add multimer inference (#59)

* add multimer inference

* add dada pipeline

fastfold/data/data_pipeline.py

@@ -19,6 +19,7 @@ import contextlib
 import dataclasses
 import datetime
 import json
+import copy
 from multiprocessing import cpu_count
 import tempfile
 from typing import Mapping, Optional, Sequence, Any, MutableMapping, Union
@@ -56,7 +57,7 @@ def empty_template_feats(n_res) -> FeatureDict:
 def make_template_features(
     input_sequence: str,
     hits: Sequence[Any],
-    template_featurizer: Any,
+    template_featurizer: Union[hhsearch.HHSearch, hmmsearch.Hmmsearch],
     query_pdb_code: Optional[str] = None,
     query_release_date: Optional[str] = None,
 ) -> FeatureDict:
@@ -64,12 +65,18 @@ def make_template_features(
     if(len(hits_cat) == 0 or template_featurizer is None):
         template_features = empty_template_feats(len(input_sequence))
     else:
-        templates_result = template_featurizer.get_templates(
-            query_sequence=input_sequence,
-            query_pdb_code=query_pdb_code,
-            query_release_date=query_release_date,
-            hits=hits_cat,
-        )
+        if type(template_featurizer) == hhsearch.HHSearch:
+            templates_result = template_featurizer.get_templates(
+                query_sequence=input_sequence,
+                query_pdb_code=query_pdb_code,
+                query_release_date=query_release_date,
+                hits=hits_cat,
+            )
+        else:
+            templates_result = template_featurizer.get_templates(
+                query_sequence=input_sequence,
+                hits=hits_cat,
+            )
         template_features = templates_result.features
 
         # The template featurizer doesn't format empty template features
@@ -242,7 +249,7 @@ def run_msa_tool(
     if(msa_format == "sto" and max_sto_sequences is not None):
         result = msa_runner.query(fasta_path, max_sto_sequences)[0]
     else:
-        result = msa_runner.query(fasta_path)[0]
+        result = msa_runner.query(fasta_path)
   
     with open(msa_out_path, "w") as f:
         f.write(result[msa_format])
@@ -262,7 +269,6 @@ class AlignmentRunner:
         bfd_database_path: Optional[str] = None,
         uniclust30_database_path: Optional[str] = None,
         pdb70_database_path: Optional[str] = None,
-        template_searcher: Optional[TemplateSearcher] = None,
         use_small_bfd: Optional[bool] = None,
         no_cpus: Optional[int] = None,
         uniref_max_hits: int = 10000,
@@ -447,6 +453,225 @@ class AlignmentRunner:
                     f.write(hhblits_bfd_uniclust_result["a3m"])
 
 
+
+
+class AlignmentRunnerMultimer(AlignmentRunner):
+    """Runs alignment tools and saves the results"""
+
+    def __init__(
+        self,
+        jackhmmer_binary_path: Optional[str] = None,
+        hhblits_binary_path: Optional[str] = None,
+        uniref90_database_path: Optional[str] = None,
+        mgnify_database_path: Optional[str] = None,
+        bfd_database_path: Optional[str] = None,
+        uniclust30_database_path: Optional[str] = None,
+        uniprot_database_path: Optional[str] = None,
+        template_searcher: Optional[TemplateSearcher] = None,
+        use_small_bfd: Optional[bool] = None,
+        no_cpus: Optional[int] = None,
+        uniref_max_hits: int = 10000,
+        mgnify_max_hits: int = 5000,
+        uniprot_max_hits: int = 50000,
+    ):
+        """
+        Args:
+            jackhmmer_binary_path:
+                Path to jackhmmer binary
+            hhblits_binary_path:
+                Path to hhblits binary
+            uniref90_database_path:
+                Path to uniref90 database. If provided, jackhmmer_binary_path
+                must also be provided
+            mgnify_database_path:
+                Path to mgnify database. If provided, jackhmmer_binary_path
+                must also be provided
+            bfd_database_path:
+                Path to BFD database. Depending on the value of use_small_bfd,
+                one of hhblits_binary_path or jackhmmer_binary_path must be 
+                provided.
+            uniclust30_database_path:
+                Path to uniclust30. Searched alongside BFD if use_small_bfd is 
+                false.
+            use_small_bfd:
+                Whether to search the BFD database alone with jackhmmer or 
+                in conjunction with uniclust30 with hhblits.
+            no_cpus:
+                The number of CPUs available for alignment. By default, all
+                CPUs are used.
+            uniref_max_hits:
+                Max number of uniref hits
+            mgnify_max_hits:
+                Max number of mgnify hits
+        """
+        # super().__init__()
+        db_map = {
+            "jackhmmer": {
+                "binary": jackhmmer_binary_path,
+                "dbs": [
+                    uniref90_database_path,
+                    mgnify_database_path,
+                    bfd_database_path if use_small_bfd else None,
+                    uniprot_database_path,
+                ],
+            },
+            "hhblits": {
+                "binary": hhblits_binary_path,
+                "dbs": [
+                    bfd_database_path if not use_small_bfd else None,
+                ],
+            },
+        }
+
+        for name, dic in db_map.items():
+            binary, dbs = dic["binary"], dic["dbs"]
+            if(binary is None and not all([x is None for x in dbs])):
+                raise ValueError(
+                    f"{name} DBs provided but {name} binary is None"
+                )
+
+        self.uniref_max_hits = uniref_max_hits
+        self.mgnify_max_hits = mgnify_max_hits
+        self.uniprot_max_hits = uniprot_max_hits
+        self.use_small_bfd = use_small_bfd
+
+        if(no_cpus is None):
+            no_cpus = cpu_count()
+
+        self.jackhmmer_uniref90_runner = None
+        if(jackhmmer_binary_path is not None and 
+            uniref90_database_path is not None
+        ):
+            self.jackhmmer_uniref90_runner = jackhmmer.Jackhmmer(
+                binary_path=jackhmmer_binary_path,
+                database_path=uniref90_database_path,
+                n_cpu=no_cpus,
+            )
+   
+        self.jackhmmer_small_bfd_runner = None
+        self.hhblits_bfd_uniclust_runner = None
+        if(bfd_database_path is not None):
+            if use_small_bfd:
+                self.jackhmmer_small_bfd_runner = jackhmmer.Jackhmmer(
+                    binary_path=jackhmmer_binary_path,
+                    database_path=bfd_database_path,
+                    n_cpu=no_cpus,
+                )
+            else:
+                dbs = [bfd_database_path]
+                if(uniclust30_database_path is not None):
+                    dbs.append(uniclust30_database_path)
+                self.hhblits_bfd_uniclust_runner = hhblits.HHBlits(
+                    binary_path=hhblits_binary_path,
+                    databases=dbs,
+                    n_cpu=no_cpus,
+                )
+
+        self.jackhmmer_mgnify_runner = None
+        if(mgnify_database_path is not None):
+            self.jackhmmer_mgnify_runner = jackhmmer.Jackhmmer(
+                binary_path=jackhmmer_binary_path,
+                database_path=mgnify_database_path,
+                n_cpu=no_cpus,
+            )
+
+        self.jackhmmer_uniprot_runner = None
+        if(uniprot_database_path is not None):
+            self.jackhmmer_uniprot_runner = jackhmmer.Jackhmmer(
+                binary_path=jackhmmer_binary_path,
+                database_path=uniprot_database_path
+            )
+
+        if(template_searcher is not None and 
+           self.jackhmmer_uniref90_runner is None
+        ):
+            raise ValueError(
+                "Uniref90 runner must be specified to run template search"
+            )
+
+        self.template_searcher = template_searcher
+    
+    def run(
+        self,
+        fasta_path: str,
+        output_dir: str,
+    ):
+        """Runs alignment tools on a sequence"""
+        if(self.jackhmmer_uniref90_runner is not None):
+            uniref90_out_path = os.path.join(output_dir, "uniref90_hits.sto")
+
+            jackhmmer_uniref90_result = run_msa_tool(
+                msa_runner=self.jackhmmer_uniref90_runner,
+                fasta_path=fasta_path,
+                msa_out_path=uniref90_out_path,
+                msa_format='sto',
+                max_sto_sequences=self.uniref_max_hits,
+            )
+
+            template_msa = jackhmmer_uniref90_result["sto"]
+            template_msa = parsers.deduplicate_stockholm_msa(template_msa)
+            template_msa = parsers.remove_empty_columns_from_stockholm_msa(
+                template_msa
+            )
+
+            if(self.template_searcher is not None):
+                if(self.template_searcher.input_format == "sto"):
+                    pdb_templates_result = self.template_searcher.query(
+                        template_msa,
+                        output_dir=output_dir
+                    )
+                elif(self.template_searcher.input_format == "a3m"):
+                    uniref90_msa_as_a3m = parsers.convert_stockholm_to_a3m(
+                        template_msa
+                    )
+                    pdb_templates_result = self.template_searcher.query(
+                        uniref90_msa_as_a3m,
+                        output_dir=output_dir
+                    )
+                else:
+                    fmt = self.template_searcher.input_format
+                    raise ValueError(
+                        f"Unrecognized template input format: {fmt}"
+                    )
+
+        if(self.jackhmmer_mgnify_runner is not None):
+            mgnify_out_path = os.path.join(output_dir, "mgnify_hits.sto")
+            jackhmmer_mgnify_result = run_msa_tool(
+                msa_runner=self.jackhmmer_mgnify_runner,
+                fasta_path=fasta_path,
+                msa_out_path=mgnify_out_path,
+                msa_format='sto',
+                max_sto_sequences=self.mgnify_max_hits
+            )
+
+        if(self.use_small_bfd and self.jackhmmer_small_bfd_runner is not None):
+            bfd_out_path = os.path.join(output_dir, "small_bfd_hits.sto")
+            jackhmmer_small_bfd_result = run_msa_tool(
+                msa_runner=self.jackhmmer_small_bfd_runner,
+                fasta_path=fasta_path,
+                msa_out_path=bfd_out_path,
+                msa_format="sto",
+            )
+        elif(self.hhblits_bfd_uniclust_runner is not None):
+            bfd_out_path = os.path.join(output_dir, "bfd_uniclust_hits.a3m")
+            hhblits_bfd_uniclust_result = run_msa_tool(
+                msa_runner=self.hhblits_bfd_uniclust_runner,
+                fasta_path=fasta_path,
+                msa_out_path=bfd_out_path,
+                msa_format="a3m",
+            )
+
+        if(self.jackhmmer_uniprot_runner is not None):
+            uniprot_out_path = os.path.join(output_dir, 'uniprot_hits.sto')
+            result = run_msa_tool(
+                self.jackhmmer_uniprot_runner, 
+                fasta_path=fasta_path, 
+                msa_out_path=uniprot_out_path, 
+                msa_format='sto',
+                max_sto_sequences=self.uniprot_max_hits,
+            )
+
+
 @contextlib.contextmanager
 def temp_fasta_file(fasta_str: str):
     with tempfile.NamedTemporaryFile('w', suffix='.fasta') as fasta_file:
@@ -722,7 +947,12 @@ class DataPipeline:
         input_description = input_descs[0]
         num_res = len(input_sequence)
 
-        hits = self._parse_template_hits(alignment_dir, _alignment_index)
+        hits = self._parse_template_hits(
+            alignment_dir, 
+            input_sequence,
+            _alignment_index,
+        )
+        
         template_features = make_template_features(
             input_sequence,
             hits,
@@ -893,8 +1123,8 @@ class DataPipelineMultimer:
         uniprot_msa_path = os.path.join(alignment_dir, "uniprot_hits.sto")
         with open(uniprot_msa_path, "r") as fp:
             uniprot_msa_string = fp.read()
-        msa = parsers.parse_stockholm(uniprot_msa_string)
-        all_seq_features = make_msa_features([msa])
+        msa, deletion_matrix, _ = parsers.parse_stockholm(uniprot_msa_string)
+        all_seq_features = make_msa_features(msa, deletion_matrix)
         valid_feats = msa_pairing.MSA_FEATURES + (
             'msa_species_identifiers',
         )

fastfold/data/templates.py

@@ -188,9 +188,9 @@ def _assess_hhsearch_hit(
     hit: parsers.TemplateHit,
     hit_pdb_code: str,
     query_sequence: str,
-    query_pdb_code: Optional[str],
     release_dates: Mapping[str, datetime.datetime],
     release_date_cutoff: datetime.datetime,
+    query_pdb_code: Optional[str] = None,
     max_subsequence_ratio: float = 0.95,
     min_align_ratio: float = 0.1,
 ) -> bool:
@@ -752,12 +752,12 @@ class SingleHitResult:
 
 def _prefilter_hit(
     query_sequence: str,
-    query_pdb_code: Optional[str],
     hit: parsers.TemplateHit,
     max_template_date: datetime.datetime,
     release_dates: Mapping[str, datetime.datetime],
     obsolete_pdbs: Mapping[str, str],
     strict_error_check: bool = False,
+    query_pdb_code: Optional[str] = None,
 ):
     # Fail hard if we can't get the PDB ID and chain name from the hit.
     hit_pdb_code, hit_chain_id = _get_pdb_id_and_chain(hit)
@@ -794,7 +794,6 @@ def _prefilter_hit(
 
 def _process_single_hit(
     query_sequence: str,
-    query_pdb_code: Optional[str],
     hit: parsers.TemplateHit,
     mmcif_dir: str,
     max_template_date: datetime.datetime,
@@ -803,6 +802,7 @@ def _process_single_hit(
     kalign_binary_path: str,
     strict_error_check: bool = False,
     _zero_center_positions: bool = True,
+    query_pdb_code: Optional[str] = None,
 ) -> SingleHitResult:
     """Tries to extract template features from a single HHSearch hit."""
     # Fail hard if we can't get the PDB ID and chain name from the hit.
@@ -996,9 +996,9 @@ class TemplateHitFeaturizer:
     def get_templates(
         self,
         query_sequence: str,
-        query_pdb_code: Optional[str],
         query_release_date: Optional[datetime.datetime],
         hits: Sequence[parsers.TemplateHit],
+        query_pdb_code: Optional[str] = None,
     ) -> TemplateSearchResult:
         """Computes the templates for given query sequence (more details above)."""
         logging.info("Searching for template for: %s", query_pdb_code)
@@ -1155,7 +1155,7 @@ class HmmsearchHitFeaturizer(TemplateHitFeaturizer):
             idx[:stk] = np.random.permutation(idx[:stk])
 
         for i in idx:
-            if(len(already_seen) >= self._max_hits):
+            if(len(already_seen) >= self.max_hits):
                 break
 
             hit = filtered[i]

fastfold/data/tools/jackhmmer.py

@@ -23,6 +23,7 @@ import subprocess
 from typing import Any, Callable, Mapping, Optional, Sequence
 from urllib import request
 
+from fastfold.data import parsers
 from fastfold.data.tools import utils
 
 
@@ -93,7 +94,10 @@ class Jackhmmer:
         self.streaming_callback = streaming_callback
 
     def _query_chunk(
-        self, input_fasta_path: str, database_path: str
+        self, 
+        input_fasta_path: str, 
+        database_path: str,
+        max_sequences: Optional[int] = None
     ) -> Mapping[str, Any]:
         """Queries the database chunk using Jackhmmer."""
         with utils.tmpdir_manager(base_dir="/tmp") as query_tmp_dir:
@@ -167,8 +171,11 @@ class Jackhmmer:
                 with open(tblout_path) as f:
                     tbl = f.read()
 
-            with open(sto_path) as f:
-                sto = f.read()
+            if(max_sequences is None):
+                with open(sto_path) as f:
+                    sto = f.read()
+            else:
+                sto = parsers.truncate_stockholm_msa(sto_path, max_sequences)
 
         raw_output = dict(
             sto=sto,
@@ -180,10 +187,16 @@ class Jackhmmer:
 
         return raw_output
 
-    def query(self, input_fasta_path: str) -> Sequence[Mapping[str, Any]]:
+    def query(self,
+    input_fasta_path: str, 
+    max_sequences: Optional[int] = None
+    ) -> Sequence[Mapping[str, Any]]:
         """Queries the database using Jackhmmer."""
         if self.num_streamed_chunks is None:
-            return [self._query_chunk(input_fasta_path, self.database_path)]
+            single_chunk_result = self._query_chunk(
+                input_fasta_path, self.database_path, max_sequences,
+            )
+            return [single_chunk_result]
 
         db_basename = os.path.basename(self.database_path)
         db_remote_chunk = lambda db_idx: f"{self.database_path}.{db_idx}"
@@ -217,12 +230,20 @@ class Jackhmmer:
                 # Run Jackhmmer with the chunk
                 future.result()
                 chunked_output.append(
-                    self._query_chunk(input_fasta_path, db_local_chunk(i))
+                    self._query_chunk(
+                        input_fasta_path, 
+                        db_local_chunk(i), 
+                        max_sequences
+                    )
                 )
 
                 # Remove the local copy of the chunk
                 os.remove(db_local_chunk(i))
                 future = next_future
+                # Do not set next_future for the last chunk so that this works
+                # even for databases with only 1 chunk
+                if(i < self.num_streamed_chunks):
+                    future = next_future
                 if self.streaming_callback:
                     self.streaming_callback(i)
         return chunked_output

inference.py

@@ -19,6 +19,8 @@ import random
 import sys
 import time
 from datetime import date
+import tempfile
+import contextlib
 
 import numpy as np
 import torch
@@ -39,6 +41,12 @@ from fastfold.data.parsers import parse_fasta
 from fastfold.utils.import_weights import import_jax_weights_
 from fastfold.utils.tensor_utils import tensor_tree_map
 
+@contextlib.contextmanager
+def temp_fasta_file(fasta_str: str):
+    with tempfile.NamedTemporaryFile('w', suffix='.fasta') as fasta_file:
+        fasta_file.write(fasta_str)
+        fasta_file.seek(0)
+        yield fasta_file.name
 
 def add_data_args(parser: argparse.ArgumentParser):
     parser.add_argument(
@@ -66,10 +74,22 @@ def add_data_args(parser: argparse.ArgumentParser):
         type=str,
         default=None,
     )
+    parser.add_argument(
+        "--pdb_seqres_database_path",
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        "--uniprot_database_path",
+        type=str,
+        default=None,
+    )
     parser.add_argument('--jackhmmer_binary_path', type=str, default='/usr/bin/jackhmmer')
     parser.add_argument('--hhblits_binary_path', type=str, default='/usr/bin/hhblits')
     parser.add_argument('--hhsearch_binary_path', type=str, default='/usr/bin/hhsearch')
     parser.add_argument('--kalign_binary_path', type=str, default='/usr/bin/kalign')
+    parser.add_argument("--hmmsearch_binary_path", type=str, default="hmmsearch")
+    parser.add_argument("--hmmbuild_binary_path", type=str, default="hmmbuild")
     parser.add_argument(
         '--max_template_date',
         type=str,
@@ -79,6 +99,7 @@ def add_data_args(parser: argparse.ArgumentParser):
     parser.add_argument('--release_dates_path', type=str, default=None)
     parser.add_argument('--enable_workflow', default=False, action='store_true', help='run inference with ray workflow or not')
 
+
 def inference_model(rank, world_size, result_q, batch, args):
     os.environ['RANK'] = str(rank)
     os.environ['LOCAL_RANK'] = str(rank)
@@ -120,7 +141,7 @@ def main(args):
 
 def inference_multimer_model(args):
     print("running in multimer mode...")
-
+    config = model_config(args.model_name)
     # feature_dict = pickle.load(open("/home/lcmql/data/features_pdb1o5d.pkl", "rb"))
     
     predict_max_templates = 4
@@ -143,6 +164,81 @@ def inference_multimer_model(args):
         obsolete_pdbs_path=args.obsolete_pdbs_path,
     )
 
+    if(not args.use_precomputed_alignments):
+        alignment_runner = data_pipeline.AlignmentRunnerMultimer(
+            jackhmmer_binary_path=args.jackhmmer_binary_path,
+            hhblits_binary_path=args.hhblits_binary_path,
+            uniref90_database_path=args.uniref90_database_path,
+            mgnify_database_path=args.mgnify_database_path,
+            bfd_database_path=args.bfd_database_path,
+            uniclust30_database_path=args.uniclust30_database_path,
+            uniprot_database_path=args.uniprot_database_path,
+            template_searcher=template_searcher,
+            use_small_bfd=(args.bfd_database_path is None),
+            no_cpus=args.cpus,
+        )
+    else:
+        alignment_runner = None
+
+    monomer_data_processor = data_pipeline.DataPipeline(
+        template_featurizer=template_featurizer,
+    )
+
+
+    data_processor = data_pipeline.DataPipelineMultimer(
+            monomer_data_pipeline=monomer_data_processor,
+    )
+
+    output_dir_base = args.output_dir
+    random_seed = args.data_random_seed
+    if random_seed is None:
+        random_seed = random.randrange(sys.maxsize)
+    
+    feature_processor = feature_pipeline.FeaturePipeline(
+        config.data
+    )
+
+    if not os.path.exists(output_dir_base):
+        os.makedirs(output_dir_base)
+    if(not args.use_precomputed_alignments):
+        alignment_dir = os.path.join(output_dir_base, "alignments")
+    else:
+        alignment_dir = args.use_precomputed_alignments
+
+    # Gather input sequences
+    fasta_path = args.fasta_path
+    with open(fasta_path, "r") as fp:
+        data = fp.read()
+
+    lines = [
+        l.replace('\n', '') 
+        for prot in data.split('>') for l in prot.strip().split('\n', 1)
+    ][1:]
+    tags, seqs = lines[::2], lines[1::2]
+
+
+    for tag, seq in zip(tags, seqs):
+        local_alignment_dir = os.path.join(alignment_dir, tag)
+        if(args.use_precomputed_alignments is None):
+            if not os.path.exists(local_alignment_dir):
+                os.makedirs(local_alignment_dir)
+            
+            chain_fasta_str = f'>chain_{tag}\n{seq}\n'
+            with temp_fasta_file(chain_fasta_str) as chain_fasta_path:
+                alignment_runner.run(
+                    chain_fasta_path, local_alignment_dir
+                )
+                print(f"Finished running alignment for {tag}")
+                
+    local_alignment_dir = alignment_dir
+
+    feature_dict = data_processor.process_fasta(
+        fasta_path=fasta_path, alignment_dir=local_alignment_dir
+    )
+
+    processed_feature_dict = feature_processor.process_features(
+        feature_dict, mode='predict', is_multimer=True,
+    )
 
 def inference_monomer_model(args):
     print("running in monomer mode...")
@@ -282,6 +378,7 @@ def inference_monomer_model(args):
         with open(relaxed_output_path, 'w') as f:
             f.write(relaxed_pdb_str)
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument(