Featurize Negative Sites
=======================================

### Leak Summary:
    definitely lost: 186,946,272 bytes in 1,298,308 blocks
    indirectly lost: 0 bytes in 0 blocks
      possibly lost: 1,728 bytes in 12 blocks
    still reachable: 415,519 bytes in 6,546 blocks
         suppressed: 0 bytes in 0 blocks

    Profiling timer expired

### Run Timer:
    real: 6m47.897s
    user: 6m42.730s
    sys:  0m3.820s

From Command: 

### Call Graph Summary:
Each sample counts as 0.01 seconds.

     % time | cumulative  seconds | self seconds | calls   | self s/call | total s/call | name 
    --------------------------------------------------------------------------------------------------------------------
     83.22  |         36.65       |    36.65     |  458963 |    0.00     |    0.00      | Protein::parseAtom(char const*)
     14.99  |         43.25       |     6.60     |   53891 |    0.00     |    0.00      | Protein::parseDSSPLine(char const*)
      0.39  |         43.42       |     0.17     |         |             |              | Neighbor::Neighbor(std::vector<Point3D*...
                                                          ...
      0.07  |         43.75       |     0.03     | 1312774 |    0.00     |    0.00      | Atom::Atom() 

Only Shows frequently called functions. Click for full graph.

[![Summary of Featurize Negative Sites Call Grap](featurize-neg.png)](featurize-neg-full.png "View full, un-trimmed graph")

From Command(s) (Note: Makefile modified to add `-pg` to g++ flags):

    make
    featurize -P examples/serprot/trypsin_ser_og.neg.ptf > examples/serprot/trypsin_ser_og.neg.ff
    gprof ./featurize > profile/featurize-neg.gprof
    ~/ggprof2do/tprof2dot.py -s profile/featurize-neg.gprof | dot -Tpng -o profile/featurize-neg.png
    ~/ggprof2do/tprof2dot.py -n0 -e0 -s profile/featurize-neg.gprof | dot -Tpng -o profile/featurize-pos-full.png
    time valgrind --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes featurize -P examples/serprot/trypsin_ser_og.neg.ptf > examples/serprot/trypsin_ser_og.neg.ff 2> profile/featurize-neg.valgrid
    grep '^==' profile/featurize-neg.valgrid | sed 's/==[0-9]\+== //' > profile/featurize-neg-clean.valgrid

* * *

Featurize Positive Sites
=======================================

Leak Summary:
-------------
    definitely lost: 28,747,264 bytes in 199,668 blocks
    indirectly lost: 0 bytes in 0 blocks
      possibly lost: 288 bytes in 2 blocks
    still reachable: 415,519 bytes in 6,546 blocks
         suppressed: 0 bytes in 0 blocks

    Profiling timer expired
    
Run Timer:
----------
    real: 0m20.547s
    user: 0m19.910s
    sys:  0m0.440s

### Call Graph Summary:

Only Shows frequently called functions. Click for full graph.

Each sample counts as 0.01 seconds.

     % time | cumulative  seconds | self seconds | calls  | self s/call | total s/call | name 
    --------------------------------------------------------------------------------------------------------------------
     56.87  |          0.29       |     0.29     |  68848 |    0.00     |    0.00      | Protein::parseAtom(char const*)
     15.69  |          0.37       |     0.08     |   8064 |    0.01     |    0.01      | Protein::parseDSSPLine(char const*)
      7.84  |          0.41       |     0.04     |        |             |              | Neighbor::Neighbor(std::vector<Point3D*...
                                                         ...
      0.00  |          0.51       |     0.00     | 199671 |    0.00     |    0.00      | Atom::Atom() 

[![Summary of Featurize Positive Sites Call Grap](featurize-pos.png)](featurize-pos-full.png "View full, un-trimmed graph")

From Command(s) (Note: Makefile modified to add `-pg` to g++ flags):

    make
    featurize -P examples/serprot/trypsin_ser_og.pos.ptf > examples/serprot/trypsin_ser_og.pos.ff
    gprof ./featurize > profile/featurize-pos.gprof
    ~/ggprof2do/tprof2dot.py -s profile/featurize-pos.gprof | dot -Tpng -o profile/featurize-pos.png
    ~/ggprof2do/tprof2dot.py -n0 -e0 -s profile/featurize-pos.gprof | dot -Tpng -o profile/featurize-pos-full.png
    time valgrind --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes featurize -P examples/serprot/trypsin_ser_og.pos.ptf > examples/serprot/trypsin_ser_og.pos.ff 2> profile/featurize-pos.valgrid
    grep '^==' profile/featurize-pos.valgrid | sed 's/==[0-9]\+== //' > profile/featurize-pos-clean.valgrid