def binaries(gmxpath, gmxsuff):
"""Locate the paths to the best available gromacs binaries. """
def gmx_path(binary_path):
return os.path.join(gmxpath, binary_path + gmxsuff)
if which('gmx_d'):
logger.debug("Using double precision binaries for gromacs")
main_binary = gmx_path('gmx_d')
grompp_bin = [main_binary, 'grompp']
mdrun_bin = [main_binary, 'mdrun']
genergy_bin = [main_binary, 'energy']
elif which('grompp_d') and which('mdrun_d') and which('g_energy_d'):
logger.debug("Using double precision binaries")
grompp_bin = [gmx_path('grompp_d')]
mdrun_bin = [gmx_path('mdrun_d')]
genergy_bin = [gmx_path('g_energy_d')]
elif which('gmx'):
logger.debug("Using double precision binaries")
main_binary = gmx_path('gmx')
grompp_bin = [main_binary, 'grompp']
mdrun_bin = [main_binary, 'mdrun']
genergy_bin = [main_binary, 'energy']
elif which('grompp') and which('mdrun') and which('g_energy'):
logger.debug("Using single precision binaries")
grompp_bin = [gmx_path('grompp')]
mdrun_bin = [gmx_path('mdrun')]
genergy_bin = [gmx_path('g_energy')]
else:
raise IOError('Unable to find gromacs executables.')
return grompp_bin, mdrun_bin, genergy_bin
def binaries(gmxpath, gmxsuff):
"""Locate the paths to the best available gromacs binaries. """
def gmx_path(binary_path):
return os.path.join(gmxpath, binary_path + gmxsuff)
if which('gmx_d'):
logger.debug("Using double precision binaries for gromacs")
main_binary = gmx_path('gmx_d')
grompp_bin = [main_binary, 'grompp']
mdrun_bin = [main_binary, 'mdrun']
genergy_bin = [main_binary, 'energy']
elif which('grompp_d') and which('mdrun_d') and which('g_energy_d'):
logger.debug("Using double precision binaries")
grompp_bin = [gmx_path('grompp_d')]
mdrun_bin = [gmx_path('mdrun_d')]
genergy_bin = [gmx_path('g_energy_d')]
elif which('gmx'):
logger.debug("Using double precision binaries")
main_binary = gmx_path('gmx')
grompp_bin = [main_binary, 'grompp']
mdrun_bin = [main_binary, 'mdrun']
genergy_bin = [main_binary, 'energy']
elif which('grompp') and which('mdrun') and which('g_energy'):
logger.debug("Using single precision binaries")
grompp_bin = [gmx_path('grompp')]
mdrun_bin = [gmx_path('mdrun')]
genergy_bin = [gmx_path('g_energy')]
else:
raise IOError('Unable to find gromacs executables.')
return grompp_bin, mdrun_bin, genergy_bin
def amber_energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, 'parm.prmtop')
if not crd:
crd = os.path.join(directory, 'ener.edr')
mdout = os.path.join(directory, 'amber.out')
stdout_path = os.path.join(directory, 'amber_stdout.txt')
stderr_path = os.path.join(directory, 'amber_stderr.txt')
# did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == 'sander':
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, 'sander')
if not which(amber_bin):
raise IOError('Unable to find AMBER executable (sander).')
# run sander
cmd = [amber_bin, '-i', input, '-c', crd, '-p', prmtop, '-o', mdout, '-O']
proc = run_subprocess(cmd, 'amber', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('sander failed. See %s' % stderr_path)
# Extract energies from amber output
return _group_energy_terms(mdout)
def amber_energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info("Evaluating energy of {0}".format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, "parm.prmtop")
if not crd:
crd = os.path.join(directory, "ener.edr")
mdout = os.path.join(directory, "amber.out")
stdout_path = os.path.join(directory, "amber_stdout.txt")
stderr_path = os.path.join(directory, "amber_stderr.txt")
# did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == "sander":
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, "sander")
if not which(amber_bin):
raise IOError("Unable to find AMBER executable (sander).")
# run sander
cmd = [amber_bin, "-i", input, "-c", crd, "-p", prmtop, "-o", mdout, "-O"]
proc = run_subprocess(cmd, "amber", stdout_path, stderr_path)
if proc.returncode != 0:
logger.error("sander failed. See %s" % stderr_path)
# Extract energies from amber output
return _group_energy_terms(mdout)
def energies(inpfile, crm_path):
"""Compute single-point energies using CHARMM.
Args:
inpfile (str)
crm_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(inpfile))
# find the directory the input file is in.
directory, _ = os.path.split(os.path.abspath(inpfile))
# create files for output
stdout_path = os.path.join(directory, 'charmm_stdout.txt')
stderr_path = os.path.join(directory, 'charmm_stderr.txt')
# delete previous stdout and stderr
if os.path.isfile(stdout_path):
os.remove(stdout_path)
if os.path.isfile(stderr_path):
os.remove(stderr_path)
if not which(crm_path):
raise IOError('Unable to find CHARMM executable (charmm).')
if os.path.isdir(crm_path):
charmm_bin = os.path.join(crm_path, 'charmm')
else:
charmm_bin = crm_path
# run charmm - this assumes all files required in the input file are present
cmd = [charmm_bin, '-i', inpfile]
proc = run_subprocess(cmd, 'charmm', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('charmm failed. See %s' % stderr_path)
# Extract energies from charmm output
return _group_energy_terms(stdout_path)
def charmm_energies(inpfile, crm_path):
"""Compute single-point energies using CHARMM.
Args:
inpfile (str)
crm_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(inpfile))
# find the directory the input file is in.
directory, _ = os.path.split(os.path.abspath(inpfile))
# create files for output
stdout_path = os.path.join(directory, 'charmm_stdout.txt')
stderr_path = os.path.join(directory, 'charmm_stderr.txt')
# delete previous stdout and stderr
if os.path.isfile(stdout_path):
os.remove(stdout_path)
if os.path.isfile(stderr_path):
os.remove(stderr_path)
if not which(crm_path):
raise IOError('Unable to find CHARMM executable (charmm).')
if os.path.isdir(crm_path):
charmm_bin = os.path.join(crm_path, 'charmm')
else:
charmm_bin = crm_path
# run charmm - this assumes all files required in the input file are present
cmd = [charmm_bin, '-i', inpfile]
proc = run_subprocess(cmd, 'charmm', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('charmm failed. See %s' % stderr_path)
# Extract energies from charmm output
return _group_energy_terms(stdout_path)
def energies(prmtop, crd, input, amb_path):
"""Compute single-point energies using AMBER.
Args:
prmtop (str):
crd (str):
input (str)
amb_path (str):
Returns:
e_out:
ener_xvg:
"""
logger.info('Evaluating energy of {0}'.format(crd))
directory, _ = os.path.split(os.path.abspath(prmtop))
if not prmtop:
prmtop = os.path.join(directory, 'parm.prmtop')
if not crd:
crd = os.path.join(directory, 'ener.edr')
mdout = os.path.join(directory, 'amber.out')
stdout_path = os.path.join(directory, 'amber_stdout.txt')
stderr_path = os.path.join(directory, 'amber_stderr.txt')
# Did they give a path, or the name of the file?
islastbin = os.path.basename(os.path.normpath(amb_path))
if islastbin == 'sander':
amber_bin = amb_path
else:
amber_bin = os.path.join(amb_path, 'sander')
if not which(amber_bin):
raise IOError('Unable to find AMBER executable (sander).')
# Run sander.
cmd = [amber_bin, '-i', input, '-c', crd, '-p', prmtop, '-o', mdout, '-O']
proc = run_subprocess(cmd, 'amber', stdout_path, stderr_path)
if proc.returncode != 0:
logger.error('sander failed. See %s' % stderr_path)
return _group_energy_terms(mdout)
from intermol.utils import run_subprocess, which
from intermol.lammps.lammps_parser import load, save
# Python 2/3 compatibility.
try:
FileNotFoundError
except NameError:
FileNotFoundError = OSError
logger = logging.getLogger('InterMolLog')
for exe in ['lammps', 'lmp_mpi', 'lmp_serial', 'lmp_openmpi',
'lmp_mac_mpi']:
if which(exe):
LMP_PATH = exe
break
else:
warnings.warn('Found no LAMMPS executable.')
def energies(input_file, lmp_path=None):
"""Evaluate energies of LAMMPS files
Args:
input_file = path to input file (expects data file in same folder)
lmp_path = path to LAMMPS binaries
"""
if lmp_path is None:
lmp_path = LMP_PATH
import simtk.unit as units
from intermol.utils import run_subprocess, which
from intermol.lammps.lammps_parser import load, save
# Python 2/3 compatibility.
try:
FileNotFoundError
except NameError:
FileNotFoundError = OSError
logger = logging.getLogger('InterMolLog')
for exe in ['lammps', 'lmp_mpi', 'lmp_serial', 'lmp_openmpi', 'lmp_mac_mpi']:
if which(exe):
LMP_PATH = exe
break
else:
warnings.warn('Found no LAMMPS executable.')
def energies(input_file, lmp_path=None):
"""Evaluate energies of LAMMPS files
Args:
input_file = path to input file (expects data file in same folder)
lmp_path = path to LAMMPS binaries
"""
if lmp_path is None:
lmp_path = LMP_PATH