From 316b2ac6067a10426ae9d255e5159d2cba0dcc76 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Fri, 29 Mar 2024 17:48:35 -0700 Subject: [PATCH 1/3] fixing header --- src/schema/chemrof.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/schema/chemrof.yaml b/src/schema/chemrof.yaml index a9ceb9c..e7eaa70 100644 --- a/src/schema/chemrof.yaml +++ b/src/schema/chemrof.yaml @@ -2,18 +2,12 @@ id: https://w3id.org/chemrof name: chemrof title: Chemical Entities Mixtures and Reactions Ontological Framework description: 'A data model for managing information about chemical entities, ranging - from atoms - - through molecules to complex mixtures. - + from atoms through molecules to complex mixtures. Aspects of this have been cribbed from various sources including CHEBI, SIO, - Wikipedia/Wikidata, the NCATS Translator Chemical Working Group, but all mistakes - are my own. - For full context/motivation see the [GitHub repo](https://github.com/chemkg/chemrof).' license: https://creativecommons.org/publicdomain/zero/1.0/ version: 0.0.1 From 672ef4ec67cb733a2a39344f7ac6b5b8f828bf65 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Fri, 29 Mar 2024 19:11:13 -0700 Subject: [PATCH 2/3] Adding missing --- poetry.lock | 3748 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 25 + 2 files changed, 3773 insertions(+) create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..dbf9bba --- /dev/null +++ b/poetry.lock @@ -0,0 +1,3748 @@ +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. + +[[package]] +name = "airium" +version = "0.2.6" +description = "Easy and quick html builder with natural syntax correspondence (python->html). 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src/data/examples/valid/ChemicalElement-carbon.yaml create mode 100644 src/data/examples/valid/Collection-nitrites.yaml create mode 100644 src/data/examples/valid/PolyatomicIon-ammonium.yaml diff --git a/Makefile b/Makefile index d68deb2..088353c 100644 --- a/Makefile +++ b/Makefile @@ -46,7 +46,8 @@ t: echo: echo $(patsubst %,gen-%,$(TGTS)) -test: all +#test: all +test: test-examples install: . environment.sh diff --git a/src/data/examples/valid/ChemicalElement-carbon.yaml b/src/data/examples/valid/ChemicalElement-carbon.yaml new file mode 100644 index 0000000..7ee429b --- /dev/null +++ b/src/data/examples/valid/ChemicalElement-carbon.yaml @@ -0,0 +1,11 @@ +id: CHEBI:27594 ## carbon atom +name: carbon +symbol: C +smiles_string: + - "[C]" +inchi_string: "InChI=1S/C" +atomic_number: 6 +# in_periodic_table_group: 14 +#in_periodic_table_group: p-block +#in_periodic_table_block: p-block + diff --git a/src/data/examples/valid/Collection-nitrites.yaml b/src/data/examples/valid/Collection-nitrites.yaml new file mode 100644 index 0000000..0aa7f6e --- /dev/null +++ b/src/data/examples/valid/Collection-nitrites.yaml @@ -0,0 +1,55 @@ +entities: +- + id: CHEBI:16301 + name: nitrite + type: chemrof:PolyatomicIon + empirical_formula: "NO−2" + smiles_string: + - "N(=O)[O-]" +# molar_mass: 46.005 +# conjugate_base_of: CHEBI:25567 + has_atom_occurrences: + - name: _:nitrite-o1 + occurrence_of: oxygen + - name: _:nitrite-o2 + occurrence_of: oxygen + - name: _:nitrite-n1 + occurrence_of: nitrogen + has_bonds: + - subject: _:nitrite-o1 + object: _:nitrite-n1 + bond_type: sigma + bond_order: 2 + - subject: _:nitrite-o2 + object: _:nitrite-n1 + bond_type: sigma + bond_order: 1 +- + id: CHEBI:25567 + name: nitrous acid + type: chemrof:BronstedAcid + empirical_formula: "HNO2" +# molar_mass: 47.013 +# acidity: 3.398 + smiles_string: + - "N(=O)O" + has_atom_occurrences: + - name: _:nitrous_acid-o1 + occurrence_of: oxygen + - name: _:nitrous_acid-o2 + occurrence_of: oxygen + - name: _:nitrous_acid-n1 + occurrence_of: nitrogen + - name: _:nitrous_acid-h1 + occurrence_of: hydrogen + has_bonds: + - subject: _:nitrous_acid-o1 + object: _:nitrous_acid-n1 + bond_order: 2 + - subject: _:nitrous_acid-o2 + object: _:nitrous_acid-n1 + bond_order: 1 + - subject: _:nitrous_acid-o2 + object: _:nitrous_acid-h1 + bond_order: 1 + diff --git a/src/data/examples/valid/PolyatomicIon-ammonium.yaml b/src/data/examples/valid/PolyatomicIon-ammonium.yaml new file mode 100644 index 0000000..0206f61 --- /dev/null +++ b/src/data/examples/valid/PolyatomicIon-ammonium.yaml @@ -0,0 +1,36 @@ +id: CHEBI:28938 +name: ammonium +type: chemrof:PolyatomicIon +empirical_formula: "NH+4" +smiles_string: + - "[NH4+]" +#conjugate_base_of: CHEBI:16134 +has_atom_occurrences: + - name: ammonium-n + occurrence_of: N + - name: ammonium-h1 + occurrence_of: H + - name: ammonium-h2 + occurrence_of: H + - name: ammonium-h3 + occurrence_of: H + - name: ammonium-h4 + occurrence_of: H +has_bonds: + - subject: ammonium-n + object: ammonium-h1 + bond_order: 1 + bond_type: polar covalent + - subject: ammonium-n + object: ammonium-h2 + bond_order: 1 + bond_type: polar covalent + - subject: ammonium-n + object: ammonium-h3 + bond_order: 1 + bond_type: polar covalent + - subject: ammonium-n + object: ammonium-h4 + bond_order: 1 + bond_type: polar covalent +