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