def test_mapall(self):
try:
qfep = os.path.join(os.environ["QBIN_DIR"], "Qfep6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qmapping/testrep1", "data/qmapping/testrep2",
"data/qmapping/testrep3"
]
qmapper_parms = {
"mapdirs": dirs,
"hij": 100.0,
"alpha": 10.0,
"nthreads": 1,
"temperature": 298.0,
"points_skip": 1,
"minpts_bin": 1,
"gap_bins": 20,
"qfep_exec": qfep,
"en_list_fn": "q_enfiles.list",
"gas_const": 0.0019872041
}
qmapper = QMapper(**qmapper_parms)
try:
qmapper.mapall()
except KeyboardInterrupt:
qmapper.kill_event.set()
raise
for md, (qfep_inp, qfep_out) in six.iteritems(qmapper.mapped):
fn = "data/qmapping/qfep_" + os.path.basename(md) + ".inp"
#open(fn, "w").write(qfep_inp)
assert open(fn, "r").read() == qfep_inp
qfep_out = re.sub(".*Number of energy files",
"Number of energy files", qfep_out, 0, re.DOTALL)
fn = "data/qmapping/qfep_" + os.path.basename(md) + ".out"
#open(fn, "w").write(qfep_out)
qfep_out = re.sub(" +", " ", qfep_out)
ref_out = open(fn, "r").read()
ref_out = re.sub(" +", " ", ref_out)
assert ref_out == qfep_out
def test_mapall(self):
try:
qfep = os.path.join(os.environ["QBIN_DIR"], "Qfep6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qmapping/testrep1", "data/qmapping/testrep2",
"data/qmapping/testrep3"
]
qmapper_parms = {
"mapdirs": dirs,
"hij": 100.0,
"alpha": 10.0,
"nthreads": 1,
"temperature": 298.0,
"points_skip": 1,
"minpts_bin": 1,
"gap_bins": 20,
"qfep_exec": qfep,
"en_list_fn": "q_enfiles.list",
"gas_const": 0.0019872041
}
qmapper = QMapper(**qmapper_parms)
try:
qmapper.mapall()
except KeyboardInterrupt:
qmapper.kill_event.set()
raise
assert qmapper.input_parms_str == \
"q_mapper.py 100.0 10.0 --bins 20 --skip 1 --min 1 --temp 298.0 "
for md, (qfep_inp, qfep_out) in qmapper.mapped.iteritems():
fn = "data/qmapping/qfep_" + os.path.basename(md) + ".inp"
#open(fn, "w").write(qfep_inp)
assert open(fn, "r").read() == qfep_inp
fn = "data/qmapping/qfep_" + os.path.basename(md) + ".out"
#open(fn, "w").write(qfep_out)
assert open(fn, "r").read() == re.sub("Current .*", "", qfep_out)
def test_fit_to_reference(self):
try:
qfep = os.path.join(os.environ["QBIN_DIR"], "Qfep6")
except KeyError:
raise Exception("QBIN_DIR environment variable not defined.")
dirs = [
"data/qmapping/testrep1", "data/qmapping/testrep2",
"data/qmapping/testrep3"
]
qmapper_parms = {
"mapdirs": dirs,
"hij": 0.0,
"alpha": 0.0,
"nthreads": 1,
"temperature": 298.0,
"points_skip": 1,
"minpts_bin": 1,
"gap_bins": 50,
"qfep_exec": qfep,
"en_list_fn": "q_enfiles.list",
"gas_const": 0.0019872041
}
qmapper = QMapper(**qmapper_parms)
try:
qmapper.fit_to_reference(12, -5, 10, 0.001, 10)
except KeyboardInterrupt:
qmapper.kill_event.set()
raise
assert is_close(qmapper.parms["hij"], 82.120105)
assert is_close(qmapper.parms["alpha"], 4.567082)
assert is_close(qmapper.parms["gas_const"], 0.0019872041)
assert is_close(qmapper.parms["temperature"], 298.0)
assert qmapper.parms["gap_bins"] == 50
assert qmapper.parms["points_skip"] == 1
assert qmapper.parms["minpts_bin"] == 1
def main():
logger = init_logger('Qpyl')
parser = argparse.ArgumentParser(description="""
Fits EVB parameters Hij and alpha to reproduce
reference activation and reaction free energies.
By default, all subdirectories in current dir will be used
for mapping, or current dir if no subdirs are found.
This can be changed with --dirs.
Initial guess values for Hij and alpha should be relatively close to
their correct values (+-50) otherwise qfep crashes. If it doesn't converge,
change the step size (--step), number of iterations (--iter) or the threshold
(--threshold).
""",
add_help=False)
reqarg = parser.add_argument_group("Required")
reqarg.add_argument("ref_dga",
type=float,
help="Reference activation free energy.")
reqarg.add_argument("ref_dg0",
type=float,
help="Reference reaction free energy.")
reqarg.add_argument("init_hij",
type=float,
help="Initial guess for Hij (offdiagonal)")
reqarg.add_argument("init_alpha",
type=float,
help="Initial guess for alpha (state 2 shift)")
optarg = parser.add_argument_group("Optional")
optarg.add_argument("--nt",
dest='nthreads',
type=int,
default=QScfg.get("mapping", "nthreads"),
help="Number of threads (default = {})"
"".format(QScfg.get("mapping", "nthreads")))
optarg.add_argument("--bins",
dest="gap_bins",
type=int,
default=QScfg.get("mapping", "gap_bins"),
help="Number of gap-bins (default={})."
"".format(QScfg.get("mapping", "gap_bins")))
optarg.add_argument("--skip",
dest="points_skip",
type=int,
default=QScfg.get("mapping", "points_skip"),
help="Number of points to skip in each frame "
"(default={})."
"".format(QScfg.get("mapping", "points_skip")))
optarg.add_argument("--min",
dest="minpts_bin",
type=int,
default=QScfg.get("mapping", "minpts_bin"),
help="Minimum points for gap-bin (default={})."
"".format(QScfg.get("mapping", "minpts_bin")))
optarg.add_argument("--temp",
dest="temperature",
type=float,
default=QScfg.get("mapping", "temperature"),
help="Temperature (default={})."
"".format(QScfg.get("mapping", "temperature")))
optarg.add_argument("--dirs",
nargs="+",
dest="mapdirs",
default=[],
help="Directories to map (default=all subdirs "
"in cwd that contain the energy-files list {})."
"".format(QScfg.get("files", "en_list_fn")))
optarg.add_argument("--out",
dest="outfile",
default=QScfg.get("files", "automapper_log"),
help="Logfile name (default={})."
"".format(QScfg.get("files", "automapper_log")))
_args, _, _, _defaults = inspect.getargspec(QMapper.fit_to_reference)
defs = dict(zip(_args[-len(_defaults):], _defaults))
optarg.add_argument("--step",
dest="step_size",
type=float,
help="Step size (default={})."
"".format(defs["step_size"]),
default=defs["step_size"])
optarg.add_argument("--threshold",
dest="threshold",
type=float,
help="Convergence threshold for dG# and dG0 "
"(default={}).".format(defs["threshold"]),
default=defs["threshold"])
optarg.add_argument("--iter",
dest="max_iterations",
type=int,
help="Max number of iterations (default={})."
"".format(defs["max_iterations"]),
default=defs["max_iterations"])
optarg.add_argument("--nosingle",
dest="nosingle",
action="store_true",
help="Do not run the first iteration on only 1 dir.")
optarg.add_argument("--qfep_exec",
dest="qfep_exec",
default=QScfg.get("qexec", "qfep"),
help="qfep executable path (default={})."
"".format(QScfg.get("qexec", "qfep")))
optarg.add_argument("-v",
"--version",
action="version",
version=get_version_full())
optarg.add_argument("-h",
"--help",
action="help",
help="show this help "
" message and exit")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
print """\
Attempting to fit to dG# = {} and dG0 = {}
(stepsize = {}, threshold = {}, max iterations = {})
""".format(args.ref_dga, args.ref_dg0, args.step_size, args.threshold,
args.max_iterations)
mapdirs = args.mapdirs
# if mapping directories were not passed in as an argument,
# store all directories in the current folder
if not mapdirs:
lsdir = os.listdir(os.getcwd())
mapdirs = [md for md in lsdir if os.path.isdir(md)]
mapdirs.sort()
# if there are no folders in the current working directory,
# map just the current one
if not mapdirs:
mapdirs = [
os.getcwd(),
]
print "No subdirectories. Mapping files in current directory only."
else:
print "Will use these directories for mapping (use --dirs to "\
"change this): {}".format(", ".join(mapdirs))
qmapper_parms = {
"hij": args.init_hij,
"alpha": args.init_alpha,
"nthreads": args.nthreads,
"temperature": args.temperature,
"points_skip": args.points_skip,
"minpts_bin": args.minpts_bin,
"gap_bins": args.gap_bins,
"qfep_exec": args.qfep_exec,
"en_list_fn": QScfg.get("files", "en_list_fn"),
"gas_const": QScfg.get("mapping", "gas_const")
}
# automap with only the first replica (when we have 3 or more)
# to get a better init guess quickly
if not args.nosingle and len(mapdirs) > 2:
print "\nInitial fit, using only the first folder (disable this "\
"with --nosingle)."
# create QMapper instance with all arguments
qmapper_parms["mapdirs"] = mapdirs[:1]
qmapper_single = QMapper(**qmapper_parms)
try:
qmapper_single.fit_to_reference(args.ref_dga,
args.ref_dg0,
step_size=args.step_size,
threshold=args.threshold,
max_iterations=1)
except QMapperError:
print "...failed, will try with all dirs anyhow..."
except KeyboardInterrupt:
qmapper_single.kill_event.set()
raise
else:
qmapper_parms.update({
"hij": qmapper_single.parms["hij"],
"alpha": qmapper_single.parms["alpha"]
})
print "\nSwitching to all directories..."
qmapper_parms["mapdirs"] = mapdirs
qmapper = QMapper(**qmapper_parms)
try:
rcode = qmapper.fit_to_reference(args.ref_dga,
args.ref_dg0,
step_size=args.step_size,
threshold=args.threshold,
max_iterations=args.max_iterations)
except QMapperError as error_msg:
print "\nMassive fail:\n{}\n".format(error_msg)
sys.exit(1)
except KeyboardInterrupt:
qmapper.kill_event.set()
raise
if not rcode:
print "Did not converge. Try changing the step (--step), increasing "\
"number of iterations (--iter) or raising the threshold "\
"(--threshold)\n"
else:
print """
Well done! Use this on your non-reference simulations:
{}
""".format(qmapper.input_parms_str)
# write out the inputs and outputs from the last step
qfep_inp_fn = QScfg.get("files", "qfep_inp")
qfep_out_fn = QScfg.get("files", "qfep_out")
for mapdir, (qfep_inp_str, qfep_out_str) in qmapper.mapped.iteritems():
qfep_inp = os.path.join(mapdir, qfep_inp_fn)
qfep_out = os.path.join(mapdir, qfep_out_fn)
open(qfep_inp, "w").write(qfep_inp_str)
open(qfep_out, "w").write(qfep_out_str)
# analyse the outputs
output_files = [os.path.join(md, qfep_out_fn) for md in qmapper.mapped]
qafs = QAnalyseFeps(output_files)
fails = "\n".join([
"{}: {}".format(qfo, err) for qfo, err in qafs.failed.iteritems()
])
outstr = """
{mapper_details}
Analysis Stats:
{analysis_stats}
Analysis Fails:
{analysis_fails}
""".format(mapper_details=qmapper.details,
analysis_stats=qafs.stats_str,
analysis_fails=fails or "None")
if fails or qmapper.failed:
print """
WARNING! Some dirs failed to map/analyse! Look at the log!
"""
print "Writting out the logfile..."
backup = backup_file(args.outfile)
if backup:
print "# Backed up '{}' to '{}'".format(args.outfile, backup)
open(args.outfile, "w").write(outstr)
print "Wrote '{}'...".format(args.outfile)
def main():
logger = init_logger('Qpyl')
parser = argparse.ArgumentParser(description="""
Command-line interface for mapping EVB (or just plain old FEP) simulations
with QFep. At the moment, supports only single Hij (constant) and alpha.
For FEP, use Hij=alpha=0.
By default, all subdirectories in current dir will be used
for mapping, or current dir if no subdirs are found.
This can be changed with --dirs.
""",
add_help=False)
reqarg = parser.add_argument_group("Required")
reqarg.add_argument("hij", type=float, help="Hij coupling constant")
reqarg.add_argument("alpha", type=float, help="state 2 shift (alpha)")
optarg = parser.add_argument_group("Optional")
optarg.add_argument("--nt",
dest='nthreads',
type=int,
default=QScfg.get("mapping", "nthreads"),
help="Number of threads (default = {})"
"".format(QScfg.get("mapping", "nthreads")))
optarg.add_argument("--bins",
dest="gap_bins",
type=int,
default=QScfg.get("mapping", "gap_bins"),
help="Number of gap-bins (default={})."
"".format(QScfg.get("mapping", "gap_bins")))
optarg.add_argument("--skip",
dest="points_skip",
type=int,
default=QScfg.get("mapping", "points_skip"),
help="Number of points to skip in each frame "
"(default={})."
"".format(QScfg.get("mapping", "points_skip")))
optarg.add_argument("--min",
dest="minpts_bin",
type=int,
default=QScfg.get("mapping", "minpts_bin"),
help="Minimum points for gap-bin (default={})."
"".format(QScfg.get("mapping", "minpts_bin")))
optarg.add_argument("--temp",
dest="temperature",
type=float,
default=QScfg.get("mapping", "temperature"),
help="Temperature (default={})."
"".format(QScfg.get("mapping", "temperature")))
optarg.add_argument("--dirs",
nargs="+",
dest="mapdirs",
default=[],
help="Directories to map (default=all subdirs "
"in cwd or current dir)")
optarg.add_argument("--out",
dest="outfile",
default=QScfg.get("files", "mapper_log"),
help="Logfile name (default={})."
"".format(QScfg.get("files", "mapper_log")))
optarg.add_argument("--qfep_exec",
dest="qfep_exec",
default=QScfg.get("qexec", "qfep"),
help="qfep executable path (default={})."
"".format(QScfg.get("qexec", "qfep")))
optarg.add_argument("-v",
"--version",
action="version",
version=get_version_full())
optarg.add_argument("-h",
"--help",
action="help",
help="show this "
"help message and exit")
if len(sys.argv) == 1:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
mapdirs = args.mapdirs
# if mapping directories were not passed in as an argument,
# store all directories in the current folder
if not mapdirs:
lsdir = os.listdir(os.getcwd())
mapdirs = [md for md in lsdir if os.path.isdir(md)]
mapdirs.sort()
# if there are no folders in the current working directory,
# map just the current one
if not mapdirs:
mapdirs = [
os.getcwd(),
]
print "No subdirectories. Mapping files in current directory only."
else:
print "Will use these directories for mapping (use --dirs to "\
"change this): {}".format(", ".join(mapdirs))
qmapper_parms = {
"mapdirs": mapdirs,
"hij": args.hij,
"alpha": args.alpha,
"nthreads": args.nthreads,
"temperature": args.temperature,
"points_skip": args.points_skip,
"minpts_bin": args.minpts_bin,
"gap_bins": args.gap_bins,
"qfep_exec": args.qfep_exec,
"en_list_fn": QScfg.get("files", "en_list_fn"),
"gas_const": QScfg.get("mapping", "gas_const")
}
qmapper = QMapper(**qmapper_parms)
try:
qmapper.mapall()
except KeyboardInterrupt:
qmapper.kill_event.set()
raise
qfep_inp_fn = QScfg.get("files", "qfep_inp")
qfep_out_fn = QScfg.get("files", "qfep_out")
# write out the inputs and outputs
for mapdir, (qfep_inp_str, qfep_out_str) in qmapper.mapped.iteritems():
qfep_inp = os.path.join(mapdir, qfep_inp_fn)
qfep_out = os.path.join(mapdir, qfep_out_fn)
open(qfep_inp, "w").write(qfep_inp_str)
open(qfep_out, "w").write(qfep_out_str)
# analyse the outputs
output_files = [os.path.join(md, qfep_out_fn) for md in qmapper.mapped]
qafs = QAnalyseFeps(output_files)
outstr = """
{mapper_details}
Analysis Stats:
{analysis_stats}
Analysis Fails:
FEP: {fails}, EVB: {fails_dg}
Run q_analysefeps.py for more info...
""".format(mapper_details=qmapper.details,
analysis_stats=qafs.stats_str,
fails=len(qafs.failed) or "None",
fails_dg=len(qafs.failed_dg) or "None")
print outstr
backup = backup_file(args.outfile)
if backup:
print "# Backed up '{}' to '{}'".format(args.outfile, backup)
open(args.outfile, "w").write(outstr)
print "Wrote '{}'...".format(args.outfile)