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update ruff and apply
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@DomFijan
DomFijan committed Apr 9, 2024
1 parent 3682c9e commit 00fa040
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Showing 4 changed files with 1,003 additions and 73 deletions.
2 changes: 1 addition & 1 deletion .ruff.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,4 +63,4 @@ ignore = [
convention = "google"

[format]
quote-style = "double"
quote-style = "double"
17 changes: 10 additions & 7 deletions ConservedWaterSearch/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,8 @@ def _check_mpl_installation():
try:
import matplotlib.pyplot as plt
except ModuleNotFoundError:
raise Exception(
"install matplotlib using conda install -c conda-forge matplotlib or pip install matplotlib"
)
msg = "install matplotlib using conda install -c conda-forge matplotlib or pip install matplotlib"
raise Exception(msg)
return plt


Expand Down Expand Up @@ -137,8 +136,9 @@ def get_orientations_from_positions(
a: np.ndarray = h1 - o
b: np.ndarray = h2 - o
if (np.linalg.norm(h1 - o) > 1.2) or (np.linalg.norm(h2 - o) > 1.2):
msg = "bad input HO bonds in water longer than 1.2A; value:"
raise ValueError(
"bad input HO bonds in water longer than 1.2A; value:",
msg,
np.linalg.norm(h1 - o),
np.linalg.norm(h2 - o),
)
Expand All @@ -148,7 +148,8 @@ def get_orientations_from_positions(
H2orientdata: np.ndarray = np.asarray(v2)
return Odata, H1orientdata, H2orientdata
else:
raise Exception("Hydrogen array of wrong length")
msg = "Hydrogen array of wrong length"
raise Exception(msg)


def _make_protein_surface_with_ligand():
Expand Down Expand Up @@ -667,7 +668,8 @@ def _initialize_pymol(reinitialize: bool, finish: bool):
import pymol
from pymol import cmd
except ModuleNotFoundError:
raise Exception("pymol not installed. Either install pymol or use nglview")
msg = "pymol not installed. Either install pymol or use nglview"
raise Exception(msg)
if finish:
pymol.finish_launching(["pymol", "-q"])
if reinitialize:
Expand Down Expand Up @@ -730,7 +732,8 @@ def visualise_nglview(
try:
import nglview as ngl
except ModuleNotFoundError:
raise Exception("nglview not installed. Either install pymol or nglview")
msg = "nglview not installed. Either install pymol or nglview"
raise Exception(msg)

if aligned_protein is not None:
view: NGLWidget = ngl.show_file(aligned_protein, default_representation=False)
Expand Down
135 changes: 70 additions & 65 deletions ConservedWaterSearch/water_clustering.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,19 +65,10 @@ def __init__(
self,
nsnaps: int,
clustering_algorithm: str = "OPTICS",
water_types_to_find: list[str] = ["FCW", "HCW", "WCW"],
water_types_to_find: list[str] | None = None,
restart_after_found: bool = False,
min_samples: list[int] = None,
xis: list[float] = [
0.1,
0.05,
0.01,
0.005,
0.001,
0.0005,
0.0001,
0.00001,
],
min_samples: list[int] | None = None,
xis: list[float] | None = None,
numbpct_oxygen: float = 0.8,
normalize_orientations: bool = True,
numbpct_hyd_orient_analysis: float = 0.85,
Expand All @@ -90,9 +81,9 @@ def __init__(
HCW_angstd_cutoff: float = 17,
WCW_angstd_cutoff: float = 20,
weakly_explained: float = 0.7,
xiFCW: list[float] = [0.03],
xiHCW: list[float] = [0.05, 0.01],
xiWCW: list[float] = [0.05, 0.001],
xiFCW: list[float] | None = None,
xiHCW: list[float] | None = None,
xiWCW: list[float] | None = None,
njobs: int = 1,
verbose: int = 0,
debugO: int = 0,
Expand Down Expand Up @@ -199,10 +190,22 @@ def __init__(
``output_file`` have to be provided for clustering
restarting. Defaults to None.
"""
if xiWCW is None:
xiWCW = [0.05, 0.001]
if xiHCW is None:
xiHCW = [0.05, 0.01]
if xiFCW is None:
xiFCW = [0.03]
if water_types_to_find is None:
water_types_to_find = ["FCW", "HCW", "WCW"]
if xis is None:
xis = [0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 1e-05]
if nsnaps <= 0:
raise Exception(f"nsnaps must be positive {nsnaps}")
msg = f"nsnaps must be positive {nsnaps}"
raise Exception(msg)
if not isinstance(nsnaps, int):
raise Exception(f"nsnaps must be an integer, but its {type(nsnaps)}")
msg = f"nsnaps must be an integer, but its {type(nsnaps)}"
raise Exception(msg)
self.nsnaps: int = nsnaps
self.clustering_algorithm = clustering_algorithm
self.water_types_to_find = water_types_to_find
Expand Down Expand Up @@ -274,17 +277,8 @@ def multi_stage_reclustering(
clustering_algorithm: str = "OPTICS",
lower_minsamp_pct: float = 0.25,
every_minsamp: int = 1,
xis: list[float] = [
0.1,
0.05,
0.01,
0.005,
0.001,
0.0005,
0.0001,
0.00001,
],
whichH: list[str] = ["FCW", "HCW", "WCW"],
xis: list[float] | None = None,
whichH: list[str] | None = None,
) -> None:
"""Multi Stage ReClustering (MSRC) procedure for obtaining conserved
water molecules.
Expand Down Expand Up @@ -322,6 +316,10 @@ def multi_stage_reclustering(
allowed, or "onlyO" for oxygen clustering only.
Defaults to ["FCW", "HCW", "WCW"].
"""
if whichH is None:
whichH = ["FCW", "HCW", "WCW"]
if xis is None:
xis = [0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 1e-05]
self.restart_after_find = True
self.clustering_algorithm = clustering_algorithm
self.xis = xis
Expand All @@ -338,17 +336,8 @@ def quick_multi_stage_reclustering(
clustering_algorithm: str = "OPTICS",
lower_minsamp_pct: float = 0.25,
every_minsamp: int = 1,
xis: list[float] = [
0.1,
0.05,
0.01,
0.005,
0.001,
0.0005,
0.0001,
0.00001,
],
whichH: list[str] = ["FCW", "HCW", "WCW"],
xis: list[float] | None = None,
whichH: list[str] | None = None,
) -> None:
"""Quick Multi Stage ReClustering (QMSRC) procedure for
obtaining conserved water molecules.
Expand Down Expand Up @@ -387,6 +376,10 @@ def quick_multi_stage_reclustering(
allowed, or "onlyO" for oxygen clustering only.
Defaults to ["FCW", "HCW", "WCW"].
"""
if whichH is None:
whichH = ["FCW", "HCW", "WCW"]
if xis is None:
xis = [0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 1e-05]
self.restart_after_find = False
self.clustering_algorithm = clustering_algorithm
self.xis = xis
Expand All @@ -403,7 +396,7 @@ def single_clustering(
clustering_algorithm: str = "OPTICS",
minsamp: int | None = None,
xi: float | None = None,
whichH: list[str] = ["FCW", "HCW", "WCW"],
whichH: list[str] | None = None,
) -> None:
"""Single clustering procedure.
Expand Down Expand Up @@ -432,6 +425,8 @@ def single_clustering(
allowed, or "onlyO" for oxygen clustering only.
Defaults to ["FCW", "HCW", "WCW"].
"""
if whichH is None:
whichH = ["FCW", "HCW", "WCW"]
self.restart_after_find = False
self.clustering_algorithm = clustering_algorithm
self.water_types_to_find = whichH
Expand Down Expand Up @@ -489,14 +484,16 @@ def restart_cluster(
H1 = data[:, 3:6]
H2 = data[:, 6:9]
else:
raise Exception("data file not found")
msg = "data file not found"
raise Exception(msg)
if os.path.isfile(partial_results_file):
self.read_and_set_water_clust_options(partial_results_file)
self._water_type, self._waterO, self._waterH1, self._waterH2 = read_results(
partial_results_file
)
else:
raise Exception("partial results file not found")
msg = "partial results file not found"
raise Exception(msg)
self.run(Odata, H1, H2)

def read_and_set_water_clust_options(self, file_name: str) -> None:
Expand Down Expand Up @@ -539,7 +536,8 @@ def read_and_set_water_clust_options(self, file_name: str) -> None:
self.plotreach = lines[25] == "True"
self.plotend = lines[26] == "True"
else:
raise Exception("output file not found")
msg = "output file not found"
raise Exception(msg)

@classmethod
def create_from_file(
Expand Down Expand Up @@ -1040,24 +1038,24 @@ def _delete_data(
return Odata, H1, H2

def _check_cls_alg_and_whichH(self):
if (
self.clustering_algorithm != "OPTICS"
and self.clustering_algorithm != "HDBSCAN"
):
raise Exception("clustering algorithm must be OPTICS or HDBSCAN")
if self.clustering_algorithm not in ("OPTICS", "HDBSCAN"):
msg = "clustering algorithm must be OPTICS or HDBSCAN"
raise Exception(msg)
for i in self.water_types_to_find:
if i not in ["FCW", "HCW", "WCW", "onlyO"]:
raise Exception(
"whichH supports onlyO or any combination of FCW, HCW and WCW"
)
msg = "whichH supports onlyO or any combination of FCW, HCW and WCW"
raise Exception(msg)
if "onlyO" in self.water_types_to_find and len(self.water_types_to_find) > 1:
raise Exception("onlyO cannot be used with other water types")
msg = "onlyO cannot be used with other water types"
raise Exception(msg)
if self.clustering_algorithm == "OPTICS":
for i in self.xis:
if not isinstance(i, float):
raise Exception("xis must contain floats")
msg = "xis must contain floats"
raise Exception(msg)
if i > 1 or i < 0:
raise Exception("xis should be between 0 and 1")
msg = "xis should be between 0 and 1"
raise Exception(msg)
elif self.clustering_algorithm == "HDBSCAN":
self.xis = [0.0]
# sort min_samples in descending order
Expand All @@ -1068,24 +1066,31 @@ def _check_and_setup_single(self, xis, minsamp):
if minsamp is None:
minsamp = int(self.numbpct_oxygen * self.nsnaps)
elif not isinstance(minsamp, int):
raise Exception("minsamp must be an int")
msg = "minsamp must be an int"
raise Exception(msg)
elif minsamp > self.nsnaps or minsamp <= 0:
raise Exception("minsamp must be between 0 and nsnaps")
msg = "minsamp must be between 0 and nsnaps"
raise Exception(msg)
if xis is None:
xis = 0.05
elif not isinstance(xis, float):
raise Exception("xi must be a float")
msg = "xi must be a float"
raise Exception(msg)
elif xis < 0 or xis > 1:
raise Exception("xis should be between 0 and 1")
msg = "xis should be between 0 and 1"
raise Exception(msg)
return [minsamp], [xis]

def _check_and_setup_MSRC(self, lower_minsamp_pct, every_minsamp):
if lower_minsamp_pct > 1.0000001 or lower_minsamp_pct < 0:
raise Exception("lower_misamp_pct must be between 0 and 1")
msg = "lower_misamp_pct must be between 0 and 1"
raise Exception(msg)
if not isinstance(every_minsamp, int):
raise Exception("every_minsamp must be integer")
msg = "every_minsamp must be integer"
raise Exception(msg)
if every_minsamp <= 0 or every_minsamp > self.nsnaps:
raise Exception("every_minsamp must be 0<every_minsamp<=nsnaps")
msg = "every_minsamp must be 0<every_minsamp<=nsnaps"
raise Exception(msg)
minsamps: list = list(
reversed(
range(
Expand All @@ -1099,12 +1104,12 @@ def _check_and_setup_MSRC(self, lower_minsamp_pct, every_minsamp):

def _check_data(self, Odata, H1, H2):
if (H1 is None or H2 is None) and "onlyO" not in self.water_types_to_find:
raise Exception(
f"H1 and H2 have to be provided for non oxygen only search. Run type {self.water_types_to_find}"
)
msg = f"H1 and H2 have to be provided for non oxygen only search. Run type {self.water_types_to_find}"
raise Exception(msg)
if H1 is not None and H2 is not None:
if len(Odata) != len(H1) or len(Odata) != len(H2) or len(H1) != len(H2):
raise Exception("Odata, H1 and H2 have to be of same length")
msg = "Odata, H1 and H2 have to be of same length"
raise Exception(msg)

def _save_intermediate_data(self, Oxygen, H1, H2) -> None:
if self.restart_data_file is not None:
Expand Down
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