From 6baaa6950ce23693ef34948f460ae09315a4af6e Mon Sep 17 00:00:00 2001 From: Augustin Zidek Date: Wed, 14 Apr 2021 14:07:38 +0100 Subject: [PATCH] Fix documentation issue reported in https://github.com/deepmind/deepmind-research/issues/200. PiperOrigin-RevId: 368415190 --- alphafold_casp13/README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/alphafold_casp13/README.md b/alphafold_casp13/README.md index 7f63b65..73dd348 100644 --- a/alphafold_casp13/README.md +++ b/alphafold_casp13/README.md @@ -342,12 +342,16 @@ def extract_hmm_profile(hhm_file, sequence, asterisks_replace=0.0): # The first and the last values in line_values are metadata, skip them. for j, t in enumerate(line_values[2:-1]): aa_profile[count_aa, j] = ( - 2**(-float(t) / 1000.) if t != '*' else asterisks_replace) + 2**(-float(t) / 1000.0) if t != '*' else asterisks_replace) count_aa += 1 elif len(line_values) == 10: for j, t in enumerate(line_values): - gap_profile[count_gap, j] = ( - 2**(-float(t) / 1000.) if t != '*' else asterisks_replace) + if j <= 6: + gap_profile[count_gap, j] = ( + 2**(-float(t) / 1000.0) if t != '*' else asterisks_replace) + else: + # Neff_M, Neff_I, and Neff_D are given in units of 0.001. + gap_profile[count_gap, j] = float(t) / 1000.0 count_gap += 1 elif not line_values: pass