Commit 1a43c881 authored by Jacob Durrant's avatar Jacob Durrant

Added testing examples.

parent 48862808
# NNScore 2.02 is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html).
# If you have any questions, comments, or suggestions, please don't hesitate to contact me, Jacob
# Durrant, at jdurrant [at] ucsd [dot] edu. If you use NNScore 2.02 in your work, please cite [REFERENCE HERE].
# NNScore 2.02 is released under the GNU General Public License (see
# http://www.gnu.org/licenses/gpl.html). If you have any questions, comments,
# or suggestions, please don't hesitate to contact me, Jacob Durrant, at
# durrantj [at] pitt [dot] edu. If you use NNScore 2.02 in your work, please
# cite [REFERENCE HERE].
import __future__
......@@ -2178,7 +2180,7 @@ def networks():
print("\nNNScore 2.02")
print("============\n")
print((textwrap.fill("NNScore 2.02 is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html). If you have any questions, comments, or suggestions, please contact the author, Jacob Durrant, at jdurrant [at] ucsd [dot] edu. If you use NNScore 2.02 in your work, please cite [REFERENCE HERE].")))
print((textwrap.fill("NNScore 2.02 is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html). If you have any questions, comments, or suggestions, please contact the author, Jacob Durrant, at durrantj [at] pitt [dot] edu. If you use NNScore 2.02 in your work, please cite NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. Jacob D. Durrant, Andrew McCammon. Journal of Chemical Information and Modeling, 2011, 51 (11), pp 2897-2903.")))
print("")
MODEL 1
REMARK VINA RESULT: -1.2 0.000 0.000
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 48.233 24.577 26.619 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 2
REMARK VINA RESULT: -1.2 17.163 17.163
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 37.195 22.393 13.660 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 3
REMARK VINA RESULT: -1.1 16.879 16.879
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 37.428 22.239 13.864 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 4
REMARK VINA RESULT: -1.1 17.513 17.513
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 36.920 22.553 13.405 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 5
REMARK VINA RESULT: -1.1 21.797 21.797
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 30.376 27.084 14.373 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 6
REMARK VINA RESULT: -1.1 21.743 21.743
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 30.324 27.028 14.536 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 7
REMARK VINA RESULT: -1.0 17.580 17.580
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 52.178 28.660 9.982 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 8
REMARK VINA RESULT: -1.0 15.067 15.067
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 51.700 26.543 12.089 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
MODEL 9
REMARK VINA RESULT: -0.9 17.861 17.861
REMARK 2 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: O_3 and C_4
REMARK 2 A between atoms: C_7 and C_10
ROOT
ATOM 1 CL LIG 38.026 24.348 11.963 0.00 0.00 0.000 C
ENDROOT
TORSDOF 2
ENDMDL
This source diff could not be displayed because it is too large. You can view the blob instead.
# You must set your own path to the vina executable
export VINA_EXEC=/Applications/autodock_vina_1_1_2_mac/bin/vina
# Run NNScore2
python ../NNScore2.py -receptor myreceptor.pdbqt -ligand myligand.pdbqt -vina_executable $VINA_EXEC
# If it works, you should get this output:
echo "====================================="
echo " CORRECT OUTPUT (TO VERIFY IT WORKS) "
echo "====================================="
echo
cat << EOF
When the poses were ranked by the best of the 20 network scores
associated with each pose, the best-scoring pose was MODEL 3 (Score =
7.9 = 12.59 nM)
When the poses were ranked by the average of the 20 network scores
associated with each pose, the best-scoring pose was MODEL 1 (Score =
1.765 +/- 2.274 = 17.18 mM). This is the recommended ranking/scoring
metric.
EOF
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