Merge pull request #331 from theGreatHerrLebert/feature/timsim-gui

Feature/timsim gui
theGreatHerrLebert · Feb 26, 2025 · 373ab62 · 373ab62
2 parents cb87b81 + 42895db
commit 373ab62
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/imspy/imspy/simulation/timsim/jobs/simulate_ion_mobilities_and_variance.py b/imspy/imspy/simulation/timsim/jobs/simulate_ion_mobilities_and_variance.py
@@ -10,7 +10,7 @@ def simulate_ion_mobilities_and_variance(
         im_upper: float,
         verbose: bool = False,
         epsilon: float = 1e-6,
-        remove_unimod_annotation: bool = False
+        remove_mods: bool = False
 ) -> pd.DataFrame:
     """Simulate ion mobilities.
 
@@ -20,7 +20,7 @@ def simulate_ion_mobilities_and_variance(
         im_upper: Upper ion mobility.
         verbose: Verbosity.
         epsilon: Epsilon value to be added to the variance.
-        remove_unimod_annotation: Remove Unimod annotation.
+        remove_mods: Remove Unimod annotation.
 
     Returns:
         pd.DataFrame: Ions DataFrame.
@@ -43,7 +43,7 @@ def simulate_ion_mobilities_and_variance(
         sequences=ions.sequence.values,
         batch=True,
         shuffle=False,
-        remove_unimod=remove_unimod_annotation,
+        remove_unimod=remove_mods,
     )
 
     ccs, ccs_std, _ = model.predict(tf_ds)

diff --git a/imspy/imspy/simulation/timsim/simulator.py b/imspy/imspy/simulation/timsim/simulator.py
@@ -486,7 +486,7 @@ def main():
 
             peptides_tmp = simulate_peptides(
                 protein_table=proteins_tmp,
-                num_peptides_total=2_000_000,
+                num_peptides_total=250_000,
                 verbose=not args.silent_mode,
                 exclude_accumulated_gradient_start=True,
                 min_rt_percent=2.0,
@@ -617,6 +617,7 @@ def main():
             im_lower=acquisition_builder.tdf_writer.helper_handle.im_lower,
             im_upper=acquisition_builder.tdf_writer.helper_handle.im_upper,
             verbose=not args.silent_mode,
+            remove_mods=True,
         )
 
         # JOB 7: Precursor isotopic distributions