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Create chemical record from SMILES using rdkit#191

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prehner merged 4 commits into
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fragmentation_chemical_record
Oct 15, 2023
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Create chemical record from SMILES using rdkit#191
prehner merged 4 commits into
mainfrom
fragmentation_chemical_record

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@prehner prehner commented Oct 10, 2023 •
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Replacement for #188

Adds ChemicalRecord.from_smiles that uses rdkit and a user-provided set of SMARTS to convert a SMILES string into a chemical record (including bonds).

ChemicalRecord.from_smiles("CCCOCC", smarts)
ChemicalRecord(
	identifier=Identifier(smiles=CCCOCC),
	segments=["CH3", "CH2", "OCH2", "CH2", "CH3"],
	bonds=[[0, 1], [1, 2], [2, 3], [3, 4]]
)

You can also pass an Identifier to directly fill out the remaining fields

ChemicalRecord.from_smiles(Identifier(name="1-propanol", smiles="CCCO"), smarts)
ChemicalRecord(
	identifier=Identifier(name=1-propanol, smiles=CCCO),
	segments=["CH3", "CH2", "CH2", "OH"],
	bonds=[[0, 1], [1, 2], [2, 3]]
)

@prehner
prehner marked this pull request as ready for review October 11, 2023 08:53
g-bauer
g-bauer approved these changes Oct 15, 2023
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Looks good. Found some typos in the docstrings but can be merged as soon those are fixed.

Comment thread feos-core/src/python/parameter/mod.rs Outdated
Comment thread feos-core/src/python/parameter/mod.rs Outdated
Comment thread feos-core/src/python/parameter/fragmentation.rs Outdated
@prehner prehner added this to the v0.5.0 milestone Oct 15, 2023
@prehner prehner added python Python related feature or issue pcsaft Related to the PC-SAFT model gc-pcsaft Related to the gc-PC-SAFT model core related to features in feos-core labels Oct 15, 2023
@prehner
prehner merged commit 0fc8bfa into main Oct 15, 2023
@prehner
prehner deleted the fragmentation_chemical_record branch October 15, 2023 13:47
g-bauer pushed a commit that referenced this pull request Oct 16, 2023
@prehner @g-bauer
Create chemical record from SMILES using rdkit (#191)
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core related to features in feos-core gc-pcsaft Related to the gc-PC-SAFT model pcsaft Related to the PC-SAFT model python Python related feature or issue

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