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Tweaks to remove a few print statements when being run from RAW. #32

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Tweaks to remove a few print statements when being run from RAW. #32

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19 changes: 12 additions & 7 deletions denss/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2537,7 +2537,7 @@ def binary_average(rhos, cores=1, thorough=True, abort_event=None, single_proc=F


def iterative_average(rhos, cycles=5, cores=1, thorough=True, abort_event=None, single_proc=False, my_logger=None,
enan=False, refrho_start=None):
enan=False, refrho_start=None, avg_queue=None):
"""
Generate a reference map using iterative alignment and averaging.

Expand All @@ -2558,12 +2558,15 @@ def iterative_average(rhos, cycles=5, cores=1, thorough=True, abort_event=None,
alignment (align_multiple).
refrho_start (np.ndarray): Optional starting reference map. If None,
the first map in rhos is used.
avg_queue (Queue): Optional queue for sending progress messages to GUI.
"""
def log_info(message):
"""Helper to print or log information."""
if avg_queue is not None:
avg_queue.put_nowait(message + '\n')
if my_logger:
my_logger.info(message)
else:
elif avg_queue is None:
print(message)

if rhos.shape[0] < 2:
Expand Down Expand Up @@ -2870,7 +2873,8 @@ def optimize_alpha(self, quiet=False):
chi2.append(chi2value)
al = np.array(al)
chi2 = np.array(chi2)
print()
if not quiet:
print()
# find optimal alpha value based on where chi2 begins to rise, to 10% above the ideal chi2
# interpolate between tested alphas to find more precise value
x = np.linspace(al[0], al[-1], 1000)
Expand Down Expand Up @@ -3973,7 +3977,7 @@ def __init__(self,
self.pdb.calculate_unique_volume()
elif self.pdb.unique_volume is None:
if not self.quiet: print("Looking up unique atomic volumes...")
self.pdb.lookup_unique_volume()
self.pdb.lookup_unique_volume(quiet=quiet)
self.pdb.unique_radius = sphere_radius_from_volume(self.pdb.unique_volume)
if radii_sf is None:
self.radii_sf = np.ones(len(self.modifiable_atom_types))
Expand Down Expand Up @@ -4197,9 +4201,9 @@ def make_grids(self):
n=nsamples)
optimal_values_warning = """
To ensure the highest accuracy, manually set the -s option to {os:.2f} and
the -v option to {ov:.2f}, which will set -n option to {on:d} and thus
the -v option to {ov:.2f}, which will set -n option to {on:d} and thus
may take a long time to calculate and use a lot of memory.
If that requires too much computation, set -s first, and -n to the
If that requires too much computation, set -s first, and -n to the
limit you prefer (n=512 may approach an upper limit for many computers).
""".format(os=optimal_side, ov=optimal_voxel, on=optimal_nsamples)

Expand Down Expand Up @@ -4347,7 +4351,8 @@ def calculate_hydration_shell(self):
self.water_shell_idx = water_shell_idx = uniform_shell.astype(bool)

if self.dx > 2 * self.r_water and self.shell_type == "water":
print("Voxel size too large for water form factor hydration shell. Changing shell type to uniform.")
if not self.quiet:
print("Voxel size too large for water form factor hydration shell. Changing shell type to uniform.")
self.shell_type = "uniform"

if self.shell_mrcfile is not None:
Expand Down