Commit d71807ea authored by Jacob Durrant's avatar Jacob Durrant

Updated README.md.

parent 196e150f
......@@ -93,7 +93,7 @@ highly system dependent. Including positive controls (known inhibitors) in
virtual screens is a useful way to identify which scoring function is best
suited to your needs.
### REQUIREMENTS ###
### Requirements ###
* Python3: A copy of the Python interpreter can be downloaded from
[http://www.python.org/getit/](http://www.python.org/getit/).
......@@ -107,11 +107,11 @@ suited to your needs.
PDBQT format using scripts included in MGLTools (`prepare_receptor4.py` and
`prepare_ligand4.py`). MGLTools can be obtained from
[http://mgltools.scripps.edu/downloads](http://mgltools.scripps.edu/downloads).
**Be sure to use MGLTools to convert from PDB to PDBQT, not Open Babel.
**Be sure to use MGLTools to convert from PDB to PDBQT, not Open Babel.**
These two programs do not assign the same partial atomic charges, and
NNScore was trained using MGLTools-assigned charges.**
NNScore was trained using MGLTools-assigned charges.
### COMMAND-LINE PARAMETERS ###
### Command-Line Parameters ###
`-receptor`: File name of the receptor PDBQT file.
......@@ -123,7 +123,7 @@ don't wish to specify the location of this file every time you use NNScore
2.0, simply edit the `vina_executable` variable defined near the beginning of
the NNScore2.py script.
### PROGRAM OUTPUT ###
### Program Output ###
NNScore 2.0 evaluates each of the ligand poses contained in the file specified
by the -ligand tag using 20 distinct neural-network scoring functions. The
......@@ -136,7 +136,7 @@ affinity using several metrics:
3) The poses are ranked by the average of the scores given by the 20 networks.
**This is the recommended metric.**
### EXAMPLE OF USAGE ###
### Example of Usage ###
```bash
python NNScore2.py -receptor myreceptor.pdbqt -ligand myligand.pdbqt -vina_executable /PATH/TO/VINA/1.1.2/vina
......
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