Merge pull request #8 from chemkg/hdr-change

fixing header

Makefile

@@ -46,7 +46,8 @@ t:
 echo:
 	echo $(patsubst %,gen-%,$(TGTS))
 
-test: all
+#test: all
+test: test-examples
 
 install:
 	. environment.sh

pyproject.toml

@@ -0,0 +1,25 @@
+[tool.poetry]
+name = "chemrof"
+version = "0.0.0"
+description = "Chemical Entities, Materials, and Reactions Ontological Framework"
+authors = ["cmungall <[email protected]>"]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+linkml-runtime = ">=1.7.0"
+oaklib = "^0.5.20"
+linkml-transformer = "^0.2.2"
+linkml = "^1.6.7"
+linkml-owl = "^0.3.0"
+
+[tool.poetry.group.dev.dependencies]
+linkml-owl = ">=0.2.0"
+linkml = ">=1.7.0"
+mkdocs = ">=1.2.3"
+mkdocs-material = ">=8.1.8"
+mkdocs-mermaid2-plugin = ">=0.6.0"
+linkml-datalog = ">=0.2.0"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

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
+

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
+

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
+

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