def add_parser(subparsers, *args, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*subparsers*: argparse subparsers object to add subparser
:*args*: Passed to subparsers.add_parser(...)
:*kwargs*: Passed to subparsers.add_parser(...)
"""
from MDclt import overridable_defaults
subparser = secondary.add_parser(subparsers,
name = "association",
help = "Analyzes molecular association")
arg_groups = {ag.title:ag for ag in subparser._action_groups}
arg_groups["input"].add_argument(
"-log",
type = str,
required = True,
nargs = "+",
metavar = ("H5_FILE", "ADDRESS"),
action = overridable_defaults(nargs = 2, defaults = {1: "log"}),
help = "H5 file and optionally address from which to load " +
"simulation log (default ADDRESS: log)")
arg_groups["input"].add_argument(
"-coord",
type = str,
required = True,
nargs = 2,
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load coordinate")
arg_groups["action"].add_argument(
"-bound",
type = float,
required = True,
help = "Bound state cutoff along coordinate")
arg_groups["action"].add_argument(
"-unbound",
type = float,
required = True,
help = "Unbound state cutoff along coordinate")
arg_groups["output"].add_argument(
"-output",
type = str,
required = True,
metavar = "H5_FILE",
help = "H5 file in which to output data")
subparser.set_defaults(analysis = command_line)
def add_parser(tool_subparsers, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*tool_subparsers*: Argparse subparsers object to add subparser
:*args*: Passed to tool_subparsers.add_parser(...)
:*\*\*kwargs*: Passed to tool_subparsers.add_parser(...)
.. todo:
- Implement nested subparser (should be 'amber log', not just 'log')
"""
from MDclt import overridable_defaults
subparser = primary.add_parser(tool_subparsers,
name = "log",
help = "Load AMBER logs")
arg_groups = {ag.title:ag for ag in subparser._action_groups}
arg_groups["input"].add_argument(
"-frames_per_file",
type = int,
required = False,
help = "Number of frames in each file; used to check if new data " +
"is present")
arg_groups["input"].add_argument(
"-start_time",
type = float,
required = False,
help = "Time of first frame (ns) (optional)")
arg_groups["output"].add_argument(
"-output",
type = str,
required = True,
nargs = "+",
action = overridable_defaults(nargs = 2, defaults = {1: "/log"}),
help = "H5 file and optionally address in which to output data " +
"(default address: /log)")
subparser.set_defaults(analysis = command_line)
def add_parser(tool_subparsers, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*tool_subparsers*: argparse subparsers object to add subparser
:*args*: Passed to tool_subparsers.add_parser(...)
:*kwargs*: Passed to tool_subparsers.add_parser(...)
"""
from MDclt import overridable_defaults
subparser = primary.add_parser(tool_subparsers,
name = "raw",
help = "Load raw text files")
arg_groups = {ag.title: ag for ag in subparser._action_groups}
arg_groups["input"].add_argument(
"-frames_per_file",
type = int,
required = False,
help = "Number of frames in each file; used to check if new data " +
"is present")
arg_groups["input"].add_argument(
"-dimensions",
type = int,
required = False,
nargs = "*",
help = "Additional dimensions in dataset; if multidimensional " +
"(optional)")
arg_groups["output"].add_argument(
"-output",
type = str,
required = True,
nargs = "+",
action = overridable_defaults(nargs = 2, defaults = {1: "/dataset"}),
help = "H5 file and optionally address in which to output data " +
"(default address: /dataset)")
subparser.set_defaults(analysis = command_line)
def add_parser(tool_subparsers, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*tool_subparsers*: <argparse._SubParsersAction> to which to add
:*\*\*kwargs*: Passed to *subparsers*.add_parser(...)
"""
from MDclt import h5_default_path, overridable_defaults
tool_subparser = tool_subparsers.add_parser(
name = "pdist",
help = "Calculates probability density function along a coordinate")
mode_subparsers = tool_subparser.add_subparsers(
dest = "mode",
description = "")
hist_subparser = secondary.add_parser(mode_subparsers,
name = "hist",
help = "Calculates probability density function along a coordinate " +
"using a histogram")
kde_subparser = secondary.add_parser(mode_subparsers,
name = "kde",
help = "Calculates probability density function along a coordinate " +
"using a kernal density estimate")
arg_groups = {
hist_subparser:
{ag.title: ag for ag in hist_subparser._action_groups},
kde_subparser:
{ag.title: ag for ag in kde_subparser._action_groups}}
# Input
for mode_subparser in [hist_subparser, kde_subparser]:
arg_groups[mode_subparser]["input"].add_argument(
"-coord",
type = str,
required = True,
nargs = "+",
action = h5_default_path(),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load coordinate")
# Action
arg_groups[hist_subparser]["action"].add_argument(
"-frames_per_block",
type = int,
default = 128,
help = "Number of frames included in each block of analysis; " +
"may influence results of block averaging error analysis, " +
"frames_per_block is minimum potential length of block " +
"(default: %(default)s)")
arg_groups[kde_subparser]["action"].add_argument(
"-frames_per_block",
type = int,
default = 128,
help = "Number of frames included in each block of analysis; " +
"may influence results of block averaging error analysis, " +
"frames_per_block is minimum potential length of block " +
"(default: %(default)s)")
arg_groups[hist_subparser]["action"].add_argument(
"-bins",
type = str,
required = True,
metavar = "BINEXPR",
help = "Python expression used to generate bins")
arg_groups[kde_subparser]["action"].add_argument(
"-grid",
type = str,
required = True,
metavar = "GRIDEXPR",
help = "Python expression used to generate grid")
arg_groups[kde_subparser]["action"].add_argument(
"-bandwidth",
type = float,
required = True,
help = "Bandwidth of kernel density estimate")
for mode_subparser in [hist_subparser, kde_subparser]:
arg_groups[mode_subparser]["action"].add_argument(
"-zero_point",
type = str,
required = False,
help = "Point at which to shift PMF to 0; " +
"alternatively range of points (e.g. 10-12) " +
"over which to adjust average to 0 (optional)")
arg_groups[mode_subparser]["action"].add_argument(
"-temperature",
type = str,
default = 298.0,
help = "System temperature (default: %(default)s)")
# Output
for mode_subparser in [hist_subparser, kde_subparser]:
arg_groups[mode_subparser]["output"].add_argument(
"-output",
type = str,
required = True,
nargs = "+",
action = overridable_defaults(nargs = 2, defaults = {1: "/pdist"}),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and optionally address in which to output data " +
"(default ADDRESS: /pdist)")
hist_subparser.set_defaults(
analysis = command_line(Hist_Block_Generator, Hist_Block_Accumulator))
kde_subparser.set_defaults(
analysis = command_line(KDE_Block_Generator, KDE_Block_Accumulator))
def add_parser(tool_subparsers, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*tool_subparsers*: <argparse._SubParsersAction> to which to add
:*\*\*kwargs*: Passed to *tool_subparsers*.add_parser(...)
"""
from MDclt import h5_default_path, overridable_defaults
tool_subparser = secondary.add_parser(tool_subparsers,
name = "assign",
help = "Assigns states")
mode_subparsers = tool_subparser.add_subparsers(
dest = "mode",
description = "")
coord_subparser = secondary.add_parser(mode_subparsers,
name = "from_coord",
help = "Assigns states based on coordinates")
assign_subparser = secondary.add_parser(mode_subparsers,
name = "from_assign",
help = "Assigns states based on previous state assignments")
arg_groups = {
coord_subparser:
{ag.title: ag for ag in coord_subparser._action_groups},
assign_subparser:
{ag.title: ag for ag in assign_subparser._action_groups}}
# Input
arg_groups[coord_subparser]["input"].add_argument(
"-coord",
type = str,
required = True,
nargs = "+",
action = h5_default_path(),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load coordinate")
arg_groups[assign_subparser]["input"].add_argument(
"-assign",
type = str,
required = True,
nargs = "+",
action = h5_default_path(),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load state "
"assignments")
# Action
arg_groups[coord_subparser]["action"].add_argument(
"-states",
type = str,
required = True,
nargs = "+",
metavar = "NAME:{<,>}CUTOFF",
help = "State definitions")
# Output
for mode_subparser in [coord_subparser, assign_subparser]:
arg_groups[mode_subparser]["output"].add_argument(
"-output",
type = str,
required = True,
nargs = "+",
action = overridable_defaults(nargs = 2, defaults = {1:"/"}),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and optionally address in which to output data " +
"(default address: /)")
coord_subparser.set_defaults(analysis = coord_command_line)
assign_subparser.set_defaults(analysis = assign_command_line)
def add_parser(tool_subparsers, **kwargs):
"""
Adds subparser for this analysis to a nascent argument parser
**Arguments:**
:*tool_subparsers*: <argparse._SubParsersAction> to which to add
:*\*\*kwargs*: Passed to *tool_subparsers*.add_parser(...)
"""
from MDclt import h5_default_path, overridable_defaults
tool_subparser = tool_subparsers.add_parser(
name = "stateprobs",
help = "Calculates state probabilities")
mode_subparsers = tool_subparser.add_subparsers(
dest = "mode",
description = "")
pdist_subparser = secondary.add_parser(mode_subparsers,
name = "from_pdist",
help = "Calculates state probabilities using the probability "
"density function")
assign_subparser = secondary.add_parser(mode_subparsers,
name = "from_assignment",
help = "Calculates state probabilities using per-frame state " +
"assignments")
arg_groups = {
pdist_subparser:
{ag.title: ag for ag in pdist_subparser._action_groups},
assign_subparser:
{ag.title: ag for ag in assign_subparser._action_groups}}
# Input
arg_groups[pdist_subparser]["input"].add_argument(
"-pdist",
type = str,
required = True,
nargs = "+",
action = h5_default_path(),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load probability "
"density function")
arg_groups[assign_subparser]["input"].add_argument(
"-assign",
type = str,
required = True,
nargs = "+",
action = h5_default_path(),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and address from which to load state "
"assignments")
# Action
arg_groups[pdist_subparser]["action"].add_argument(
"-states",
type = str,
nargs = "+",
metavar = "NAME:{<,>}CUTOFF",
help = "State definitions")
# Output
for mode_subparser in [pdist_subparser, assign_subparser]:
arg_groups[mode_subparser]["output"].add_argument(
"-output",
type = str,
required = True,
nargs = "+",
action = overridable_defaults(nargs = 2, defaults = {1: "/"}),
metavar = ("H5_FILE", "ADDRESS"),
help = "H5 file and optionally address in which to output data " +
"(default address: /)")
pdist_subparser.set_defaults(analysis = command_line(PDist_Analyzer))
assign_subparser.set_defaults(analysis = command_line(Assign_Analyzer))