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219 | class DimpleSolveParameters(ThirdPartyParameters):
"""Parameters for CCP4's dimple program.
There are many parameters. For more information on
usage, please refer to the CCP4 documentation, here:
https://ccp4.github.io/dimple/
"""
class Config(ThirdPartyParameters.Config):
"""Identical to super-class Config but includes a result."""
set_result: bool = True
"""Whether the Executor should mark a specified parameter as a result."""
result_from_params: str = ""
"""Defines a result from the parameters. Use a validator to do so."""
executable: str = Field(
"/sdf/group/lcls/ds/tools/ccp4-8.0/bin/dimple",
description="CCP4 Dimple for solving structures with MR.",
flag_type="",
)
# Positional requirements - all required.
in_file: str = Field(
"",
description="Path to input mtz.",
flag_type="",
)
pdb: str = Field("", description="Path to a PDB.", flag_type="")
out_dir: str = Field("", description="Output DIRECTORY.", flag_type="")
# Most used options
mr_thresh: PositiveFloat = Field(
0.4,
description="Threshold for molecular replacement.",
flag_type="--",
rename_param="mr-when-r",
)
slow: Optional[bool] = Field(
False, description="Perform more refinement.", flag_type="--"
)
# Other options (IO)
hklout: str = Field(
"final.mtz", description="Output mtz file name.", flag_type="--"
)
xyzout: str = Field(
"final.pdb", description="Output PDB file name.", flag_type="--"
)
icolumn: Optional[str] = Field(
# "IMEAN",
description="Name for the I column.",
flag_type="--",
)
sigicolumn: Optional[str] = Field(
# "SIG<ICOL>",
description="Name for the Sig<I> column.",
flag_type="--",
)
fcolumn: Optional[str] = Field(
# "F",
description="Name for the F column.",
flag_type="--",
)
sigfcolumn: Optional[str] = Field(
# "F",
description="Name for the Sig<F> column.",
flag_type="--",
)
libin: Optional[str] = Field(
description="Ligand descriptions for refmac (LIBIN).", flag_type="--"
)
refmac_key: Optional[str] = Field(
description="Extra Refmac keywords to use in refinement.",
flag_type="--",
rename_param="refmac-key",
)
free_r_flags: Optional[str] = Field(
description="Path to a mtz file with freeR flags.",
flag_type="--",
rename_param="free-r-flags",
)
freecolumn: Optional[Union[int, float]] = Field(
# 0,
description="Refree column with an optional value.",
flag_type="--",
)
img_format: Optional[str] = Field(
description="Format of generated images. (png, jpeg, none).",
flag_type="-",
rename_param="f",
)
white_bg: bool = Field(
False,
description="Use a white background in Coot and in images.",
flag_type="--",
rename_param="white-bg",
)
no_cleanup: bool = Field(
False,
description="Retain intermediate files.",
flag_type="--",
rename_param="no-cleanup",
)
# Calculations
no_blob_search: bool = Field(
False,
description="Do not search for unmodelled blobs.",
flag_type="--",
rename_param="no-blob-search",
)
anode: bool = Field(
False,
description="Use SHELX/AnoDe to find peaks in the anomalous map.",
flag_type="--",
)
# Run customization
no_hetatm: bool = Field(
False,
description="Remove heteroatoms from the given model.",
flag_type="--",
rename_param="no-hetatm",
)
rigid_cycles: Optional[PositiveInt] = Field(
# 10,
description="Number of cycles of rigid-body refinement to perform.",
flag_type="--",
rename_param="rigid-cycles",
)
jelly: Optional[PositiveInt] = Field(
# 4,
description="Number of cycles of jelly-body refinement to perform.",
flag_type="--",
)
restr_cycles: Optional[PositiveInt] = Field(
# 8,
description="Number of cycles of refmac final refinement to perform.",
flag_type="--",
rename_param="restr-cycles",
)
lim_resolution: Optional[PositiveFloat] = Field(
description="Limit the final resolution.", flag_type="--", rename_param="reso"
)
weight: Optional[str] = Field(
# "auto-weight",
description="The refmac matrix weight.",
flag_type="--",
)
mr_prog: Optional[str] = Field(
# "phaser",
description="Molecular replacement program. phaser or molrep.",
flag_type="--",
rename_param="mr-prog",
)
mr_num: Optional[Union[str, int]] = Field(
# "auto",
description="Number of molecules to use for molecular replacement.",
flag_type="--",
rename_param="mr-num",
)
mr_reso: Optional[PositiveFloat] = Field(
# 3.25,
description="High resolution for molecular replacement. If >10 interpreted as eLLG.",
flag_type="--",
rename_param="mr-reso",
)
itof_prog: Optional[str] = Field(
description="Program to calculate amplitudes. truncate, or ctruncate.",
flag_type="--",
rename_param="ItoF-prog",
)
@validator("in_file", always=True)
def validate_in_file(cls, in_file: str, values: Dict[str, Any]) -> str:
if in_file == "":
get_hkl_file: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "ManipulateHKL", "out_file"
)
if get_hkl_file:
return get_hkl_file
return in_file
@validator("out_dir", always=True)
def validate_out_dir(cls, out_dir: str, values: Dict[str, Any]) -> str:
if out_dir == "":
get_hkl_file: Optional[str] = read_latest_db_entry(
f"{values['lute_config'].work_dir}", "ManipulateHKL", "out_file"
)
if get_hkl_file:
return os.path.dirname(get_hkl_file)
return out_dir
@root_validator(pre=False)
def define_result(cls, values: Dict[str, Any]) -> Dict[str, Any]:
out_dir: str = values["out_dir"]
result: str
if out_dir != "":
result = f"{out_dir}/final.mtz;{out_dir}/final.pdb"
else:
result = ""
cls.Config.result_from_params = result
return values
|