Read a single protein state to :class:~pyhdx.models.HDXMeasurement.
Parameters:
| Name |
Type |
Description |
Default |
state |
str
|
Name of the protein state to read.
|
required
|
**kwargs |
Any
|
Additional keyword arguments passed to :class:~pyhdx.models.HDXMeasurement.
|
{}
|
Returns:
| Type |
Description |
HDXMeasurement
|
The requested :class:~pyhdx.models.HDXMeasurement.
|
Source code in pyhdx/legacy.py
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82 | def load_hdxm_v041(self, state: str, **kwargs: Any) -> HDXMeasurement:
"""Read a single protein state to :class:`~pyhdx.models.HDXMeasurement`.
Args:
state: Name of the protein state to read.
**kwargs: Additional keyword arguments passed to :class:`~pyhdx.models.HDXMeasurement`.
Returns:
The requested :class:`~pyhdx.models.HDXMeasurement`.
"""
state_dict = self.state_spec[state]
filenames = state_dict["filenames"]
df = self.load_data(*filenames)
pmt = PeptideMasterTable(
df,
drop_first=state_dict.get("drop_first", 1),
d_percentage=state_dict["d_percentage"],
)
if "control" in state_dict.keys(): # Use a FD control for back exchange correction
# todo control should be set from an external file
control_state = state_dict["control"]["state"]
exposure_value = state_dict["control"]["exposure"]["value"]
exposure_units = state_dict["control"]["exposure"]["unit"]
control_exposure = exposure_value * time_factors[exposure_units]
pmt.set_control((control_state, control_exposure))
elif "be_percent" in state_dict.keys(): # Flat back exchange percentage for all peptides\
pmt.set_backexchange(state_dict["be_percent"])
else:
raise ValueError("No valid back exchange control method specified")
temperature = state_dict["temperature"]["value"]
try:
t_offset = temperature_offsets[state_dict["temperature"]["unit"]]
except KeyError:
t_offset = temperature_offsets[state_dict["temperature"]["unit"].lower()]
temperature += t_offset
sequence = state_dict.get("sequence", "")
c_term = state_dict.get("c_term")
n_term = state_dict.get("n_term", 1)
if not (c_term or sequence):
raise ValueError("Must specify either 'c_term' or 'sequence'")
state_data = pmt.get_state(state_dict["state"])
for flt in self.data_filters:
state_data = flt(state_data)
if "name" not in kwargs:
kwargs["name"] = state
hdxm = HDXMeasurement(
state_data,
temperature=temperature,
pH=state_dict["pH"],
sequence=sequence,
n_term=n_term,
c_term=c_term,
**kwargs,
)
return hdxm
|