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Merge pull request #578 from avcopan/dev
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Fixes tests and allows enantiomer filtering on reaction ID
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@avcopan
avcopan authored Oct 25, 2024
2 parents 9c7e1ba + aa81b69 commit ce8071c
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Showing 3 changed files with 160 additions and 126 deletions.
176 changes: 102 additions & 74 deletions automol/reac/_5conv.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
""" Conversion functions
"""

from typing import List
from collections.abc import Sequence

from .. import amchi, geom, graph
from .. import chi as chi_
Expand All @@ -25,24 +25,26 @@

# # constructors from data types
def from_graphs(
rct_gras, prd_gras, stereo: bool = True, struc_typ: str = None
) -> List[Reaction]:
"""Get reaction objects from graphs
rct_gras: Sequence[object],
prd_gras: Sequence[object],
stereo: bool = True,
struc_typ: str | None = None,
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from graphs.
:param rct_gras: The reactant graphs
:type rct_gras: list of automol graphs
:param prd_gras: The product graphs
:type prd_gras: list of automol graphs
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to "geom"
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
rct_gras = tuple(map(graph.explicit, rct_gras))
prd_gras = tuple(map(graph.explicit, prd_gras))
rxns = find(rct_gras, prd_gras, stereo=stereo)
rxns = find(rct_gras, prd_gras, stereo=stereo, enant=enant, strained=strained)

if struc_typ is not None:
rxns = tuple(with_structures(r, struc_typ) for r in rxns)
Expand All @@ -51,62 +53,82 @@ def from_graphs(


def from_amchis(
rct_achs, prd_achs, stereo: bool = True, struc_typ: str = None
) -> List[Reaction]:
"""Get reaction objects from AMChIs
rct_achs: Sequence[str],
prd_achs: Sequence[str],
stereo: bool = True,
struc_typ: str | None = None,
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from AMChIs.
:param rct_achs: The reactant AMChI strings
:type rct_achs: list[str]
:param prd_achs: The product AMChI strings
:type prd_achs: list[str]
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to None
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
return from_chis(rct_achs, prd_achs, stereo=stereo, struc_typ=struc_typ)
return from_chis(
rct_achs,
prd_achs,
stereo=stereo,
struc_typ=struc_typ,
enant=enant,
strained=strained,
)


def from_inchis(
rct_ichs, prd_ichs, stereo: bool = True, struc_typ: str = None
) -> List[Reaction]:
"""Get reaction objects from InChIs
rct_ichs: Sequence[str],
prd_ichs: Sequence[str],
stereo: bool = True,
struc_typ: str | None = None,
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from InChIs.
:param rct_ichs: The reactant InChI strings
:type rct_ichs: list[str]
:param prd_ichs: The product InChI strings
:type prd_ichs: list[str]
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to None
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
return from_chis(rct_ichs, prd_ichs, stereo=stereo, struc_typ=struc_typ)
return from_chis(
rct_ichs,
prd_ichs,
stereo=stereo,
struc_typ=struc_typ,
enant=enant,
strained=strained,
)


def from_chis(
rct_chis, prd_chis, stereo: bool = True, struc_typ: str = None
) -> List[Reaction]:
"""Get reaction objects from ChIs
rct_chis: Sequence[str],
prd_chis: Sequence[str],
stereo: bool = True,
struc_typ: str | None = None,
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from ChIs.
:param rct_chis: The reactant ChI (InChI or AMChI) strings
:type rct_chis: list[str]
:param prd_chis: The product ChI (InChI or AMChI) strings
:type prd_chis: list[str]
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to None
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
rct_gras = tuple(map(graph.explicit, map(chi_.graph, rct_chis)))
prd_gras = tuple(map(graph.explicit, map(chi_.graph, prd_chis)))
rxns = find(rct_gras, prd_gras, stereo=stereo)
rxns = find(rct_gras, prd_gras, stereo=stereo, enant=enant, strained=strained)

if struc_typ is not None:
rxns = tuple(with_structures(r, struc_typ) for r in rxns)
Expand All @@ -115,24 +137,26 @@ def from_chis(


def from_smiles(
rct_smis, prd_smis, stereo: bool = True, struc_typ: str = None
) -> List[Reaction]:
"""Get reaction objects from SMILES
rct_smis: Sequence[str],
prd_smis: Sequence[str],
stereo: bool = True,
struc_typ: str | None = None,
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from SMILES.
:param rct_smis: The reactant SMILES strings
:type rct_smis: list[str]
:param prd_smis: The product SMILES strings
:type prd_smis: list[str]
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to None
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
rct_gras = tuple(map(graph.explicit, map(smiles_.graph, rct_smis)))
prd_gras = tuple(map(graph.explicit, map(smiles_.graph, prd_smis)))
rxns = find(rct_gras, prd_gras, stereo=stereo)
rxns = find(rct_gras, prd_gras, stereo=stereo, enant=enant, strained=strained)

if struc_typ is not None:
rxns = tuple(with_structures(r, struc_typ) for r in rxns)
Expand All @@ -141,24 +165,26 @@ def from_smiles(


def from_geometries(
rct_geos, prd_geos, stereo: bool = True, struc_typ: str = "geom"
) -> List[Reaction]:
"""Get reaction objects from geometries
rct_geos: Sequence[object],
prd_geos: Sequence[object],
stereo: bool = True,
struc_typ: str | None = "geom",
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from geometries.
:param rct_geos: The reactant geometries
:type rct_geos: list of automol geometries
:param prd_geos: The product geometries
:type prd_geos: list of automol geometries
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to "geom"
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
rct_gras = tuple(map(geom.graph, rct_geos))
prd_gras = tuple(map(geom.graph, prd_geos))
rxns = find(rct_gras, prd_gras, stereo=stereo)
rxns = find(rct_gras, prd_gras, stereo=stereo, enant=enant, strained=strained)

if struc_typ is not None:
rxns = tuple(
Expand All @@ -171,24 +197,26 @@ def from_geometries(


def from_zmatrices(
rct_zmas, prd_zmas, stereo: bool = True, struc_typ: str = "zmat"
) -> List[Reaction]:
"""Get reaction objects from z-matrices
rct_zmas: Sequence[object],
prd_zmas: Sequence[object],
stereo: bool = True,
struc_typ: str | None = "zmat",
enant: bool = True,
strained: bool = True,
) -> tuple[Reaction, ...]:
"""Get reaction objects from z-matrices.
:param rct_zmas: The reactant z-matrices
:type rct_zmas: list of automol z-matrices
:param prd_zmas: The product z-matrices
:type prd_zmas: list of automol z-matrices
:param stereo: Include stereoassignments?
:type stereo: bool
:param struc_typ: Add structures of this type; defaults to "zmat"
:type struc_typ: str, optional
:param enant: If expanding stereo, include enantiomers?
:param strained: If expanding stereo, include strained stereoisomers?
:returns: A series of reaction objects
:rtype: List[Reaction]
"""
rct_gras = tuple(map(zmat_.graph, rct_zmas))
prd_gras = tuple(map(zmat_.graph, prd_zmas))
rxns = find(rct_gras, prd_gras, stereo=stereo)
rxns = find(rct_gras, prd_gras, stereo=stereo, enant=enant, strained=strained)

if struc_typ is not None:
rxns = tuple(
Expand All @@ -202,7 +230,7 @@ def from_zmatrices(

# # converters to various data types
def graphs(rxn: Reaction, stereo: bool = True, shift_keys: bool = False):
"""Convert the reaction object to graphs
"""Convert the reaction object to graphs.
:param rxn: the reaction object
:param stereo: Include stereo? defaults to True
Expand All @@ -218,7 +246,7 @@ def graphs(rxn: Reaction, stereo: bool = True, shift_keys: bool = False):


def amchis(rxn: Reaction, stereo: bool = True):
"""Convert the reaction object to AMChIs
"""Convert the reaction object to AMChIs.
:param rxn: the reaction object
:param stereo: Include stereo?
Expand All @@ -232,7 +260,7 @@ def amchis(rxn: Reaction, stereo: bool = True):


def inchis(rxn: Reaction, stereo: bool = True):
"""Convert the reaction object to InChIs
"""Convert the reaction object to InChIs.
:param rxn: the reaction object
:param stereo: Include stereo?
Expand All @@ -248,7 +276,7 @@ def inchis(rxn: Reaction, stereo: bool = True):


def chis(rxn: Reaction, stereo: bool = True):
"""Convert the reaction object to ChIs
"""Convert the reaction object to ChIs.
:param rxn: the reaction object
:param stereo: Include stereo?
Expand All @@ -264,7 +292,7 @@ def chis(rxn: Reaction, stereo: bool = True):


def smiles(rxn: Reaction, stereo=True, res_stereo=True, exp_singles=False):
"""Convert the reaction object to SMILESs
"""Convert the reaction object to SMILESs.
:param rxn: the reaction object
:param stereo: Include stereo?
Expand All @@ -288,7 +316,7 @@ def smiles(rxn: Reaction, stereo=True, res_stereo=True, exp_singles=False):


def geometries(rxn: Reaction):
"""Convert the reaction object to geometries
"""Convert the reaction object to geometries.
:param rxn: the reaction object
:returns: geometries for the reactants and products
Expand All @@ -307,7 +335,7 @@ def geometries(rxn: Reaction):


def zmatrices(rxn: Reaction):
"""Convert the reaction object to z-matrices
"""Convert the reaction object to z-matrices.
:param rxn: the reaction object
:returns: z-matrices for the reactants and products
Expand All @@ -327,7 +355,7 @@ def zmatrices(rxn: Reaction):

# # additional data types
def ts_amchi(rxn: Reaction, stereo: bool = True) -> str:
"""Get the AMChI for the reaction TS
"""Get the AMChI for the reaction TS.
:param rxn: The reaction object
:type rxn: Reaction
Expand All @@ -345,7 +373,7 @@ def ts_amchi(rxn: Reaction, stereo: bool = True) -> str:


def reaction_smiles(rxn) -> str:
"""Convert the Reaction object to a reaction SMILES string
"""Convert the Reaction object to a reaction SMILES string.
:param rxn: The reaction object
:type rxn: Reaction
Expand All @@ -358,7 +386,7 @@ def reaction_smiles(rxn) -> str:


def display(rxn: Reaction, stereo=True, exp=False, label=False, label_dct=None):
"""Display reaction object to IPython using the RDKit visualizer
"""Display reaction object to IPython using the RDKit visualizer.
:param rxn: the reaction object
:param stereo: Include stereochemistry information?
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