missing: tutorial, fix clapeyron writer

SalvadorBrandolin · SalvadorBrandolin · commit 99f85856a987 · 2025-01-03T16:55:51.000-03:00
diff --git a/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani.rst b/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Class
+====================
+
+.. automodule:: ugropy.core.frag_classes.abdulelah_gani.abdulelah_gani
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_pst.rst b/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_pst.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani PST Class
+========================
+
+.. automodule:: ugropy.core.frag_classes.abdulelah_gani.abdulelah_gani_pst
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_pst_result.rst b/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_pst_result.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani PST Result
+=========================
+
+.. automodule:: ugropy.core.frag_classes.abdulelah_gani.abdulelah_gani_pst_result
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_result.rst b/docs/source/core/frag_classes/abdulelah_gani/abdulelah_gani_result.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Result Class
+===========================
+
+.. automodule:: ugropy.core.frag_classes.abdulelah_gani.abdulelah_gani_result
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/core/frag_classes/abdulelah_gani/init.rst b/docs/source/core/frag_classes/abdulelah_gani/init.rst
@@ -0,0 +1,15 @@
+Abdulelah-Gani fragmentation Classes
+====================================
+
+.. automodule:: ugropy.core.frag_classes.abdulelah_gani
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 1
+
+   abdulelah_gani_pst_result
+   abdulelah_gani_pst
+   abdulelah_gani_result
+   abdulelah_gani
diff --git a/docs/source/core/frag_classes/init.rst b/docs/source/core/frag_classes/init.rst
@@ -12,3 +12,4 @@ Fragmentation Classes
    base/init
    gibbs_model/init
    joback_model/init
+   abdulelah_gani/init
diff --git a/docs/source/models/abdulelah_gani_mod.rst b/docs/source/models/abdulelah_gani_mod.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Model
+====================
+
+.. automodule:: ugropy.models.abdulelah_gani_mod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/abdulelah_gani_pmod.rst b/docs/source/models/abdulelah_gani_pmod.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Primary Model
+============================
+
+.. automodule:: ugropy.models.abdulelah_gani_pmod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/abdulelah_gani_smod.rst b/docs/source/models/abdulelah_gani_smod.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Secondary Model
+==============================
+
+.. automodule:: ugropy.models.abdulelah_gani_smod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/abdulelah_gani_tmod.rst b/docs/source/models/abdulelah_gani_tmod.rst
@@ -0,0 +1,7 @@
+Abdulelah-Gani Tertiary Model
+=============================
+
+.. automodule:: ugropy.models.abdulelah_gani_tmod
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/models/init.rst b/docs/source/models/init.rst
@@ -9,6 +9,10 @@ Models
 .. toctree::
    :maxdepth: 1
 
+   abdulelah_gani_mod
+   abdulelah_gani_pmod
+   abdulelah_gani_smod
+   abdulelah_gani_tmod
    jobackmod
    psrkmod
    unifacmod
diff --git a/docs/source/tutorial/database/critical.csv b/docs/source/tutorial/database/critical.csv
@@ -1,6 +1,6 @@
 Clapeyron Database File,,,,,
 Critical Single Parameters,,,,,
 species,CAS,Tc,Pc,Vc,acentricfactor
-limonene,,657.4486692170663,2755561.066677689,0.0004965,0.3219127551737521
-adrenaline,,953.7486693594541,5569169.079973267,0.0004115,1.6071531017924205
-Trinitrotoluene,,1146.7095578060987,4067315.701790919,0.0005654999999999999,1.0796561474496789
+limonene,,657.4486692170663 kelvin,2755561.066677689 bar,0.0004965 centimeter ** 3 / mole,0.3219127551737521 dimensionless
+adrenaline,,953.7486693594541 kelvin,5569169.079973267 bar,0.0004115 centimeter ** 3 / mole,1.6071531017924205 dimensionless
+Trinitrotoluene,,1146.7095578060987 kelvin,4067315.701790919 bar,0.0005654999999999999 centimeter ** 3 / mole,1.0796561474496789 dimensionless
diff --git a/docs/source/tutorial/database/molarmass.csv b/docs/source/tutorial/database/molarmass.csv
@@ -1,6 +1,6 @@
 Clapeyron Database File,,
 Molar Mases Single Params,,
 species,CAS,Mw
-limonene,,136.238
-adrenaline,,183.207
-Trinitrotoluene,,227.13199999999998
+limonene,,136.238 gram / mole
+adrenaline,,183.207 gram / mole
+Trinitrotoluene,,227.13199999999998 gram / mole
diff --git a/ugropy/constants.py b/ugropy/constants.py
@@ -4,6 +4,8 @@
 ----------
 R : float
     Gas constant [J/mol/K]
+ureg : pint.UnitRegistry
+    Unit registry of Pint library
 """
 
 from pathlib import Path
diff --git a/ugropy/core/frag_classes/abdulelah_gani/abdulelah_gani_pst.py b/ugropy/core/frag_classes/abdulelah_gani/abdulelah_gani_pst.py
@@ -17,10 +17,10 @@
 
 
 class AbdulelahGaniPSTModel(FragmentationModel):
-    """Abdulelah-Gani model dedicated to properties estimation models.
+    """Abdulelah-Gani model dedicated to properties estimation.
 
-    Class to construct the primary structures detector for the Abdulelah-Gani
-    properties estimation model :cite:p:`gani`.
+    Class to construct the primary, secondary and tertiary structures detector
+    for the Abdulelah-Gani properties estimation model :cite:p:`gani`.
 
     Parameters
     ----------
@@ -112,8 +112,7 @@ def mol_preprocess(self, mol: Chem.rdchem.Mol) -> Chem.rdchem.Mol:
         1. Kekulize the molecule.
         2. Identify the aromatic rings.
         3. Check the aromaticity of the rings.
-        4. Make the rings aromatic or non-aromatic based on the aromaticity
-        check.
+        4. Make the rings aromatic or non-aromatic based on the setp 3 check.
 
         The criteria to check the aromaticity of the rings are based on the
         criteria proposed by Abdulelah-Gani in the original paper datase
diff --git a/ugropy/core/frag_classes/abdulelah_gani/abdulelah_gani_pst_result.py b/ugropy/core/frag_classes/abdulelah_gani/abdulelah_gani_pst_result.py
@@ -10,7 +10,10 @@
 
 
 class AGaniPSTFragmentationResult(FragmentationResult):
-    """Abdulelah-Gani primary group contribution properties estimator.
+    """Abdulelah-Gani group contribution properties estimator.
+
+    This class is to instantiate the Abdulelah-Gani primary, secondary and
+    tertiary models.
 
     Parameters
     ----------
@@ -26,11 +29,11 @@ class AGaniPSTFragmentationResult(FragmentationResult):
     Attributes
     ----------
     subgroups : dict
-        Abdulelah-Gani primary functional groups of the molecule.
+        Abdulelah-Gani groups of the molecule.
     subgroups_atoms_indexes : dict
-        Abdulelah-Gani primary functional groups atoms indexes.
+        Abdulelah-Gani groups atoms indexes.
     subgroups_numbers : dict
-        Abdulelah-Gani primary functional groups numbers.
+        Abdulelah-Gani groups numbers.
     """
 
     def __init__(
diff --git a/ugropy/groups.py b/ugropy/groups.py
@@ -4,38 +4,47 @@
 
 from rdkit.Chem import Descriptors
 
+from .core.frag_classes.abdulelah_gani.abdulelah_gani_result import (
+    AGaniFragmentationResult,
+)
 from .core.frag_classes.gibbs_model.gibbs_result import (
     GibbsFragmentationResult,
 )
 from .core.frag_classes.joback.joback_result import JobackFragmentationResult
 from .core.get_rdkit_object import instantiate_mol_object
 from .core.ilp_solvers.default_solver import DefaultSolver
 from .core.ilp_solvers.ilp_solver import ILPSolver
+from .models.abdulelah_gani_mod import abdulelah_gani
 from .models.jobackmod import joback
 from .models.psrkmod import psrk
 from .models.unifacmod import unifac
 
 
 class Groups:
-    """Group class.
+    """Groups class.
 
-    Stores the solved FragmentationModels subgroups of a molecule.
+    Stores the solved FragmentationModels subgroups of a molecule. This class
+    was implemented on an early version of the `ugropy` library. Is not really
+    meant to be used, instead is recommended to use directly the corresponding
+    FragmentationModel independently since it provides more flexibility and
+    control over the results. The class is kept since in most cases is very
+    comfortable to have all the results in a single object.
 
     Parameters
     ----------
-    identifier : str or rdkit.Chem.rdchem.Mol
-        Identifier of a molecule (name, SMILES or Chem.rdchem.Mol). Example:
-        hexane or CCCCCC.
+    identifier : Union[str, Chem.rdchem.Mol]
+            Identifier of the molecule. You can use either the name of the
+            molecule, the SMILEs of the molecule or a rdkit Mol object.
     identifier_type : str, optional
-        Use 'name' to search a molecule by name, 'smiles' to provide the
-        molecule SMILES representation or 'mol' to provide a
-        rdkit.Chem.rdchem.Mol object, by default "name".
+        Identifier type of the molecule. Use "name" if you are providing
+        the molecules' name, "smiles" if you are providing the SMILES
+        or "mol" if you are providing a rdkir mol object, by default "name"
     solver : ILPSolver, optional
-        ILP solver to use, by default DefaultSolver.
+        ILP solver class, by default DefaultSolver
     search_multiple_solutions : bool, optional
-        If True, the solver will search for multiple solutions. If set to true,
-        the model's results will be lists of FragmentationResults objects, by
-        default False.
+        Weather search for multiple solutions or not, by default False
+        If False the return will be a FragmentationResult object, if True
+        the return will be a list of FragmentationResult objects.
     normal_boiling_temperature : float, optional
         If provided, will be used to estimate critical temperature, acentric
         factor, and vapor pressure instead of the estimated normal boiling
@@ -59,6 +68,9 @@ class Groups:
     joback : Union[JobackFragmentationResult, List[JobackFragmentationResult]]
         JobackFragmentationResult object that contains the Joback subgroups and
         the estimated properties of the molecule.
+    agani : Union[AGaniFragmentationResult, List[AGaniFragmentationResult]]
+        AGaniFragmentationResult object that contains the Abdulelah-Gani
+        subgroups and the estimated properties of the molecule.
     """
 
     def __init__(
@@ -104,3 +116,13 @@ def __init__(
             search_multiple_solutions=search_multiple_solutions,
             normal_boiling_point=normal_boiling_temperature,
         )
+
+        # Abdulelah-Gani
+        self.agani: Union[
+            AGaniFragmentationResult, List[AGaniFragmentationResult]
+        ] = abdulelah_gani.get_groups(
+            self.identifier,
+            self.identifier_type,
+            solver=solver,
+            search_multiple_solutions=search_multiple_solutions,
+        )
diff --git a/ugropy/models/__init__.py b/ugropy/models/__init__.py
@@ -4,7 +4,7 @@
 
 .. code-block:: python
 
-    from ugropy import joback, psrk, unifac
+    from ugropy import joback, psrk, unifac, abdulelah_gani
 
 You can check the group list and their SMARTS representation with:
 
@@ -19,6 +19,9 @@
     joback.get_groups("n-hexane").subgroups
     unifac.get_groups("toluene").subgroups
     psrk.get_groups("CCO", "smiles").subgroups
+    abdulelah_gani.get_groups("CCO", "smiles").primary.subgroups
+    abdulelah_gani.get_groups("CCO", "smiles").secondary.subgroups
+    abdulelah_gani.get_groups("CCO", "smiles").tertiary.subgroups
 
 Attributes
 ----------
@@ -30,8 +33,14 @@
     unifac3, unifac4, unifac5, unifac6`
 joback: JobackModel
     Joback FragmentationModel :cite:p:`joback1, joback2`
-abdulelah_gani_p: AbdulelahGaniPrimaryModel
+abdulelah_gani_p: AbdulelahGaniPSTModel
     Abdulelah-Gani Primary Structures FragmentationModel :cite:p:`gani`
+abdulelah_gani_s: AbdulelahGaniPSTModel
+    Abdulelah-Gani Secondary Structures FragmentationModel :cite:p:`gani`
+abdulelah_gani_t: AbdulelahGaniPSTModel
+    Abdulelah-Gani Tertiary Structures FragmentationModel :cite:p:`gani`
+abdulelah_gani: AbdulelahGaniModel
+    Abdulelah-Gani properties estimation model :cite:p:`gani`
 """
 
 from . import (
diff --git a/ugropy/models/abdulelah_gani_mod.py b/ugropy/models/abdulelah_gani_mod.py
@@ -10,6 +10,9 @@
     tol = abdulelah_gani.get_groups("toluene")
 
     print(tol.critical_temperature)
+    print(tol.primary.subgroups)
+    print(tol.secondary.subgroups)
+    print(tol.tertiary.subgroups)
 
     # Get groups from molecule's SMILES
     eth = abdulelah_gani.get_groups("CCO", "smiles")
diff --git a/ugropy/models/abdulelah_gani_pmod.py b/ugropy/models/abdulelah_gani_pmod.py
@@ -18,8 +18,8 @@
 
 Attributes
 ----------
-abdulelah_gani_p: AbdulelahGaniPrimaryModel
-    AbdulelahGaniPrimaryModel FragmentationModel :cite:p:`gani`
+abdulelah_gani_p: AbdulelahGaniPSTModel
+    AbdulelahGaniPSTModel FragmentationModel :cite:p:`gani`
 """
 
 from ugropy.constants import _csvs
diff --git a/ugropy/models/abdulelah_gani_smod.py b/ugropy/models/abdulelah_gani_smod.py
@@ -4,22 +4,22 @@
 
 .. code-block:: python
 
-    from ugropy import abdulelah_gani_p
+    from ugropy import abdulelah_gani_s
 
     # Get groups from molecule's name
-    tol = abdulelah_gani_p.get_groups("toluene")
+    tol = abdulelah_gani_s.get_groups("toluene")
 
     print(tol.subgroups)
 
     # Get groups from molecule's SMILES
-    eth = abdulelah_gani_p.get_groups("CCO", "smiles")
+    eth = abdulelah_gani_s.get_groups("CCO", "smiles")
 
     print(eth.subgroups)
 
 Attributes
 ----------
-abdulelah_gani_p: AbdulelahGaniPrimaryModel
-    AbdulelahGaniPrimaryModel FragmentationModel :cite:p:`gani`
+abdulelah_gani_s: AbdulelahGaniPSTModel
+    AbdulelahGaniPSTModel FragmentationModel :cite:p:`gani`
 """
 
 from ugropy.constants import _csvs
diff --git a/ugropy/models/abdulelah_gani_tmod.py b/ugropy/models/abdulelah_gani_tmod.py
@@ -4,22 +4,22 @@
 
 .. code-block:: python
 
-    from ugropy import abdulelah_gani_p
+    from ugropy import abdulelah_gani_t
 
     # Get groups from molecule's name
-    tol = abdulelah_gani_p.get_groups("toluene")
+    tol = abdulelah_gani_t.get_groups("toluene")
 
     print(tol.subgroups)
 
     # Get groups from molecule's SMILES
-    eth = abdulelah_gani_p.get_groups("CCO", "smiles")
+    eth = abdulelah_gani_t.get_groups("CCO", "smiles")
 
     print(eth.subgroups)
 
 Attributes
 ----------
-abdulelah_gani_p: AbdulelahGaniPrimaryModel
-    AbdulelahGaniPrimaryModel FragmentationModel :cite:p:`gani`
+abdulelah_gani_t: AbdulelahGaniPSTModel
+    AbdulelahGaniPSTModel FragmentationModel :cite:p:`gani`
 """
 
 from ugropy.constants import _csvs
