From 3d1b620be92ae55903651dac1eab40a2a3764d29 Mon Sep 17 00:00:00 2001 From: Logan Ward Date: Wed, 16 Aug 2023 09:41:44 -0400 Subject: [PATCH] Initial draft of a data model (#16) * Initial draft of a data model * Update example of what a node could be called * Add an example MOF * Ability to read a CIF and parse it * Update interfaces to use MOFRecord --- mofa/generator.py | 4 +- mofa/model.py | 96 ++ mofa/scoring/base.py | 35 +- mofa/scoring/geometry.py | 4 +- tests/conftest.py | 25 + tests/files/check.cif | 1819 ++++++++++++++++++++++++++++++++ tests/scoring/test_geometry.py | 3 +- tests/test_model.py | 9 + 8 files changed, 1987 insertions(+), 8 deletions(-) create mode 100644 mofa/model.py create mode 100644 tests/conftest.py create mode 100644 tests/files/check.cif create mode 100644 tests/test_model.py diff --git a/mofa/generator.py b/mofa/generator.py index 8a1bb0ae..9b46823d 100644 --- a/mofa/generator.py +++ b/mofa/generator.py @@ -3,10 +3,12 @@ import ase +from mofa.model import MOFRecord + def train_generator( starting_model: str | Path, - examples: list[object], + examples: list[MOFRecord], num_epochs: int ) -> Path: """Retrain a generative model for MOFs diff --git a/mofa/model.py b/mofa/model.py new file mode 100644 index 00000000..8e57fea6 --- /dev/null +++ b/mofa/model.py @@ -0,0 +1,96 @@ +"""Data models for a MOF class""" +from dataclasses import dataclass, field +from functools import cached_property +from pathlib import Path +from io import StringIO + +from ase.io.cif import read_cif + +import ase + + +@dataclass +class NodeDescription: + """The inorganic components of a MOF""" + + name: str = ... + """Human-readable name of the node (e.g., "Cu paddlewheel")""" + xyz: str | None = None + """XYZ coordinates of each atom in the node + + Uses At or Fr as an identifier of the the anchor points + where the linkers attach to the node + - At designates a carbon-carbon bond anchor + - Fr designates other types of linkages + """ + + +@dataclass +class LigandDescription: + """Description of organic sections which connect inorganic nodes""" + + name: str | None = ... + """Human-readable name of the linker""" + smiles: str = ... + """SMILES-format designation of the molecule""" + xyz: str | None = None + """XYZ coordinates of each atom in the linker""" + + fragment_atoms: list[list[int]] | None = None + """Groups of atoms which attach to the nodes + + There are typically two groups of fragment atoms, and these are + never altered during MOF generation.""" + + @property + def linker_atoms(self) -> list[int]: + """All atoms which are not part of a fragment""" + raise NotImplementedError() + + +@dataclass +class MOFRecord: + """Information available about a certain MOF""" + # Data describing what the MOF is + identifiers: dict[str, str] = field(default_factory=dict) + """Names of this MOFs is registries (e.g., hMOF)""" + topology: str | None = None + """Description of the 3D network structure (e.g., pcu) as the topology""" + catenation: int | None = None + """Degree of catenation. 0 corresponds to no interpenetrating lattices""" + nodes: tuple[NodeDescription] = field(default_factory=tuple) + """Description of the nodes within the structure""" + ligands: tuple[LigandDescription] = field(default_factory=tuple) + """Description of each linker within the structure""" + + # Information about the 3D structure of the MOF + structure: str = ... + """A representative 3D structure of the MOF in POSCAR format""" + + # Properties + gas_storage: dict[tuple[str, float], float] = field(default_factory=dict) + """Storage capacity of the MOF for different gases and pressures""" + structure_stability: dict[str, float] = field(default_factory=dict) + """How likely the structure is to be stable according to different assays + + A score of 1 equates to most likely to be stable, 0 as least likely.""" + + @classmethod + def from_file(cls, cif_path: Path | str, **kwargs) -> 'MOFRecord': + """Create a MOF description from a CIF file on disk + + Keyword arguments can include identifiers of the MOF and + should be passed to the constructor. + + Args: + cif_path: Path to the CIF file + Returns: + A MOF record before fragmentation + """ + + return MOFRecord(structure=Path(cif_path).read_text(), **kwargs) + + @cached_property + def atoms(self) -> ase.Atoms: + """The structure as an ASE Atoms object""" + return next(read_cif(StringIO(self.structure), index=slice(None))) diff --git a/mofa/scoring/base.py b/mofa/scoring/base.py index 36f1eccf..60b5d3a6 100644 --- a/mofa/scoring/base.py +++ b/mofa/scoring/base.py @@ -2,19 +2,43 @@ import ase +from mofa.model import MOFRecord -class LinkerScorer: - """Scoring functions which operate on the linkers produced by the generator + +class Scorer: + """Base class for tools which score a MOF + + Most implementations should be subclasses of the :class:`LigandScorer` or + :class:`MOFScorer`, which provide utility that - for example - extract + the information about the linker. + """ + + def score_mof(self, record: MOFRecord) -> float: + """Score a MOF given the full MOF record + + Args: + record: Record to be scored + Returns: + Score value + """ + + +class LigandScorer(Scorer): + """Scoring functions which operate on the ligands between nodes in the MOF Examples: - - Verify the linker is chemically reasonable (e.g., SAScore, SCScore) + - Verify the ligand is chemically reasonable (e.g., SAScore, SCScore) """ def __call__(self, linker: ase.Atoms) -> float: raise NotImplementedError() + def score_mof(self, record: MOFRecord) -> float: + assert len(record.ligands) == 1, 'We do not yet know how to score a MOF with >1 type of linker' # TOOD + raise NotImplementedError() -class MOFScorer: + +class MOFScorer(Scorer): """Scoring functions which produce a quick estimate of the quality of a MOF Examples: @@ -24,3 +48,6 @@ class MOFScorer: def __call__(self, mof: ase.Atoms) -> float: raise NotImplementedError() + + def score_mof(self, record: MOFRecord) -> float: + return self(record.atoms) diff --git a/mofa/scoring/geometry.py b/mofa/scoring/geometry.py index 6eb26362..9cfd5952 100644 --- a/mofa/scoring/geometry.py +++ b/mofa/scoring/geometry.py @@ -2,10 +2,10 @@ import numpy as np import ase -from mofa.scoring.base import LinkerScorer +from mofa.scoring.base import MOFScorer -class MinimumDistance(LinkerScorer): +class MinimumDistance(MOFScorer): """Rate molecules based on the closest distance between atoms""" def __call__(self, linker: ase.Atoms) -> float: diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 00000000..7c0a4572 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,25 @@ + +from pytest import fixture +from pathlib import Path +from ase.io.cif import read_cif +import ase + +from mofa.model import MOFRecord + +_files_path = Path(__file__).parent / 'files' + + +@fixture() +def example_cif() -> Path: + return _files_path / 'check.cif' + + +@fixture() +def example_mof(example_cif) -> ase.Atoms: + with open(example_cif) as fp: + return next(read_cif(fp, index=slice(None))) + + +@fixture() +def example_record(example_cif) -> MOFRecord: + return MOFRecord.from_file(example_cif) diff --git a/tests/files/check.cif b/tests/files/check.cif new file mode 100644 index 00000000..a6fe1df4 --- /dev/null +++ b/tests/files/check.cif @@ -0,0 +1,1819 @@ +data_check +_audit_creation_date 2023-05-29 +_audit_creation_method 'cif2lammps' +_symmetry_space_group_name_H-M 'P1' +_symmetry_Int_Tables_number 1 +_symmetry_cell_setting triclinic +loop_ +_symmetry_equiv_pos_as_xyz + x,y,z +_cell_length_a 39.87968858000001 +_cell_length_b 25.576616020000003 +_cell_length_c 25.57662568 +_cell_angle_alpha 89.97005461 +_cell_angle_beta 90.80598709 +_cell_angle_gamma 88.29381776 +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_charge +Zn1 Zn 0.381462 0.251897 0.379238 0.000000 +Zn2 Zn 0.325262 0.342179 0.377843 0.000000 +Zn3 Zn 0.325365 0.254870 0.465839 0.000000 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+C43 C45 1.421 A +C45 C46 1.52 S +C45 C47 1.427 S +C47 C48 1.411 A +C47 C56 1.425 A +C48 C49 1.396 S +C49 C50 1.401 A +C49 C54 1.403 A +C50 H432 17.127 S +C50 C481 1.405 A +C51 C61 1.419 A +C51 C52 1.511 S +C51 C473 1.411 A +C52 H119 22.866 S +C53 O92 1.4 S +C53 C54 1.41 A +C53 C471 17.889 A +C54 C55 1.415 S +C55 C56 1.43 A +C55 C58 1.495 S +C56 C57 1.408 S +C58 C59 1.333 D +C59 O92 1.396 S +C59 H123 22.626 S +C60 C89 1.49 S +C61 C87 1.49 S +C61 C470 17.119 A +C62 C273 1.206 T +C63 C64 1.471 S +C63 C272 22.823 T +C64 C275 1.524 S +C64 N300 1.464 S +C65 C66 1.402 A +C65 C274 22.227 S +C65 C282 1.417 A +C66 C71 1.399 A +C67 C69 1.422 A +C67 C71 1.418 A +C67 C173 1.516 S +C68 H127 22.993 S +C68 C172 23.078 S +C69 C280 1.518 S +C69 C282 1.421 A +C70 H130 23.443 S +C70 H341 19.015 S +C70 C279 22.301 S +C71 C88 1.49 S +C72 C85 1.49 S +C72 C275 22.402 A +C72 C279 22.355 A +C73 C74 1.206 T +C74 C75 1.471 S +C75 N91 1.464 S +C75 C76 1.524 S +C76 C77 1.402 A +C76 C83 1.417 A +C77 C82 1.399 A +C78 C82 1.418 A +C78 C79 1.516 S +C78 C80 1.422 A +C80 C83 1.421 A +C80 C81 1.518 S +C82 C86 1.49 S +C83 C84 1.49 S +C84 O100 1.262 A +C84 O102 1.262 A +C85 O105 1.262 A +C85 O104 1.262 A +C86 O97 1.267 A +C86 O94 1.267 A +C87 O101 1.267 A +C87 O103 1.267 A +C88 O96 1.267 A +C88 O98 1.267 A +C89 O99 1.262 A +C89 O95 1.262 A +N90 C274 22.44 S +O100 Zn108 23.683 S +O102 Zn109 23.655 S +Zn106 O203 1.922 S +Zn106 O198 1.941 S +Zn106 O208 1.922 S +Zn106 O199 1.922 S +Zn107 O200 1.922 S +Zn107 O202 1.922 S +Zn107 O198 1.941 S +Zn107 O209 1.922 S +Zn108 O201 1.922 S +Zn108 O198 1.941 S +Zn108 O204 1.922 S +Zn109 O198 1.941 S +Zn109 O206 1.922 S +Zn109 O210 1.922 S +H110 C149 1.11 S +H111 C149 1.109 S +H112 C149 1.11 S +H113 C151 1.11 S +H114 C151 1.11 S +H115 C151 1.107 S +H116 C153 1.082 S +H117 C575 1.085 S +H118 C157 1.11 S +H120 C157 1.11 S +H121 C162 1.077 S +H122 C163 1.077 S +H124 C167 1.058 S +H125 C169 1.11 S +H126 C171 1.084 S +H128 C173 1.109 S +H129 C173 1.11 S +H131 C280 1.11 S +H132 C175 1.109 S +H133 N195 1.046 S +H134 N195 1.047 S +H135 C178 1.058 S +H136 C180 1.11 S +H137 C182 1.084 S +H138 C184 1.11 S +H139 C184 1.109 S +H140 C184 1.11 S +H141 C186 1.11 S +H142 C186 1.11 S +H143 C186 1.109 S +H144 N196 1.046 S +H145 N196 1.047 S +C146 C147 1.446 S +C146 C165 1.206 T +C147 C162 1.394 A +C147 C148 1.41 A +C148 C149 1.517 S +C148 C150 1.421 A +C150 C151 1.52 S +C150 C152 1.427 S +C152 C153 1.411 A +C152 C161 1.425 A +C153 C154 1.396 S +C154 C155 1.401 A +C154 C159 1.403 A +C155 H537 1.085 S +C155 C586 1.405 A +C156 C166 1.419 A +C156 C578 1.411 A +C156 C157 1.511 S +C158 C576 1.411 A +C158 O197 1.4 S +C158 C159 1.41 A +C159 C160 1.415 S +C160 C161 1.43 A +C160 C163 1.495 S +C161 C162 1.408 S +C163 C164 1.333 D +C164 O197 1.396 S +C165 C194 1.49 S +C166 C575 1.405 A +C166 C192 1.49 S +C167 C378 1.206 T +C168 C377 1.206 T +C168 C169 1.471 S +C169 C380 1.524 S +C169 N405 1.464 S +C170 C379 1.524 S +C170 C171 1.402 A +C170 C387 1.417 A +C171 C176 1.399 A +C172 C174 1.422 A +C172 C176 1.418 A +C174 C385 1.518 S +C174 C387 1.421 A +C175 H236 1.11 S +C175 C384 1.518 S +C176 C193 1.49 S +C177 C380 1.417 A +C177 C384 1.421 A +C177 C190 1.49 S +C178 C179 1.206 T +C179 C180 1.471 S +C180 N196 1.464 S +C180 C181 1.524 S +C181 C182 1.402 A +C181 C188 1.417 A +C182 C187 1.399 A +C183 C187 1.418 A +C183 C184 1.516 S +C183 C185 1.422 A +C185 C188 1.421 A +C185 C186 1.518 S +C187 C191 1.49 S +C188 C189 1.49 S +C189 O205 1.262 A +C189 O207 1.262 A +C190 O210 1.262 A +C190 O209 1.262 A +C191 O202 1.267 A +C191 O199 1.267 A +C192 O206 1.267 A +C192 O208 1.267 A +C193 O201 1.267 A +C193 O203 1.267 A +C194 O204 1.262 A +C194 O200 1.262 A +N195 C379 1.464 S +Zn211 O308 1.922 S +Zn211 O303 1.941 S +Zn211 O313 1.922 S +Zn211 O304 1.922 S +Zn212 O305 1.922 S +Zn212 O307 1.922 S +Zn212 O303 1.941 S +Zn212 O314 1.922 S +Zn213 O306 1.922 S +Zn213 O303 1.941 S +Zn213 O309 1.922 S +Zn213 O415 1.922 S +Zn214 O417 1.922 S +Zn214 O303 1.941 S +Zn214 O311 1.922 S +Zn214 O315 1.922 S +H215 C254 1.11 S +H216 C254 1.109 S +H217 C254 1.11 S +H218 C256 1.11 S +H219 C256 1.11 S +H220 C256 1.107 S +H221 C258 1.082 S +H222 C680 1.085 S +H223 C262 1.11 S +H224 C367 1.11 S +H225 C262 1.11 S +H226 C267 1.077 S +H227 C268 1.077 S +H228 C374 1.082 S +H229 C272 1.058 S +H230 C274 1.11 S +H231 C276 1.084 S +H232 C383 1.11 S +H233 C278 1.109 S +H234 C278 1.11 S +H235 C385 1.11 S +H237 C280 1.109 S +H238 N300 1.046 S +H239 N300 1.047 S +H240 C283 1.058 S +H241 C285 1.11 S +H242 C287 1.084 S +H243 C289 1.11 S +H244 C289 1.109 S +H245 C289 1.11 S +H246 C291 1.11 S +H247 C291 1.11 S +H248 C291 1.109 S +H249 N301 1.046 S +H250 N301 1.047 S +C251 C252 1.446 S +C251 C270 1.206 T +C252 C267 1.394 A +C252 C253 1.41 A +C253 C254 1.517 S +C253 C255 1.421 A +C255 C256 1.52 S +C255 C257 1.427 S +C257 C258 1.411 A +C257 C266 1.425 A +C258 C259 1.396 S +C259 C260 1.401 A +C259 C264 1.403 A +C260 H642 1.085 S +C260 C691 1.405 A +C261 C271 1.419 A +C261 C683 1.411 A +C261 C262 1.511 S +C262 H329 1.11 S +C263 C681 1.411 A +C263 O302 1.4 S +C263 C264 1.41 A +C264 C265 1.415 S +C265 C266 1.43 A +C265 C268 1.495 S +C266 C267 1.408 S +C268 C269 1.333 D +C269 H333 1.082 S +C269 O302 1.396 S +C270 C299 1.49 S +C271 C680 1.405 A +C271 C297 1.49 S +C273 C274 1.471 S +C275 C276 1.402 A +C276 C281 1.399 A +C277 C383 1.516 S +C277 C279 1.422 A +C277 C281 1.418 A +C278 H337 1.11 S +C278 C382 1.516 S +C280 H340 1.11 S +C281 C298 1.49 S +C282 C295 1.49 S +C283 C284 1.206 T +C284 C285 1.471 S +C285 N301 1.464 S +C285 C286 1.524 S +C286 C287 1.402 A +C286 C293 1.417 A +C287 C292 1.399 A +C288 C292 1.418 A +C288 C289 1.516 S +C288 C290 1.422 A +C290 C293 1.421 A +C290 C291 1.518 S +C292 C296 1.49 S +C293 C294 1.49 S +C294 O310 1.262 A +C294 O312 1.262 A +C295 O315 1.262 A +C295 O314 1.262 A +C296 O307 1.267 A +C296 O304 1.267 A +C297 O311 1.267 A +C297 O313 1.267 A +C298 O306 1.267 A +C298 O308 1.267 A +C299 O309 1.262 A +C299 O305 1.262 A +O310 Zn318 1.922 S +O312 Zn319 1.922 S +Zn316 O413 1.922 S +Zn316 O408 1.941 S +Zn316 O418 1.922 S +Zn316 O409 1.922 S +Zn317 O410 1.922 S +Zn317 O412 1.922 S +Zn317 O408 1.941 S +Zn317 O419 1.922 S +Zn318 O411 1.922 S +Zn318 O408 1.941 S +Zn318 O414 1.922 S +Zn319 O408 1.941 S +Zn319 O416 1.922 S +Zn319 O420 1.922 S +H320 C359 1.11 S +H321 C359 1.109 S +H322 C359 1.11 S +H323 C361 1.11 S +H324 C361 1.11 S +H325 C361 1.107 S +H326 C363 1.082 S +H327 C785 1.085 S +H328 C367 1.11 S +H330 C367 1.11 S +H331 C372 1.077 S +H332 C373 1.077 S +H334 C377 1.058 S +H335 C379 1.11 S +H336 C381 1.084 S +H338 C383 1.109 S +H339 C383 1.11 S +H342 C385 1.109 S +H343 N405 1.046 S +H344 N405 1.047 S +H345 C388 1.058 S +H346 C390 1.11 S +H347 C392 1.084 S +H348 C394 1.11 S +H349 C394 1.109 S +H350 C394 1.11 S +H351 C396 1.11 S +H352 C396 1.11 S +H353 C396 1.109 S +H354 N406 1.046 S +H355 N406 1.047 S +C356 C357 1.446 S +C356 C375 1.206 T +C357 C372 1.394 A +C357 C358 1.41 A +C358 C359 1.517 S +C358 C360 1.421 A +C360 C361 1.52 S +C360 C362 1.427 S +C362 C363 1.411 A +C362 C371 1.425 A +C363 C364 1.396 S +C364 C365 1.401 A +C364 C369 1.403 A +C365 H747 1.085 S +C365 C796 1.405 A +C366 C376 1.419 A +C366 C788 1.411 A +C366 C367 1.511 S +C368 C786 1.411 A +C368 O407 1.4 S +C368 C369 1.41 A +C369 C370 1.415 S +C370 C371 1.43 A +C370 C373 1.495 S +C371 C372 1.408 S +C373 C374 1.333 D +C374 O407 1.396 S +C375 C404 1.49 S +C376 C785 1.405 A +C376 C402 1.49 S +C378 C379 1.471 S +C380 C381 1.402 A +C381 C386 1.399 A +C382 C384 1.422 A +C382 C386 1.418 A +C386 C403 1.49 S +C387 C400 1.49 S +C388 C389 1.206 T +C389 C390 1.471 S +C390 N406 1.464 S +C390 C391 1.524 S +C391 C392 1.402 A +C391 C398 1.417 A +C392 C397 1.399 A +C393 C397 1.418 A +C393 C394 1.516 S +C393 C395 1.422 A +C395 C398 1.421 A +C395 C396 1.518 S +C397 C401 1.49 S +C398 C399 1.49 S +C399 O415 1.262 A +C399 O417 1.262 A +C400 O420 1.262 A +C400 O419 1.262 A +C401 O412 1.267 A +C401 O409 1.267 A +C402 O416 1.267 A +C402 O418 1.267 A +C403 O411 1.267 A +C403 O413 1.267 A +C404 O414 1.262 A +C404 O410 1.262 A +Zn421 O518 1.922 S +Zn421 O513 1.941 S +Zn421 O523 1.922 S +Zn421 O514 1.922 S +Zn422 O515 1.922 S +Zn422 O517 1.922 S +Zn422 O513 1.941 S +Zn422 O524 1.922 S +Zn423 O516 1.922 S +Zn423 O513 1.941 S +Zn423 O519 1.922 S +Zn423 O625 1.922 S +Zn424 O627 1.922 S +Zn424 O513 1.941 S +Zn424 O521 1.922 S +Zn424 O525 1.922 S +H425 C464 1.11 S +H426 C464 1.109 S +H427 C464 1.11 S +H428 C466 1.11 S +H429 C466 1.11 S +H430 C466 1.107 S +H431 C468 1.082 S +H433 C472 1.11 S +H434 C577 1.11 S +H435 C472 1.11 S +H436 C477 1.077 S +H437 C478 1.077 S +H438 C584 1.082 S +H439 C482 1.058 S +H440 C484 1.11 S +H441 C486 1.084 S +H442 C593 1.11 S +H443 C488 1.109 S +H444 C488 1.11 S +H445 C595 1.11 S +H446 C805 1.11 S +H447 C490 1.109 S +H448 N510 1.046 S +H449 N510 1.047 S +H450 C493 1.058 S +H451 C495 1.11 S +H452 C497 1.084 S +H453 C499 1.11 S +H454 C499 1.109 S +H455 C499 1.11 S +H456 C501 1.11 S +H457 C501 1.11 S +H458 C501 1.109 S +H459 N511 1.046 S +H460 N511 1.047 S +C461 C462 1.446 S +C461 C480 1.206 T +C462 C477 1.394 A +C462 C463 1.41 A +C463 C464 1.517 S +C463 C465 1.421 A +C465 C466 1.52 S +C465 C467 1.427 S +C467 C468 1.411 A +C467 C476 1.425 A +C468 C469 1.396 S +C469 C470 1.401 A +C469 C474 1.403 A +C471 C481 1.419 A +C471 C472 1.511 S +C472 H539 1.11 S +C473 O512 1.4 S +C473 C474 1.41 A +C474 C475 1.415 S +C475 C476 1.43 A +C475 C478 1.495 S +C476 C477 1.408 S +C478 C479 1.333 D +C479 H543 1.082 S +C479 O512 1.396 S +C480 C509 1.49 S +C481 C507 1.49 S +C482 C693 1.206 T +C483 C692 1.206 T +C483 C484 1.471 S +C484 C695 1.524 S +C484 N720 1.464 S +C485 C694 1.524 S +C485 C486 1.402 A +C485 C702 1.417 A +C486 C491 1.399 A +C487 C593 1.516 S +C487 C489 1.422 A +C487 C491 1.418 A +C488 H547 1.11 S +C488 C592 1.516 S +C489 C700 1.518 S +C489 C702 1.421 A +C490 H550 1.11 S +C490 H761 1.11 S +C490 C699 1.518 S +C491 C508 1.49 S +C492 C695 1.417 A +C492 C699 1.421 A +C492 C505 1.49 S +C493 C494 1.206 T +C494 C495 1.471 S +C495 N511 1.464 S +C495 C496 1.524 S +C496 C497 1.402 A +C496 C503 1.417 A +C497 C502 1.399 A +C498 C502 1.418 A +C498 C499 1.516 S +C498 C500 1.422 A +C500 C503 1.421 A +C500 C501 1.518 S +C502 C506 1.49 S +C503 C504 1.49 S +C504 O520 1.262 A +C504 O522 1.262 A +C505 O525 1.262 A +C505 O524 1.262 A +C506 O517 1.267 A +C506 O514 1.267 A +C507 O521 1.267 A +C507 O523 1.267 A +C508 O516 1.267 A +C508 O518 1.267 A +C509 O519 1.262 A +C509 O515 1.262 A +N510 C694 1.464 S +O520 Zn528 1.922 S +O522 Zn529 1.922 S +Zn526 O623 1.922 S +Zn526 O618 1.941 S +Zn526 O628 1.922 S +Zn526 O619 1.922 S +Zn527 O620 1.922 S +Zn527 O622 1.922 S +Zn527 O618 1.941 S +Zn527 O629 1.922 S +Zn528 O621 1.922 S +Zn528 O618 1.941 S +Zn528 O624 1.922 S +Zn529 O618 1.941 S +Zn529 O626 1.922 S +Zn529 O630 1.922 S +H530 C569 1.11 S +H531 C569 1.109 S +H532 C569 1.11 S +H533 C571 1.11 S +H534 C571 1.11 S +H535 C571 1.107 S +H536 C573 1.082 S +H538 C577 1.11 S +H540 C577 1.11 S +H541 C582 1.077 S +H542 C583 1.077 S +H544 C587 1.058 S +H545 C589 1.11 S +H546 C591 1.084 S +H548 C593 1.109 S +H549 C593 1.11 S +H551 C700 1.11 S +H552 C595 1.109 S +H553 N615 1.046 S +H554 N615 1.047 S +H555 C598 1.058 S +H556 C600 1.11 S +H557 C602 1.084 S +H558 C604 1.11 S +H559 C604 1.109 S +H560 C604 1.11 S +H561 C606 1.11 S +H562 C606 1.11 S +H563 C606 1.109 S +H564 N616 1.046 S +H565 N616 1.047 S +C566 C567 1.446 S +C566 C585 1.206 T +C567 C582 1.394 A +C567 C568 1.41 A +C568 C569 1.517 S +C568 C570 1.421 A +C570 C571 1.52 S +C570 C572 1.427 S +C572 C573 1.411 A +C572 C581 1.425 A +C573 C574 1.396 S +C574 C575 1.401 A +C574 C579 1.403 A +C576 C586 1.419 A +C576 C577 1.511 S +C578 O617 1.4 S +C578 C579 1.41 A +C579 C580 1.415 S +C580 C581 1.43 A +C580 C583 1.495 S +C581 C582 1.408 S +C583 C584 1.333 D +C584 O617 1.396 S +C585 C614 1.49 S +C586 C612 1.49 S +C587 C798 1.206 T +C588 C797 1.206 T +C588 C589 1.471 S +C589 C800 1.524 S +C589 N825 1.464 S +C590 C799 1.524 S +C590 C591 1.402 A +C590 C807 1.417 A +C591 C596 1.399 A +C592 C594 1.422 A +C592 C596 1.418 A +C594 C805 1.518 S +C594 C807 1.421 A +C595 H656 1.11 S +C595 C804 1.518 S +C596 C613 1.49 S +C597 C800 1.417 A +C597 C804 1.421 A +C597 C610 1.49 S +C598 C599 1.206 T +C599 C600 1.471 S +C600 N616 1.464 S +C600 C601 1.524 S +C601 C602 1.402 A +C601 C608 1.417 A +C602 C607 1.399 A +C603 C607 1.418 A +C603 C604 1.516 S +C603 C605 1.422 A +C605 C608 1.421 A +C605 C606 1.518 S +C607 C611 1.49 S +C608 C609 1.49 S +C609 O625 1.262 A +C609 O627 1.262 A +C610 O630 1.262 A +C610 O629 1.262 A +C611 O622 1.267 A +C611 O619 1.267 A +C612 O626 1.267 A +C612 O628 1.267 A +C613 O621 1.267 A +C613 O623 1.267 A +C614 O624 1.262 A +C614 O620 1.262 A +N615 C799 1.464 S +Zn631 O728 1.922 S +Zn631 O723 1.941 S +Zn631 O733 1.922 S +Zn631 O724 1.922 S +Zn632 O725 1.922 S +Zn632 O727 1.922 S +Zn632 O723 1.941 S +Zn632 O734 1.922 S +Zn633 O726 1.922 S +Zn633 O723 1.941 S +Zn633 O729 1.922 S +Zn633 O835 1.922 S +Zn634 O837 1.922 S +Zn634 O723 1.941 S +Zn634 O731 1.922 S +Zn634 O735 1.922 S +H635 C674 1.11 S +H636 C674 1.109 S +H637 C674 1.11 S +H638 C676 1.11 S +H639 C676 1.11 S +H640 C676 1.107 S +H641 C678 1.082 S +H643 C682 1.11 S +H644 C787 1.11 S +H645 C682 1.11 S +H646 C687 1.077 S +H647 C688 1.077 S +H648 C794 1.082 S +H649 C692 1.058 S +H650 C694 1.11 S +H651 C696 1.084 S +H652 C803 1.11 S +H653 C698 1.109 S +H654 C698 1.11 S +H655 C805 1.11 S +H657 C700 1.109 S +H658 N720 1.046 S +H659 N720 1.047 S +H660 C703 1.058 S +H661 C705 1.11 S +H662 C707 1.084 S +H663 C709 1.11 S +H664 C709 1.109 S +H665 C709 1.11 S +H666 C711 1.11 S +H667 C711 1.11 S +H668 C711 1.109 S +H669 N721 1.046 S +H670 N721 1.047 S +C671 C672 1.446 S +C671 C690 1.206 T +C672 C687 1.394 A +C672 C673 1.41 A +C673 C674 1.517 S +C673 C675 1.421 A +C675 C676 1.52 S +C675 C677 1.427 S +C677 C678 1.411 A +C677 C686 1.425 A +C678 C679 1.396 S +C679 C680 1.401 A +C679 C684 1.403 A +C681 C691 1.419 A +C681 C682 1.511 S +C682 H749 1.11 S +C683 O722 1.4 S +C683 C684 1.41 A +C684 C685 1.415 S +C685 C686 1.43 A +C685 C688 1.495 S +C686 C687 1.408 S +C688 C689 1.333 D +C689 H753 1.082 S +C689 O722 1.396 S +C690 C719 1.49 S +C691 C717 1.49 S +C693 C694 1.471 S +C695 C696 1.402 A +C696 C701 1.399 A +C697 C803 1.516 S +C697 C699 1.422 A +C697 C701 1.418 A +C698 H757 1.11 S +C698 C802 1.516 S +C700 H760 1.11 S +C701 C718 1.49 S +C702 C715 1.49 S +C703 C704 1.206 T +C704 C705 1.471 S +C705 N721 1.464 S +C705 C706 1.524 S +C706 C707 1.402 A +C706 C713 1.417 A +C707 C712 1.399 A +C708 C712 1.418 A +C708 C709 1.516 S +C708 C710 1.422 A +C710 C713 1.421 A +C710 C711 1.518 S +C712 C716 1.49 S +C713 C714 1.49 S +C714 O730 1.262 A +C714 O732 1.262 A +C715 O735 1.262 A +C715 O734 1.262 A +C716 O727 1.267 A +C716 O724 1.267 A +C717 O731 1.267 A +C717 O733 1.267 A +C718 O726 1.267 A +C718 O728 1.267 A +C719 O729 1.262 A +C719 O725 1.262 A +O730 Zn738 1.922 S +O732 Zn739 1.922 S +Zn736 O833 1.922 S +Zn736 O828 1.941 S +Zn736 O838 1.922 S +Zn736 O829 1.922 S +Zn737 O830 1.922 S +Zn737 O832 1.922 S +Zn737 O828 1.941 S +Zn737 O839 1.922 S +Zn738 O831 1.922 S +Zn738 O828 1.941 S +Zn738 O834 1.922 S +Zn739 O828 1.941 S +Zn739 O836 1.922 S +Zn739 O840 1.922 S +H740 C779 1.11 S +H741 C779 1.109 S +H742 C779 1.11 S +H743 C781 1.11 S +H744 C781 1.11 S +H745 C781 1.107 S +H746 C783 1.082 S +H748 C787 1.11 S +H750 C787 1.11 S +H751 C792 1.077 S +H752 C793 1.077 S +H754 C797 1.058 S +H755 C799 1.11 S +H756 C801 1.084 S +H758 C803 1.109 S +H759 C803 1.11 S +H762 C805 1.109 S +H763 N825 1.046 S +H764 N825 1.047 S +H765 C808 1.058 S +H766 C810 1.11 S +H767 C812 1.084 S +H768 C814 1.11 S +H769 C814 1.109 S +H770 C814 1.11 S +H771 C816 1.11 S +H772 C816 1.11 S +H773 C816 1.109 S +H774 N826 1.046 S +H775 N826 1.047 S +C776 C777 1.446 S +C776 C795 1.206 T +C777 C792 1.394 A +C777 C778 1.41 A +C778 C779 1.517 S +C778 C780 1.421 A +C780 C781 1.52 S +C780 C782 1.427 S +C782 C783 1.411 A +C782 C791 1.425 A +C783 C784 1.396 S +C784 C785 1.401 A +C784 C789 1.403 A +C786 C796 1.419 A +C786 C787 1.511 S +C788 O827 1.4 S +C788 C789 1.41 A +C789 C790 1.415 S +C790 C791 1.43 A +C790 C793 1.495 S +C791 C792 1.408 S +C793 C794 1.333 D +C794 O827 1.396 S +C795 C824 1.49 S +C796 C822 1.49 S +C798 C799 1.471 S +C800 C801 1.402 A +C801 C806 1.399 A +C802 C804 1.422 A +C802 C806 1.418 A +C806 C823 1.49 S +C807 C820 1.49 S +C808 C809 1.206 T +C809 C810 1.471 S +C810 N826 1.464 S +C810 C811 1.524 S +C811 C812 1.402 A +C811 C818 1.417 A +C812 C817 1.399 A +C813 C817 1.418 A +C813 C814 1.516 S +C813 C815 1.422 A +C815 C818 1.421 A +C815 C816 1.518 S +C817 C821 1.49 S +C818 C819 1.49 S +C819 O835 1.262 A +C819 O837 1.262 A +C820 O840 1.262 A +C820 O839 1.262 A +C821 O832 1.267 A +C821 O829 1.267 A +C822 O836 1.267 A +C822 O838 1.267 A +C823 O831 1.267 A +C823 O833 1.267 A +C824 O834 1.262 A +C824 O830 1.262 A diff --git a/tests/scoring/test_geometry.py b/tests/scoring/test_geometry.py index f3cac986..a758bf72 100644 --- a/tests/scoring/test_geometry.py +++ b/tests/scoring/test_geometry.py @@ -3,9 +3,10 @@ from mofa.scoring.geometry import MinimumDistance -def test_distance(): +def test_distance(example_record): # Make a 2x2x2 simple cubic cell atoms = Atoms(positions=[[0, 0, 0]], cell=[1., 1., 1.]) atoms *= [2, 2, 2] assert MinimumDistance()(atoms) == 1. + assert MinimumDistance().score_mof(example_record) > 0 diff --git a/tests/test_model.py b/tests/test_model.py new file mode 100644 index 00000000..efc332ed --- /dev/null +++ b/tests/test_model.py @@ -0,0 +1,9 @@ +from math import isclose + +from mofa.model import MOFRecord + + +def test_create(example_cif): + mof = MOFRecord.from_file(example_cif, identifiers={'local': 'test'}) + assert mof.identifiers['local'] == 'test' + assert isclose(mof.atoms.cell.lengths()[0], 39.87968858)