Merge pull request #7 from ecrl/dev

Updates to GNN structure

README.md

@@ -1,16 +1,15 @@
 [![UML Energy & Combustion Research Laboratory](http://faculty.uml.edu/Hunter_Mack/uploads/9/7/1/3/97138798/1481826668_2.png)](http://faculty.uml.edu/Hunter_Mack/)
 
-# GraphChem: Graph-based machine learning for chemical property prediction
+# GraphChem: Graph-based machine learning for fuel property prediction
 
 [![GitHub version](https://badge.fury.io/gh/ecrl%2FGraphChem.svg)](https://badge.fury.io/gh/ecrl%2FGraphChem)
 [![PyPI version](https://badge.fury.io/py/graphchem.svg)](https://badge.fury.io/py/graphchem)
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ecrl/GraphChem/master/LICENSE.txt)
 
-**GraphChem** is an open source Python package for constructing graph-based machine learning models with a focus on chemical property prediction. 
+**GraphChem** is an open source Python package for constructing graph-based machine learning models with a focus on fuel property prediction. 
 
 Future plans for GraphChem include:
-- Full API documentation, in-code documentation
-- A robust hyper-parameter and model architecture tuning runtime
+- Robust hyper-parameter and model architecture tuning runtimes
 - Molecule visualization via RDKit
 - Extensive automated testing
 
@@ -25,15 +24,15 @@ Future plans for GraphChem include:
 $ pip install graphchem
 ```
 
-If any installation issues occur with PyTorch or torch-dependent packages (notably torch-geometric), visit their installation pages and follow the installation instructions: [PyTorch](https://pytorch.org/get-started/locally/), [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html)
-
 ### Method 2: From Source
 ```
 $ git clone https://github.com/ecrl/graphchem
 $ cd graphchem
 $ python setup.py install
 ```
 
+If any errors occur when installing dependencies, namely with PyTorch or torch-geometric, visit their installation pages and follow the installation instructions: [PyTorch](https://pytorch.org/get-started/locally/), [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html)
+
 # Usage:
 
 API documentation is coming in the future! In the meantime, take a look at some [examples](https://github.com/ecrl/GraphChem/tree/master/examples).

examples/schweidtmann_test.csv

@@ -0,0 +1,76 @@
+Compounds, SMILES,Meas DCN,Meas MON,Meas RON
+δ-undecalactone,CCCCCCC1CCCC(=O)O1,48.6,n.a.,n.a.
+"3,4,4-Trimethyl-2-pentene", C/C=C(\C)C(C)(C)C,n.a.,86.1,103.0
+"2,3-Dimethyl-2-pentene", CCC(C)=C(C)C,n.a.,80.0,97.5
+2-methyl furan, Cc1ccco1,9.0,86.0,103.0
+Methylcyclopropane, CC1CC1,n.a.,81.2,102.5
+"1,2-dimethylbenzene", Cc1ccccc1C,8.3,100.0,105.0
+furan, c1ccoc1,7.0,91.6,108.6
+4-Methyl-2-pentene (trans), C/C=C/C(C)C,n.a.,82.6,98.0
+"2,3-Dimethyl-2-hexene", CCCC(C)=C(C)C,n.a.,79.3,93.1
+"4,4-Dimethyl-2-pentene (trans)", C/C=C/C(C)(C)C,n.a.,90.9,105.3
+"2,2-Dimethyloctane", CCCCCCC(C)(C)C,n.a.,46.0,49.0
+methyl erucate, CCCCCCCC/C=C\CCCCCCCCCCCC(=O)OC,74.2,n.a.,n.a.
+3-Ethyl-1-pentene, C=CC(CC)CC,n.a.,81.6,95.6
+Sec-Butylcyclohexane, CCC(C)C1CCCCC1,n.a.,55.2,51.0
+aceticacid-2-methylpropylester, CC(=O)OCC(C)C,n.a.,112.3,108.7
+menthone, CC1CCC(C(C)C)C(=O)C1,20.6,n.a.,n.a.
+4-Methylcyclohexene, CC1CC=CCC1,n.a.,67.0,84.1
+tetrahydrofuran, C1CCOC1,21.9,64.8,72.9
+2-Octene, C/C=C\CCCCC,n.a.,56.5,56.3
+1-decene, C=CCCCCCCCC,49.1,n.a.,n.a.
+methyl-9-decenoate, C=CCCCCCCCC(=O)OC,38.3,n.a.,n.a.
+"1,3-Dimethylcyclohexane (trans)", C[C@H]1CCC[C@H](C)C1,n.a.,64.2,66.9
+1-Methylcyclohexene, CC1=CCCCC1,n.a.,72.1,89.2
+2-Phenylpentane, CCCC(C)c1ccccc1,n.a.,92.1,103.5
+2-octanone, CCCCCCC(C)=O,36.6,n.a.,n.a.
+n-Propylbenzene, CCCc1ccccc1,n.a.,98.7,101.5
+3-Ethylhexane, CCCC(CC)CC,n.a.,52.4,33.5
+2-heptanol, CCCCCC(C)O,25.0,n.a.,n.a.
+"2,2-dimethylbutane", CCC(C)(C)C,24.4,93.4,91.8
+"1,2,3-Trimethylcyclohexane (cis, trans, cis)", CC1[C@@H](C)CCC[C@H]1C,n.a.,81.0,83.4
+4-methoxybenzaldehyde, COc1ccc(C=O)cc1,25.8,n.a.,n.a.
+iso-Butylbenzene, CC(C)Cc1ccccc1,n.a.,98.0,111.4
+geraniol, CC(C)=CCC/C(C)=C/CO,19.3,n.a.,n.a.
+trans-3-octene, CC/C=C/CCCC,34.0,n.a.,n.a.
+dipropylene glycol monomethyl ether, COC(C)COC(C)CO,43.9,n.a.,n.a.
+2-methylpropanoicacidmethylester, COC(=O)C(C)C,n.a.,104.7,103.6
+"1,5-Hexadiene", C=CCCC=C,n.a.,37.6,71.1
+dibutyl ether, CCCCOCCCC,115.4,n.a.,n.a.
+1-Methyl-4-isopropylbenzene, Cc1ccc(C(C)C)cc1,n.a.,97.7,101.4
+tert-Butylbenzene, CC(C)(C)c1ccccc1,n.a.,107.4,115.5
+"3,3-Dimethyl-1-pentene", C=CC(C)(C)CC,n.a.,86.1,103.5
+4-ethyl guaiacol, CCc1ccc(OC)c(O)c1,19.6,n.a.,n.a.
+butanal, CCCC=O,41.1,n.a.,n.a.
+"1,4-Diethylbenzene", CCc1ccc(CC)cc1,n.a.,95.2,106.0
+"2,5-Dimethyl-3-hexene (cis)", CC(C)/C=C\C(C)C,n.a.,87.4,104.0
+3-methyl-2-butanone, CC(=O)C(C)C,n.a.,102.2,108.9
+"1,3,5triisopropylbenzene", CC(C)c1cc(C(C)C)cc(C(C)C)c1,2.8,n.a.,n.a.
+"2,2,3-Trimethylpentane", CCC(C)C(C)(C)C,n.a.,99.9,109.6
+ocimene, C=C/C(C)=C/C=C/C(C)C,28.0,n.a.,n.a.
+1-Methyl-2-ethylbenzene, CCc1ccccc1C,n.a.,92.1,102.5
+"2,2-Dimethyl-3-hexene (cis)", CC/C=C\C(C)(C)C,n.a.,88.0,106.7
+2-Methyl-1-pentene, C=C(C)CCC,n.a.,81.5,94.2
+6-Methyl-1-heptene, C=CCCCC(C)C,n.a.,62.6,63.6
+1-Methyl-2-n-propylcyclohexane (trans), CCC[C@@H]1CCCC[C@H]1C,n.a.,38.8,29.4
+2-methylheptane, CCCCCC(C)C,49.8,23.0,20.7
+dodecyl vinyl ether, C=COCCCCCCCCCCCC,101.7,n.a.,n.a.
+"1,1,3-Trimethylcyclohexane", CC1CCCC(C)(C)C1,n.a.,82.6,81.3
+2-Methyl-2-pentene, CCC=C(C)C,n.a.,83.0,97.8
+"1,4-dimethylbenzene", Cc1ccc(C)cc1,6.2,101.2,103.4
+Methyl-2-methylbutanoate, CCC(C)C(=O)OC,n.a.,99.1,110.5
+"3,3-Dimethylhexane", CCCC(C)(C)CC,n.a.,83.4,75.5
+methyl α-linolenate, CC/C=C\C/C=C\C/C=C\CCCCCCCC(=O)OC,22.7,n.a.,n.a.
+n-pentanol, CCCCCO,n.a.,74.0,78.0
+1-Methyl-3-n-propylbenzene, CCCc1cccc(C)c1,n.a.,100.5,111.9
+propylene glycol monomethyl ether acetate, COCC(C)OC(C)=O,24.0,n.a.,n.a.
+4-Octene (trans), CCC/C=C/CCC,n.a.,74.3,73.3
+6-undecanone, CCCCCC(=O)CCCCC,49.0,n.a.,n.a.
+methyl caproate, CCCCCC(=O)OC,24.6,n.a.,n.a.
+"1,2,3,4-Tetramethylbenzene", Cc1ccc(C)c(C)c1C,n.a.,100.3,105.3
+"2,4-Hexadiene", C/C=C\C=C\C,n.a.,80.7,97.1
+4-nonanone, CCCCCC(=O)CCC,43.0,n.a.,n.a.
+n-butylbenzene, CCCCc1ccccc1,12.5,94.4,104.4
+Allylcyclopentane, C=CCC1CCCC1,n.a.,45.6,52.1
+diisobutylether, CC(C)COCC(C)C,59.7,n.a.,n.a.
+β-citronellol, CC(C)=CCCC(C)CCO,25.6,n.a.,n.a.