Flat profile:

Each sample counts as 0.01 seconds.
  %   cumulative   self              self     total           
 time   seconds   seconds    calls   s/call   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*, std::allocator<Point3D*> > const*, float)
  0.32     43.56     0.14                             LispParser::GetLine(std::string&)
  0.23     43.66     0.10       45     0.00     0.00  assign_types(Protein*, ForceFieldParametersSet*, char const*)
  0.14     43.72     0.06   858489     0.00     0.00  Atoms::addAtom(Atom*, bool)
  0.07     43.75     0.03  1312774     0.00     0.00  Atom::Atom()
  0.07     43.78     0.03   509715     0.00     0.00  Protein::parsePDBLine(char const*)
  0.07     43.81     0.03       45     0.00     0.00  MarkHetatm(Atoms*)
  0.05     43.83     0.02   569286     0.00     0.00  std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&)
  0.05     43.85     0.02       45     0.00     0.00  GetResidues(Protein*)
  0.05     43.87     0.02                             parseString(char*, char const*, int, int)
  0.05     43.89     0.02                             std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_erase(std::_Rb_tree_node<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >*)
  0.02     43.90     0.01   858489     0.00     0.00  Atom::operator=(Atom&)
  0.02     43.91     0.01   416377     0.00     0.00  Atom::setSecondaryStructure(char)
  0.02     43.92     0.01   405593     0.00     0.00  std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&)
  0.02     43.93     0.01    72792     0.00     0.00  Atom::getCharge()
  0.02     43.94     0.01    18334     0.00     0.00  Atom::getHydroxyl()
  0.02     43.95     0.01    18334     0.00     0.00  Atom::isRingSystem()
  0.02     43.96     0.01    18334     0.00     0.00  Atom::getRadius()
  0.02     43.97     0.01        1     0.01     0.01  global constructors keyed to Atom::operator=(Atom&)
  0.02     43.98     0.01                             warning(char const*, ...)
  0.02     43.99     0.01                             parseLong(long*, char const*, int, int)
  0.02     44.00     0.01                             Neighbor::~Neighbor()
  0.02     44.01     0.01                             Point3D::getDistanceSqr(Point3D const&) const
  0.02     44.02     0.01                             std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> const&)
  0.01     44.03     0.01   454285     0.00     0.00  Atom::setResidueFullSequence(Atom*)
  0.01     44.03     0.01    53750     0.00     0.00  std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*)
  0.01     44.04     0.01    52586     0.00     0.00  std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*)
  0.01     44.04     0.01                             Atom::getResidueLabel(char*) const
  0.00     44.04     0.00  2671689     0.00     0.00  Atoms::getAtom(int)
  0.00     44.04     0.00  2671689     0.00     0.00  Atoms::operator[](int)
  0.00     44.04     0.00  1319583     0.00     0.00  Atoms::size()
  0.00     44.04     0.00   480096     0.00     0.00  Atom::parsePDBAtom(char const*)
  0.00     44.04     0.00   418748     0.00     0.00  std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, char const* const&)
  0.00     44.04     0.00   405593     0.00     0.00  std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, int> const&)
  0.00     44.04     0.00    73336     0.00     0.00  Atom::isBackbone()
  0.00     44.04     0.00    52586     0.00     0.00  std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique(std::pair<char const* const, int> const&)
  0.00     44.04     0.00    23520     0.00     0.00  Properties::get(int)
  0.00     44.04     0.00    21133     0.00     0.00  Protein::parseHetAtom(char const*)
  0.00     44.04     0.00    20993     0.00     0.00  Atoms::decrementAtomMark(int)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setPeptide(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setNegCharge(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setPosCharge(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setVDWVolume(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setRingSystem(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setResidueName(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setChargeWithHis(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setPartialCharge(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setResidueClass1(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setResidueClass2(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setSecondaryStructure1(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setSecondaryStructure2(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::calculateAtomProperties(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setName(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  AtomProperties::setType(Atom*)
  0.00     44.04     0.00    18334     0.00     0.00  Atom::getCarbonyl()
  0.00     44.04     0.00    18334     0.00     0.00  Atom::getChainDistance()
  0.00     44.04     0.00    18334     0.00     0.00  Atom::getHydrophobicity()
  0.00     44.04     0.00    18334     0.00     0.00  Atom::getAmide()
  0.00     44.04     0.00    18334     0.00     0.00  Atom::getAmine()
  0.00     44.04     0.00    14544     0.00     0.00  Atom::~Atom()
  0.00     44.04     0.00     3211     0.00     0.00  Properties::include(AtomProperties*)
  0.00     44.04     0.00     2250     0.00     0.00  std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&)
  0.00     44.04     0.00     1252     0.00     0.00  std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&)
  0.00     44.04     0.00      665     0.00     0.00  InSameResidue(Atom*, Atom*)
  0.00     44.04     0.00      516     0.00     0.00  std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&)
  0.00     44.04     0.00      294     0.00     0.00  PrintEnvironment(Properties&, _IO_FILE*)
  0.00     44.04     0.00      294     0.00     0.00  Properties::Properties()
  0.00     44.04     0.00      294     0.00     0.00  Properties::~Properties()
  0.00     44.04     0.00       45     0.00     0.00  GetCoordList(Protein*)
  0.00     44.04     0.00       45     0.00     0.00  GetNonExcludedResidues(Atoms*, Strings&)
  0.00     44.04     0.00       45     0.00     0.00  Atoms::extractMarkedAtoms(int)
  0.00     44.04     0.00       45     0.00     0.00  Atoms::~Atoms()
  0.00     44.04     0.00       45     0.00     0.00  Atoms::~Atoms()
  0.00     44.04     0.00       45     0.00     0.82  Protein::readPDBFile(char const*)
  0.00     44.04     0.00       45     0.00     0.15  Protein::readDSSPFile(char const*)
  0.00     44.04     0.00       45     0.00     0.82  Protein::Protein(char const*)
  0.00     44.04     0.00       45     0.00     0.00  Protein::~Protein()
  0.00     44.04     0.00        8     0.00     0.00  std::vector<std::string, std::allocator<std::string> >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::string*, std::vector<std::string, std::allocator<std::string> > >, std::string const&)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to DEFAULT_VERBOSITY
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to IsFullName(Atom&, void*)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to InSameResidue(Atom*, Atom*)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to Properties::Properties()
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to Environment::Environment(int)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to AtomProperties::setName(Atom*)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to Protein::Protein()
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to Property::Property(std::string const&)
  0.00     44.04     0.00        1     0.00     0.00  global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double)
  0.00     44.04     0.00        1     0.00    43.61  Featurize::RunPointEnvironmentMode()
  0.00     44.04     0.00        1     0.00    43.61  Featurize::main(int, char**)

 %         the percentage of the total running time of the
time       program used by this function.

cumulative a running sum of the number of seconds accounted
 seconds   for by this function and those listed above it.

 self      the number of seconds accounted for by this
seconds    function alone.  This is the major sort for this
           listing.

calls      the number of times this function was invoked, if
           this function is profiled, else blank.
 
 self      the average number of milliseconds spent in this
ms/call    function per call, if this function is profiled,
	   else blank.

 total     the average number of milliseconds spent in this
ms/call    function and its descendents per call, if this 
	   function is profiled, else blank.

name       the name of the function.  This is the minor sort
           for this listing. The index shows the location of
	   the function in the gprof listing. If the index is
	   in parenthesis it shows where it would appear in
	   the gprof listing if it were to be printed.

		     Call graph (explanation follows)


granularity: each sample hit covers 2 byte(s) for 0.02% of 44.04 seconds

index % time    self  children    called     name
                                                 <spontaneous>
[1]     99.0    0.00   43.61                 main [1]
                0.00   43.61       1/1           Featurize::main(int, char**) [3]
-----------------------------------------------
                0.00   43.61       1/1           Featurize::main(int, char**) [3]
[2]     99.0    0.00   43.61       1         Featurize::RunPointEnvironmentMode() [2]
                0.00   36.88      45/45          Protein::Protein(char const*) [5]
                0.00    6.61      45/45          Protein::readDSSPFile(char const*) [9]
                0.00    0.04      45/45          Atoms::extractMarkedAtoms(int) [14]
                0.00    0.04   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
                0.00    0.03      45/45          GetNonExcludedResidues(Atoms*, Strings&) [18]
                0.00    0.00  437082/2671689     Atoms::getAtom(int) [52]
                0.00    0.00  437082/2671689     Atoms::operator[](int) [53]
                0.00    0.00   18334/18334       AtomProperties::setSecondaryStructure2(Atom*) [67]
                0.00    0.00    3211/3211        Properties::include(AtomProperties*) [76]
                0.00    0.00     623/1252        std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [78]
                0.00    0.00     294/294         Properties::Properties() [82]
                0.00    0.00     294/294         PrintEnvironment(Properties&, _IO_FILE*) [81]
                0.00    0.00     294/294         Properties::~Properties() [83]
                0.00    0.00     135/1319583     Atoms::size() [54]
                0.00    0.00      45/45          Atoms::~Atoms() [85]
                0.00    0.00      45/45          Protein::~Protein() [87]
-----------------------------------------------
                0.00   43.61       1/1           main [1]
[3]     99.0    0.00   43.61       1         Featurize::main(int, char**) [3]
                0.00   43.61       1/1           Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00       8/8           std::vector<std::string, std::allocator<std::string> >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::string*, std::vector<std::string, std::allocator<std::string> > >, std::string const&) [88]
-----------------------------------------------
                0.00   36.88      45/45          Protein::Protein(char const*) [5]
[4]     83.7    0.00   36.88      45         Protein::readPDBFile(char const*) [4]
                0.03   36.71  509715/509715      Protein::parsePDBLine(char const*) [6]
                0.10    0.04      45/45          assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
-----------------------------------------------
                0.00   36.88      45/45          Featurize::RunPointEnvironmentMode() [2]
[5]     83.7    0.00   36.88      45         Protein::Protein(char const*) [5]
                0.00   36.88      45/45          Protein::readPDBFile(char const*) [4]
-----------------------------------------------
                0.03   36.71  509715/509715      Protein::readPDBFile(char const*) [4]
[6]     83.4    0.03   36.71  509715         Protein::parsePDBLine(char const*) [6]
               36.65    0.06  458963/458963      Protein::parseAtom(char const*) [7]
                0.00    0.00   21133/21133       Protein::parseHetAtom(char const*) [44]
-----------------------------------------------
               36.65    0.06  458963/458963      Protein::parsePDBLine(char const*) [6]
[7]     83.4   36.65    0.06  458963         Protein::parseAtom(char const*) [7]
                0.03    0.01  418748/858489      Atoms::addAtom(Atom*, bool) [13]
                0.00    0.01  458963/480096      Atom::parsePDBAtom(char const*) [23]
                0.00    0.00   14544/14544       Atom::~Atom() [75]
                0.00    0.00     623/2250        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [77]
-----------------------------------------------
                6.60    0.01   53891/53891       Protein::readDSSPFile(char const*) [9]
[8]     15.0    6.60    0.01   53891         Protein::parseDSSPLine(char const*) [8]
                0.01    0.00  416377/416377      Atom::setSecondaryStructure(char) [25]
-----------------------------------------------
                0.00    6.61      45/45          Featurize::RunPointEnvironmentMode() [2]
[9]     15.0    0.00    6.61      45         Protein::readDSSPFile(char const*) [9]
                6.60    0.01   53891/53891       Protein::parseDSSPLine(char const*) [8]
-----------------------------------------------
                                                 <spontaneous>
[10]     0.4    0.17    0.02                 Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float) [10]
                0.02    0.00  569286/569286      std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&) [19]
-----------------------------------------------
                                                 <spontaneous>
[11]     0.3    0.14    0.00                 LispParser::GetLine(std::string&) [11]
-----------------------------------------------
                0.10    0.04      45/45          Protein::readPDBFile(char const*) [4]
[12]     0.3    0.10    0.04      45         assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
                0.02    0.00      45/45          GetResidues(Protein*) [20]
                0.01    0.00  405593/405593      std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&) [26]
                0.01    0.00   53750/53750       std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*) [41]
                0.01    0.00   52586/52586       std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*) [42]
                0.00    0.00  915339/2671689     Atoms::getAtom(int) [52]
                0.00    0.00  915339/2671689     Atoms::operator[](int) [53]
                0.00    0.00  418748/418748      std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, char const* const&) [55]
                0.00    0.00     665/665         InSameResidue(Atom*, Atom*) [79]
                0.00    0.00      45/1319583     Atoms::size() [54]
                0.00    0.00      45/45          GetCoordList(Protein*) [84]
-----------------------------------------------
                0.00    0.00   20993/858489      Protein::parseHetAtom(char const*) [44]
                0.03    0.01  418748/858489      Atoms::extractMarkedAtoms(int) [14]
                0.03    0.01  418748/858489      Protein::parseAtom(char const*) [7]
[13]     0.2    0.06    0.03  858489         Atoms::addAtom(Atom*, bool) [13]
                0.02    0.00  858489/1312774     Atom::Atom() [16]
                0.01    0.00  858489/858489      Atom::operator=(Atom&) [24]
                0.00    0.00    1252/2250        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [77]
-----------------------------------------------
                0.00    0.04      45/45          Featurize::RunPointEnvironmentMode() [2]
[14]     0.1    0.00    0.04      45         Atoms::extractMarkedAtoms(int) [14]
                0.03    0.01  418748/858489      Atoms::addAtom(Atom*, bool) [13]
-----------------------------------------------
                0.00    0.04   18334/18334       Featurize::RunPointEnvironmentMode() [2]
[15]     0.1    0.00    0.04   18334         AtomProperties::calculateAtomProperties(Atom*) [15]
                0.01    0.00   18334/18334       Atom::getHydroxyl() [29]
                0.00    0.01   18334/18334       AtomProperties::setRingSystem(Atom*) [28]
                0.00    0.01   18334/18334       AtomProperties::setVDWVolume(Atom*) [27]
                0.00    0.00   18334/72792       Atom::getCharge() [39]
                0.00    0.00   18334/18334       AtomProperties::setPosCharge(Atom*) [46]
                0.00    0.00   18334/18334       AtomProperties::setNegCharge(Atom*) [45]
                0.00    0.00   18334/18334       AtomProperties::setChargeWithHis(Atom*) [47]
                0.00    0.00   18334/18334       AtomProperties::setName(Atom*) [68]
                0.00    0.00   18334/18334       Atom::getAmide() [73]
                0.00    0.00   18334/18334       Atom::getAmine() [74]
                0.00    0.00   18334/18334       Atom::getCarbonyl() [70]
                0.00    0.00   18334/18334       AtomProperties::setType(Atom*) [69]
                0.00    0.00   18334/18334       AtomProperties::setPeptide(Atom*) [61]
                0.00    0.00   18334/18334       AtomProperties::setPartialCharge(Atom*) [63]
                0.00    0.00   18334/18334       Atom::getHydrophobicity() [72]
                0.00    0.00   18334/18334       Atom::getChainDistance() [71]
                0.00    0.00   18334/18334       AtomProperties::setResidueClass1(Atom*) [64]
                0.00    0.00   18334/18334       AtomProperties::setResidueName(Atom*) [62]
                0.00    0.00   18334/18334       AtomProperties::setResidueClass2(Atom*) [65]
                0.00    0.00   18334/18334       AtomProperties::setSecondaryStructure1(Atom*) [66]
-----------------------------------------------
                0.01    0.00  454285/1312774     Atom::parsePDBAtom(char const*) [23]
                0.02    0.00  858489/1312774     Atoms::addAtom(Atom*, bool) [13]
[16]     0.1    0.03    0.00 1312774         Atom::Atom() [16]
-----------------------------------------------
                0.03    0.00      45/45          GetNonExcludedResidues(Atoms*, Strings&) [18]
[17]     0.1    0.03    0.00      45         MarkHetatm(Atoms*) [17]
                0.00    0.00  439786/1319583     Atoms::size() [54]
                0.00    0.00  439741/2671689     Atoms::getAtom(int) [52]
                0.00    0.00  439741/2671689     Atoms::operator[](int) [53]
                0.00    0.00   20993/20993       Atoms::decrementAtomMark(int) [60]
-----------------------------------------------
                0.00    0.03      45/45          Featurize::RunPointEnvironmentMode() [2]
[18]     0.1    0.00    0.03      45         GetNonExcludedResidues(Atoms*, Strings&) [18]
                0.03    0.00      45/45          MarkHetatm(Atoms*) [17]
-----------------------------------------------
                0.02    0.00  569286/569286      Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float) [10]
[19]     0.0    0.02    0.00  569286         std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&) [19]
-----------------------------------------------
                0.02    0.00      45/45          assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[20]     0.0    0.02    0.00      45         GetResidues(Protein*) [20]
                0.00    0.00  439831/1319583     Atoms::size() [54]
                0.00    0.00  439786/2671689     Atoms::getAtom(int) [52]
                0.00    0.00  439786/2671689     Atoms::operator[](int) [53]
                0.00    0.00     516/516         std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&) [80]
-----------------------------------------------
                                                 <spontaneous>
[21]     0.0    0.02    0.00                 parseString(char*, char const*, int, int) [21]
-----------------------------------------------
                                                 <spontaneous>
[22]     0.0    0.02    0.00                 std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_erase(std::_Rb_tree_node<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >*) [22]
-----------------------------------------------
                0.00    0.00   21133/480096      Protein::parseHetAtom(char const*) [44]
                0.00    0.01  458963/480096      Protein::parseAtom(char const*) [7]
[23]     0.0    0.00    0.02  480096         Atom::parsePDBAtom(char const*) [23]
                0.01    0.00  454285/1312774     Atom::Atom() [16]
                0.01    0.00  454285/454285      Atom::setResidueFullSequence(Atom*) [40]
-----------------------------------------------
                0.01    0.00  858489/858489      Atoms::addAtom(Atom*, bool) [13]
[24]     0.0    0.01    0.00  858489         Atom::operator=(Atom&) [24]
-----------------------------------------------
                0.01    0.00  416377/416377      Protein::parseDSSPLine(char const*) [8]
[25]     0.0    0.01    0.00  416377         Atom::setSecondaryStructure(char) [25]
-----------------------------------------------
                0.01    0.00  405593/405593      assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[26]     0.0    0.01    0.00  405593         std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&) [26]
                0.00    0.00  353007/405593      std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, int> const&) [56]
                0.00    0.00   52586/52586       std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique(std::pair<char const* const, int> const&) [58]
-----------------------------------------------
                0.00    0.01   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[27]     0.0    0.00    0.01   18334         AtomProperties::setVDWVolume(Atom*) [27]
                0.01    0.00   18334/18334       Atom::getRadius() [31]
-----------------------------------------------
                0.00    0.01   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[28]     0.0    0.00    0.01   18334         AtomProperties::setRingSystem(Atom*) [28]
                0.01    0.00   18334/18334       Atom::isRingSystem() [30]
-----------------------------------------------
                0.01    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[29]     0.0    0.01    0.00   18334         Atom::getHydroxyl() [29]
-----------------------------------------------
                0.01    0.00   18334/18334       AtomProperties::setRingSystem(Atom*) [28]
[30]     0.0    0.01    0.00   18334         Atom::isRingSystem() [30]
-----------------------------------------------
                0.01    0.00   18334/18334       AtomProperties::setVDWVolume(Atom*) [27]
[31]     0.0    0.01    0.00   18334         Atom::getRadius() [31]
-----------------------------------------------
                0.01    0.00       1/1           __do_global_ctors_aux [38]
[32]     0.0    0.01    0.00       1         global constructors keyed to Atom::operator=(Atom&) [32]
-----------------------------------------------
                                                 <spontaneous>
[33]     0.0    0.01    0.00                 warning(char const*, ...) [33]
-----------------------------------------------
                                                 <spontaneous>
[34]     0.0    0.01    0.00                 parseLong(long*, char const*, int, int) [34]
-----------------------------------------------
                                                 <spontaneous>
[35]     0.0    0.01    0.00                 Neighbor::~Neighbor() [35]
-----------------------------------------------
                                                 <spontaneous>
[36]     0.0    0.01    0.00                 Point3D::getDistanceSqr(Point3D const&) const [36]
-----------------------------------------------
                                                 <spontaneous>
[37]     0.0    0.01    0.00                 std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> const&) [37]
-----------------------------------------------
                                                 <spontaneous>
[38]     0.0    0.00    0.01                 __do_global_ctors_aux [38]
                0.01    0.00       1/1           global constructors keyed to Atom::operator=(Atom&) [32]
                0.00    0.00       1/1           global constructors keyed to DEFAULT_VERBOSITY [89]
                0.00    0.00       1/1           global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*) [91]
                0.00    0.00       1/1           global constructors keyed to IsFullName(Atom&, void*) [90]
                0.00    0.00       1/1           global constructors keyed to Environment::Environment(int) [94]
                0.00    0.00       1/1           global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double) [99]
                0.00    0.00       1/1           global constructors keyed to Properties::Properties() [93]
                0.00    0.00       1/1           global constructors keyed to Property::Property(std::string const&) [98]
                0.00    0.00       1/1           global constructors keyed to Protein::Protein() [97]
                0.00    0.00       1/1           global constructors keyed to InSameResidue(Atom*, Atom*) [92]
                0.00    0.00       1/1           global constructors keyed to AtomProperties::setName(Atom*) [95]
                0.00    0.00       1/1           global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double) [96]
-----------------------------------------------
                0.00    0.00   17790/72792       AtomProperties::setChargeWithHis(Atom*) [47]
                0.00    0.00   18334/72792       AtomProperties::setPosCharge(Atom*) [46]
                0.00    0.00   18334/72792       AtomProperties::setNegCharge(Atom*) [45]
                0.00    0.00   18334/72792       AtomProperties::calculateAtomProperties(Atom*) [15]
[39]     0.0    0.01    0.00   72792         Atom::getCharge() [39]
-----------------------------------------------
                0.01    0.00  454285/454285      Atom::parsePDBAtom(char const*) [23]
[40]     0.0    0.01    0.00  454285         Atom::setResidueFullSequence(Atom*) [40]
-----------------------------------------------
                              418748             std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*) [41]
                0.01    0.00   53750/53750       assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[41]     0.0    0.01    0.00   53750+418748  std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*) [41]
                              418748             std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*) [41]
-----------------------------------------------
                              405593             std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*) [42]
                0.01    0.00   52586/52586       assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[42]     0.0    0.01    0.00   52586+405593  std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*) [42]
                              405593             std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*) [42]
-----------------------------------------------
                                                 <spontaneous>
[43]     0.0    0.01    0.00                 Atom::getResidueLabel(char*) const [43]
-----------------------------------------------
                0.00    0.00   21133/21133       Protein::parsePDBLine(char const*) [6]
[44]     0.0    0.00    0.00   21133         Protein::parseHetAtom(char const*) [44]
                0.00    0.00   20993/858489      Atoms::addAtom(Atom*, bool) [13]
                0.00    0.00   21133/480096      Atom::parsePDBAtom(char const*) [23]
                0.00    0.00     375/2250        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [77]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[45]     0.0    0.00    0.00   18334         AtomProperties::setNegCharge(Atom*) [45]
                0.00    0.00   18334/72792       Atom::getCharge() [39]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[46]     0.0    0.00    0.00   18334         AtomProperties::setPosCharge(Atom*) [46]
                0.00    0.00   18334/72792       Atom::getCharge() [39]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[47]     0.0    0.00    0.00   18334         AtomProperties::setChargeWithHis(Atom*) [47]
                0.00    0.00   17790/72792       Atom::getCharge() [39]
-----------------------------------------------
                0.00    0.00  437082/2671689     Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00  439741/2671689     MarkHetatm(Atoms*) [17]
                0.00    0.00  439741/2671689     GetCoordList(Protein*) [84]
                0.00    0.00  439786/2671689     GetResidues(Protein*) [20]
                0.00    0.00  915339/2671689     assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[52]     0.0    0.00    0.00 2671689         Atoms::getAtom(int) [52]
-----------------------------------------------
                0.00    0.00  437082/2671689     Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00  439741/2671689     MarkHetatm(Atoms*) [17]
                0.00    0.00  439741/2671689     GetCoordList(Protein*) [84]
                0.00    0.00  439786/2671689     GetResidues(Protein*) [20]
                0.00    0.00  915339/2671689     assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[53]     0.0    0.00    0.00 2671689         Atoms::operator[](int) [53]
-----------------------------------------------
                0.00    0.00      45/1319583     assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
                0.00    0.00     135/1319583     Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00  439786/1319583     MarkHetatm(Atoms*) [17]
                0.00    0.00  439786/1319583     GetCoordList(Protein*) [84]
                0.00    0.00  439831/1319583     GetResidues(Protein*) [20]
[54]     0.0    0.00    0.00 1319583         Atoms::size() [54]
-----------------------------------------------
                0.00    0.00  418748/418748      assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[55]     0.0    0.00    0.00  418748         std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, char const* const&) [55]
-----------------------------------------------
                0.00    0.00   52586/405593      std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique(std::pair<char const* const, int> const&) [58]
                0.00    0.00  353007/405593      std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&) [26]
[56]     0.0    0.00    0.00  405593         std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, int> const&) [56]
-----------------------------------------------
                0.00    0.00   18334/73336       Atom::getChainDistance() [71]
                0.00    0.00   18334/73336       Atom::getAmide() [73]
                0.00    0.00   18334/73336       Atom::getHydrophobicity() [72]
                0.00    0.00   18334/73336       AtomProperties::setPeptide(Atom*) [61]
[57]     0.0    0.00    0.00   73336         Atom::isBackbone() [57]
-----------------------------------------------
                0.00    0.00   52586/52586       std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&) [26]
[58]     0.0    0.00    0.00   52586         std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique(std::pair<char const* const, int> const&) [58]
                0.00    0.00   52586/405593      std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, int> const&) [56]
-----------------------------------------------
                0.00    0.00   23520/23520       PrintEnvironment(Properties&, _IO_FILE*) [81]
[59]     0.0    0.00    0.00   23520         Properties::get(int) [59]
-----------------------------------------------
                0.00    0.00   20993/20993       MarkHetatm(Atoms*) [17]
[60]     0.0    0.00    0.00   20993         Atoms::decrementAtomMark(int) [60]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[61]     0.0    0.00    0.00   18334         AtomProperties::setPeptide(Atom*) [61]
                0.00    0.00   18334/73336       Atom::isBackbone() [57]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[62]     0.0    0.00    0.00   18334         AtomProperties::setResidueName(Atom*) [62]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[63]     0.0    0.00    0.00   18334         AtomProperties::setPartialCharge(Atom*) [63]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[64]     0.0    0.00    0.00   18334         AtomProperties::setResidueClass1(Atom*) [64]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[65]     0.0    0.00    0.00   18334         AtomProperties::setResidueClass2(Atom*) [65]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[66]     0.0    0.00    0.00   18334         AtomProperties::setSecondaryStructure1(Atom*) [66]
-----------------------------------------------
                0.00    0.00   18334/18334       Featurize::RunPointEnvironmentMode() [2]
[67]     0.0    0.00    0.00   18334         AtomProperties::setSecondaryStructure2(Atom*) [67]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[68]     0.0    0.00    0.00   18334         AtomProperties::setName(Atom*) [68]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[69]     0.0    0.00    0.00   18334         AtomProperties::setType(Atom*) [69]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[70]     0.0    0.00    0.00   18334         Atom::getCarbonyl() [70]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[71]     0.0    0.00    0.00   18334         Atom::getChainDistance() [71]
                0.00    0.00   18334/73336       Atom::isBackbone() [57]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[72]     0.0    0.00    0.00   18334         Atom::getHydrophobicity() [72]
                0.00    0.00   18334/73336       Atom::isBackbone() [57]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[73]     0.0    0.00    0.00   18334         Atom::getAmide() [73]
                0.00    0.00   18334/73336       Atom::isBackbone() [57]
-----------------------------------------------
                0.00    0.00   18334/18334       AtomProperties::calculateAtomProperties(Atom*) [15]
[74]     0.0    0.00    0.00   18334         Atom::getAmine() [74]
-----------------------------------------------
                0.00    0.00   14544/14544       Protein::parseAtom(char const*) [7]
[75]     0.0    0.00    0.00   14544         Atom::~Atom() [75]
-----------------------------------------------
                0.00    0.00    3211/3211        Featurize::RunPointEnvironmentMode() [2]
[76]     0.0    0.00    0.00    3211         Properties::include(AtomProperties*) [76]
-----------------------------------------------
                0.00    0.00     375/2250        Protein::parseHetAtom(char const*) [44]
                0.00    0.00     623/2250        Protein::parseAtom(char const*) [7]
                0.00    0.00    1252/2250        Atoms::addAtom(Atom*, bool) [13]
[77]     0.0    0.00    0.00    2250         std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [77]
-----------------------------------------------
                0.00    0.00     623/1252        Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00     629/1252        GetCoordList(Protein*) [84]
[78]     0.0    0.00    0.00    1252         std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [78]
-----------------------------------------------
                0.00    0.00     665/665         assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[79]     0.0    0.00    0.00     665         InSameResidue(Atom*, Atom*) [79]
-----------------------------------------------
                0.00    0.00     516/516         GetResidues(Protein*) [20]
[80]     0.0    0.00    0.00     516         std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&) [80]
-----------------------------------------------
                0.00    0.00     294/294         Featurize::RunPointEnvironmentMode() [2]
[81]     0.0    0.00    0.00     294         PrintEnvironment(Properties&, _IO_FILE*) [81]
                0.00    0.00   23520/23520       Properties::get(int) [59]
-----------------------------------------------
                0.00    0.00     294/294         Featurize::RunPointEnvironmentMode() [2]
[82]     0.0    0.00    0.00     294         Properties::Properties() [82]
-----------------------------------------------
                0.00    0.00     294/294         Featurize::RunPointEnvironmentMode() [2]
[83]     0.0    0.00    0.00     294         Properties::~Properties() [83]
-----------------------------------------------
                0.00    0.00      45/45          assign_types(Protein*, ForceFieldParametersSet*, char const*) [12]
[84]     0.0    0.00    0.00      45         GetCoordList(Protein*) [84]
                0.00    0.00  439786/1319583     Atoms::size() [54]
                0.00    0.00  439741/2671689     Atoms::getAtom(int) [52]
                0.00    0.00  439741/2671689     Atoms::operator[](int) [53]
                0.00    0.00     629/1252        std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [78]
-----------------------------------------------
                0.00    0.00      45/45          Featurize::RunPointEnvironmentMode() [2]
[85]     0.0    0.00    0.00      45         Atoms::~Atoms() [85]
-----------------------------------------------
                0.00    0.00      45/45          Protein::~Protein() [87]
[86]     0.0    0.00    0.00      45         Atoms::~Atoms() [86]
-----------------------------------------------
                0.00    0.00      45/45          Featurize::RunPointEnvironmentMode() [2]
[87]     0.0    0.00    0.00      45         Protein::~Protein() [87]
                0.00    0.00      45/45          Atoms::~Atoms() [86]
-----------------------------------------------
                0.00    0.00       8/8           Featurize::main(int, char**) [3]
[88]     0.0    0.00    0.00       8         std::vector<std::string, std::allocator<std::string> >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::string*, std::vector<std::string, std::allocator<std::string> > >, std::string const&) [88]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[89]     0.0    0.00    0.00       1         global constructors keyed to DEFAULT_VERBOSITY [89]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[90]     0.0    0.00    0.00       1         global constructors keyed to IsFullName(Atom&, void*) [90]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[91]     0.0    0.00    0.00       1         global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*) [91]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[92]     0.0    0.00    0.00       1         global constructors keyed to InSameResidue(Atom*, Atom*) [92]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[93]     0.0    0.00    0.00       1         global constructors keyed to Properties::Properties() [93]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[94]     0.0    0.00    0.00       1         global constructors keyed to Environment::Environment(int) [94]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[95]     0.0    0.00    0.00       1         global constructors keyed to AtomProperties::setName(Atom*) [95]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[96]     0.0    0.00    0.00       1         global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double) [96]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[97]     0.0    0.00    0.00       1         global constructors keyed to Protein::Protein() [97]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[98]     0.0    0.00    0.00       1         global constructors keyed to Property::Property(std::string const&) [98]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [38]
[99]     0.0    0.00    0.00       1         global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double) [99]
-----------------------------------------------

 This table describes the call tree of the program, and was sorted by
 the total amount of time spent in each function and its children.

 Each entry in this table consists of several lines.  The line with the
 index number at the left hand margin lists the current function.
 The lines above it list the functions that called this function,
 and the lines below it list the functions this one called.
 This line lists:
     index	A unique number given to each element of the table.
		Index numbers are sorted numerically.
		The index number is printed next to every function name so
		it is easier to look up where the function in the table.

     % time	This is the percentage of the `total' time that was spent
		in this function and its children.  Note that due to
		different viewpoints, functions excluded by options, etc,
		these numbers will NOT add up to 100%.

     self	This is the total amount of time spent in this function.

     children	This is the total amount of time propagated into this
		function by its children.

     called	This is the number of times the function was called.
		If the function called itself recursively, the number
		only includes non-recursive calls, and is followed by
		a `+' and the number of recursive calls.

     name	The name of the current function.  The index number is
		printed after it.  If the function is a member of a
		cycle, the cycle number is printed between the
		function's name and the index number.


 For the function's parents, the fields have the following meanings:

     self	This is the amount of time that was propagated directly
		from the function into this parent.

     children	This is the amount of time that was propagated from
		the function's children into this parent.

     called	This is the number of times this parent called the
		function `/' the total number of times the function
		was called.  Recursive calls to the function are not
		included in the number after the `/'.

     name	This is the name of the parent.  The parent's index
		number is printed after it.  If the parent is a
		member of a cycle, the cycle number is printed between
		the name and the index number.

 If the parents of the function cannot be determined, the word
 `<spontaneous>' is printed in the `name' field, and all the other
 fields are blank.

 For the function's children, the fields have the following meanings:

     self	This is the amount of time that was propagated directly
		from the child into the function.

     children	This is the amount of time that was propagated from the
		child's children to the function.

     called	This is the number of times the function called
		this child `/' the total number of times the child
		was called.  Recursive calls by the child are not
		listed in the number after the `/'.

     name	This is the name of the child.  The child's index
		number is printed after it.  If the child is a
		member of a cycle, the cycle number is printed
		between the name and the index number.

 If there are any cycles (circles) in the call graph, there is an
 entry for the cycle-as-a-whole.  This entry shows who called the
 cycle (as parents) and the members of the cycle (as children.)
 The `+' recursive calls entry shows the number of function calls that
 were internal to the cycle, and the calls entry for each member shows,
 for that member, how many times it was called from other members of
 the cycle.


Index by function name

  [89] global constructors keyed to DEFAULT_VERBOSITY (featurize.cc) [28] AtomProperties::setRingSystem(Atom*) [52] Atoms::getAtom(int)
  [90] global constructors keyed to IsFullName(Atom&, void*) (Atoms.cc) [62] AtomProperties::setResidueName(Atom*) [85] Atoms::~Atoms()
  [91] global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc) [47] AtomProperties::setChargeWithHis(Atom*) [86] Atoms::~Atoms()
  [92] global constructors keyed to InSameResidue(Atom*, Atom*) (ResidueHelper.cc) [63] AtomProperties::setPartialCharge(Atom*) [53] Atoms::operator[](int)
  [93] global constructors keyed to Properties::Properties() (Properties.cc) [64] AtomProperties::setResidueClass1(Atom*) [4] Protein::readPDBFile(char const*)
  [94] global constructors keyed to Environment::Environment(int) (Environments.cc) [65] AtomProperties::setResidueClass2(Atom*) [44] Protein::parseHetAtom(char const*)
  [95] global constructors keyed to AtomProperties::setName(Atom*) (AtomProperties.cc) [66] AtomProperties::setSecondaryStructure1(Atom*) [6] Protein::parsePDBLine(char const*)
  [96] global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double) (StatisticsFile.cc) [67] AtomProperties::setSecondaryStructure2(Atom*) [9] Protein::readDSSPFile(char const*)
  [32] global constructors keyed to Atom::operator=(Atom&) (Atom.cc) [15] AtomProperties::calculateAtomProperties(Atom*) [8] Protein::parseDSSPLine(char const*)
  [97] global constructors keyed to Protein::Protein() (Protein.cc) [68] AtomProperties::setName(Atom*) [7] Protein::parseAtom(char const*)
  [98] global constructors keyed to Property::Property(std::string const&) (Property.cc) [69] AtomProperties::setType(Atom*) [5] Protein::Protein(char const*)
  [99] global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double) (ModelFile.cc) [57] Atom::isBackbone() [87] Protein::~Protein()
  [17] MarkHetatm(Atoms*)     [70] Atom::getCarbonyl()    [10] Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float)
  [20] GetResidues(Protein*)  [29] Atom::getHydroxyl()    [35] Neighbor::~Neighbor()
  [21] parseString(char*, char const*, int, int) [30] Atom::isRingSystem() [2] Featurize::RunPointEnvironmentMode()
  [84] GetCoordList(Protein*) [23] Atom::parsePDBAtom(char const*) [3] Featurize::main(int, char**)
  [12] assign_types(Protein*, ForceFieldParametersSet*, char const*) [71] Atom::getChainDistance() [43] Atom::getResidueLabel(char*) const
  [79] InSameResidue(Atom*, Atom*) [72] Atom::getHydrophobicity() [36] Point3D::getDistanceSqr(Point3D const&) const
  [81] PrintEnvironment(Properties&, _IO_FILE*) [25] Atom::setSecondaryStructure(char) [80] std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&)
  [18] GetNonExcludedResidues(Atoms*, Strings&) [40] Atom::setResidueFullSequence(Atom*) [77] std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&)
  [33] warning(char const*, ...) [73] Atom::getAmide()    [78] std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&)
  [34] parseLong(long*, char const*, int, int) [74] Atom::getAmine() [88] std::vector<std::string, std::allocator<std::string> >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::string*, std::vector<std::string, std::allocator<std::string> > >, std::string const&)
  [11] LispParser::GetLine(std::string&) [39] Atom::getCharge() [19] std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&)
  [59] Properties::get(int)   [31] Atom::getRadius()      [37] std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> const&)
  [76] Properties::include(AtomProperties*) [16] Atom::Atom() [22] std::_Rb_tree<Neighbor::Cell, std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*>, std::_Select1st<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >, Neighbor::Cell::compare, std::allocator<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> > >::_M_erase(std::_Rb_tree_node<std::pair<Neighbor::Cell const, std::vector<int, std::allocator<int> >*> >*)
  [82] Properties::Properties() [75] Atom::~Atom()        [55] std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, char const* const&)
  [83] Properties::~Properties() [24] Atom::operator=(Atom&) [41] std::_Rb_tree<char const*, char const*, std::_Identity<char const*>, compare_cstring, std::allocator<char const*> >::_M_erase(std::_Rb_tree_node<char const*>*)
  [61] AtomProperties::setPeptide(Atom*) [60] Atoms::decrementAtomMark(int) [56] std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, int> const&)
  [45] AtomProperties::setNegCharge(Atom*) [14] Atoms::extractMarkedAtoms(int) [58] std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique(std::pair<char const* const, int> const&)
  [46] AtomProperties::setPosCharge(Atom*) [54] Atoms::size() [26] std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, int> >, std::pair<char const* const, int> const&)
  [27] AtomProperties::setVDWVolume(Atom*) [13] Atoms::addAtom(Atom*, bool) [42] std::_Rb_tree<char const*, std::pair<char const* const, int>, std::_Select1st<std::pair<char const* const, int> >, compare_cstring, std::allocator<std::pair<char const* const, int> > >::_M_erase(std::_Rb_tree_node<std::pair<char const* const, int> >*)