Fix a few typos.

PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab

README.md

@@ -107,7 +107,7 @@ $DOWNLOAD_DIR/                             # Total: ~ 2.2 TB (download: 438 GB)
         mmcif_files/
             # About 180,000 .cif files.
         obsolete.dat
-    small_fbd/                             # ~ 17 GB (download: 9.6 GB)
+    small_bfd/                             # ~ 17 GB (download: 9.6 GB)
         bfd-first_non_consensus_sequences.fasta
     uniclust30/                            # ~ 86 GB (download: 24.9 GB)
         uniclust30_2018_08/

alphafold/common/protein.py

@@ -194,7 +194,7 @@ def ideal_atom_mask(prot: Protein) -> np.ndarray:
 
   `Protein.atom_mask` typically is defined according to the atoms that are
   reported in the PDB. This function computes a mask according to heavy atoms
-  that should be present in the given seqence of amino acids.
+  that should be present in the given sequence of amino acids.
 
   Args:
     prot: `Protein` whose fields are `numpy.ndarray` objects.

alphafold/data/templates.py

@@ -885,7 +885,7 @@ class TemplateHitFeaturizer:
         errors.append(result.error)
 
       # There could be an error even if there are some results, e.g. thrown by
-      # other unparseable chains in the same mmCIF file.
+      # other unparsable chains in the same mmCIF file.
       if result.warning:
         warnings.append(result.warning)
 

alphafold/model/all_atom.py

@@ -578,10 +578,10 @@ def extreme_ca_ca_distance_violations(
     residue_index: jnp.ndarray,  # (N)
     max_angstrom_tolerance=1.5
     ) -> jnp.ndarray:
-  """Counts residues whose Ca is a large distance from its neighbor.
+  """Counts residues whose Ca is a large distance from its neighbour.
 
-  Measures the fraction of CA-CA pairs between consectutive amino acids that
-  are more than 'max_angstrom_tolerance' apart.
+  Measures the fraction of CA-CA pairs between consecutive amino acids that are
+  more than 'max_angstrom_tolerance' apart.
 
   Args:
     pred_atom_positions: Atom positions in atom37/14 representation

alphafold/model/tf/protein_features.py

@@ -93,7 +93,7 @@ def shape(feature_name: str,
 
   Args:
     feature_name: String identifier for the feature. If the feature name ends
-      with "_unnormalized", theis suffix is stripped off.
+      with "_unnormalized", this suffix is stripped off.
     num_residues: The number of residues in the current domain - some elements
       of the shape can be dynamic and will be replaced by this value.
     msa_length: The number of sequences in the multiple sequence alignment, some

docker/Dockerfile

@@ -42,7 +42,7 @@ RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh
     && popd \
     && rm -rf /tmp/hh-suite
 
-# Install Miniconda package manger.
+# Install Miniconda package manager.
 RUN wget -q -P /tmp \
   https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \