def _get_db_options(args):
"""Parse through a command line of arguments to over-ride the values
in the users .dbrc file.
If no user name is given then the environment variable $USERNAME is
used. If $USERNAME is not defined then prompt for input.
"""
import optik, getpass, sys
from optik import OptionParser
parser = OptionParser()
parser.add_option("-d",
"--database",
action="store",
type="string",
dest="database",
default="cfht",
help="Name of the SYBASE database containing TABLE",
metavar="FILE")
parser.add_option("-u",
"--user",
action="store",
type="string",
dest="user",
default=getpass.getuser(),
help="User name to access db with",
metavar="USER")
(opt, unused_args) = parser.parse_args(args)
return opt.database, opt.user, unused_args
#* $Date: 2006/01/09 13:36:44 $
#*
#* Programmer : <your name>
#*
#* Modification History:
#*
#**** C A N A D I A N A S T R O N O M Y D A T A C E N T R E *****
# Run J-M.'s and Matt's object finding systems... then intersect the
# results.
if __name__ == '__main__':
### Must be running as a script
import optik, sys
from optik import OptionParser
parser = OptionParser()
parser.add_option("--verbose",
"-v",
action="store_true",
dest="verbose",
help="Provide feedback on what I'm doing")
parser.add_option("--triple",
"-t",
action="store",
type="int",
dest="triple",
help="Triple to search")
parser.add_option("--block",
"-b",
action="store",
default=None,
def main():
usage = "usage: %prog [options] sysName [ctp_id | rtpFileName=Run.rtp] [buildMode] [buildOpts]"
dataSource = {"db2": 0, "xml": 1, "ff": 2}
parser = OptionParser(usage)
rtpName = 'Run.rtp'
# sys_class option:
parser.add_option("-c",
"--sys_class",
type="string",
action="store",
dest="sys_class",
default="testing",
help="(scratch | [testing] | production)")
# source options:
parser.add_option("-d",
"--from-database",
action="store_const",
dest="source",
const=dataSource["db2"],
default=dataSource["db2"],
help="look for system in database")
parser.add_option("-x",
"--from-xml",
action="store_const",
dest="source",
const=dataSource["xml"],
help="look for system in xml file")
parser.add_option("-p",
"--from-package",
action="store_const",
dest="source",
const=dataSource["ff"],
help="look for system in force field files")
# force field identifier option (only used if source=package)
parser.add_option("-f",
"--forcefield",
action="store",
dest="forceField",
default="unknown",
help="define force field of system")
# system id option (only used if source=db2)
parser.add_option("-i",
"--system-id",
action="store",
dest="sysId",
default="-1",
help="identify system in db2")
# verbose/quiet options
parser.add_option("-v",
"--verbose",
action="store_true",
dest="verbose",
default="store_false",
help="sets output to be verbose")
parser.add_option("-q",
"--quiet",
action="store_false",
dest="verbose",
help="sets output to be quiet")
(options, args) = parser.parse_args()
buildMode = "Opt"
buildOpts = ''
if len(args) < 1:
parser.error("incorrect number of args")
sysName = args[0]
if len(args) == 2:
rtpName = args[1]
if len(args) == 3:
buildMode = args[2]
if len(args) == 4:
buildOpts = args[3]
if options.verbose:
print("sys_class:", options.sys_class)
print("source:", options.source)
print("rtp file:", rtpName)
print("force field:", options.forceField)
# set xml creation object based on force field setting
creator = None
if options.forceField == 'charmm':
creator = BuildUtils.createXmlForCharmm()
elif options.forceField == 'oplsaa':
creator = BuildUtils.createXmlForOplsaa()
else:
create = BuildUtils.createXml()
sysId = options.sysId
ctpId = -1
if options.source == dataSource["ff"]:
if options.verbose:
print("calling creator.fromSource()")
creator.fromSource(sysName, None, options.verbose)
if options.source == dataSource["xml"] or \
options.source == dataSource["ff"]:
if options.verbose:
print("calling BuildUtils.xml2db2(), BuildUtils.rtp2db2()")
sysId=BuildUtils.xml2db2(sysName + '.' + options.forceField, \
options.verbose)
if options.verbose:
print("sysId =", str(sysId))
if rtpName.isdigit():
ctpId = rtpName
else:
ctpId = BuildUtils.rtp2db2(rtpName, options.verbose)
if options.source == dataSource["xml"] or \
options.source == dataSource["ff"] or \
options.source == dataSource["db2"]:
if options.verbose:
print("calling BuildUtils.db2cpp(), BuildUtils.cpp2exe()")
BuildUtils.db2cpp(
str(sysName) + '.' + str(options.forceField), sysId, ctpId,
options.verbose)
BuildUtils.cpp2exe(
str(sysName) + '.' + str(options.forceField), buildMode, buildOpts,
options.verbose)
return (0)
def main():
usage = "usage: %prog [options] epsilon sigma/Rmin"
parser = OptionParser(usage)
parser.add_option("-s",
"--sigma",
action="store_true",
dest="sigma",
default="store_false",
help="sets input type of sigma/Rmin to sigma")
parser.add_option("-r",
"--rmin",
action="store_false",
dest="sigma",
default="store_false",
help="sets input type of sigma/Rmin to Rmin")
parser.add_option("-n",
"--number",
action="store",
dest="count",
default=4,
help="particle count")
parser.add_option("-c",
"--chemcomp",
action="store",
dest="chemcomp",
default="AR",
help="chemical component")
parser.add_option("-e",
"--element",
action="store",
dest="element",
default="Ar",
help="element symbol")
parser.add_option("-t",
"--atomtag",
action="store",
dest="atomtag",
default="AR_",
help="atom tag")
parser.add_option("-m",
"--mass",
action="store",
dest="mass",
default="39.948",
help="mass (amu)")
parser.add_option("-d",
"--moleculename",
action="store",
dest="moleculename",
default="Argon",
help="molecule name")
parser.add_option("-k",
"--kelvin",
action="store_true",
dest="kelvin",
default="store_false",
help="energy units in kelvin")
(options, args) = parser.parse_args()
if len(args) < 2:
parser.error("incorrect number of args")
if int(options.count) <= 0:
parser.error("Illegal value for particle number")
epsilon = args[0]
if options.kelvin:
epsilon = epsilon + "*SciConst::KBoltzmann_IU"
rMinValue = args[1]
if options.sigma:
rMinValue = rMinValue + "*SciConst::SixthRootOfTwo"
outputXmlHeaderWithDtd()
print("<ffparams>")
outputHeaderParameterList()
outputMoleculeName(options.moleculename, "SALT")
outputChemicalComponentInstanceList(int(options.count), options.chemcomp)
outputMoleculeInstanceList(int(options.count))
outputSiteList(int(options.count), options.mass, options.atomtag, epsilon,
rMinValue, options.element)
print("</ffparams>")
