def insert_to_db():
toolset_dict = {
'display_name': 'Quantum ESPRESSO',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'espresso',
'description': 'Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure '
'calculations and materials modeling at the nanoscale. It is based on density-functional theory, '
'plane waves, and pseudopotentials.',
'source_url': 'http://www.quantum-espresso.org/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Quantum ESPRESSO',
'description': 'Supports PWscf/pw.x, CPV/cp.x'
},
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'GAMESS',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'gamess',
'description': 'The General Atomic and Molecular Electronic Structure System (GAMESS) '
'is a general ab initio quantum chemistry package. '
'Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF.',
'source_url': 'http://www.msg.ameslab.gov/gamess/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'GAMESS',
# "executable_name": "GAMESSExecutable",
# "view_name":"GAMESSView",
'description': 'GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF'
},
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'Impi',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'impi',
'description': 'Image processing tool that runs in parallel via MPI',
# 'source_url': 'http://www.quantum-espresso.org/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Impi',
# "executable_name": "QuantumESPRESSOExecutable",
# "view_name":"QuantumESPRESSOView",
'description': 'Image processing tool for JPEG format',
},
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'Dock 6',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'dock6',
'description': 'The new features of DOCK 6 include: additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening; PB/SA solvation scoring; and AMBER scoring-including receptor flexibility, the full AMBER molecular mechanics scoring function with implicit solvent, conjugate gradient minimization, and molecular dynamics simulation capabilities. Because DOCK 6 is an extension of DOCK 5, it also includes all previous features. ',
'source_url': 'http://dock.compbio.ucsf.edu/DOCK_6/index.htm'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'dock6',
'description': 'Screen molecules for complementarily with receptor'
},
{'display_name': 'grid',
'description': 'Precompute score grids for rapid dock evaluation'
},
# not yet supported
# {'display_name': 'sphgen',
# 'description': 'Site characterization negative image of the site',
# }
]
add_tools_to_toolset(tools, toolset) # add tool db entries and associate them to the toolset
def insert_to_db():
toolset_dict = {
'display_name': 'Ray',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'ray',
'description': 'Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.',
'source_url': 'http://denovoassembler.sourceforge.net/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Ray',
'description': 'The main executable for Ray'
# "executable_name": "RayExecutable",
# "view_name":"RayView",
},
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'Dock 6',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'dock6',
'description': 'The new features of DOCK 6 include: additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening; PB/SA solvation scoring; and AMBER scoring-including receptor flexibility, the full AMBER molecular mechanics scoring function with implicit solvent, conjugate gradient minimization, and molecular dynamics simulation capabilities. Because DOCK 6 is an extension of DOCK 5, it also includes all previous features. ',
'source_url': 'http://dock.compbio.ucsf.edu/DOCK_6/index.htm'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'dock6',
'description': 'Screen molecules for complementarily with receptor'
},
{'display_name': 'grid',
'description': 'Precompute score grids for rapid dock evaluation'
},
# not yet supported
# {'display_name': 'sphgen',
# 'description': 'Site characterization negative image of the site',
# }
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'Ray',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'ray',
'description': 'Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.',
'source_url': 'http://denovoassembler.sourceforge.net/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Ray',
'description': 'The main executable for Ray'
# "executable_name": "RayExecutable",
# "view_name":"RayView",
},
]
add_tools_to_toolset(tools, toolset) # add tool db entries and associate them with toolset
def insert_to_db():
toolset_dict = {
'display_name': 'Impi',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'impi',
'description': 'Image processing tool that runs in parallel via MPI',
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Impi',
'description': 'Image processing tool for JPEG format',
},
]
add_tools_to_toolset(tools, toolset) # add tool db entries and associate them with toolset
def insert_to_db():
toolset_dict = {
'display_name': 'GAMESS',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'gamess',
'description': 'The General Atomic and Molecular Electronic Structure System (GAMESS) '
'is a general ab initio quantum chemistry package. '
'Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF.',
'source_url': 'http://www.msg.ameslab.gov/gamess/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'GAMESS',
# "executable_name": "GAMESSExecutable",
# "view_name":"GAMESSView",
'description': 'GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF'
},
]
add_tools_to_toolset(tools, toolset) # add tool db entries and associate to toolset
def insert_to_db():
toolset_dict = {
'display_name':
'AutoDock 4',
'package_name':
__name__.replace('.install', ''),
'p2ctool_name':
'autodock',
'description':
'AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, '
'such as substrates or drug candidates, bind to a receptor of known 3D structure.',
'source_url':
'http://autodock.scripps.edu/'
}
toolset, created = ToolSet.objects.update_or_create(
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={
'display_name':
toolset_dict['display_name'],
'description':
toolset_dict.get('description', 'No description provided'),
'source_url':
toolset_dict.get('source_url', 'No link provided'),
'package_name':
toolset_dict.get('package_name')
})
# Ff you followed the naming convention for classes,
# you do not need to provide values for executable_name and view_name
tools = [
{
'display_name': 'autogrid4',
# 'executable_name': 'AutoGrid4Executable',
# 'view_name': 'AutogridView',
'description': 'Pre-calculates grids to be used by autodock4',
},
{
'display_name':
'autodock4',
# 'executable_name': 'AutoDock4Executable',
# 'view_name': 'Autodoc4kView',
'description':
'Performs the docking of the ligand to a set of grids describing the target protein',
},
]
add_tools_to_toolset(tools, toolset) # associate tools to toolset
def insert_to_db():
toolset_dict = {
'display_name':
'Quantum ESPRESSO',
'package_name':
__name__.replace('.install', ''),
'p2ctool_name':
'espresso',
'description':
'Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure '
'calculations and materials modeling at the nanoscale. It is based on density-functional theory, '
'plane waves, and pseudopotentials.',
'source_url':
'http://www.quantum-espresso.org/'
}
toolset, created = ToolSet.objects.update_or_create(
package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={
'display_name':
toolset_dict['display_name'],
'description':
toolset_dict.get('description', 'No description provided'),
'source_url':
toolset_dict.get('source_url', 'No link provided')
})
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{
'display_name': 'Quantum ESPRESSO',
'description': 'Supports PWscf/pw.x, CPV/cp.x'
},
]
add_tools_to_toolset(
tools, toolset) # add tool db entries and associate them with toolset
def insert_to_db():
toolset_dict = {
'display_name': 'AutoDock Vina',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'vina',
'description': 'AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. ',
'source_url': 'http://vina.scripps.edu/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Vina',
'description': 'The main executable for AutoDock Vina'
# 'executable_name': 'VinaExecutable',
# 'view_name':'VinaView',
},
{'display_name': 'Vina split',
# 'executable_name': 'VinaSplitExecutable',
# 'view_name':'VinaSplitView',
'description': 'You split the receptor into two parts: rigid and flexible, '
'with the latter represented somewhat similarly to how the ligand is represented.',
},
]
add_tools_to_toolset(tools, toolset)
def insert_to_db():
toolset_dict = {
'display_name': 'AutoDock Vina',
'package_name': __name__.replace('.install', ''),
'p2ctool_name': 'vina',
'description': 'AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. ',
'source_url': 'http://vina.scripps.edu/'
}
toolset, created = ToolSet.objects.update_or_create(package_name=toolset_dict['package_name'],
p2ctool_name=toolset_dict['p2ctool_name'],
defaults={'display_name': toolset_dict['display_name'],
'description': toolset_dict.get('description',
'No description provided'),
'source_url': toolset_dict.get('source_url',
'No link provided')
}
)
# if you followed the naming convention for classes, you do not need to provide values for executable_name and view_name
tools = [
{'display_name': 'Vina',
'description': 'The main executable for AutoDock Vina'
# 'executable_name': 'VinaExecutable',
# 'view_name':'VinaView',
},
{'display_name': 'Vina split',
# 'executable_name': 'VinaSplitExecutable',
# 'view_name':'VinaSplitView',
'description': 'You split the receptor into two parts: rigid and flexible, '
'with the latter represented somewhat similarly to how the ligand is represented.',
},
]
add_tools_to_toolset(tools, toolset) # add tool db entries and associate them with toolset