def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except error:
print('Unable to create {} folder. Will not check for new HTMD versions.'.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
if not os.path.isfile(__file) or time.time() > os.path.getmtime(__file) + 86400: #86400: # Check if one day has passed since last version check
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print('Unable to open {} file for reading. Will not check for new HTMD versions.'.format(__file))
return
latestver = f.read()
f.close()
currver = version()
if currver != 'unpackaged' and natsorted((latestver, currver))[1] != currver:
print('New HTMD version ({}) is available. You are currently on ({}). Use \'conda update htmd\' to update to the new version.'.format(latestver, currver))
else:
print('You are on the latest HTMD version ({}).'.format(currver))
def compareVersions():
from htmd.home import home
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
__file = os.path.join(home(), '.latestversion')
if not os.path.isfile(__file) or time.time() > os.path.getmtime(
__file
) + 86400: #86400: # Check if one day has passed since last version check
_writeLatestVersionFile(__file)
f = open(__file, 'r')
latestver = f.read()
f.close()
currver = version()
if currver != 'unpackaged' and natsorted(
(latestver, currver))[1] != currver:
print(
'New HTMD version ({}) is available. You are currently on ({}). Use \'conda update htmd\' to update to the new version.'
.format(latestver, currver))
else:
print('You are on the latest HTMD version ({}).'.format(currver))
def getArgumentParser():
parser = argparse.ArgumentParser(description='Acellera small molecule parameterization tool')
parser.add_argument('filename', help='Molecule file in MOL2 format')
parser.add_argument('-c', '--charge', type=int,
help='Total charge of the molecule (default: sum of partial charges)')
parser.add_argument('-l', '--list', action='store_true', help='List parameterizable dihedral angles')
parser.add_argument('--rtf-prm', nargs=2, metavar='<filename>', help='CHARMM RTF and PRM files')
parser.add_argument('-ff', '--forcefield', default='GAFF2', choices=fftypemethods,
help='Initial atom type and parameter assignment (default: %(default)s)')
parser.add_argument('--fix-charge', nargs='+', default=[], metavar='<atom name>',
help='Fix atomic charge during charge fitting (default: none)')
parser.add_argument('-d', '--dihedral', nargs='+', default=[], metavar='A1-A2-A3-A4',
help='Select dihedral angle to parameterize (default: all parameterizable dihedral angles)')
parser.add_argument('--code', default='Psi4', choices=['Psi4', 'Gaussian'],
help='QM code (default: %(default)s)')
parser.add_argument('--theory', default='B3LYP', choices=['HF', 'B3LYP', 'wB97X-D'],
help='QM level of theory (default: %(default)s)')
parser.add_argument('--basis', default='cc-pVDZ', choices=['6-31G*', '6-31+G*', '6-311G**', '6-311++G**', 'cc-pVDZ',
'aug-cc-pVDZ'],
help='QM basis set (default: %(default)s)')
parser.add_argument('--environment', default='vacuum', choices=['vacuum', 'PCM'],
help='QM environment (default: %(default)s)')
parser.add_argument('--no-min', action='store_false', dest='minimize',
help='DDEPRECATED: use `--min-type` instead')
parser.add_argument('--min-type', default='qm', dest='min_type', choices=['None', 'qm', 'mm'],
help='Type of initial structure optimization (default: %(default)s)')
parser.add_argument('--charge-type', default='ESP', choices=['None', 'Gasteiger', 'AM1-BCC', 'ESP'],
help='Partial atomic charge type (default: %(default)s)')
parser.add_argument('--no-dihed', action='store_false', dest='fit_dihedral',
help='Do not perform QM scanning of dihedral angles')
parser.add_argument('--no-dihed-opt', action='store_false', dest='optimize_dihedral',
help='DEPRECATED: use `--scan-type` instead')
parser.add_argument('--scan-type', default='qm', dest='dihed_opt_type', choices=['None', 'qm', 'mm'],
help='Type of structure optimization when scanning dihedral angles (default: %(default)s)')
parser.add_argument('--dihed-num-searches', default=None, type=int,
help='Number of random searches during the dihedral parameter fitting')
parser.add_argument('-q', '--queue', default='local', choices=['local', 'Slurm', 'LSF', 'AceCloud'],
help='QM queue (default: %(default)s)')
parser.add_argument('-n', '--ncpus', default=None, type=int, help='Number of CPU per QM job (default: queue '
'defaults)')
parser.add_argument('-m', '--memory', default=None, type=int, help='Maximum amount of memory in MB to use.')
parser.add_argument('--groupname', default=None, help=argparse.SUPPRESS)
parser.add_argument('-o', '--outdir', default='./', help='Output directory (default: %(default)s)')
parser.add_argument('--seed', default=20170920, type=int,
help='Random number generator seed (default: %(default)s)')
parser.add_argument('--version', action='version', version=version())
# Enable replacement of any real QM class with FakeQM.
# This is intedended for debugging only and should be kept hidden.
parser.add_argument('--fake-qm', action='store_true', default=False, dest='fake_qm', help=argparse.SUPPRESS)
# NNP module name
parser.add_argument('--nnp', help=argparse.SUPPRESS)
# Debug mode
parser.add_argument('--debug', action='store_true', default=False, dest='debug', help=argparse.SUPPRESS)
return parser
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except:
print('Unable to create {} folder. Will not check for new HTMD versions.'.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
# Check if one day has passed since last version check. If yes, get new version and write to file
if not os.path.isfile(__file) or time.time() > os.path.getmtime(__file) + 86400:
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print('Unable to open {} file for reading. Will not check for new HTMD versions.'.format(__file))
return
latestversions = f.readlines()
f.close()
currver = version()
if currver != 'unpackaged' and len(latestversions) == 2: # Supporting users which still haven't passed the one day limit. Can remove in next
if _is_stable(currver):
latest = latestversions[0].strip()
verstring = 'stable'
else:
latest = latestversions[1].strip()
verstring = 'devel'
elif len(latestversions) == 1: # Supporting users which still haven't passed the one day limit. Can remove in next version
latest = latestversions[0].strip()
verstring = ''
elif currver == 'unpackaged':
pass
else:
return
if currver != 'unpackaged' and natsorted((latest, currver))[1] != currver:
print('New {} HTMD version ({}) is available. You are currently on ({}). Use \'conda update -c acellera htmd\' to '
'update to the new version.'.format(verstring, latest, currver))
else:
if currver != 'unpackaged':
print('You are on the latest HTMD version ({}).'.format(currver))
else:
from htmd import home
print('You are on the latest HTMD version ({} : {}).'.format(currver, home()))
print("")
def getArgumentParser():
parser = argparse.ArgumentParser(description='Acellera small molecule parameterization tool')
parser.add_argument('filename', help='Molecule file in MOL2 format')
parser.add_argument('-c', '--charge', type=int,
help='Total charge of the molecule (default: sum of partial charges)')
parser.add_argument('-l', '--list', action='store_true', help='List parameterizable dihedral angles')
parser.add_argument('--rtf-prm', nargs=2, metavar='<filename>', help='CHARMM RTF and PRM files')
parser.add_argument('-ff', '--forcefield', nargs='+', default=['GAFF2'], choices=['GAFF', 'GAFF2', 'CGENFF'],
help='Inital force field guess (default: %(default)s)')
parser.add_argument('--fix-charge', nargs='+', default=[], metavar='<atom name>',
help='Fix atomic charge during charge fitting (default: none)')
parser.add_argument('-d', '--dihedral', nargs='+', default=[], metavar='A1-A2-A3-A4',
help='Select dihedral angle to parameterize (default: all parameterizable dihedral angles)')
parser.add_argument('--code', default='Psi4', choices=['Psi4', 'Gaussian'], help='QM code (default: %(default)s)')
parser.add_argument('--theory', default='B3LYP', choices=['HF', 'B3LYP'],
help='QM level of theory (default: %(default)s)')
parser.add_argument('--basis', default='cc-pVDZ', choices=['6-31G*', '6-31+G*', 'cc-pVDZ', 'aug-cc-pVDZ'],
help='QM basis set (default: %(default)s)')
parser.add_argument('--environment', default='vacuum', choices=['vacuum', 'PCM'],
help='QM environment (default: %(default)s)')
parser.add_argument('--no-min', action='store_false', dest='minimize',
help='Do not perform QM structure minimization')
parser.add_argument('--no-esp', action='store_false', dest='fit_charges', help='Do not perform QM charge fitting')
parser.add_argument('--no-dihed', action='store_false', dest='fit_dihedral',
help='Do not perform QM scanning of dihedral angles')
parser.add_argument('--no-dihed-opt', action='store_false', dest='optimize_dihedral',
help='Do not perform QM structure optimisation when scanning dihedral angles')
parser.add_argument('-q', '--queue', default='local', choices=['local', 'Slurm', 'LSF', 'AceCloud'],
help='QM queue (default: %(default)s)')
parser.add_argument('-n', '--ncpus', default=None, type=int, help='Number of CPU per QM job (default: queue '
'defaults)')
parser.add_argument('-m', '--memory', default=None, type=int, help='Maximum amount of memory in MB to use.')
parser.add_argument('--groupname', default=None, help=argparse.SUPPRESS)
parser.add_argument('-o', '--outdir', default='./', help='Output directory (default: %(default)s)')
parser.add_argument('--seed', default=20170920, type=int,
help='Random number generator seed (default: %(default)s)')
parser.add_argument('--version', action='version', version=version())
# Enable replacement of any real QM class with FakeQM.
# This is intedended for debugging only and should be kept hidden.
parser.add_argument('--fake-qm', action='store_true', default=False, dest='fake_qm', help=argparse.SUPPRESS)
return parser
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except error:
print(
'Unable to create {} folder. Will not check for new HTMD versions.'
.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
if not os.path.isfile(__file) or time.time() > os.path.getmtime(
__file
) + 86400: #86400: # Check if one day has passed since last version check
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print(
'Unable to open {} file for reading. Will not check for new HTMD versions.'
.format(__file))
return
latestver = f.read()
f.close()
currver = version()
if currver != 'unpackaged' and natsorted(
(latestver, currver))[1] != currver:
print(
'New HTMD version ({}) is available. You are currently on ({}). Use \'conda update htmd\' to update to the new version.'
.format(latestver, currver))
else:
print('You are on the latest HTMD version ({}).'.format(currver))
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except:
print(
'Unable to create {} folder. Will not check for new HTMD versions.'
.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
# Check if one day has passed since last version check. If yes, get new version and write to file
if not os.path.isfile(__file) or time.time(
) > os.path.getmtime(__file) + 86400 or os.stat(__file).st_size == 0:
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print(
'Unable to open {} file for reading. Will not check for new HTMD versions.'
.format(__file))
return
latestversions = f.readlines()
f.close()
if len(latestversions) != 2:
print(
'There is something wrong with your {} file. Will not check for new HTMD versions.'
.format(__file))
return
currver = version()
if currver != 'unpackaged':
if _is_stable(currver):
pieces = latestversions[0].split()
latest = pieces[0].strip()
verstring = 'stable'
else:
pieces = latestversions[1].split()
latest = pieces[0].strip()
verstring = 'devel'
pydeps = ''
if len(pieces) > 1:
pydeps = ' python[{}]'.format(pieces[1])
elif currver == 'unpackaged':
pass
else:
return
if currver != 'unpackaged' and natsorted((latest, currver))[1] != currver:
print(
'New {} HTMD version ({}{}) is available. You are currently on ({}). Use \'conda update -c '
'acellera htmd\' to update to the new version. You might need to update your python version as well '
'if there is no release for your current version.'.format(
verstring, latest, pydeps, currver))
else:
if currver != 'unpackaged':
print('You are on the latest HTMD version ({}).'.format(currver))
else:
from htmd.home import home
print('You are on the latest HTMD version ({} : {}).'.format(
currver, home()))
print("")
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, ".htmd")
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except Exception:
print(
f"Unable to create {__htmdconf} folder. Will not check for new HTMD versions."
)
return
__file = os.path.join(__htmdconf, ".latestversion")
# Check if one day has passed since last version check. If yes, get new version and write to file
if (not os.path.isfile(__file)
or time.time() > os.path.getmtime(__file) + 86400
or os.stat(__file).st_size == 0):
_writeLatestVersionFile(__file)
try:
f = open(__file, "r")
except Exception:
print(
f"Unable to open {__file} file for reading. Will not check for new HTMD versions."
)
return
latestversions = f.readlines()
f.close()
if len(latestversions) != 2:
print(
f"There is something wrong with your {__file} file. Will not check for new HTMD versions."
)
return
currver = version()
if currver != "unpackaged":
if _is_stable(currver):
pieces = latestversions[0].split()
latest = pieces[0].strip()
verstring = "stable"
else:
pieces = latestversions[1].split()
latest = pieces[0].strip()
verstring = "devel"
pydeps = ""
if len(pieces) > 1:
pydeps = f" python[{pieces[1]}]"
elif currver == "unpackaged":
pass
else:
return
if currver != "unpackaged" and natsorted((latest, currver))[1] != currver:
print(
f"New {verstring} HTMD version ({latest}{pydeps}) is available. You are currently on ({currver})."
"There are several methods to update:"
f" - Create a new conda env. using `conda create -n htmd{latest} htmd={latest} -c acellera -c conda-forge`"
" - Create a brand new conda installation and run `conda install htmd -c acellera -c conda-forge`"
" - Run: `conda update htmd -c acellera -c conda-forge` (NOT RECOMMENDED!)"
)
else:
if currver != "unpackaged":
print(f"You are on the latest HTMD version ({currver}).")
else:
from htmd.home import home
print(
f"You are on the latest HTMD version ({currver} : {home()}).")
print("")
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except:
print('Unable to create {} folder. Will not check for new HTMD versions.'.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
# Check if one day has passed since last version check. If yes, get new version and write to file
if not os.path.isfile(__file) or time.time() > os.path.getmtime(__file) + 86400 or os.stat(__file).st_size == 0:
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print('Unable to open {} file for reading. Will not check for new HTMD versions.'.format(__file))
return
latestversions = f.readlines()
f.close()
if len(latestversions) != 2:
print('There is something wrong with your {} file. Will not check for new HTMD versions.'.format(__file))
return
currver = version()
if currver != 'unpackaged':
if _is_stable(currver):
pieces = latestversions[0].split()
latest = pieces[0].strip()
verstring = 'stable'
else:
pieces = latestversions[1].split()
latest = pieces[0].strip()
verstring = 'devel'
pydeps = ''
if len(pieces) > 1:
pydeps = ' python[{}]'.format(pieces[1])
elif currver == 'unpackaged':
pass
else:
return
if currver != 'unpackaged' and natsorted((latest, currver))[1] != currver:
print('New {} HTMD version ({}{}) is available. You are currently on ({}). Use \'conda update -c '
'acellera htmd\' to update to the new version. You might need to update your python version as well '
'if there is no release for your current version.'.format(verstring, latest, pydeps, currver))
else:
if currver != 'unpackaged':
print('You are on the latest HTMD version ({}).'.format(currver))
else:
from htmd.home import home
print('You are on the latest HTMD version ({} : {}).'.format(currver, home()))
print("")
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except:
print(
'Unable to create {} folder. Will not check for new HTMD versions.'
.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
# Check if one day has passed since last version check. If yes, get new version and write to file
if not os.path.isfile(
__file) or time.time() > os.path.getmtime(__file) + 86400:
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print(
'Unable to open {} file for reading. Will not check for new HTMD versions.'
.format(__file))
return
latestversions = f.readlines()
f.close()
currver = version()
if currver != 'unpackaged' and len(
latestversions
) == 2: # Supporting users which still haven't passed the one day limit. Can remove in next
if _is_stable(currver):
latest = latestversions[0].strip()
verstring = 'stable'
else:
latest = latestversions[1].strip()
verstring = 'devel'
elif len(
latestversions
) == 1: # Supporting users which still haven't passed the one day limit. Can remove in next version
latest = latestversions[0].strip()
verstring = ''
elif currver == 'unpackaged':
pass
else:
return
if currver != 'unpackaged' and natsorted((latest, currver))[1] != currver:
print(
'New {} HTMD version ({}) is available. You are currently on ({}). Use \'conda update htmd\' to '
'update to the new version.'.format(verstring, latest, currver))
else:
if currver != 'unpackaged':
print('You are on the latest HTMD version ({}).'.format(currver))
else:
from htmd import home
print('You are on the latest HTMD version ({} : {}).'.format(
currver, home()))
def compareVersions():
from htmd.version import version
from natsort import natsorted
import os
import time
from os.path import expanduser
__home = expanduser("~")
__htmdconf = os.path.join(__home, '.htmd')
if not os.path.exists(__htmdconf):
try:
os.makedirs(__htmdconf)
except:
print(
'Unable to create {} folder. Will not check for new HTMD versions.'
.format(__htmdconf))
return
__file = os.path.join(__htmdconf, '.latestversion')
# Check if one day has passed since last version check. If yes, get new version and write to file
if not os.path.isfile(__file) or time.time(
) > os.path.getmtime(__file) + 86400 or os.stat(__file).st_size == 0:
_writeLatestVersionFile(__file)
try:
f = open(__file, 'r')
except:
print(
'Unable to open {} file for reading. Will not check for new HTMD versions.'
.format(__file))
return
latestversions = f.readlines()
f.close()
if len(latestversions) != 2:
print(
'There is something wrong with your {} file. Will not check for new HTMD versions.'
.format(__file))
return
currver = version()
if currver != 'unpackaged':
if _is_stable(currver):
pieces = latestversions[0].split()
latest = pieces[0].strip()
verstring = 'stable'
else:
pieces = latestversions[1].split()
latest = pieces[0].strip()
verstring = 'devel'
pydeps = ''
if len(pieces) > 1:
pydeps = ' python[{}]'.format(pieces[1])
elif currver == 'unpackaged':
pass
else:
return
if currver != 'unpackaged' and natsorted((latest, currver))[1] != currver:
print(
'New {verstring} HTMD version ({latest}{pydeps}) is available. You are currently on ({currver}).'
'There are several methods to update:'
' - Create a new conda env. using `conda create -n htmd{latest} htmd={latest} -c acellera -c psi4`'
' - Create a brand new conda installation and run `conda install htmd -c acellera -c psi4`'
' - Run: `conda update htmd -c acellera -c psi4` (NOT RECOMMENDED)'
''.format(verstring=verstring,
latest=latest,
pydeps=pydeps,
currver=currver))
else:
if currver != 'unpackaged':
print('You are on the latest HTMD version ({}).'.format(currver))
else:
from htmd.home import home
print('You are on the latest HTMD version ({} : {}).'.format(
currver, home()))
print("")