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Documentation update per conversion/database tool changes
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Kessler authored and Kessler committed May 30, 2019
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Expand Up @@ -6,9 +6,7 @@ ECNet databases are comma-separated value (CSV) formatted files that provide inf

Our [databases](https://github.com/ECRL/ECNet/tree/master/databases) directory on GitHub contains databases for cetane number, cloud point, kinetic viscosity, pour point and yield sooting index, as well as a database template.

You can create an ECNet-formatted database with molecule names or SMILES and (optionally) target values. The following programs must be installed for you to do so:
- [Open Babel](http://openbabel.org/wiki/Main_Page) software
- [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6 and above
You can create an ECNet-formatted database with molecule names or SMILES and (optionally) target values. [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6 and above is required to create a database.

Supplied names or SMILES must exist in a text file, one entry per line:
```
Expand Down Expand Up @@ -70,6 +68,8 @@ smiles = get_smiles('Molecule Name')

### SMILES string to MDL Molfile

Creating an MDL file requires [Open Babel](http://openbabel.org/wiki/Main_Page) to be installed.

A text file containing SMILES strings, one per line, is required:

```
Expand Down Expand Up @@ -100,6 +100,19 @@ from ecnet.tools.conversions import mdl_to_descriptors
mdl_to_descriptors('molfile.md', 'descriptors.csv')
```

### SMILES string to QSPR descriptors

A text file containing SMILES strings, one per line, is required, as well as an installation of [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html).

*Note: the file extension for the text file containing SMILES strings must be ".smi"

```python
from ecnet.tools.conversions import smiles_to_descriptors

# A CSV file with descriptors is generated
smiles_to_descriptors('molecules.smi', 'descriptors.csv')
```

## ECNet .prj file usage

Once an ECNet project has been created, the resulting .prj file can be used to predict properties for new molecules. A text file containing names or SMILES strings of new molecules, one per line, is required in addition to the .prj file.
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