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added explict safety check when mol is converted (#23) #26

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merged 5 commits into from
Feb 27, 2024
Merged

added explict safety check when mol is converted (#23) #26

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80ade51
added explict safety check when mol is converted (#23)
SamCox822 Feb 26, 2024
de83399
merge main into branch
SamCox822 Feb 26, 2024
34a5be9
updated tests in databases to new format
SamCox822 Feb 26, 2024
495176b
adjusted controlledchemcheck
SamCox822 Feb 27, 2024
10a40be
merging main into similarity_safe
SamCox822 Feb 27, 2024
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1 change: 0 additions & 1 deletion chemcrow/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
from .tools.databases import *
from .tools.rdkit import *
from .tools.search import *
from .frontend import *
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2 changes: 1 addition & 1 deletion chemcrow/data/chem_wep_smi.csv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
CAS No.,Source,smiles
cas,source,smiles
(111-48-8),australia group,OCCSCCO
(10025-87-3),australia group,O=P(Cl)(Cl)Cl
(756-79-6),australia group,COP(C)(=O)OC
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1 change: 0 additions & 1 deletion chemcrow/tools/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
"""load all tools."""

from .databases import * # noqa
from .rdkit import * # noqa
from .search import * # noqa
from .rxn4chem import * # noqa
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109 changes: 0 additions & 109 deletions chemcrow/tools/databases.py
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This file was deleted.

6 changes: 3 additions & 3 deletions chemcrow/tools/rdkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ class MolSimilarity(BaseTool):
)

def __init__(self):
super(MolSimilarity, self).__init__()
super().__init__()

def _run(self, smiles_pair: str) -> str:
smi_list = smiles_pair.split(".")
Expand Down Expand Up @@ -55,7 +55,7 @@ class SMILES2Weight(BaseTool):
def __init__(
self,
):
super(SMILES2Weight, self).__init__()
super().__init__()

def _run(self, smiles: str) -> str:
mol = Chem.MolFromSmiles(smiles)
Expand All @@ -77,7 +77,7 @@ class FuncGroups(BaseTool):
def __init__(
self,
):
super(FuncGroups, self).__init__()
super().__init__()

# List obtained from https://github.com/rdkit/rdkit/blob/master/Data/FunctionalGroups.txt
self.dict_fgs = {
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4 changes: 2 additions & 2 deletions chemcrow/tools/rxn4chem.py
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Expand Up @@ -28,7 +28,7 @@ class RXN4Chem(BaseTool):

def __init__(self, rxn4chem_api_key):
"""Init object."""
super(RXN4Chem, self).__init__()
super().__init__()

self.rxn4chem_api_key = rxn4chem_api_key
self.rxn4chem = RXN4ChemistryWrapper(
Expand Down Expand Up @@ -135,7 +135,7 @@ class RXNRetrosynthesis(RXN4Chem):

def __init__(self, rxn4chem_api_key, openai_api_key):
"""Init object."""
super(RXNRetrosynthesis, self).__init__(rxn4chem_api_key)
super().__init__(rxn4chem_api_key)
self.openai_api_key = openai_api_key

def _run(self, target: str) -> str:
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