def get_available_platforms():
from simtk.openmm import Platform
platform_names = []
for i in range(Platform.getNumPlatforms()):
p = Platform.getPlatform(i)
name = p.getName()
platform_names.append(name)
return platform_names
platform_properties = {
'CUDA': [
'Cuda_Device_Index', 'Cuda_Precision', 'Cuda_Use_Cpu_Pme',
'Cuda_Cuda_Compiler', 'Cuda_Temp_Directory',
'Cuda_Use_Blocking_Sync', 'Cuda_Deterministic_Forces'
],
'OpenCL': [
'OpenCL_Device_Index', 'OpenCL_Precision', 'OpenCL_Use_Cpu_Pme',
'OpenCL_OpenCL_Platform_Index'
],
'CPU': ['CPU_Threads'],
'Reference': []
}
platform_names = [
Platform.getPlatform(no_platform).getName()
for no_platform in range(Platform.getNumPlatforms())
]
parser = argparse.ArgumentParser(
description='Run an MD simulation using OpenMM')
parser.add_argument('output',
metavar='output/',
help='the output directory',
type=str)
parser.add_argument('-l',
'--length',
dest='length',
type=int,
funcs = {'get_platform': [get_platform, platform],
'get_pdbfile': [get_pdbfile, pdbfile],
'get_system': [get_xml, system],
'get_integrator': [get_xml, integrator]}
kfuncs = list(funcs.keys())
random.shuffle(kfuncs)
returns = dict()
while kfuncs:
op_name = kfuncs.pop(0)
func, arg = funcs[op_name]
returns.update({op_name: func(arg)})
return [returns[nxt] for nxt in return_order]
platformNames = [Platform.getPlatform(i).getName() for i in range(Platform.getNumPlatforms())]
print(platformNames)
parser = argparse.ArgumentParser()
parser.add_argument('--save_traj',dest='save_traj',required=True,type=str)
parser.add_argument('--md_steps',dest='md_steps',required=True,type=int)
parser.add_argument('--trajstride',dest='trajstride', required=False, type=int, default=10)
parser.add_argument('--idxstart',dest='idxstart',required=True,type=int)
parser.add_argument('--idxend',dest='idxend',required=True,type=int)
parser.add_argument('--iter',dest='iter',required=True,type=int)
parser.add_argument('--path',dest='path',required=True,type=str)
args = parser.parse_args()
#grofile_name='start2.gro
#pdb=mdtraj.load(grofile_name)
pdb_in = sys.argv[1]
mol_in = sys.argv[2]
output_complex = sys.argv[3] + '_complex.pdb'
output_traj_pdb = sys.argv[3] + '_traj.pdb'
output_traj_dcd = sys.argv[3] + '_traj.dcd'
output_min = sys.argv[3] + '_minimised.pdb'
num_steps = int(sys.argv[4])
print('Processing', pdb_in, 'and', mol_in, 'with', num_steps,
'steps generating outputs', output_complex, output_min, output_traj_pdb,
output_traj_dcd)
# check whether we have a GPU platform and if so set the precision to mixed
speed = 0
for i in range(Platform.getNumPlatforms()):
p = Platform.getPlatform(i)
# print(p.getName(), p.getSpeed())
if p.getSpeed() > speed:
platform = p
speed = p.getSpeed()
if platform.getName() == 'CUDA' or platform.getName() == 'OpenCL':
platform.setPropertyDefaultValue('Precision', 'mixed')
print('Set precision for platform', platform.getName(), 'to mixed')
# Read the molfile into RDKit, add Hs and create an openforcefield Molecule object
print('Reading ligand')
rdkitmol = Chem.MolFromMolFile(mol_in)
print('Adding hydrogens')
rdkitmolh = Chem.AddHs(rdkitmol, addCoords=True)
# ensure the chiral centers are all defined
"""
Houses all of the "extra" test cases to run for OpenMM
"""
__all__ = ['testhewl', 'available_platforms']
import testhewl
# Construct the list of available platforms
available_platforms = []
from simtk.openmm import Platform
for i in range(Platform.getNumPlatforms()):
available_platforms.append(Platform.getPlatform(i).getName())
# Cleanup the namespace a bit
del i, Platform
'get_pdbfile': [get_pdbfile, pdbfile],
'get_system': [get_xml, system],
'get_integrator': [get_xml, integrator]
}
kfuncs = list(funcs.keys())
random.shuffle(kfuncs)
returns = dict()
while kfuncs:
op_name = kfuncs.pop(0)
func, arg = funcs[op_name]
returns.update({op_name: func(arg)})
return [returns[nxt] for nxt in return_order]
platformNames = [
Platform.getPlatform(i).getName()
for i in range(Platform.getNumPlatforms())
]
print(platformNames)
parser = argparse.ArgumentParser()
#parser.add_argument('--save_traj',dest='save_traj',required=True,type=str)
#parser.add_argument('--md_steps',dest='md_steps',required=True,type=int)
#parser.add_argument('--trajstride',dest='trajstride', required=False, type=int, default=10)
parser.add_argument('--idxstart', dest='idxstart', required=True, type=int)
parser.add_argument('--idxend', dest='idxend', required=True, type=int)
#parser.add_argument('--iter',dest='iter',required=True,type=int)
parser.add_argument('--path', dest='path', required=True, type=str)
parser.add_argument("--Kconfig", type=str, dest="Kconfig", required=True)
#parser.add_argument("--extend", type=str, dest="extend", default='True')
args = parser.parse_args()
