diff --git a/.release-please-manifest.json b/.release-please-manifest.json index 256c881..7b51ca0 100644 --- a/.release-please-manifest.json +++ b/.release-please-manifest.json @@ -1,3 +1,3 @@ { - ".": "0.16.1" + ".": "0.17.0" } diff --git a/CHANGELOG.md b/CHANGELOG.md index 26cca9e..f319fab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,26 @@ # Changelog +## 0.17.0 (2026-08-22) + + +### ⚠ BREAKING CHANGES + +* **molecules:** Complex no longer sorts chains by ID. Chains iterate and serialize in insertion order, so code relying on get_chains() returning alphabetical order must sort explicitly. Combining with & or | appends the new chain last rather than sorting it into place, and both now return a new Complex instead of mutating the left operand. Complex is also no longer hashable, matching its mutable-mapping semantics. Structures parsed from CIF or PDB are unaffected. + +### Features + +* expose unnumbered_policy and job warnings on alignments +* **prompt:** curated antibody prompts (VH, VL, VH-VL, VL-VH) as attributes on the prompt API +* **molecules:** dict-like Complex interface with insertion-ordered chains + + +## 0.16.2 (2026-07-20) + + +### Bug Fixes + +* export single site future + ## 0.16.1 (2026-07-14) diff --git a/flake.lock b/flake.lock index 18b197d..65dff8e 100644 --- a/flake.lock +++ b/flake.lock @@ -22,18 +22,15 @@ }, "nixpkgs": { "locked": { - "lastModified": 1762156382, - "narHash": "sha256-Yg7Ag7ov5+36jEFC1DaZh/12SEXo6OO3/8rqADRxiqs=", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "7241bcbb4f099a66aafca120d37c65e8dda32717", - "type": "github" + "lastModified": 1785747939, + "narHash": "sha256-NqaCaIITVSDaBYdcWcfCyEu1erL7paTPEQbISQp9xwQ=", + "rev": "104240a772428cc2e20d8fd86c9ddbb886bbaff2", + "type": "tarball", + "url": "https://releases.nixos.org/nixpkgs/nixpkgs-26.11pre1046984.104240a77242/nixexprs.tar.xz" }, "original": { - "owner": "NixOS", - "ref": "nixpkgs-unstable", - "repo": "nixpkgs", - "type": "github" + "id": "nixpkgs", + "type": "indirect" } }, "root": { diff --git a/flake.nix b/flake.nix index dd7e9bb..88d186e 100644 --- a/flake.nix +++ b/flake.nix @@ -1,6 +1,6 @@ { description = "A basic flake with a shell"; - inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable"; + inputs.nixpkgs.url = "nixpkgs"; inputs.systems.url = "github:nix-systems/default"; inputs.flake-utils = { url = "github:numtide/flake-utils"; diff --git a/openprotein/align/align.py b/openprotein/align/align.py index 1258247..7645bfa 100644 --- a/openprotein/align/align.py +++ b/openprotein/align/align.py @@ -11,7 +11,7 @@ from . import api from .msa import MSAFuture -from .schemas import AbNumberScheme, AlignType +from .schemas import AbNumberScheme, AlignType, UnnumberedPolicy class AlignAPI: @@ -190,6 +190,7 @@ def abnumber( names: Sequence[str] | None = None, scheme: AbNumberScheme = AbNumberScheme.CHOTHIA, drop_minority_chains: bool = False, + unnumbered_policy: UnnumberedPolicy = UnnumberedPolicy.ERROR, ) -> MSAFuture: """ Align antibody sequences using `AbNumber`. @@ -210,6 +211,11 @@ def abnumber( If True, drop sequences belonging to chain types that are in the minority (e.g. heavy vs light) so the resulting alignment contains only the dominant chain type. + unnumbered_policy : UnnumberedPolicy, default=UnnumberedPolicy.ERROR + What to do with residues outside the numbered variable domain -- + a constant/Fc region, an N-terminal tag. ERROR fails the job, DROP + aligns the numbered residues only, RETAIN keeps them padded against + the numbered-domain boundary. Returns ------- @@ -241,7 +247,10 @@ def abnumber( content = b"\n".join(lines) stream = BytesIO(content) return self.abnumber_file( - stream, scheme=scheme, drop_minority_chains=drop_minority_chains + stream, + scheme=scheme, + drop_minority_chains=drop_minority_chains, + unnumbered_policy=unnumbered_policy, ) def abnumber_file( @@ -249,6 +258,7 @@ def abnumber_file( file, scheme: AbNumberScheme = AbNumberScheme.CHOTHIA, drop_minority_chains: bool = False, + unnumbered_policy: UnnumberedPolicy = UnnumberedPolicy.ERROR, ) -> MSAFuture: """ Align antibody sequences using `AbNumber`. @@ -267,6 +277,11 @@ def abnumber_file( If True, drop sequences belonging to chain types that are in the minority (e.g. heavy vs light) so the resulting alignment contains only the dominant chain type. + unnumbered_policy : UnnumberedPolicy, default=UnnumberedPolicy.ERROR + What to do with residues outside the numbered variable domain -- + a constant/Fc region, an N-terminal tag. ERROR fails the job, DROP + aligns the numbered residues only, RETAIN keeps them padded against + the numbered-domain boundary. Returns ------- @@ -278,6 +293,7 @@ def abnumber_file( file, scheme=scheme, drop_minority_chains=drop_minority_chains, + unnumbered_policy=unnumbered_policy, ) return MSAFuture.create(session=self.session, job=job) diff --git a/openprotein/align/api.py b/openprotein/align/api.py index a57be67..bdb1b10 100644 --- a/openprotein/align/api.py +++ b/openprotein/align/api.py @@ -11,7 +11,12 @@ from openprotein.errors import APIError, InvalidParameterError, MissingParameterError from openprotein.jobs import Job -from .schemas import AbNumberScheme, AlignType, MSASamplingMethod +from .schemas import ( + AbNumberScheme, + AlignType, + MSASamplingMethod, + UnnumberedPolicy, +) def get_align_job_inputs( @@ -270,6 +275,7 @@ def abnumber_post( sequence_file: BinaryIO, scheme: AbNumberScheme | str = AbNumberScheme.IMGT, drop_minority_chains: bool = False, + unnumbered_policy: UnnumberedPolicy | str = UnnumberedPolicy.ERROR, ) -> Job: """ Align antibody sequences using AbNumber. @@ -289,6 +295,9 @@ def abnumber_post( If True, drop sequences belonging to chain types that are in the minority (e.g. heavy vs light) so the resulting alignment contains only the dominant chain type. Default is False. + unnumbered_policy : UnnumberedPolicy, optional + What to do with residues outside the numbered variable domain. + Default is ERROR, which fails the job. Returns ------- @@ -300,18 +309,28 @@ def abnumber_post( if isinstance(scheme, str): if scheme not in {value.value for value in AbNumberScheme}: raise InvalidParameterError(f"Antibody numbering {scheme} not recognized") + if isinstance(unnumbered_policy, str): + if unnumbered_policy not in {value.value for value in UnnumberedPolicy}: + raise InvalidParameterError( + f"Unnumbered residue policy {unnumbered_policy} not recognized" + ) files = {"file": sequence_file} params = { "scheme": scheme if isinstance(scheme, str) else scheme.value, "drop_minority_chains": drop_minority_chains, + "unnumbered_policy": ( + unnumbered_policy + if isinstance(unnumbered_policy, str) + else unnumbered_policy.value + ), } response = session.post(endpoint, files=files, params=params) return Job.model_validate(response.json()) -def antibody_schema_get(session: APISession, job_id: str): +def antibody_schema_get(session: APISession, job_id: str) -> dict: """ Retrieve the antibody numbering for an AbNumber job. @@ -322,16 +341,16 @@ def antibody_schema_get(session: APISession, job_id: str): job_id : str The job identifier. - Raises - ------ - NotImplementedError - This function is not yet implemented. - Returns ------- - None + dict + The job's extras: a ``chains`` entry per chain position carrying the + numbering and CDR regions, and a ``warnings`` list. """ - raise NotImplementedError() + endpoint = "v1/align/antibody_schema" + + response = session.get(endpoint, params={"job_id": job_id}) + return response.json() def prompt_post( diff --git a/openprotein/align/msa.py b/openprotein/align/msa.py index 25ab969..9835ca9 100644 --- a/openprotein/align/msa.py +++ b/openprotein/align/msa.py @@ -1,5 +1,6 @@ """MSA results represented as a future.""" +import warnings from typing import Iterator from openprotein import config @@ -12,6 +13,7 @@ from .schemas import ( AbNumberJob, ClustalOJob, + JobWarning, MafftJob, MSAJob, MSASamplingMethod, @@ -44,6 +46,7 @@ def __init__( super().__init__(session, job) self.page_size = page_size self.msa_id = self.job.job_id + self._warned = False def _get(self, verbose: bool = False) -> Iterator[tuple[str, str]]: """ @@ -59,8 +62,54 @@ def _get(self, verbose: bool = False) -> Iterator[tuple[str, str]]: Iterator[tuple[str, str]] An iterator over names and sequences of the MSA data. """ + self._warn_once() return api.get_msa(session=self.session, job_id=self.job.job_id) + def _warn_once(self) -> None: + """Surface what the job reported about its own output, once.""" + if self._warned or not isinstance(self.job, AbNumberJob): + return + self._warned = True + try: + job_warnings = self.get_warnings() + except Exception: + # reading the results cannot depend on the schema endpoint answering + return + for job_warning in job_warnings: + warnings.warn(f"{job_warning.code}: {job_warning.message}") + + def get_antibody_schema(self) -> dict: + """ + Retrieve the antibody numbering for an AbNumber job. + + Returns + ------- + dict + One ``chains`` entry per chain position, carrying that position's + numbering, CDR regions and chain type, plus a ``warnings`` list. + + Raises + ------ + HTTPError + If the job did not use AbNumber. + """ + return api.antibody_schema_get(session=self.session, job_id=self.job.job_id) + + def get_warnings(self) -> list[JobWarning]: + """ + Retrieve what the job reported about its own output. + + A job that succeeds can still have changed the data, e.g. by dropping + residues AbNumber could not number. + + Returns + ------- + list[JobWarning] + Empty if the job had nothing to report. + """ + schema = self.get_antibody_schema() + return [JobWarning.model_validate(w) for w in schema.get("warnings", [])] + def sample_prompt( self, num_sequences: int | None = None, diff --git a/openprotein/align/schemas.py b/openprotein/align/schemas.py index bdf8b81..9761ad4 100644 --- a/openprotein/align/schemas.py +++ b/openprotein/align/schemas.py @@ -180,3 +180,47 @@ class AbNumberScheme(str, Enum): CHOTHIA = "chothia" KABAT = "kabat" AHO = "aho" + + +class UnnumberedPolicy(str, Enum): + """ + What to do with residues the numbering scheme gives no antibody position. + + ANARCI numbers one variable domain per sequence. Residues outside it -- a + constant/Fc region, an N-terminal tag -- have no antibody position and + cannot share the numbering coordinate system. + + Attributes + ---------- + ERROR : str + Fail the job if any sequence carries unnumbered residues. + DROP : str + Align the numbered residues only, discarding the rest. + RETAIN : str + Keep the unnumbered residues, padded against the numbered-domain + boundary. They are preserved, not aligned to each other. + """ + + ERROR = "error" + DROP = "drop" + RETAIN = "retain" + + +class JobWarning(BaseModel): + """ + Something a job reports about its own output while still succeeding. + + Attributes + ---------- + code : str + Machine-readable identifier, e.g. ``UNNUMBERED_RESIDUES_DROPPED``. + message : str + Human-readable description. + metadata : dict or None + Code-specific detail. For the unnumbered-residue codes this carries a + ``chains`` list, one entry per affected chain position. + """ + + code: str + message: str + metadata: dict | None = None diff --git a/openprotein/embeddings/__init__.py b/openprotein/embeddings/__init__.py index f818176..9a05e9d 100644 --- a/openprotein/embeddings/__init__.py +++ b/openprotein/embeddings/__init__.py @@ -25,4 +25,5 @@ EmbeddingsGenerateFuture, EmbeddingsResultFuture, EmbeddingsScoreFuture, + EmbeddingsScoreSingleSiteFuture, ) diff --git a/openprotein/molecules/chains.py b/openprotein/molecules/chains.py index 98c1c93..ae0364d 100644 --- a/openprotein/molecules/chains.py +++ b/openprotein/molecules/chains.py @@ -109,6 +109,8 @@ def __len__(self): def copy(self) -> "DNA": return replace(self) + # TODO - support (&) and (|) operators for combining into Complexes (like Protein) + @staticmethod def _from_structure_block( structure_block: _cif_utils.StructureCIFBlock, chain_id: str, model_idx: int @@ -159,6 +161,8 @@ def __len__(self): def copy(self) -> "RNA": return replace(self) + # TODO - support (&) and (|) operators for combining into Complexes (like Protein) + @staticmethod def _from_structure_block( structure_block: _cif_utils.StructureCIFBlock, chain_id: str, model_idx: int @@ -210,6 +214,8 @@ def __post_init__(self): def copy(self) -> "Ligand": return replace(self) + + # TODO - support (&) and (|) operators for combining into Complexes (like Protein) @staticmethod def _from_structure_block( diff --git a/openprotein/molecules/complex.py b/openprotein/molecules/complex.py index a424e81..8ebcd85 100644 --- a/openprotein/molecules/complex.py +++ b/openprotein/molecules/complex.py @@ -1,6 +1,6 @@ import gzip import operator -from collections.abc import Mapping, Sequence +from collections.abc import Mapping, Sequence, MutableMapping from functools import reduce from pathlib import Path from types import MappingProxyType @@ -20,8 +20,14 @@ from .template import Template +Chain = Protein | DNA | RNA | Ligand | str + +def _is_chain_type(chain): + return isinstance(chain, Chain) + + # TODO: deserialization note about plddt parsed per residue -class Complex: +class Complex(MutableMapping): def __init__( self, chains: Mapping[str, Protein | DNA | RNA | Ligand] | None = None, @@ -33,10 +39,14 @@ def __init__( if not isinstance(key, str): raise TypeError(f"chain id must be str; got {key!r}") collected[key] = value - self._chains = dict(sorted(collected.items())) + # preserve insertion order of the chains by not sorting the dictionary + # Note that as of python 3.7 dicts preserve insertion order (OrderedDict not needed) + self._chains = collected self._templates: "Sequence[Protein | Complex | Template]" = () self.name = name + # --- NAME methods --- + @property def name(self) -> str | None: return self._name @@ -52,6 +62,8 @@ def set_name(self, x: bytes | str | None) -> "Complex": self.name = x return self + # --- TEMPLATE methods --- + @property def templates(self) -> "Sequence[Protein | Complex | Template]": """A list of templates for guiding the structure prediction of this molecular complex.""" @@ -70,9 +82,150 @@ def set_templates( self.templates = templates return self + # --- dict-like methods and other general ops --- + + def get_chain_ids(self): + """Returns the Chain IDs in this Complex""" + return self._chains.keys() + def get_chains(self) -> Mapping[str, Protein | DNA | RNA | Ligand]: + """Get all chains as a {chain_id: chain} mapping""" return MappingProxyType(self._chains) + def get_chain(self, chain_id: str): + """Get the chain for this chain_id""" + return self._chains[chain_id] + + def set_chain( + self, chain_id: str, value: Protein | DNA | RNA | Ligand + ) -> "Complex": + """Add a new chain to this complex or overwrite an existing one with the same chain_id""" + self._chains[chain_id] = value + return self + + def remove_chain(self, chain_id: str): + """Remove a chain from this complex""" + del self._chains[chain_id] + + def insert_chain(self, chain: Protein | DNA | RNA | Ligand | str): + """Inserts a new chain into this Complex with an auto-generated chain_id. Casts strings into Proteins.""" + assert _is_chain_type(chain) + id_gen = _chain_id_utils.id_generator(list(self._chains.keys())) + if isinstance(chain, str): + chain = Protein.from_expr(chain) + + chain_id = next(id_gen) + self.set_chain(chain_id, chain) + return self + + def __len__(self): + """Returns the number of chains in the complex""" + return len(self._chains) + + def __getitem__(self, key): + """Retrieve the given chain""" + return self.get_chain(key) + + def __setitem__(self, key, value): + """Add a chain or overwrite a chain with the given chain_id""" + self.set_chain(key, value) + + def __delitem__(self, key): + """Remove the given chain from this complex""" + self.remove_chain(key) + + def __contains__(self, chain_id): + return chain_id in self._chains + + def __eq__(self, other): + if isinstance(other, Complex): + if self._chains != other._chains: + return False + if self._templates != other._templates: + return False + return True + return False + + def __iter__(self): + """Iterate the chains in this complex""" + return iter(self._chains) + + def keys(self): + return self._chains.keys() + + def values(self): + return self._chains.values() + + def items(self): + return self._chains.items() + + def update(self, **kwargs): + """Add a collection of chains to this complex""" + overlapping_chain_ids = [] + for key, value in kwargs.items(): + if not isinstance(key, str): + raise TypeError(f"chain id must be str; got {key!r}") + # TODO - assert that chain objects are the right types too + # assert _is_chain_type(value) + + # strictly do not allow replacing existing chain_ids + if key in self._chains: + overlapping_chain_ids.append(key) + if len(overlapping_chain_ids) > 0: + raise ValueError( + f"Trying to combine two sets of chains with overlapping chain ids: {overlapping_chain_ids}" + ) + + # update chains + self._chains.update(**kwargs) + + def clear(self): + """Remove all chains and templates from this complex""" + self._chains.clear() + # also deletes the templates if you clear this complex + self._templates = () + + def copy(self) -> "Complex": + """Copy this Complex. Returns a deep copy of the contained Chains""" + # TODO - should this deepcopy the chain objects themselves? + chains_copy: dict[str, Protein | DNA | RNA | Ligand] = { + chain_id: chain.copy() for chain_id, chain in self._chains.items() + } + return Complex(chains=chains_copy, name=self._name) + + # --- other dictionary operators like set combine --- + + # python actually uses the or operator for dict combine + def __ior__(self, other) -> "Complex": + """In-place update to this Complex using |= """ + + # other is either a single Chain or a Complex + # if single chain, we insert it with an autogenerated ID + # if complex, we add all of its chains + if _is_chain_type(other): + self.insert_chain(other) + else: + self.update(**other) + return self + + def __or__(self, right) -> "Complex": + """Create a combined copy: self | right""" + a = self.copy() + a |= right # handles right being Complex or single Chain + return a + + def __ror__(self, left) -> "Complex": + if isinstance(left, str): + left = Protein.from_expr(expr=left) + return left | self + + # NOTE - python uses the or operator (|) for set and dict unions, but we also + # support this using the and operator (&) + __rand__ = __ror__ + __and__ = __or__ + + # -- Chain-type specific methods --- + def get_proteins(self) -> Mapping[str, Protein]: return MappingProxyType( {k: v for k, v in self._chains.items() if isinstance(v, Protein)} @@ -113,41 +266,7 @@ def get_ligand(self, chain_id: str) -> Ligand: assert isinstance(chain, Ligand) return chain - def set_chain( - self, chain_id: str, value: Protein | DNA | RNA | Ligand - ) -> "Complex": - self._chains[chain_id] = value - self._chains = dict(sorted(self._chains.items())) - return self - - def __rand__(self, left: "Complex | Protein | str") -> "Complex": - if isinstance(left, str): - left = Protein.from_expr(expr=left) - return left & self - - def __and__(self, right: "Complex | Protein | str") -> "Complex": - """Combine multiple objects into a single Complex.""" - - assert ( - isinstance(right, Complex) - or isinstance(right, Protein) - or isinstance(right, str) - ) - id_gen = _chain_id_utils.id_generator(list(self._chains.keys())) - if isinstance(right, str): - right = Protein.from_expr(right) - if isinstance(right, Protein): - self.set_chain(chain_id=next(id_gen), value=right) - else: - if ( - len(overlapping_chain_ids := self._chains.keys() & right._chains.keys()) - > 0 - ): - raise ValueError( - f"Trying to combine two sets of chains with overlapping chain ids: {overlapping_chain_ids}" - ) - self._chains = dict(sorted((self._chains | right._chains).items())) - return self + # --- structure comparison and geometry methods --- @overload def rmsd( @@ -208,6 +327,8 @@ def superimpose_onto( _, R, t = tgt.rmsd(self, backbone_only=backbone_only, return_transform=True) return self.transform(R=R, t=t) + # --- read and write PDB and CIF files and strings --- + def to_string(self, format: Literal["cif", "pdb"] = "cif") -> str: """ Serialize this Complex to a string. Note that format="pdb" may not serialize all @@ -268,12 +389,6 @@ def from_string( verbose=verbose, ) - def copy(self) -> "Complex": - chains_copy: dict[str, Protein | DNA | RNA | Ligand] = { - chain_id: chain.copy() for chain_id, chain in self._chains.items() - } - return Complex(chains=chains_copy, name=self._name) - def _assert_valid_templates(self): from .template import Template diff --git a/openprotein/molecules/protein.py b/openprotein/molecules/protein.py index 084738d..21e28d0 100644 --- a/openprotein/molecules/protein.py +++ b/openprotein/molecules/protein.py @@ -216,6 +216,10 @@ def __add__(self, right: "Protein | str") -> "Protein": } return new + # --- complex set operations to support & and | operators between proteins and Complexes --- + # NOTE - in python, the or operator (|) is used to combine sets and dicts, but we also support + # the and operator (&) to do the same thing + def __rand__(self, left: "Complex | Protein | str") -> "Complex": if isinstance(left, str): left = self.from_expr(expr=left) @@ -235,7 +239,15 @@ def __and__(self, right: "Complex | Protein | str") -> "Complex": if isinstance(right, Protein): id_gen = _chain_id_utils.id_generator() return Complex({next(id_gen): self, next(id_gen): right}) - return right & self + # NOTE - this inserts this protein at the _end_ of the Complex even though the operation + # was Protein & Complex + return right & self + + # map the (|) or operator to the and operators + __ror__ = __rand__ + __or__ = __and__ + + # --- end set operator definitions --- def at(self, positions: Sequence[int] | npt.NDArray[np.integer]) -> "Protein": """ diff --git a/openprotein/prompt/api.py b/openprotein/prompt/api.py index 544ad82..ba1a404 100644 --- a/openprotein/prompt/api.py +++ b/openprotein/prompt/api.py @@ -11,11 +11,25 @@ from .schemas import Context, PromptMetadata, QueryMetadata -def _coerce_sequence(name: str, sequence: bytes | str) -> Protein | Complex: - """Parse a raw sequence into a Protein, or a Complex if it contains ':' chain breaks.""" +def _coerce_sequence( + name: str, sequence: bytes | str, allow_empty_chains: bool = False +) -> Protein | Complex: + """Parse a raw sequence into a Protein, or a Complex if it contains ':' chain breaks. + + With ``allow_empty_chains`` a chain may hold no residues. That is how a prompt + sampled from a multi-chain MSA describes coverage: it carries one slot per chain + of the complex, so a homolog that only matches one of them renders as ``":SEQ"`` + and the empty slot says which chain the residues belong to. A query has no such + layout to describe, so an empty chain there is malformed. Either way, an entry + with no residues in any chain carries nothing and is rejected. + """ raw = sequence.encode() if isinstance(sequence, str) else sequence parts = raw.split(b":") - if any(len(p) == 0 for p in parts): + if all(len(p) == 0 for p in parts): + raise InvalidParameterError( + f"sequence {raw.decode()!r} has no residues in any chain" + ) + if not allow_empty_chains and any(len(p) == 0 for p in parts): raise InvalidParameterError("Invalid chain break usage in sequence") if len(parts) == 1: return Protein(name=name, sequence=parts[0]) @@ -52,7 +66,10 @@ def create_prompt( Context or list of contexts, each of which is a list of sequences/structures. Entries may be raw sequences (``bytes``/``str``), :py:class:`Protein`, or :py:class:`Complex`. Raw sequences may include ``:`` chain breaks to denote - a multichain protein (e.g. ``"ACDE:GHIK"`` becomes a two-chain Complex). + a multichain protein (e.g. ``"ACDE:GHIK"`` becomes a two-chain Complex). A + chain of a context entry may be empty (``":GHIK"``), which says the entry + covers only the chains that do have residues; an entry empty in every chain + is rejected. Currently only protein chains are accepted; passing a Complex with DNA, RNA, or Ligand chains raises :py:class:`InvalidParameterError`. This restriction may be relaxed in the future. @@ -147,8 +164,10 @@ def get_prompt(session: APISession, prompt_id: str) -> list[list[Protein | Compl Get the prompt content for a given prompt ID. Single-chain entries collapse to :py:class:`Protein`; multichain entries are - returned as :py:class:`Complex`. For a uniform return type, see - :py:meth:`Prompt.get_as_complexes` or :py:meth:`Prompt.get_as_proteins`. + returned as :py:class:`Complex`, empty chains included - a prompt sampled from a + multi-chain MSA has an empty chain wherever the entry covers only part of the + complex. For a uniform return type, see :py:meth:`Prompt.get_as_complexes` or + :py:meth:`Prompt.get_as_proteins`. Parameters ---------- @@ -242,7 +261,11 @@ def zip_prompt( context_files: list[tuple[str, io.BytesIO]] = [] for i, x in enumerate(this_context): if isinstance(x, (bytes, str)): - x = _coerce_sequence(name=f"unnamed-{i:06}", sequence=x) + # a sampled prompt marks the chains an entry does not cover with an + # empty slot + x = _coerce_sequence( + name=f"unnamed-{i:06}", sequence=x, allow_empty_chains=True + ) elif not isinstance(x, (Protein, Complex)): raise InvalidParameterError( f"unexpected context entry type: {type(x).__name__}" @@ -364,7 +387,11 @@ def __parse_prompt( name.decode() if isinstance(name, bytes) else name ) entries_in_context.append( - _coerce_sequence(name=entry_name, sequence=sequence) + _coerce_sequence( + name=entry_name, + sequence=sequence, + allow_empty_chains=True, + ) ) else: diff --git a/openprotein/prompt/prompt.py b/openprotein/prompt/prompt.py index 3803859..f07c5f9 100644 --- a/openprotein/prompt/prompt.py +++ b/openprotein/prompt/prompt.py @@ -10,6 +10,11 @@ from .models import Prompt, Query from .schemas import Context +HUMAN_ANTIBODY_VH_V1 = "c044b1b9-9842-536a-83e0-e81400199f67" +HUMAN_ANTIBODY_VH_VL_V1 = "0ddde5dc-d140-5d53-bebf-e69fff5a05c5" +HUMAN_ANTIBODY_VL_V1 = "3da24801-7032-5b79-a0b9-6e687581de60" +HUMAN_ANTIBODY_VL_VH_V1 = "6de556eb-a739-5986-ab20-cf574a780f69" + class PromptAPI: """Prompt API providing the interface to create prompts for use with PoET models.""" @@ -143,6 +148,96 @@ def get_query(self, query_id: str) -> Query: metadata=api.get_query_metadata(session=self.session, query_id=query_id), ) + @property + def human_antibody_vh(self) -> Prompt: + """ + Curated prompt of naive human antibody heavy chains (VH). + + Tracks the latest version of this prompt, currently + :py:attr:`human_antibody_vh_v1`. Use the versioned attribute directly to + pin a version that will not change in a later release. + """ + return self.human_antibody_vh_v1 + + @property + def human_antibody_vh_v1(self) -> Prompt: + """ + Curated prompt of naive human antibody heavy chains (VH), version 1. + + An ensemble of 10 replicates, each a random sample of 200 naive human + antibody heavy chain (VH) sequences from the OAS paired database, + clustered at 70% sequence identity. + """ + return self.get_prompt(HUMAN_ANTIBODY_VH_V1) + + @property + def human_antibody_vl(self) -> Prompt: + """ + Curated prompt of naive human antibody light chains (VL). + + Tracks the latest version of this prompt, currently + :py:attr:`human_antibody_vl_v1`. Use the versioned attribute directly to + pin a version that will not change in a later release. + """ + return self.human_antibody_vl_v1 + + @property + def human_antibody_vl_v1(self) -> Prompt: + """ + Curated prompt of naive human antibody light chains (VL), version 1. + + An ensemble of 10 replicates, each a random sample of 200 naive human + antibody light chain (VL) sequences from the OAS paired database, + clustered at 70% sequence identity. + """ + return self.get_prompt(HUMAN_ANTIBODY_VL_V1) + + @property + def human_antibody_vh_vl(self) -> Prompt: + """ + Curated prompt of naive paired human antibodies, heavy chain first. + + Tracks the latest version of this prompt, currently + :py:attr:`human_antibody_vh_vl_v1`. Use the versioned attribute directly + to pin a version that will not change in a later release. + """ + return self.human_antibody_vh_vl_v1 + + @property + def human_antibody_vh_vl_v1(self) -> Prompt: + """ + Curated prompt of naive paired human antibodies (VH-VL), version 1. + + An ensemble of 10 replicates, each a random sample of 200 naive paired + human antibody sequences from the OAS paired database, clustered at 70% + sequence identity. Each complex is the heavy chain (VH) followed by the + light chain (VL). + """ + return self.get_prompt(HUMAN_ANTIBODY_VH_VL_V1) + + @property + def human_antibody_vl_vh(self) -> Prompt: + """ + Curated prompt of naive paired human antibodies, light chain first. + + Tracks the latest version of this prompt, currently + :py:attr:`human_antibody_vl_vh_v1`. Use the versioned attribute directly + to pin a version that will not change in a later release. + """ + return self.human_antibody_vl_vh_v1 + + @property + def human_antibody_vl_vh_v1(self) -> Prompt: + """ + Curated prompt of naive paired human antibodies (VL-VH), version 1. + + An ensemble of 10 replicates, each a random sample of 200 naive paired + human antibody sequences from the OAS paired database, clustered at 70% + sequence identity. Each complex is the light chain (VL) followed by the + heavy chain (VH). + """ + return self.get_prompt(HUMAN_ANTIBODY_VL_VH_V1) + def _resolve_query( self, query: ( diff --git a/pixi.lock b/pixi.lock index c783a81..4c43dc3 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,8 +1,22 @@ version: 7 platforms: - name: linux-64 + virtual-packages: + - __unix=0=0 + - __linux=4.18 + - __glibc=2.28 + - __archspec=0=x86_64 - name: linux-aarch64 + virtual-packages: + - __unix=0=0 + - __linux=4.18 + - __glibc=2.28 + - __archspec=0=aarch64 - name: osx-arm64 + virtual-packages: + - __unix=0=0 + - __osx=13.0 + - __archspec=0=m1 environments: default: channels: @@ -11,124 +25,121 @@ environments: - https://pypi.org/simple packages: linux-64: - - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - - conda: 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extra == 'telegram' + - envwrap ; extra == 'telegram' + - ipywidgets>=6 ; extra == 'notebook' + requires_python: '>=3.8' diff --git a/pyproject.toml b/pyproject.toml index dce5769..9578146 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,31 +17,31 @@ classifiers = [ "Programming Language :: Python :: 3", ] dependencies = [ - "requests>=2.32.3,<3", - "pydantic>=2.5,<3", - "tqdm>=4.66.4,<5", - "pandas>=2.2.2,<3", - "numpy>=1.9,<3", + "requests>=2.32.3", + "pydantic>=2.5", + "tqdm>=4.66.4", + "pandas>=2.2.2", + "numpy>=1.9", "gemmi>=0.6.0,<0.8", - "tomli>=2.3.0,<3", - "filelock>=3.13,<4", + "tomli>=2.3.0", + "filelock>=3.13", ] requires-python = ">=3.10,<3.15" [dependency-groups] dev = [ - "pip>=24.2,<25", - "ipykernel>=6.29.5,<7", - "pytest>=9,<10", - "pytest-xdist>=3.6.1,<4", - "pandas-stubs>=2.1.4.240909,<3", - "matplotlib>=3.9.2,<4", - "scipy>=1.14.1,<2", + "pip>=24.2", + "ipykernel>=6.29.5", + "pytest>=9", + "pytest-xdist>=3.6.1", + "pandas-stubs>=2.1.4.240909", + "matplotlib>=3.9.2", + "scipy>=1.14.1", "hatchling>=1.26.1", - "hatch-vcs>=0.5,<1", - "editables>=0.5,<0.6", - "seaborn>=0.13.2,<0.14", - "jupyterlab>=4.4.1,<5", + "hatch-vcs>=0.5", + "editables>=0.5", + "seaborn>=0.13.2", + "jupyterlab>=4.4.1", "torch>=2.2.0,<3", ] diff --git a/tests/align/test_align_api.py b/tests/align/test_align_api.py index 5fd65d0..87d3ccc 100644 --- a/tests/align/test_align_api.py +++ b/tests/align/test_align_api.py @@ -5,6 +5,7 @@ from openprotein.align.api import ( abnumber_post, + antibody_schema_get, clustalo_post, get_align_job_inputs, get_input, @@ -14,7 +15,7 @@ msa_post, prompt_post, ) -from openprotein.align.schemas import AlignType, MSASamplingMethod +from openprotein.align.schemas import AlignType, MSASamplingMethod, UnnumberedPolicy from openprotein.base import APISession from openprotein.errors import HTTPError, InvalidParameterError, MissingParameterError from openprotein.jobs import Job, JobStatus, JobType @@ -165,6 +166,63 @@ def test_abnumber_post_with_drop_minority_chains( assert kwargs["params"]["drop_minority_chains"] is True +def test_abnumber_post_default_unnumbered_policy( + mock_session: MagicMock, sample_job_dict: dict +): + """abnumber_post should default unnumbered_policy to error, so dropping + residues is always a choice the caller made.""" + mock_session.post.return_value.json.return_value = sample_job_dict + abnumber_post(mock_session, io.BytesIO(b"test")) + + _args, kwargs = mock_session.post.call_args + assert kwargs["params"]["unnumbered_policy"] == "error" + + +@pytest.mark.parametrize("policy", ["drop", "retain"]) +def test_abnumber_post_forwards_unnumbered_policy( + mock_session: MagicMock, sample_job_dict: dict, policy: str +): + """abnumber_post should forward the policy as its wire value.""" + mock_session.post.return_value.json.return_value = sample_job_dict + abnumber_post(mock_session, io.BytesIO(b"test"), unnumbered_policy=policy) + + _args, kwargs = mock_session.post.call_args + assert kwargs["params"]["unnumbered_policy"] == policy + + +def test_abnumber_post_accepts_policy_enum( + mock_session: MagicMock, sample_job_dict: dict +): + """The enum and its string value are interchangeable on the wire.""" + mock_session.post.return_value.json.return_value = sample_job_dict + abnumber_post( + mock_session, io.BytesIO(b"test"), unnumbered_policy=UnnumberedPolicy.RETAIN + ) + + _args, kwargs = mock_session.post.call_args + assert kwargs["params"]["unnumbered_policy"] == "retain" + + +def test_abnumber_post_invalid_unnumbered_policy(mock_session: MagicMock): + """abnumber_post rejects an unknown policy before submitting.""" + with pytest.raises( + Exception, match="Unnumbered residue policy maybe not recognized" + ): + abnumber_post(mock_session, io.BytesIO(), unnumbered_policy="maybe") + + +def test_antibody_schema_get(mock_session: MagicMock): + """antibody_schema_get returns the job's extras as sent.""" + extras = {"chains": [{"chain_type": "H"}], "warnings": []} + mock_session.get.return_value.json.return_value = extras + + assert antibody_schema_get(mock_session, "job123") == extras + + args, kwargs = mock_session.get.call_args + assert args[0] == "v1/align/antibody_schema" + assert kwargs["params"] == {"job_id": "job123"} + + def test_prompt_post_valid(mock_session: MagicMock, sample_job_dict: dict): """Test prompt_post with valid parameters.""" mock_session.post.return_value.json.return_value = sample_job_dict diff --git a/tests/align/test_align_msa.py b/tests/align/test_align_msa.py index 54fdb41..fbdcc37 100644 --- a/tests/align/test_align_msa.py +++ b/tests/align/test_align_msa.py @@ -1,11 +1,18 @@ from datetime import datetime +import warnings import pytest from unittest.mock import MagicMock, patch from openprotein.base import APISession +from openprotein.errors import APIError from openprotein.jobs import Job, JobStatus, JobType from openprotein.align.msa import MSAFuture -from openprotein.align.schemas import MafftJob, MSASamplingMethod +from openprotein.align.schemas import ( + AbNumberJob, + JobWarning, + MafftJob, + MSASamplingMethod, +) from openprotein.prompt import Prompt @@ -74,3 +81,182 @@ def test_msa_future_sample_prompt( ) assert prompt == mock_prompt_future + + +_UNNUMBERED_WARNING = { + "code": "UNNUMBERED_RESIDUES_DROPPED", + "message": "Residues outside the region AbNumber numbered were dropped.", + "metadata": { + "residue_count": 103, + "chain_count": 1, + "chains": [ + { + "chain_index": 0, + "sequence_count": 3, + "residue_count": 103, + "max_prefix_length": 0, + "max_suffix_length": 103, + "sampled": False, + "sequences": [{"name": "s0", "prefix_length": 0, "suffix_length": 103}], + } + ], + }, +} + + +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_antibody_schema(mock_schema_get, msa_future: MSAFuture): + """get_antibody_schema passes the job through to the API helper.""" + msa_future.get_antibody_schema() + mock_schema_get.assert_called_once_with( + session=msa_future.session, job_id=msa_future.job.job_id + ) + + +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_warnings(mock_schema_get, msa_future: MSAFuture): + """get_warnings parses the extras' warnings into models.""" + mock_schema_get.return_value = {"chains": [], "warnings": [_UNNUMBERED_WARNING]} + + (warning,) = msa_future.get_warnings() + + assert isinstance(warning, JobWarning) + assert warning.code == "UNNUMBERED_RESIDUES_DROPPED" + assert warning.metadata is not None + assert warning.metadata["chains"][0]["max_suffix_length"] == 103 + + +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_warnings_empty(mock_schema_get, msa_future: MSAFuture): + """A job with nothing to report has no warnings.""" + mock_schema_get.return_value = {"chains": [], "warnings": []} + + assert msa_future.get_warnings() == [] + + +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_warnings_absent_key(mock_schema_get, msa_future: MSAFuture): + """Extras with no ``warnings`` key report nothing.""" + mock_schema_get.return_value = {"chains": []} + + assert msa_future.get_warnings() == [] + + +@pytest.fixture +def abnumber_job() -> AbNumberJob: + """Fixture for a sample AbNumberJob object.""" + return AbNumberJob( + job_id="job456", + status=JobStatus.SUCCESS, + job_type=JobType.abnumber, + created_date=datetime.fromisoformat("2023-01-01T00:00:00"), + ) + + +@pytest.fixture +def abnumber_future(mock_session: MagicMock, abnumber_job: AbNumberJob) -> MSAFuture: + """Fixture for an MSAFuture over an AbNumber job.""" + return MSAFuture(mock_session, abnumber_job) + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_warns_on_reported_warning( + mock_schema_get, mock_get_msa, abnumber_future: MSAFuture +): + """Fetching the results surfaces what the job reported about them.""" + mock_schema_get.return_value = { + "chains": [], + "warnings": [ + { + "code": "UNNUMBERED_RESIDUES_DROPPED", + "message": "16 residues were dropped", + "metadata": None, + } + ], + } + + with pytest.warns(UserWarning, match="UNNUMBERED_RESIDUES_DROPPED"): + abnumber_future.get() + + mock_get_msa.assert_called_once() + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_wait_warns_on_reported_warning( + mock_schema_get, mock_get_msa, abnumber_future: MSAFuture +): + """`wait` reaches the results through `get`, so it warns too.""" + mock_schema_get.return_value = { + "warnings": [{"code": "UNNUMBERED_RESIDUES_RETAINED", "message": "kept 16"}] + } + + with ( + patch.object(MSAFuture, "_wait_job", return_value=abnumber_future.job), + patch("time.sleep"), + ): + with pytest.warns(UserWarning, match="UNNUMBERED_RESIDUES_RETAINED"): + abnumber_future.wait() + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_warns_once_per_future( + mock_schema_get, mock_get_msa, abnumber_future: MSAFuture +): + """The schema is fetched once, however many times the results are read.""" + mock_schema_get.return_value = { + "warnings": [{"code": "UNNUMBERED_RESIDUES_DROPPED", "message": "dropped 16"}] + } + + with pytest.warns(UserWarning): + abnumber_future.get() + with warnings.catch_warnings(record=True) as caught: + warnings.simplefilter("always") + abnumber_future.get() + + assert caught == [] + mock_schema_get.assert_called_once() + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_silent_without_warnings( + mock_schema_get, mock_get_msa, abnumber_future: MSAFuture +): + """A job that reported nothing warns about nothing.""" + mock_schema_get.return_value = {"chains": [], "warnings": []} + + with warnings.catch_warnings(record=True) as caught: + warnings.simplefilter("always") + abnumber_future.get() + + assert caught == [] + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_skips_schema_for_other_methods( + mock_schema_get, mock_get_msa, msa_future: MSAFuture +): + """Only AbNumber jobs have an antibody schema to read.""" + msa_future.get() + + mock_schema_get.assert_not_called() + + +@patch("openprotein.align.api.get_msa") +@patch("openprotein.align.api.antibody_schema_get") +def test_msa_future_get_survives_unreachable_schema( + mock_schema_get, mock_get_msa, abnumber_future: MSAFuture +): + """Results stay readable when the schema endpoint does not answer.""" + mock_schema_get.side_effect = APIError("no such endpoint") + + with warnings.catch_warnings(record=True) as caught: + warnings.simplefilter("always") + abnumber_future.get() + + assert caught == [] + mock_get_msa.assert_called_once() diff --git a/tests/e2e/test_fold_e2e.py b/tests/e2e/test_fold_e2e.py index 64207ca..8e2f7d9 100644 --- a/tests/e2e/test_fold_e2e.py +++ b/tests/e2e/test_fold_e2e.py @@ -6,13 +6,13 @@ import numpy as np import pytest - from openprotein import OpenProtein from openprotein.align.msa import MSAFuture from openprotein.errors import APIError, HTTPError from openprotein.fold.future import FoldResultFuture from openprotein.molecules import Complex, Ligand, Protein, Structure from openprotein.molecules.template import Template + from tests.e2e.config import scaled_timeout E2E_TIMEOUT = scaled_timeout(1.5) @@ -108,7 +108,9 @@ def test_e2e_fold_rejects_total_sequence_length_above_model_max( if uses_multichain_entity: chain_a_len = max_len // 2 - chain_b_len = max_len - chain_a_len + overage # total length is max_len + overage + chain_b_len = ( + max_len - chain_a_len + overage + ) # total length is max_len + overage chain_a = Protein("A" * chain_a_len) chain_a.msa = Protein.single_sequence_mode @@ -156,6 +158,142 @@ def test_e2e_fold_rejects_invalid_chain_ids( model.fold(sequences=[complex_input]) +# Oseltamivir phosphate as a user actually submitted it. The phosphate carries +# one oxygen too many, leaving P with valence 6, so RDKit refuses to parse it. +# It reached a protenix worker, where RDKit returned None and the resulting +# Boost.Python error could not be pickled, taking the LitServe worker process +# down with it. Validation has to reject this at submission. +UNPARSEABLE_LIGAND_SMILES = "CCOC(=O)C1=CC(C(CC1NC(=O)C)OC(CC)CC)N.OP(=O)(O)(O)O" + +MALFORMED_LIGAND_SMILES = [ + UNPARSEABLE_LIGAND_SMILES, + "not a smiles", + "CC(", # unbalanced parens + "c1ccccc", # unclosed aromatic ring +] + +# The same molecule written correctly: a two-fragment salt. +OSELTAMIVIR_PHOSPHATE = "CCOC(=O)C1=CC(C(CC1NC(=O)C)OC(CC)CC)N.OP(=O)(O)O" + +# Models whose workers accept ligand chains, and which therefore validate them. +LIGAND_MODEL_IDS = [ + "boltz-1", + "boltz-1x", + "boltz-2", + "esmfold2", + "esmfold2-fast", + "protenix", + "protenix-v2", + "rosettafold-3", +] + + +# Variants that take no MSA. The SDK rejects an attached MSA client-side, which +# would abort the request before any ligand reached validation. +SINGLE_SEQUENCE_MODEL_IDS = {"esmfold2-fast"} + + +def _require_model(session: OpenProtein, model_id: str): + """Skip rather than fail when this backend does not serve the model.""" + if model_id not in {model.id for model in session.fold.list_models()}: + pytest.skip(f"{model_id} is not available in this backend") + return session.fold.get_model(model_id) + + +def _with_ligand(fold_complex: Complex, model_id: str, ligand: Ligand) -> Complex: + """Attach `ligand` as chain D, shedding MSAs where the model forbids them.""" + if model_id in SINGLE_SEQUENCE_MODEL_IDS: + for protein in fold_complex.get_proteins().values(): + protein.msa = Protein.single_sequence_mode + fold_complex.set_chain("D", ligand) + return fold_complex + + +@pytest.mark.e2e +@pytest.mark.parametrize("model_id", LIGAND_MODEL_IDS) +def test_e2e_fold_rejects_unparseable_ligand_smiles( + session: OpenProtein, + fold_complex: Complex, + model_id: str, +): + """Every ligand-capable model rejects a SMILES that RDKit cannot parse.""" + model = _require_model(session, model_id) + fold_complex = _with_ligand( + fold_complex, model_id, Ligand(smiles=UNPARSEABLE_LIGAND_SMILES) + ) + + with pytest.raises(HTTPError, match="Status code") as exc_info: + model.fold(sequences=[fold_complex]) + # Pin the reason: a fold rejected for some unrelated reason would otherwise + # satisfy this test and hide the fact that ligands went unchecked. + assert "ligand" in exc_info.value.text.lower() + + +@pytest.mark.e2e +@pytest.mark.parametrize("smiles", MALFORMED_LIGAND_SMILES) +def test_e2e_fold_rejects_malformed_ligand_smiles( + session: OpenProtein, + fold_complex: Complex, + smiles: str, +): + """Malformed SMILES are rejected in several shapes, not just the prod one.""" + model = _require_model(session, "boltz-2") + fold_complex.set_chain("D", Ligand(smiles=smiles)) + + with pytest.raises(HTTPError, match="Status code"): + model.fold(sequences=[fold_complex]) + + +@pytest.mark.e2e +@pytest.mark.parametrize("model_id", LIGAND_MODEL_IDS) +def test_e2e_fold_rejects_unknown_ligand_ccd( + session: OpenProtein, + fold_complex: Complex, + model_id: str, +): + """CCD ligands are checked against the PDB component set.""" + model = _require_model(session, model_id) + fold_complex = _with_ligand(fold_complex, model_id, Ligand(ccd="ZZZZ")) + + with pytest.raises(HTTPError, match="Status code") as exc_info: + model.fold(sequences=[fold_complex]) + assert "ligand" in exc_info.value.text.lower() + + +@pytest.mark.e2e +def test_e2e_fold_rejects_ccd_the_model_cannot_build( + session: OpenProtein, + fold_complex: Complex, +): + """CCD support is per model, not a single global list. + + 0IL is a real PDB component that boltz-1 cannot build, so it has to be + rejected there while remaining acceptable to models that can. + """ + model = _require_model(session, "boltz-1") + fold_complex.set_chain("D", Ligand(ccd="0IL")) + + with pytest.raises(HTTPError, match="Status code"): + model.fold(sequences=[fold_complex]) + + +@pytest.mark.e2e +def test_e2e_fold_rejects_ccd_outside_esmfold2_allowlist( + session: OpenProtein, + fold_complex: Complex, +): + """ESMFold2 ships its own CCD list rather than the universal one. + + UNL is a known PDB component that ESMFold2 does not carry, so being in the + universal set is not enough to be accepted. + """ + model = _require_model(session, "esmfold2") + fold_complex.set_chain("D", Ligand(ccd="UNL")) + + with pytest.raises(HTTPError, match="Status code"): + model.fold(sequences=[fold_complex]) + + @pytest.mark.e2e def test_e2e_fold_with_esmfold( session: OpenProtein, diff --git a/tests/e2e/test_multichain_e2e.py b/tests/e2e/test_multichain_e2e.py index 1757e05..bd8c226 100644 --- a/tests/e2e/test_multichain_e2e.py +++ b/tests/e2e/test_multichain_e2e.py @@ -19,22 +19,52 @@ length, ":" frozen at its column, never introduced elsewhere). * alignment jobs (mafft / clustalo / abnumber) on multi-chain inputs: each chain is aligned independently and rejoined with a single ":" column, and - gap-stripping each chain recovers the input chains. + gap-stripping each chain recovers the input chains. Chain order is + positional, so "L:H" is as valid as "H:L". + * multi-chain input that cannot be aligned: ragged chain counts and empty + chain positions are refused at submission; abnumber + ``drop_minority_chains`` and a chain position holding more than one chain + type fail the job. + * prompt sampling from a multi-chain MSA: sampling scores residue columns, so + the ":" break is dropped from the encoded MSA and restored in the sampled + rows. Every context entry comes back as a Complex with the seed's chain + layout, across the sequence and residue budgets, ensemble replicates, + similarity bounds, and seed inclusion. Covers both a search-built MSA and + one a user uploads directly (the non-a3m reader), including that reader's + validation of a misaligned chain break. + * prompt context entries may leave a chain slot empty -- a homolog covering + one chain of the complex -- and only an entry with no residues at all is + refused. + * abnumber ``unnumbered_policy`` on a paired row whose heavy chain carries a + constant region: the default fails the job, ``drop`` aligns the variable + domains alone, and ``retain`` keeps every residue. Either way the job + reports what it did in ``get_warnings()``, scoped to the chain position + it affected. """ from __future__ import annotations +import io + import numpy as np import pandas as pd import pytest - from openprotein import OpenProtein -from openprotein.align.schemas import AbNumberScheme +from openprotein.align.msa import MSAFuture +from openprotein.align.schemas import ( + AbNumberScheme, + MSASamplingMethod, + UnnumberedPolicy, +) from openprotein.common.reduction import ReductionType from openprotein.design import ModelCriterion +from openprotein.errors import HTTPError, InvalidParameterError +from openprotein.molecules import Complex + from tests.e2e.config import scaled_timeout from tests.e2e.correctness.support import fresh_prompt, require_embedding_model from tests.utils.sequences import ( + ANTIBODY_HEAVY_CONSTANT_SEQUENCE, ANTIBODY_HEAVY_SEQUENCE, ANTIBODY_LIGHT_SEQUENCE, mutate_sequence, @@ -469,18 +499,403 @@ def test_multichain_clustalo_alignment(session: OpenProtein): _assert_multichain_alignment(list(future.get()), seqs) +def _paired_antibodies(n: int, *, heavy_first: bool = True) -> list[str]: + """``n`` paired antibody rows. Substitution-only mutation keeps every chain + numberable (indels would break the variable-domain framing).""" + first, second = ( + (ANTIBODY_HEAVY_SEQUENCE, ANTIBODY_LIGHT_SEQUENCE) + if heavy_first + else (ANTIBODY_LIGHT_SEQUENCE, ANTIBODY_HEAVY_SEQUENCE) + ) + return [ + f"{mutate_sequence(first, mutation_rate=0.02)}:" + f"{mutate_sequence(second, mutation_rate=0.02)}" + for _ in range(n) + ] + + def test_multichain_abnumber_alignment(session: OpenProtein): """AbNumber numbers each chain of a paired heavy:light antibody independently - and rejoins with the ":" column. Substitution-only mutation keeps every chain - numberable (indels would break the variable-domain framing).""" - seqs = [ - f"{mutate_sequence(ANTIBODY_HEAVY_SEQUENCE, mutation_rate=0.02)}:" + and rejoins with the ":" column.""" + seqs = _paired_antibodies(3) + + future = session.align.abnumber(sequences=seqs, scheme=AbNumberScheme.CHOTHIA) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + assert future.status == "SUCCESS" + + _assert_multichain_alignment(list(future.get()), seqs) + assert future.get_warnings() == [], "fully numbered input has nothing to report" + + +def test_multichain_abnumber_light_heavy_order(session: OpenProtein): + """Chain order is positional, so "L:H" aligns as readily as "H:L".""" + seqs = _paired_antibodies(3, heavy_first=False) + + future = session.align.abnumber(sequences=seqs, scheme=AbNumberScheme.CHOTHIA) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + assert future.status == "SUCCESS" + + _assert_multichain_alignment(list(future.get()), seqs) + + +# --------------------------------------------------------------------------- # +# Unnumbered residues on multi-chain input +# --------------------------------------------------------------------------- # +# +# ANARCI numbers the variable domain only, so a heavy chain carrying its +# constant region has residues with no antibody position. ``unnumbered_policy`` +# decides their fate, per chain position: here only the heavy position is +# affected, the light one is numbered end to end. + + +def _paired_antibodies_with_constant(n: int) -> list[str]: + """``n`` paired rows whose heavy chain runs past the variable domain into + CH1, so every heavy position carries unnumbered residues.""" + return [ + f"{mutate_sequence(ANTIBODY_HEAVY_SEQUENCE, mutation_rate=0.02)}" + f"{ANTIBODY_HEAVY_CONSTANT_SEQUENCE}:" f"{mutate_sequence(ANTIBODY_LIGHT_SEQUENCE, mutation_rate=0.02)}" - for _ in range(3) + for _ in range(n) ] + +def _variable_domains_only(seqs: list[str]) -> set[str]: + """``seqs`` with the constant region cut off the heavy position.""" + return { + ":".join(c.replace(ANTIBODY_HEAVY_CONSTANT_SEQUENCE, "") for c in s.split(":")) + for s in seqs + } + + +def _assert_unnumbered_warning(future, code: str, seqs: list[str]) -> None: + """The job reports the unnumbered residues under ``code``, scoped to the + heavy position: only chain 0 is affected, and every constant region counts + towards the total.""" + (warning,) = future.get_warnings() + assert warning.code == code + assert warning.message + + metadata = warning.metadata + assert metadata is not None + assert metadata["chain_count"] == 1, "only the heavy position is affected" + assert metadata["residue_count"] == len(ANTIBODY_HEAVY_CONSTANT_SEQUENCE) * len( + seqs + ) + + (chain,) = metadata["chains"] + assert chain["chain_index"] == 0 + assert chain["sequence_count"] == len(seqs) + assert chain["max_prefix_length"] == 0 + assert chain["max_suffix_length"] == len(ANTIBODY_HEAVY_CONSTANT_SEQUENCE) + + +def test_multichain_abnumber_unnumbered_error_is_the_default(session: OpenProtein): + """Residues outside the numbered domain fail the job unless the caller picks + a policy, so they are never discarded by default.""" + seqs = _paired_antibodies_with_constant(2) + future = session.align.abnumber(sequences=seqs, scheme=AbNumberScheme.CHOTHIA) future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + + assert future.status == "FAILURE" + + +def test_multichain_abnumber_unnumbered_drop(session: OpenProtein): + """``drop`` aligns the numbered variable domains and discards the rest, so + gap-stripping recovers the input minus its constant region.""" + seqs = _paired_antibodies_with_constant(3) + + future = session.align.abnumber( + sequences=seqs, + scheme=AbNumberScheme.CHOTHIA, + unnumbered_policy=UnnumberedPolicy.DROP, + ) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) assert future.status == "SUCCESS" - _assert_multichain_alignment(list(future.get()), seqs) + with pytest.warns(UserWarning, match="UNNUMBERED_RESIDUES_DROPPED"): + rows = list(future.get()) + + _assert_multichain_alignment(rows, list(_variable_domains_only(seqs))) + _assert_unnumbered_warning(future, "UNNUMBERED_RESIDUES_DROPPED", seqs) + + +def test_multichain_abnumber_unnumbered_retain(session: OpenProtein): + """``retain`` keeps every unnumbered residue, so the ":" layout still holds + and gap-stripping recovers the full input including the constant region.""" + seqs = _paired_antibodies_with_constant(3) + + future = session.align.abnumber( + sequences=seqs, + scheme=AbNumberScheme.CHOTHIA, + unnumbered_policy=UnnumberedPolicy.RETAIN, + ) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + assert future.status == "SUCCESS" + + with pytest.warns(UserWarning, match="UNNUMBERED_RESIDUES_RETAINED"): + rows = list(future.get()) + + _assert_multichain_alignment(rows, seqs) + + aligned = [row[1] for row in rows] + assert all(ANTIBODY_HEAVY_CONSTANT_SEQUENCE in s for s in aligned), ( + "retain pads the constant region against the domain boundary, so it " + "stays contiguous" + ) + + _assert_unnumbered_warning(future, "UNNUMBERED_RESIDUES_RETAINED", seqs) + + +# --------------------------------------------------------------------------- # +# Multi-chain layout and semantics that are refused +# --------------------------------------------------------------------------- # +# +# Layout violations are structural and are caught at submission, before a job +# exists. Chain-type violations need ANARCI numbering, so they surface as a +# failed job. + + +def test_multichain_ragged_chain_counts_rejected(session: OpenProtein): + """Chain positions are aligned independently and rejoined by index, so every + row has to carry the same number of chains.""" + heavy0, light0 = _generic_chains() + + with pytest.raises(HTTPError, match="Status code 400"): + session.align.mafft(sequences=[f"{heavy0}:{light0}", heavy0]) + + +def test_multichain_empty_chain_rejected(session: OpenProtein): + """A trailing ":" leaves a chain position with no residues in it.""" + heavy0, light0 = _generic_chains() + + with pytest.raises(HTTPError, match="Status code 400"): + session.align.mafft(sequences=[f"{heavy0}:", f"{heavy0}:{light0}"]) + + +def test_multichain_abnumber_drop_minority_chains_rejected(session: OpenProtein): + """``drop_minority_chains`` removes whole rows, which the index-wise rejoin + cannot honour, so it is only available for single-chain input.""" + seqs = _paired_antibodies(2) + + future = session.align.abnumber( + sequences=seqs, + scheme=AbNumberScheme.CHOTHIA, + drop_minority_chains=True, + ) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + + assert future.status == "FAILURE" + + +def test_multichain_abnumber_mixed_chain_types_rejected(session: OpenProtein): + """One chain position is numbered as a single alignment, so every row must + agree on that position's chain type.""" + heavy = mutate_sequence(ANTIBODY_HEAVY_SEQUENCE, mutation_rate=0.02) + light = mutate_sequence(ANTIBODY_LIGHT_SEQUENCE, mutation_rate=0.02) + other_light = mutate_sequence(ANTIBODY_LIGHT_SEQUENCE, mutation_rate=0.02) + + future = session.align.abnumber( + sequences=[f"{heavy}:{light}", f"{other_light}:{light}"], + scheme=AbNumberScheme.CHOTHIA, + ) + future.wait_until_done(verbose=True, timeout=ALIGN_TIMEOUT) + + assert future.status == "FAILURE" + + +# --------------------------------------------------------------------------- # +# Prompt sampling from multi-chain MSAs +# --------------------------------------------------------------------------- # +# +# Sampling scores residue columns, so the ":" break is dropped from the encoded +# MSA and restored in the sampled rows. Every sampled context entry therefore +# carries the seed's chain layout and comes back as a Complex. + +PROMPT_TIMEOUT = scaled_timeout(4.0) +PROMPT_CONTEXT_SIZE = 8 + + +def _multichain_msa(session: OpenProtein, chain_a: str, chain_b: str) -> MSAFuture: + """MSA search seeded with a two-chain complex.""" + return session.align.create_msa(seed=f"{chain_a}:{chain_b}".encode()) + + +def _uploaded_multichain_msa( + session: OpenProtein, query: str, rows: list[str] +) -> MSAFuture: + """A ready-made multi-chain MSA a user uploads directly, bypassing homology + search. This is the non-a3m path: a plain FASTA block, no insertions.""" + records = [f">query\n{query}"] + [ + f">homolog_{i}\n{row}" for i, row in enumerate(rows) + ] + fasta = ("\n".join(records) + "\n").encode() + return session.align.upload_msa(io.BytesIO(fasta)) + + +def _assert_multichain_prompt(replicates, n_chains: int = 2) -> None: + """Every sampled context entry carries the seed's chain layout: a Complex of + ``n_chains`` protein chains, none of them holding a further ":".""" + assert replicates, "prompt returned no replicates" + for entries in replicates: + assert entries, "prompt replicate has no context entries" + for entry in entries: + assert isinstance(entry, Complex), ( + f"multi-chain context entry came back as {type(entry).__name__}" + ) + proteins = entry.get_proteins() + assert len(proteins) == n_chains, ( + f"expected {n_chains} chains, got {len(proteins)}" + ) + assert len(entry.get_chains()) == len(proteins), ( + "non-protein chain in prompt" + ) + for chain in proteins.values(): + assert b":" not in chain.sequence, f"chain retains a break: {chain!r}" + + +def _sample(msa: MSAFuture, **kwargs): + """Sample a prompt and return its replicates, asserting the job succeeded.""" + prompt = msa.sample_prompt(**kwargs) + prompt.wait_until_done(verbose=True, timeout=PROMPT_TIMEOUT) + assert prompt.status == "SUCCESS" + return prompt.get() + + +def test_multichain_prompt_sampling(session: OpenProtein): + """Sampling a multi-chain MSA yields context entries with the seed's layout.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + _assert_multichain_prompt(_sample(msa, num_sequences=PROMPT_CONTEXT_SIZE)) + + +def test_multichain_prompt_sampling_by_residues(session: OpenProtein): + """The residue budget counts the break column, so a token-bounded prompt keeps + the same chain layout as a sequence-bounded one.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + _assert_multichain_prompt(_sample(msa, num_residues=2048)) + + +def test_multichain_prompt_sampling_ensemble(session: OpenProtein): + """Each ensemble replicate is sampled with its own seed and keeps the layout.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + replicates = _sample(msa, num_sequences=PROMPT_CONTEXT_SIZE, num_ensemble_prompts=3) + assert len(replicates) == 3 + _assert_multichain_prompt(replicates) + + +def test_multichain_prompt_sampling_similarity_bounds(session: OpenProtein): + """Similarity bounds are measured over residue columns. A break counted as a + matching column shifts every row's similarity toward the seed's, which is what + these bounds gate on.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + _assert_multichain_prompt( + _sample( + msa, + num_sequences=PROMPT_CONTEXT_SIZE, + max_similarity=0.95, + min_similarity=0.2, + ) + ) + + +def test_multichain_prompt_sampling_random_method(session: OpenProtein): + """RANDOM skips the homology weights, so it isolates the similarity filter.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + _assert_multichain_prompt( + _sample( + msa, + num_sequences=PROMPT_CONTEXT_SIZE, + method=MSASamplingMethod.RANDOM, + ) + ) + + +def test_multichain_prompt_sampling_includes_seed(session: OpenProtein): + """``always_include_seed_sequence`` puts the seed complex in the context with + both chains at full length.""" + chain_a, chain_b = _generic_chains() + msa = _multichain_msa(session, chain_a, chain_b) + + replicates = _sample( + msa, + num_sequences=PROMPT_CONTEXT_SIZE, + always_include_seed_sequence=True, + ) + _assert_multichain_prompt(replicates) + + wanted = sorted([chain_a, chain_b]) + found = [ + sorted(p.sequence.decode() for p in entry.get_proteins().values()) + for entries in replicates + for entry in entries + ] + assert wanted in found, "seed complex is not in the sampled context" + + +def test_multichain_prompt_sampling_from_uploaded_msa(session: OpenProtein): + """A user-uploaded MSA has no homology-search a3m behind it -- it hits the + worker's plain-FASTA/CSV reader, which has to drop the chain break itself + just like the a3m reader does.""" + chain_a, chain_b = _generic_chains() + query = f"{chain_a}:{chain_b}" + homologs = _multichain_same_length_dataset(10, chain_a, chain_b) + msa = _uploaded_multichain_msa(session, query, homologs) + + _assert_multichain_prompt(_sample(msa, num_sequences=PROMPT_CONTEXT_SIZE)) + + +def test_multichain_prompt_uploaded_msa_misaligned_break_fails(session: OpenProtein): + """Every row of an uploaded MSA has to place its break at the query's column. + A homolog whose break lands one column early (same total width, wrong chain + boundary) fails the prompt job instead of sampling on a silently misaligned + complex.""" + chain_a, chain_b = _generic_chains() + query = f"{chain_a}:{chain_b}" + good = _multichain_same_length_dataset(5, chain_a, chain_b) + misaligned = f"{chain_a[:-1]}:{chain_a[-1]}{chain_b}" + msa = _uploaded_multichain_msa(session, query, good + [misaligned]) + + prompt = msa.sample_prompt(num_sequences=PROMPT_CONTEXT_SIZE) + prompt.wait_until_done(verbose=True, timeout=PROMPT_TIMEOUT) + + assert prompt.status == "FAILURE" + + +def test_multichain_prompt_empty_chain_round_trips(session: OpenProtein): + """A chain position with no residues is an empty slot, and it survives the + round trip. + + Sampling emits this shape for a homolog that covers only one chain of the + seed: the absent chain gap-strips to an empty segment, so the row renders as + ":SEQ". The empty slot is what says which chain the residues cover, so it has + to reach the service and come back rather than being refused or collapsed. + """ + chain_a, _chain_b = _generic_chains() + + for sequence, expected in [ + (f":{chain_a}", [b"", chain_a.encode()]), + (f"{chain_a}:", [chain_a.encode(), b""]), + ]: + prompt = session.prompt.create_prompt([sequence]) + (entry,) = prompt.get()[0] + assert isinstance(entry, Complex), ( + f"empty-slot entry came back as {type(entry).__name__}" + ) + assert [p.sequence for p in entry.get_proteins().values()] == expected + + +def test_multichain_prompt_entry_without_residues_rejected(session: OpenProtein): + """An entry that is empty in every chain carries nothing, so the client refuses + it rather than creating a prompt with a contentless context entry.""" + with pytest.raises(InvalidParameterError, match="no residues"): + session.prompt.create_prompt([":"]) diff --git a/tests/e2e/test_predictor_e2e.py b/tests/e2e/test_predictor_e2e.py index 09a9bb1..ebd052a 100644 --- a/tests/e2e/test_predictor_e2e.py +++ b/tests/e2e/test_predictor_e2e.py @@ -8,6 +8,7 @@ from openprotein.common.reduction import ReductionType from openprotein.data import AssayDataset from openprotein.errors import HTTPError, InvalidParameterError +from openprotein.predictor import KernelType from tests.e2e.config import scaled_timeout from tests.utils.sequences import random_sequence_fake @@ -474,3 +475,115 @@ def test_predictor_svd_batch_prediction( # Validate batch output assert mus.shape == (10, 1) assert vs.shape == (10, 1) + + +# (kernel, extra hyperparameters) for the GP kernels exposed in the client. +# period/alpha are only valid for periodic/rational_quadratic respectively. +KERNEL_CONFIGS = [ + ("linear", {}), + ("rbf", {}), + ("matern12", {}), + ("matern32", {}), + ("matern52", {}), + ("periodic", {"period": 1.0}), + ("rational_quadratic", {"alpha": 1.0}), +] + + +@pytest.mark.e2e +@pytest.mark.parametrize("kernel,kernel_kwargs", KERNEL_CONFIGS) +def test_predictor_training_kernels( + session: OpenProtein, + assay_small: AssayDataset, + kernel: str, + kernel_kwargs: dict, +): + """ + Train a GP predictor with each exposed kernel and confirm the backend + accepts the kernel (and its hyperparameters) and returns valid predictions. + """ + embedding_model = session.embedding.esm2 + property_name = assay_small.measurement_names[0] + + predictor_future = embedding_model.fit_gp( + assay=assay_small, + properties=[property_name], + reduction=ReductionType.MEAN, + kernel=kernel, + **kernel_kwargs, + ) + + assert predictor_future.wait( + timeout=TIMEOUT + ), f"Predictor training failed for kernel {kernel!r}" + predictor_model = predictor_future + + assert predictor_model.id is not None + assert predictor_model.training_assay.id == assay_small.id + + seq_len = assay_small.sequence_length or 346 + test_sequence = random_sequence_fake(seq_len) + prediction_future = predictor_model.predict(sequences=[test_sequence]) + mus, vs = prediction_future.wait(timeout=TIMEOUT) + + _assert_prediction_arrays(mus=mus, vs=vs, rows=1, cols=1) + + +@pytest.mark.e2e +def test_predictor_training_kernel_enum( + session: OpenProtein, assay_small: AssayDataset +): + """ + The KernelType enum is accepted interchangeably with its string value. + """ + embedding_model = session.embedding.esm2 + property_name = assay_small.measurement_names[0] + + predictor_future = embedding_model.fit_gp( + assay=assay_small, + properties=[property_name], + reduction=ReductionType.MEAN, + kernel=KernelType.MATERN52, + ) + + assert predictor_future.wait( + timeout=TIMEOUT + ), "Predictor training failed for KernelType.MATERN52" + + seq_len = assay_small.sequence_length or 346 + test_sequence = random_sequence_fake(seq_len) + mus, vs = predictor_future.predict(sequences=[test_sequence]).wait(timeout=TIMEOUT) + _assert_prediction_arrays(mus=mus, vs=vs, rows=1, cols=1) + + +@pytest.mark.e2e +@pytest.mark.parametrize( + "kernel_kwargs,match", + [ + ({"kernel": "bogus"}, "Unknown kernel"), + ({"kernel": "rbf", "period": 2.0}, "`period` is only valid"), + ({"kernel": "periodic", "period": 0.0}, "`period` must be > 0"), + ({"kernel": "rbf", "alpha": 2.0}, "`alpha` is only valid"), + ({"kernel": "rational_quadratic", "alpha": -1.0}, "`alpha` must be > 0"), + ], +) +def test_predictor_kernel_validation_fails_fast( + session: OpenProtein, + assay_small: AssayDataset, + kernel_kwargs: dict, + match: str, +): + """ + Invalid kernel/hyperparameter combinations are rejected client-side before + any training job is submitted. + """ + embedding_model = session.embedding.esm2 + property_name = assay_small.measurement_names[0] + + with pytest.raises(InvalidParameterError, match=match): + embedding_model.fit_gp( + assay=assay_small, + properties=[property_name], + reduction=ReductionType.MEAN, + **kernel_kwargs, + ) diff --git a/tests/molecules/test_complex_mapping.py b/tests/molecules/test_complex_mapping.py new file mode 100644 index 0000000..9f5f784 --- /dev/null +++ b/tests/molecules/test_complex_mapping.py @@ -0,0 +1,105 @@ +from openprotein.molecules import Complex, Protein, Ligand + +import gemmi + +import pytest + + +def test_chains_keep_insertion_order(): + complex = Complex({"C": Protein.from_expr(6), "A": Protein.from_expr(7)}) + assert list(complex.keys()) == ["C", "A"] + complex.set_chain("B", Protein.from_expr(8)) + assert list(complex.keys()) == ["C", "A", "B"] + + +def test_serialized_chain_order_follows_insertion_order(): + complex = Complex({"C": Protein.from_expr(6), "A": Protein.from_expr(7)}) + block = gemmi.cif.read_string(complex.to_string()).sole_block() + assert list(block.find_loop("_struct_asym.id")) == ["C", "A"] + + +def test_mapping_protocol_over_chains(): + protein = Protein.from_expr(6) + ligand = Ligand(ccd="HEM") + complex = Complex({"A": protein, "B": ligand}) + assert len(complex) == 2 + assert "A" in complex and "Z" not in complex + assert complex["A"] is protein + assert list(complex) == ["A", "B"] + assert list(complex.get_chain_ids()) == list(complex.keys()) == ["A", "B"] + assert list(complex.values()) == [protein, ligand] + assert list(complex.items()) == [("A", protein), ("B", ligand)] + replacement = Protein.from_expr(9) + complex["A"] = replacement + assert complex["A"] is replacement + del complex["B"] + assert list(complex.keys()) == ["A"] + with pytest.raises(KeyError): + complex["B"] + + +def test_complex_is_not_hashable(): + with pytest.raises(TypeError, match="unhashable"): + hash(Complex({"A": Protein.from_expr(6)})) + + +def test_insert_chain_takes_the_lowest_unused_id(): + complex = Complex({"B": Protein.from_expr(6), "C": Protein.from_expr(7)}) + complex.insert_chain(Protein.from_expr(8)) + assert list(complex.keys()) == ["B", "C", "A"] + + +def test_update_rejects_overlapping_chain_ids(): + complex = Complex({"A": Protein.from_expr(6)}) + with pytest.raises(ValueError, match="overlapping chain ids"): + complex.update(A=Protein.from_expr(7)) + + +def test_clear_drops_chains_and_templates(): + complex = Complex({"A": Protein.from_expr(6)}).set_templates( + [Protein.from_expr(8)] + ) + complex.clear() + assert len(complex) == 0 + assert complex.templates == () + + +def test_equality_compares_chains(): + protein = Protein.from_expr(6) + assert Complex({"A": protein}) == Complex({"A": protein}) + assert Complex({"A": protein}) != Complex({"B": protein}) + assert Complex({"A": protein}) != {"A": protein} + + +def test_or_returns_a_new_complex_leaving_operands_unchanged(): + left = Complex({"A": Protein.from_expr(6)}) + right = Complex({"B": Protein.from_expr(7)}) + combined = left | right + assert list(combined.keys()) == ["A", "B"] + assert list((left & right).keys()) == ["A", "B"] + assert list(left.keys()) == ["A"] + assert list(right.keys()) == ["B"] + + +def test_ior_adds_a_chain_in_place(): + complex = Complex({"A": Protein.from_expr(6)}) + complex |= Protein.from_expr(7) + assert list(complex.keys()) == ["A", "B"] + + +def test_protein_operators_build_a_two_chain_complex(): + combined = Protein.from_expr(6) | Protein.from_expr(7) + assert list(combined.keys()) == ["A", "B"] + combined = "MKV" & Protein.from_expr(6) + assert isinstance(combined["A"], Protein) + assert combined["A"].sequence == b"MKV" + + +@pytest.mark.xfail( + reason="Complex.copy() returns a Complex with no templates, so combining drops them" +) +def test_templates_survive_combining(): + complex = Complex({"A": Protein.from_expr(6)}).set_templates( + [Protein.from_expr(8)] + ) + assert len((complex | Protein.from_expr(7)).templates) == 1 diff --git a/tests/prompt/test_prompt_api.py b/tests/prompt/test_prompt_api.py index bc40cf5..b7e71de 100644 --- a/tests/prompt/test_prompt_api.py +++ b/tests/prompt/test_prompt_api.py @@ -179,11 +179,35 @@ def test_bytes_input(self): result = _coerce_sequence("foo", b"ACDE:GHIK") assert isinstance(result, Complex) - @pytest.mark.parametrize("bad", ["ACDE::GHIK", ":ACDE", "ACDE:", ":"]) - def test_invalid_chain_break_raises(self, bad: str): + @pytest.mark.parametrize( + "sequence,sequences", + [ + (":ACDE", [b"", b"ACDE"]), + ("ACDE:", [b"ACDE", b""]), + ("ACDE::GHIK", [b"ACDE", b"", b"GHIK"]), + ], + ) + def test_empty_chain_slot_is_kept(self, sequence: str, sequences: list[bytes]): + """A chain the entry does not cover is an empty slot, not an error: a prompt + sampled from a multi-chain MSA renders a homolog that only matches one chain + of the complex as ``:SEQ``, and that says which chain it covers.""" + result = _coerce_sequence("foo", sequence, allow_empty_chains=True) + assert isinstance(result, Complex) + assert [p.sequence for p in result.get_proteins().values()] == sequences + + @pytest.mark.parametrize("bad", [":ACDE", "ACDE:", "ACDE::GHIK"]) + def test_empty_chain_slot_raises_by_default(self, bad: str): + """Only a prompt context gives an empty slot a meaning, so it stays opt-in.""" with pytest.raises(InvalidParameterError, match="chain break"): _coerce_sequence("foo", bad) + @pytest.mark.parametrize("bad", ["", ":", "::"]) + def test_entry_without_residues_raises(self, bad: str): + """Empty slots say what a chain layout looks like; an entry that is empty in + every chain says nothing at all.""" + with pytest.raises(InvalidParameterError, match="no residues"): + _coerce_sequence("foo", bad, allow_empty_chains=True) + @pytest.mark.parametrize( "sequence,n_chains", [("A:B:C", 3), ("ACDE:GHIK:LMNP:QRST", 4), ("A:B:C:D:E", 5)], @@ -239,6 +263,20 @@ def test_multichain_complex_sequence_only_returns_complex(self): assert len(proteins) == 2 assert sorted(p.sequence for p in proteins.values()) == [b"ACDE", b"GHIK"] + def test_empty_chain_slot_survives_the_roundtrip(self): + """The empty slot has to reach the service and come back, or a prompt row for + a homolog covering one chain of two loses which chain that was.""" + zips = zip_prompt([":GHIK"]) + import zipfile + + zf = zipfile.ZipFile(zips[0]) + assert zf.read(zf.namelist()[0]).endswith(b"\n:GHIK\n") + + result = unzip_prompt(self._wrap(zips)) + entry = result[0][0] + assert isinstance(entry, Complex) + assert [p.sequence for p in entry.get_proteins().values()] == [b"", b"GHIK"] + def test_raw_string_with_colon_returns_complex(self): zips = zip_prompt(["ACDE:GHIK"]) outer = self._wrap(zips) diff --git a/tests/prompt/test_system_prompts.py b/tests/prompt/test_system_prompts.py new file mode 100644 index 0000000..30863f4 --- /dev/null +++ b/tests/prompt/test_system_prompts.py @@ -0,0 +1,95 @@ +"""Tests for the curated prompts exposed as attributes on ``PromptAPI``. + +The prompt IDs are written by hand in ``openprotein/prompt/prompt.py``, so the +checks here are that each attribute resolves the ID it claims, and that the +unversioned attributes stay aliases of their versioned counterparts rather than +drifting onto IDs of their own. +""" + +from unittest.mock import MagicMock + +import pytest + +from openprotein.prompt import prompt as prompt_module +from openprotein.prompt.models import Prompt +from openprotein.prompt.prompt import PromptAPI + +# Each curated prompt: the versioned attribute, the unversioned alias that +# should track it, and the ID both must resolve. +CURATED_PROMPTS = [ + ("human_antibody_vh_v1", "human_antibody_vh", prompt_module.HUMAN_ANTIBODY_VH_V1), + ("human_antibody_vl_v1", "human_antibody_vl", prompt_module.HUMAN_ANTIBODY_VL_V1), + ( + "human_antibody_vh_vl_v1", + "human_antibody_vh_vl", + prompt_module.HUMAN_ANTIBODY_VH_VL_V1, + ), + ( + "human_antibody_vl_vh_v1", + "human_antibody_vl_vh", + prompt_module.HUMAN_ANTIBODY_VL_VH_V1, + ), +] + + +@pytest.fixture +def prompt_api(mock_session: MagicMock): + """PromptAPI whose GETs return metadata echoing the requested prompt ID.""" + + def get(endpoint: str, **kwargs): + prompt_id = endpoint.rsplit("/", 1)[-1] + response = MagicMock() + response.status_code = 200 + response.json.return_value = { + "id": prompt_id, + "name": "Curated Prompt", + "created_date": "2023-01-01T00:00:00", + "num_replicates": 10, + "status": "SUCCESS", + "job_id": None, + } + return response + + mock_session.get.side_effect = get + return PromptAPI(mock_session) + + +@pytest.mark.parametrize("versioned,alias,prompt_id", CURATED_PROMPTS) +def test_versioned_attribute_resolves_its_id( + prompt_api: PromptAPI, + mock_session: MagicMock, + versioned: str, + alias: str, + prompt_id: str, +): + prompt = getattr(prompt_api, versioned) + + assert isinstance(prompt, Prompt) + assert prompt.id == prompt_id + mock_session.get.assert_called_once_with(f"v1/prompt/{prompt_id}") + + +@pytest.mark.parametrize("versioned,alias,prompt_id", CURATED_PROMPTS) +def test_unversioned_alias_tracks_latest_version( + prompt_api: PromptAPI, versioned: str, alias: str, prompt_id: str +): + assert getattr(prompt_api, alias).id == prompt_id + assert getattr(prompt_api, versioned).id == prompt_id + + +def test_curated_prompt_ids_are_distinct(): + ids = [prompt_id for _, _, prompt_id in CURATED_PROMPTS] + + assert len(set(ids)) == len(ids) + + +@pytest.mark.parametrize("versioned,alias,prompt_id", CURATED_PROMPTS) +def test_curated_attributes_are_documented_properties( + versioned: str, alias: str, prompt_id: str +): + # Properties so they read as ``session.prompt.``, documented because + # those docstrings are the published SDK docs for the curated prompts. + for name in (versioned, alias): + attribute = getattr(PromptAPI, name) + assert isinstance(attribute, property) + assert attribute.__doc__ diff --git a/tests/utils/sequences.py b/tests/utils/sequences.py index 3abef44..55dae29 100644 --- a/tests/utils/sequences.py +++ b/tests/utils/sequences.py @@ -11,6 +11,11 @@ ANTIBODY_HEAVY_SEQUENCE = "EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYYYYGMDVWGQGTTVTVSS" ANTIBODY_LIGHT_SEQUENCE = "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK" +# Human IgG1 CH1 through the upper hinge. ANARCI numbers antibody variable +# domains only, so appending this to a VH gives a sequence whose last 103 +# residues carry no antibody position. +ANTIBODY_HEAVY_CONSTANT_SEQUENCE = "ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC" + def mutate_sequence( sequence: str, mutation_rate: float = 0.05, ensure_mutation: bool = True diff --git a/uv.lock b/uv.lock index 4284dd1..cbfffb0 100644 --- a/uv.lock +++ b/uv.lock @@ -381,7 +381,7 @@ resolution-markers = [ "python_full_version < '3.11' and sys_platform == 'darwin'", ] dependencies = [ - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" } }, ] sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" } wheels = [ @@ -456,7 +456,7 @@ resolution-markers = [ "python_full_version == '3.11.*' and sys_platform == 'darwin'", ] dependencies = [ - { name = "numpy", version = "2.4.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy", version = "2.4.1", source = { registry = "https://pypi.org/simple" } }, ] sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174, upload-time = "2025-07-26T12:03:12.549Z" } wheels = [ @@ -603,7 +603,7 @@ name = "exceptiongroup" version = "1.3.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "typing-extensions", marker = "python_full_version < '3.11'" }, + { name = "typing-extensions" }, ] sdist = { url = "https://files.pythonhosted.org/packages/50/79/66800aadf48771f6b62f7eb014e352e5d06856655206165d775e675a02c9/exceptiongroup-1.3.1.tar.gz", hash = "sha256:8b412432c6055b0b7d14c310000ae93352ed6754f70fa8f7c34141f91c4e3219", size = 30371, upload-time = "2025-11-21T23:01:54.787Z" } wheels = [ @@ -887,17 +887,17 @@ resolution-markers = [ "python_full_version < '3.11' and sys_platform == 'darwin'", ] dependencies = [ - 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