirname(Utilities24.__file__)
docking_adt_python = sys.executable
except ImportError:
try:
utilities24_dir = glob('/usr/lib/python*/dist-packages/AutoDockTools/Utilities24')[0]
docking_adt_python = '/usr/bin/' + utilities24_dir.split('/')[3]
except IndexError:
utilities24_dir = ''
docking_adt_python = ''
DEFAULT_PREFS = {
'DOCKING_VINA': 'vina', # without /usr/bin, will pick it up from $PATH
'DOCKING_OBABEL': 'obabel',
'DOCKING_ADT_PYTHON': docking_adt_python,
'DOCKING_PREPARE_RECEPTOR': os.path.join(utilities24_dir, 'prepare_receptor4.py'),
'DOCKING_PREPARE_FLEXRECEPTOR': os.path.join(utilities24_dir, 'prepare_flexreceptor4.py'),
}
plugins/vina.py
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| command = ( | ||
| f'"{adt_python}"' | ||
| f' "{prepare_target}" -r "{target_pdb}"' | ||
| ) | ||
| output, success = run(command) |
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Better to remove the shlex.split call in run and do this:
command = [adt_python, prepare_target, "-r", target_pdb]
plugins/vina.py
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| def run(command): | ||
| ret = subprocess.run( | ||
| shlex.split(command), |
There was a problem hiding this comment.
better to pass a list and not do shlex.split (see other comment below)
|
Checking in to see what the status of this PR is since it's been quite some time. @pslacerda |
|
i'm needing to make this plugin public. |
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Loosely based on the original AutoDock plugin. It isn't ready yet, there is more work to do:
Must be a more convenient way to set the prefs. I'm thinking of guess the defaults for Ubuntu and Windows and let users adjust the prefs themselves if don't work.