choderalab/FreeSolv — pull request #7 by leeping (2014-10-10 20:12:00+00:00)
Title: Add a nickname column to database.txt

This pull request adds an extra column to database.txt consisting of an informal molecule nickname. The specification of the nickname is (almost by definition) not strict. I hoped to achieve a compromise between the following desired but conflicting properties:

1) Unique (i.e. minimize the number of duplicates).
2) Short - the issue with IUPAC names is that some of them became too unwieldy to print out in ForceBalance.
3) Specific - we should get results for this molecule by Googling its nickname.

I use the nickname in ForceBalance simply as a display field. I also display the mobley_ID as well. The ForceBalance printout is a fixed-width table which is easy to read (in my opinion):

```
#==============================================================================================================================================#
#| Hydration free energies (kcal/mol) |#
#| Target: FreeSolv Type: Hydration_OpenMM Objective = 1.63924e+03 |#
#| ID Nickname Reference +- StdErr Calculated +- StdErr Calc-Ref Weight Residual |#
#==============================================================================================================================================#
mobley_1017962 methyl_hexanoate -2.490 +- 0.600 -3.778 +- 0.011 -1.288 0.000 0.000
mobley_1019269 butan-1-ol -4.720 +- 0.600 -3.272 +- 0.016 1.448 1.000 2.096
mobley_1034539 2,3,3',4,4',5-hexachlorobiphenyl -3.040 +- 0.100 1.271 +- 0.005 4.311 0.000 0.000
mobley_1036761 cyclohexanamine -4.590 +- 0.600 -3.091 +- 0.029 1.499 0.000 0.000
mobley_1046331 phenyl_formate -3.820 +- 0.600 -7.897 +- 0.018 -4.077 1.000 16.619
mobley_1075836 methyl_propanoate -2.930 +- 0.600 -4.841 +- 0.009 -1.911 1.000 3.651
mobley_1079207 1,3-dichlorobenzene -0.980 +- 0.600 -0.203 +- 0.002 0.777 0.000 0.000
mobley_1107178 iodoethane -0.740 +- 0.600 -2.617 +- 0.004 -1.877 1.000 3.522
mobley_1139153 2,2,4-trimethylpentane 2.890 +- 0.600 3.055 +- 0.003 0.165 1.000 0.027
```

Thanks,

- Lee-Ping