From 7e3067b83b3cbe50cc840c6ec897453e64a1b1c8 Mon Sep 17 00:00:00 2001 From: Augustin Zidek <augustinzidek@google.com> Date: Tue, 19 Nov 2024 11:43:30 +0000 Subject: [PATCH] Remove unused MsaToolResult.num_hits PiperOrigin-RevId: 697929605 --- src/alphafold3/data/tools/jackhmmer.py | 6 +----- src/alphafold3/data/tools/msa_tool.py | 1 - src/alphafold3/data/tools/nhmmer.py | 7 +------ 3 files changed, 2 insertions(+), 12 deletions(-) diff --git a/src/alphafold3/data/tools/jackhmmer.py b/src/alphafold3/data/tools/jackhmmer.py index 1091a16..2b0fd36 100644 --- a/src/alphafold3/data/tools/jackhmmer.py +++ b/src/alphafold3/data/tools/jackhmmer.py @@ -137,12 +137,8 @@ class Jackhmmer(msa_tool.MsaTool): logging.info('Limiting MSA depth to %d', self.max_sequences) break a3m.append(f'>{name}\n{seq}') - num_hits = len(a3m) a3m = '\n'.join(a3m) return msa_tool.MsaToolResult( - target_sequence=target_sequence, - a3m=a3m, - e_value=self.e_value, - num_hits=num_hits, + target_sequence=target_sequence, a3m=a3m, e_value=self.e_value ) diff --git a/src/alphafold3/data/tools/msa_tool.py b/src/alphafold3/data/tools/msa_tool.py index 37c1ffa..a739f06 100644 --- a/src/alphafold3/data/tools/msa_tool.py +++ b/src/alphafold3/data/tools/msa_tool.py @@ -21,7 +21,6 @@ class MsaToolResult: target_sequence: str e_value: float a3m: str - num_hits: int class MsaTool(Protocol): diff --git a/src/alphafold3/data/tools/nhmmer.py b/src/alphafold3/data/tools/nhmmer.py index 36585e7..a4b4089 100644 --- a/src/alphafold3/data/tools/nhmmer.py +++ b/src/alphafold3/data/tools/nhmmer.py @@ -160,17 +160,12 @@ class Nhmmer(msa_tool.MsaTool): logging.info('Limiting MSA depth to %d', self._max_sequences) break a3m.append(f'>{name}\n{seq}') - num_hits = len(a3m) a3m = '\n'.join(a3m) else: # Nhmmer returns an empty file if there are no hits. # In this case return only the query sequence. - num_hits = 1 a3m = f'>query\n{target_sequence}' return msa_tool.MsaToolResult( - target_sequence=target_sequence, - e_value=self._e_value, - a3m=a3m, - num_hits=num_hits, + target_sequence=target_sequence, e_value=self._e_value, a3m=a3m ) -- GitLab