From cbb649d692b684ba2f847a226449c7c9a9ddbe46 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 27 Nov 2017 18:38:06 -0500
Subject: [PATCH] peptide encoding optimization
---
.../class1_affinity_prediction/class1_affinity_predictor.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
index 5d6df8c6..b424aaf5 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
@@ -753,7 +753,11 @@ class Class1AffinityPredictor(object):
mask = (
(df.normalized_allele == allele) &
df.supported_peptide_length).values
- if mask.sum() > 0:
+ if mask.all():
+ # Common case optimization
+ for (i, model) in enumerate(models):
+ df["model_single_%d" % i] = model.predict(peptides)
+ elif mask.sum() > 0:
allele_peptides = EncodableSequences.create(
df.ix[mask].peptide.values)
for (i, model) in enumerate(models):
--
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