Merge pull request #7 from SalvadorBrandolin/main

to clapeyron

MANIFEST.in

@@ -9,6 +9,7 @@ exclude tox.ini
 exclude .readthedocs.yml
 exclude requirements-dev.txt
 exclude *.png
+exclude binder.ipynb
 exclude reminder.md
 
 recursive-exclude dist *

README.md

@@ -17,13 +17,19 @@ in the molecule.
 ugropy is in an early development stage, leaving issues of examples of
 molecules that ugropy fails solving the UNIFAC's groups is very helpful.
 
+## Try ugropy now
+You can try ugropy from it's
+[Binder](https://mybinder.org/v2/gh/ipqa-research/ugropy/main). Open the
+binder.ipynb file to explore the basic features.
+
 ## Models supported v1.0.0
 - Classic liquid-vapor UNIFAC
 - Predictive Soave-Redlich-Kwong (PSRK)
 - Joback
 
 ## Example of use
-You can check the full tutorial [here](https://ugropy.readthedocs.io/en/latest/tutorial/tutorial.html).
+You can check the full tutorial 
+[here](https://ugropy.readthedocs.io/en/latest/tutorial/tutorial.html).
 
 Get UNIFAC groups from the molecule's name:
 
@@ -70,6 +76,26 @@ print(f"{limonene.joback.vapor_pressure(176 + 273.15)} bar")
     657.4486692170663 K
     1.0254019428522743 bar
 
+Write down the [Clapeyron.jl](https://github.com/ClapeyronThermo/Clapeyron.jl)
+.csv input files.
+
+```python
+from ugropy import writers
+
+names = ["limonene", "adrenaline", "Trinitrotoluene"]
+
+grps = [Groups(n) for n in names]
+
+# Write the csv files into a database directory
+writers.to_clapeyron(
+    molecules_names=names,
+    unifac_groups=[g.unifac_groups for g in grps],
+    psrk_groups=[g.psrk_groups for g in grps],
+    joback_objects=[g.joback for g in grps],
+    path="./database"
+)
+```
+
 ## Installation
 At the moment ugropy is not uploaded in PyPI (will be soon).
 

binder.ipynb

@@ -0,0 +1,183 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Welcome to the ugropy's Binder\n",
+    "\n",
+    "You can use this notebook to try the basics features of ugropy. You can \n",
+    "check the full tutorial here: https://ugropy.readthedocs.io/en/latest/index.html\n",
+    "\n",
+    "Let's use the Groups class to obtain information of the desired molecules:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ugropy import Groups\n",
+    "\n",
+    "# Write the molecule's name as it appears on pubchem\n",
+    "molecule_name = \"ethanol\"\n",
+    "\n",
+    "mol = Groups(molecule_name)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Get groups information and properties from the Joback model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'CH3': 1, 'CH2': 1, 'OH': 1}\n",
+      "{'CH3': 1, 'CH2': 1, 'OH': 1}\n",
+      "{'-CH3': 1, '-CH2-': 1, '-OH (alcohol)': 1}\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(mol.unifac_groups)\n",
+    "print(mol.psrk_groups)\n",
+    "print(mol.joback.groups)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 37,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "57.56641437226128\n",
+      "499.40737356625846\n",
+      "1.702089531406276\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Experimental value of ethanol's critical pressure is 61.37 bar\n",
+    "print(mol.joback.critical_pressure)\n",
+    "\n",
+    "# Experimental value of ethanol's critical temperature is 514.0 K\n",
+    "print(mol.joback.critical_temperature)\n",
+    "\n",
+    "# Vapor pressure at the normal boiling temperature of ethanol\n",
+    "print(mol.joback.vapor_pressure(78.37 + 273.15))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can provide the normal boiling point of the molecules to improve some \n",
+    "Joback's predictions."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mol = Groups(molecule_name, normal_boiling_temperature=78.37+273.15)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "520.0914853232541\n",
+      "1.0132499999999998\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(mol.joback.critical_temperature)\n",
+    "\n",
+    "print(mol.joback.vapor_pressure(78.37+273.15))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can also create a Groups object from the molecule's SMILES."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "520.0914853232541\n",
+      "1.0132499999999998\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Ethanol again\n",
+    "mol = Groups(\n",
+    "    \"CCO\", \n",
+    "    identifier_type=\"smiles\", \n",
+    "    normal_boiling_temperature=78.37+273.15\n",
+    ")\n",
+    "\n",
+    "print(mol.joback.critical_temperature)\n",
+    "\n",
+    "print(mol.joback.vapor_pressure(78.37+273.15))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Check the tutorial to explore more features."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "ugropy",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/source/README.rst

@@ -80,6 +80,25 @@ Estimate properties with the Joback model!
    657.4486692170663 K
    1.0254019428522743 bar
 
+Write down the Clapeyron.jl .csv input files.
+
+.. code:: python
+
+   from ugropy import writers
+
+   names = ["limonene", "adrenaline", "Trinitrotoluene"]
+
+   grps = [Groups(n) for n in names]
+
+   # Write the csv files into a database directory
+   writers.to_clapeyron(
+      molecules_names=names,
+      unifac_groups=[g.unifac_groups for g in grps],
+      psrk_groups=[g.psrk_groups for g in grps],
+      joback_objects=[g.joback for g in grps],
+      path="./database"
+   )
+
 Installation
 ============
 

docs/source/tutorial/database/PSRK/PSRK_groups.csv

@@ -0,0 +1,6 @@
+Clapeyron Database File,
+PSRK Groups [csvtype = groups,grouptype = PSRK]
+species,groups
+limonene,"[""CH3"" => 2, ""CH2"" => 3, ""CH"" => 1, ""CH2=C"" => 1, ""CH=C"" => 1]"
+adrenaline,"[""CH2"" => 1, ""ACH"" => 3, ""ACCH"" => 1, ""OH"" => 1, ""ACOH"" => 2, ""CH3NH"" => 1]"
+Trinitrotoluene,"[""ACH"" => 2, ""ACCH3"" => 1, ""ACNO2"" => 3]"

docs/source/tutorial/database/critical.csv

@@ -0,0 +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

docs/source/tutorial/database/molarmass.csv

@@ -0,0 +1,6 @@
+Clapeyron Database File,,
+Molar Mases Single Params,,
+species,CAS,Mw
+limonene,,136.23760000000001
+adrenaline,,183.20680000000002
+Trinitrotoluene,,227.132

docs/source/tutorial/database/ogUNIFAC/ogUNIFAC_groups.csv

@@ -0,0 +1,6 @@
+Clapeyron Database File,
+original UNIFAC Groups,[csvtype = groups,grouptype = originalUNIFAC]
+species,groups
+limonene,"[""CH3"" => 2, ""CH2"" => 3, ""CH"" => 1, ""CH2=C"" => 1, ""CH=C"" => 1]"
+adrenaline,"[""CH2"" => 1, ""ACH"" => 3, ""ACCH"" => 1, ""OH"" => 1, ""ACOH"" => 2, ""CH3NH"" => 1]"
+Trinitrotoluene,"[""ACH"" => 2, ""ACCH3"" => 1, ""ACNO2"" => 3]"

docs/source/tutorial/easy_way.ipynb

@@ -43,9 +43,9 @@
    "metadata": {},
    "source": [
     "Well, that was easy... `ugropy` uses\n",
-    "[`PubChemPy`](https://github.com/mcs07/PubChemPy) to access to pubchem and\n",
+    "`PubChemPy` (https://github.com/mcs07/PubChemPy) to access to pubchem and\n",
     "obtain the SMILES representation of the molecule. ugropy uses the SMILES\n",
-    "representation and the [`rdkit`](https://github.com/rdkit/rdkit) library to\n",
+    "representation and the `rdkit` (https://github.com/rdkit/rdkit) library to\n",
     "obtain the functional groups of the molecules.\n",
     "\n",
     "The complete signature of the `Groups` class is the following:"
@@ -351,7 +351,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,

docs/source/tutorial/hard_way.ipynb

@@ -81,7 +81,7 @@
    "source": [
     "#### Joback\n",
     "\n",
-    "For context, check the [Joback's article](https://doi.org/10.1080/00986448708960487).\n",
+    "For context, check the Joback's article: https://doi.org/10.1080/00986448708960487\n",
     "\n",
     "The Joback object is instantiated by the Group object as we saw in the previous \n",
     "tutorial but, a Joback object can be instantiated individually:"
@@ -314,7 +314,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,

docs/source/tutorial/installation.ipynb

@@ -9,14 +9,20 @@
     "At the moment ugropy is not uploaded in PyPI (will be soon).\n",
     "\n",
     "```\n",
-    "pip install git+https://github.com/SalvadorBrandolin/ugropy.git\n",
+    "pip install git+https://github.com/ipqa-research/ugropy.git\n",
     "```"
    ]
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "ugropy",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

docs/source/tutorial/tutorial.rst

@@ -7,4 +7,5 @@ Tutorial
    installation.ipynb
    easy_way.ipynb
    hard_way.ipynb
-   ugropy_failing.ipynb
+   ugropy_failing.ipynb
+   writers.ipynb