def __init__(self, input_structure_path: str, output_itp_path: str, input_ndx_path: str = None,
properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_structure_path": input_structure_path, "input_ndx_path": input_ndx_path},
"out": {"output_itp_path": output_itp_path}
}
# Properties specific for BB
self.force_constants = str(properties.get('force_constants', '500 500 500'))
self.restrained_group = properties.get('restrained_group', 'system')
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
output_top_zip_path: str, input_solvent_gro_path: str = None, properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_solute_gro_path": input_solute_gro_path, "input_solvent_gro_path": input_solvent_gro_path},
"out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.shell = properties.get('shell')
if not self.io_dict["in"].get('input_solvent_gro_path'):
self.io_dict["in"]['input_solvent_gro_path'] = 'spc216.gro'
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_structure_path: str,
input_ndx_path: str,
output_itp_path: str,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Input/Output files
self.io_dict = {
"in": {
"input_structure_path": input_structure_path,
"input_ndx_path": input_ndx_path
},
"out": {
"output_itp_path": output_itp_path
}
}
# Properties specific for BB
self.force_constants = str(
properties.get('force_constants', '500 500 500'))
self.restrained_group = properties.get('restrained_group', 'system')
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/data')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmxlib = properties.get('gmxlib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Properties common in all BB
self.can_write_console_log = properties.get('can_write_console_log',
True)
self.global_log = properties.get('global_log', None)
self.prefix = properties.get('prefix', None)
self.step = properties.get('step', None)
self.path = properties.get('path', '')
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
# Check the properties
fu.check_properties(self, properties)
def __init__(self, input_tpr_path: str, output_trr_path: str, output_gro_path: str, output_edr_path: str,
output_log_path: str, input_cpt_path: str = None, output_xtc_path: str = None, output_cpt_path: str = None,
output_dhdl_path: str = None, properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {"input_tpr_path": input_tpr_path, "input_cpt_path": input_cpt_path},
"out": {"output_trr_path": output_trr_path, "output_gro_path": output_gro_path,
"output_edr_path": output_edr_path, "output_log_path": output_log_path,
"output_xtc_path": output_xtc_path, "output_cpt_path": output_cpt_path,
"output_dhdl_path": output_dhdl_path}
}
# Properties specific for BB
# general mpi properties
self.mpi_bin = properties.get('mpi_bin')
self.mpi_np = properties.get('mpi_np')
self.mpi_flags = properties.get('mpi_flags')
# gromacs cpu mpi/openmp properties
self.num_threads = str(properties.get('num_threads', ''))
self.num_threads_mpi = str(properties.get('num_threads_mpi', ''))
self.num_threads_omp = str(properties.get('num_threads_omp', ''))
self.num_threads_omp_pme = str(properties.get('num_threads_omp_pme', ''))
# gromacs gpus
self.use_gpu = properties.get('use_gpu', False) # Adds: -nb gpu -pme gpu
self.gpu_id = str(properties.get('gpu_id', ''))
self.gpu_tasks = str(properties.get('gpu_tasks', ''))
# gromacs
self.checkpoint_time = properties.get('checkpoint_time')
# Not documented and not listed option, only for devs
self.dev = properties.get('dev')
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if (not self.mpi_bin) and (not self.container_path):
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_pdb_path: str,
output_gro_path: str,
output_top_zip_path: str,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {
"input_pdb_path": input_pdb_path
},
"out": {
"output_gro_path": output_gro_path,
"output_top_zip_path": output_top_zip_path
}
}
# Properties specific for BB
self.internal_top_name = properties.get(
'internal_top_name',
'p2g.top') # Excluded from documentation for simplicity
self.internal_itp_name = properties.get(
'internal_itp_name',
'posre.itp') # Excluded from documentation for simplicity
self.water_type = properties.get('water_type', 'spce')
self.force_field = properties.get('force_field', 'amber99sb-ildn')
self.ignh = properties.get('ignh', False)
self.his = properties.get('his', None)
self.merge = properties.get('merge', False)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_tpr_path: str,
output_gro_path: str,
input_top_zip_path: str,
output_top_zip_path: str,
input_ndx_path: str = None,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {
"input_tpr_path": input_tpr_path,
"input_ndx_path": input_ndx_path
},
"out": {
"output_gro_path": output_gro_path,
"output_top_zip_path": output_top_zip_path
}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.output_top_path = properties.get(
'output_top_path', 'gio.top') # Not in documentation for clarity
self.replaced_group = properties.get('replaced_group', 'SOL')
self.neutral = properties.get('neutral', False)
self.concentration = properties.get('concentration', 0.05)
self.seed = properties.get('seed', 1993)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_structure_path: str,
output_ndx_path: str,
input_ndx_path: str = None,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {
"input_structure_path": input_structure_path,
"input_ndx_path": input_ndx_path
},
"out": {
"output_ndx_path": output_ndx_path
}
}
# Properties specific for BB
self.selection = properties.get('selection', "a CA C N O")
self.append = properties.get('append', False)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_gro_path: str,
output_gro_path: str,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {
"input_gro_path": input_gro_path
},
"out": {
"output_gro_path": output_gro_path
}
}
# Properties specific for BB
self.distance_to_molecule = properties.get('distance_to_molecule', 1.0)
self.box_type = properties.get('box_type', 'cubic')
self.center_molecule = properties.get('center_molecule', True)
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_pdb_path: str,
output_gro_path: str,
output_top_zip_path: str,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Input/Output files
self.io_dict = {
"in": {
"input_pdb_path": input_pdb_path
},
"out": {
"output_gro_path": output_gro_path,
"output_top_zip_path": output_top_zip_path
}
}
# Properties specific for BB
self.output_top_path = properties.get('output_top_path', 'p2g.top')
self.output_itp_path = properties.get('output_itp_path', 'posre.itp')
self.water_type = properties.get('water_type', 'spce')
self.force_field = properties.get('force_field', 'amber99sb-ildn')
self.ignh = properties.get('ignh', False)
self.his = properties.get('his', None)
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/data')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmxlib = properties.get('gmxlib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Properties common in all BB
self.can_write_console_log = properties.get('can_write_console_log',
True)
self.global_log = properties.get('global_log', None)
self.prefix = properties.get('prefix', None)
self.step = properties.get('step', None)
self.path = properties.get('path', '')
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
# Check the properties
fu.check_properties(self, properties)
def __init__(self,
input_gro_path: str,
input_top_zip_path: str,
output_tpr_path: str,
input_cpt_path: str = None,
input_ndx_path: str = None,
input_mdp_path: str = None,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
# Input/Output files
self.io_dict = {
"in": {
"input_gro_path": input_gro_path,
"input_cpt_path": input_cpt_path,
"input_ndx_path": input_ndx_path,
"input_mdp_path": input_mdp_path
},
"out": {
"output_tpr_path": output_tpr_path
}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.output_mdp_path = properties.get('output_mdp_path', 'grompp.mdp')
self.output_top_path = properties.get('output_top_path', 'grompp.top')
self.simulation_type = properties.get('simulation_type')
self.maxwarn = str(properties.get('maxwarn', 0))
if self.simulation_type and self.simulation_type != 'index':
self.maxwarn = str(properties.get('maxwarn', 10))
self.mdp = {
k: str(v)
for k, v in properties.get('mdp', dict()).items()
}
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/data')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Check the properties
self.check_properties(properties)
def __init__(self,
input_gro_path: str,
input_top_zip_path: str,
output_tpr_path: str,
input_cpt_path: str = None,
input_ndx_path: str = None,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Input/Output files
self.io_dict = {
"in": {
"input_gro_path": input_gro_path,
"input_cpt_path": input_cpt_path,
"input_ndx_path": input_ndx_path
},
"out": {
"output_tpr_path": output_tpr_path
}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.input_mdp_path = properties.get('input_mdp_path', None)
self.output_mdp_path = properties.get('output_mdp_path', 'grompp.mdp')
self.output_top_path = properties.get('output_top_path', 'grompp.top')
#TODO REVIEW: When select is implemented.
self.maxwarn = str(properties.get('maxwarn', 10))
self.mdp = {
k: str(v)
for k, v in properties.get('mdp', dict()).items()
}
#TODO REVIEW: this two attributes
self.nsteps = ''
self.dt = ''
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/data')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmxlib = properties.get('gmxlib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Properties common in all BB
self.can_write_console_log = properties.get('can_write_console_log',
True)
self.global_log = properties.get('global_log', None)
self.prefix = properties.get('prefix', None)
self.step = properties.get('step', None)
self.path = properties.get('path', '')
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
# Check the properties
fu.check_properties(self, properties)
def __init__(self,
input_tpr_path: str,
output_gro_path: str,
input_top_zip_path: str,
output_top_zip_path: str,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Input/Output files
self.io_dict = {
"in": {
"input_tpr_path": input_tpr_path
},
"out": {
"output_gro_path": output_gro_path,
"output_top_zip_path": output_top_zip_path
}
}
# Should not be copied inside container
self.input_top_zip_path = input_top_zip_path
# Properties specific for BB
self.output_top_path = properties.get('output_top_path', 'gio.top')
self.replaced_group = properties.get('replaced_group', 'SOL')
self.neutral = properties.get('neutral', False)
self.concentration = properties.get('concentration', 0.05)
self.seed = properties.get('seed', 1993)
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/data')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmxlib = properties.get('gmxlib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.gmx_path)
# Properties common in all BB
self.can_write_console_log = properties.get('can_write_console_log',
True)
self.global_log = properties.get('global_log', None)
self.prefix = properties.get('prefix', None)
self.step = properties.get('step', None)
self.path = properties.get('path', '')
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
# Check the properties
fu.check_properties(self, properties)
def __init__(self,
input_tpr_path: str,
output_trr_path: str,
output_gro_path: str,
output_edr_path: str,
output_log_path: str,
output_xtc_path: str = None,
output_cpt_path: str = None,
output_dhdl_path: str = None,
properties: dict = None,
**kwargs) -> None:
properties = properties or {}
# Input/Output files
self.io_dict = {
"in": {
"input_tpr_path": input_tpr_path
},
"out": {
"output_trr_path": output_trr_path,
"output_gro_path": output_gro_path,
"output_edr_path": output_edr_path,
"output_log_path": output_log_path,
"output_xtc_path": output_xtc_path,
"output_cpt_path": output_cpt_path,
"output_dhdl_path": output_dhdl_path
}
}
# Properties specific for BB
self.num_threads = str(properties.get('num_threads', 0))
self.mpi_bin = properties.get('mpi_bin')
self.mpi_np = properties.get('mpi_np')
self.mpi_hostlist = properties.get('mpi_hostlist')
self.use_gpu = properties.get('use_gpu', False)
# container Specific
self.container_path = properties.get('container_path')
self.container_image = properties.get('container_image',
'gromacs/gromacs:latest')
self.container_volume_path = properties.get('container_volume_path',
'/tmp')
self.container_working_dir = properties.get('container_working_dir')
self.container_user_id = properties.get('container_user_id')
self.container_shell_path = properties.get('container_shell_path',
'/bin/bash')
# Properties common in all GROMACS BB
self.gmxlib = properties.get('gmxlib', None)
self.gmx_path = properties.get('gmx_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.gmx_path += ' -nobackup'
if self.gmx_nocopyright:
self.gmx_path += ' -nocopyright'
if (not self.mpi_bin) and (not self.container_path):
self.gmx_version = get_gromacs_version(self.gmx_path)
# Properties common in all BB
self.can_write_console_log = properties.get('can_write_console_log',
True)
self.global_log = properties.get('global_log', None)
self.prefix = properties.get('prefix', None)
self.step = properties.get('step', None)
self.path = properties.get('path', '')
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
# Check the properties
fu.check_properties(self, properties)
