Flat profile:

Each sample counts as 0.01 seconds.
  %   cumulative   self              self     total           
 time   seconds   seconds    calls  ms/call  ms/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*, std::allocator<Point3D*> > const*, float)
  1.96      0.42     0.01    77813     0.00     0.00  Atom::parsePDBAtom(char const*)
  1.96      0.43     0.01    59320     0.00     0.00  Atom::getCharge()
  1.96      0.44     0.01    59276     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&)
  1.96      0.45     0.01    14986     0.00     0.00  AtomProperties::setVDWVolume(Atom*)
  1.96      0.46     0.01    14986     0.00     0.00  AtomProperties::setChargeWithHis(Atom*)
  1.96      0.47     0.01    14986     0.00     0.00  Atom::getChainDistance()
  1.96      0.48     0.01    14986     0.00     0.00  Atom::getRadius()
  1.96      0.49     0.01       22     0.45     0.45  GetResidues(Protein*)
  1.96      0.50     0.01                             LispParser::GetLine(std::string&)
  1.96      0.51     0.01                             Neighbor::~Neighbor()
  0.00      0.51     0.00   429429     0.00     0.00  Atoms::getAtom(int)
  0.00      0.51     0.00   429429     0.00     0.00  Atoms::operator[](int)
  0.00      0.51     0.00   207566     0.00     0.00  Atoms::size()
  0.00      0.51     0.00   199671     0.00     0.00  Atom::Atom()
  0.00      0.51     0.00   130496     0.00     0.00  Atom::operator=(Atom&)
  0.00      0.51     0.00   130496     0.00     0.00  Atoms::addAtom(Atom*, bool)
  0.00      0.51     0.00    94296     0.00     0.00  Protein::parsePDBLine(char const*)
  0.00      0.51     0.00    87047     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&)
  0.00      0.51     0.00    69175     0.00     0.00  Atom::setResidueFullSequence(Atom*)
  0.00      0.51     0.00    61377     0.00     0.00  Atom::setSecondaryStructure(char)
  0.00      0.51     0.00    61366     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      0.51     0.00    59944     0.00     0.00  Atom::isBackbone()
  0.00      0.51     0.00    59276     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      0.51     0.00    14986     0.00     0.00  AtomProperties::setPeptide(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setNegCharge(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setPosCharge(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setRingSystem(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setResidueName(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setPartialCharge(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setResidueClass1(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setResidueClass2(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setSecondaryStructure1(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setSecondaryStructure2(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::calculateAtomProperties(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setName(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  AtomProperties::setType(Atom*)
  0.00      0.51     0.00    14986     0.00     0.00  Atom::getCarbonyl()
  0.00      0.51     0.00    14986     0.00     0.00  Atom::getHydroxyl()
  0.00      0.51     0.00    14986     0.00     0.00  Atom::isRingSystem()
  0.00      0.51     0.00    14986     0.00     0.00  Atom::getHydrophobicity()
  0.00      0.51     0.00    14986     0.00     0.00  Atom::getAmide()
  0.00      0.51     0.00    14986     0.00     0.00  Atom::getAmine()
  0.00      0.51     0.00    10560     0.00     0.00  Properties::get(int)
  0.00      0.51     0.00     8965     0.00     0.00  Protein::parseHetAtom(char const*)
  0.00      0.51     0.00     8039     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*>*)
  0.00      0.51     0.00     7830     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      0.51     0.00     7830     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> >*)
  0.00      0.51     0.00     7764     0.00     0.00  Atoms::decrementAtomMark(int)
  0.00      0.51     0.00     1881     0.00     0.00  Properties::include(AtomProperties*)
  0.00      0.51     0.00     1065     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      0.51     0.00      573     0.00     0.00  InSameResidue(Atom*, Atom*)
  0.00      0.51     0.00      566     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      0.51     0.00      238     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      0.51     0.00      132     0.00     0.00  PrintEnvironment(Properties&, _IO_FILE*)
  0.00      0.51     0.00      132     0.00     0.00  Properties::Properties()
  0.00      0.51     0.00      132     0.00     0.00  Properties::~Properties()
  0.00      0.51     0.00       45     0.00     0.00  Atom::~Atom()
  0.00      0.51     0.00       22     0.00     0.00  MarkHetatm(Atoms*)
  0.00      0.51     0.00       22     0.00     0.00  GetCoordList(Protein*)
  0.00      0.51     0.00       22     0.00     0.91  assign_types(Protein*, ForceFieldParametersSet*, char const*)
  0.00      0.51     0.00       22     0.00     0.00  GetNonExcludedResidues(Atoms*, Strings&)
  0.00      0.51     0.00       22     0.00     0.00  Atoms::extractMarkedAtoms(int)
  0.00      0.51     0.00       22     0.00     0.00  Atoms::~Atoms()
  0.00      0.51     0.00       22     0.00     0.00  Atoms::~Atoms()
  0.00      0.51     0.00       22     0.00    14.55  Protein::readPDBFile(char const*)
  0.00      0.51     0.00       22     0.00     3.64  Protein::readDSSPFile(char const*)
  0.00      0.51     0.00       22     0.00    14.55  Protein::Protein(char const*)
  0.00      0.51     0.00       22     0.00     0.00  Protein::~Protein()
  0.00      0.51     0.00        7     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      0.51     0.00        1     0.00     0.00  global constructors keyed to DEFAULT_VERBOSITY
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to IsFullName(Atom&, void*)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to InSameResidue(Atom*, Atom*)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to Properties::Properties()
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to Environment::Environment(int)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to AtomProperties::setName(Atom*)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to Atom::operator=(Atom&)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to Protein::Protein()
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to Property::Property(std::string const&)
  0.00      0.51     0.00        1     0.00     0.00  global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double)
  0.00      0.51     0.00        1     0.00   450.02  Featurize::RunPointEnvironmentMode()
  0.00      0.51     0.00        1     0.00   450.02  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 1.96% of 0.51 seconds

index % time    self  children    called     name
                                                 <spontaneous>
[1]     88.2    0.00    0.45                 main [1]
                0.00    0.45       1/1           Featurize::main(int, char**) [3]
-----------------------------------------------
                0.00    0.45       1/1           Featurize::main(int, char**) [3]
[2]     88.2    0.00    0.45       1         Featurize::RunPointEnvironmentMode() [2]
                0.00    0.32      22/22          Protein::Protein(char const*) [5]
                0.00    0.08      22/22          Protein::readDSSPFile(char const*) [9]
                0.00    0.05   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
                0.00    0.00   76352/429429      Atoms::getAtom(int) [30]
                0.00    0.00   76352/429429      Atoms::operator[](int) [31]
                0.00    0.00   14986/14986       AtomProperties::setSecondaryStructure2(Atom*) [49]
                0.00    0.00    1881/1881        Properties::include(AtomProperties*) [63]
                0.00    0.00     280/566         std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [66]
                0.00    0.00     132/132         Properties::Properties() [69]
                0.00    0.00     132/132         PrintEnvironment(Properties&, _IO_FILE*) [68]
                0.00    0.00     132/132         Properties::~Properties() [70]
                0.00    0.00      66/207566      Atoms::size() [32]
                0.00    0.00      22/22          Atoms::extractMarkedAtoms(int) [75]
                0.00    0.00      22/22          GetNonExcludedResidues(Atoms*, Strings&) [74]
                0.00    0.00      22/22          Atoms::~Atoms() [76]
                0.00    0.00      22/22          Protein::~Protein() [78]
-----------------------------------------------
                0.00    0.45       1/1           main [1]
[3]     88.2    0.00    0.45       1         Featurize::main(int, char**) [3]
                0.00    0.45       1/1           Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00       7/7           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&) [79]
-----------------------------------------------
                0.00    0.32      22/22          Protein::Protein(char const*) [5]
[4]     62.7    0.00    0.32      22         Protein::readPDBFile(char const*) [4]
                0.00    0.30   94296/94296       Protein::parsePDBLine(char const*) [6]
                0.00    0.02      22/22          assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
-----------------------------------------------
                0.00    0.32      22/22          Featurize::RunPointEnvironmentMode() [2]
[5]     62.7    0.00    0.32      22         Protein::Protein(char const*) [5]
                0.00    0.32      22/22          Protein::readPDBFile(char const*) [4]
-----------------------------------------------
                0.00    0.30   94296/94296       Protein::readPDBFile(char const*) [4]
[6]     58.8    0.00    0.30   94296         Protein::parsePDBLine(char const*) [6]
                0.29    0.01   68848/68848       Protein::parseAtom(char const*) [7]
                0.00    0.00    8965/8965        Protein::parseHetAtom(char const*) [25]
-----------------------------------------------
                0.29    0.01   68848/68848       Protein::parsePDBLine(char const*) [6]
[7]     58.6    0.29    0.01   68848         Protein::parseAtom(char const*) [7]
                0.01    0.00   68848/77813       Atom::parsePDBAtom(char const*) [15]
                0.00    0.00   61366/130496      Atoms::addAtom(Atom*, bool) [35]
                0.00    0.00     280/1065        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [64]
                0.00    0.00      45/45          Atom::~Atom() [71]
-----------------------------------------------
                0.08    0.00    8064/8064        Protein::readDSSPFile(char const*) [9]
[8]     15.7    0.08    0.00    8064         Protein::parseDSSPLine(char const*) [8]
                0.00    0.00   61377/61377       Atom::setSecondaryStructure(char) [38]
-----------------------------------------------
                0.00    0.08      22/22          Featurize::RunPointEnvironmentMode() [2]
[9]     15.7    0.00    0.08      22         Protein::readDSSPFile(char const*) [9]
                0.08    0.00    8064/8064        Protein::parseDSSPLine(char const*) [8]
-----------------------------------------------
                0.00    0.05   14986/14986       Featurize::RunPointEnvironmentMode() [2]
[10]     9.8    0.00    0.05   14986         AtomProperties::calculateAtomProperties(Atom*) [10]
                0.01    0.01   14986/14986       AtomProperties::setVDWVolume(Atom*) [12]
                0.01    0.00   14986/14986       AtomProperties::setChargeWithHis(Atom*) [14]
                0.01    0.00   14986/14986       Atom::getChainDistance() [18]
                0.00    0.00   14986/59320       Atom::getCharge() [16]
                0.00    0.00   14986/14986       AtomProperties::setPosCharge(Atom*) [24]
                0.00    0.00   14986/14986       AtomProperties::setNegCharge(Atom*) [23]
                0.00    0.00   14986/14986       Atom::getHydroxyl() [53]
                0.00    0.00   14986/14986       AtomProperties::setName(Atom*) [50]
                0.00    0.00   14986/14986       Atom::getAmide() [56]
                0.00    0.00   14986/14986       Atom::getAmine() [57]
                0.00    0.00   14986/14986       Atom::getCarbonyl() [52]
                0.00    0.00   14986/14986       AtomProperties::setRingSystem(Atom*) [43]
                0.00    0.00   14986/14986       AtomProperties::setType(Atom*) [51]
                0.00    0.00   14986/14986       AtomProperties::setPeptide(Atom*) [42]
                0.00    0.00   14986/14986       AtomProperties::setPartialCharge(Atom*) [45]
                0.00    0.00   14986/14986       Atom::getHydrophobicity() [55]
                0.00    0.00   14986/14986       AtomProperties::setResidueClass1(Atom*) [46]
                0.00    0.00   14986/14986       AtomProperties::setResidueName(Atom*) [44]
                0.00    0.00   14986/14986       AtomProperties::setResidueClass2(Atom*) [47]
                0.00    0.00   14986/14986       AtomProperties::setSecondaryStructure1(Atom*) [48]
-----------------------------------------------
                                                 <spontaneous>
[11]     7.8    0.04    0.00                 Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float) [11]
                0.00    0.00   87047/87047       std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&) [36]
-----------------------------------------------
                0.01    0.01   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[12]     3.9    0.01    0.01   14986         AtomProperties::setVDWVolume(Atom*) [12]
                0.01    0.00   14986/14986       Atom::getRadius() [19]
-----------------------------------------------
                0.00    0.02      22/22          Protein::readPDBFile(char const*) [4]
[13]     3.9    0.00    0.02      22         assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
                0.01    0.00   59276/59276       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&) [17]
                0.01    0.00      22/22          GetResidues(Protein*) [20]
                0.00    0.00  145665/429429      Atoms::getAtom(int) [30]
                0.00    0.00  145665/429429      Atoms::operator[](int) [31]
                0.00    0.00   61366/61366       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&) [39]
                0.00    0.00    8039/8039        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*>*) [59]
                0.00    0.00    7830/7830        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> >*) [61]
                0.00    0.00     573/573         InSameResidue(Atom*, Atom*) [65]
                0.00    0.00      22/207566      Atoms::size() [32]
                0.00    0.00      22/22          GetCoordList(Protein*) [73]
-----------------------------------------------
                0.01    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[14]     2.4    0.01    0.00   14986         AtomProperties::setChargeWithHis(Atom*) [14]
                0.00    0.00   14362/59320       Atom::getCharge() [16]
-----------------------------------------------
                0.00    0.00    8965/77813       Protein::parseHetAtom(char const*) [25]
                0.01    0.00   68848/77813       Protein::parseAtom(char const*) [7]
[15]     2.0    0.01    0.00   77813         Atom::parsePDBAtom(char const*) [15]
                0.00    0.00   69175/199671      Atom::Atom() [33]
                0.00    0.00   69175/69175       Atom::setResidueFullSequence(Atom*) [37]
-----------------------------------------------
                0.00    0.00   14362/59320       AtomProperties::setChargeWithHis(Atom*) [14]
                0.00    0.00   14986/59320       AtomProperties::setPosCharge(Atom*) [24]
                0.00    0.00   14986/59320       AtomProperties::setNegCharge(Atom*) [23]
                0.00    0.00   14986/59320       AtomProperties::calculateAtomProperties(Atom*) [10]
[16]     2.0    0.01    0.00   59320         Atom::getCharge() [16]
-----------------------------------------------
                0.01    0.00   59276/59276       assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[17]     2.0    0.01    0.00   59276         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&) [17]
                0.00    0.00   51446/59276       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&) [41]
                0.00    0.00    7830/7830        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&) [60]
-----------------------------------------------
                0.01    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[18]     2.0    0.01    0.00   14986         Atom::getChainDistance() [18]
                0.00    0.00   14986/59944       Atom::isBackbone() [40]
-----------------------------------------------
                0.01    0.00   14986/14986       AtomProperties::setVDWVolume(Atom*) [12]
[19]     2.0    0.01    0.00   14986         Atom::getRadius() [19]
-----------------------------------------------
                0.01    0.00      22/22          assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[20]     2.0    0.01    0.00      22         GetResidues(Protein*) [20]
                0.00    0.00   69174/207566      Atoms::size() [32]
                0.00    0.00   69152/429429      Atoms::getAtom(int) [30]
                0.00    0.00   69152/429429      Atoms::operator[](int) [31]
                0.00    0.00     238/238         std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&) [67]
-----------------------------------------------
                                                 <spontaneous>
[21]     2.0    0.01    0.00                 LispParser::GetLine(std::string&) [21]
-----------------------------------------------
                                                 <spontaneous>
[22]     2.0    0.01    0.00                 Neighbor::~Neighbor() [22]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[23]     0.5    0.00    0.00   14986         AtomProperties::setNegCharge(Atom*) [23]
                0.00    0.00   14986/59320       Atom::getCharge() [16]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[24]     0.5    0.00    0.00   14986         AtomProperties::setPosCharge(Atom*) [24]
                0.00    0.00   14986/59320       Atom::getCharge() [16]
-----------------------------------------------
                0.00    0.00    8965/8965        Protein::parsePDBLine(char const*) [6]
[25]     0.2    0.00    0.00    8965         Protein::parseHetAtom(char const*) [25]
                0.00    0.00    8965/77813       Atom::parsePDBAtom(char const*) [15]
                0.00    0.00    7764/130496      Atoms::addAtom(Atom*, bool) [35]
                0.00    0.00     219/1065        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [64]
-----------------------------------------------
                0.00    0.00   69130/429429      MarkHetatm(Atoms*) [72]
                0.00    0.00   69130/429429      GetCoordList(Protein*) [73]
                0.00    0.00   69152/429429      GetResidues(Protein*) [20]
                0.00    0.00   76352/429429      Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00  145665/429429      assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[30]     0.0    0.00    0.00  429429         Atoms::getAtom(int) [30]
-----------------------------------------------
                0.00    0.00   69130/429429      MarkHetatm(Atoms*) [72]
                0.00    0.00   69130/429429      GetCoordList(Protein*) [73]
                0.00    0.00   69152/429429      GetResidues(Protein*) [20]
                0.00    0.00   76352/429429      Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00  145665/429429      assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[31]     0.0    0.00    0.00  429429         Atoms::operator[](int) [31]
-----------------------------------------------
                0.00    0.00      22/207566      assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
                0.00    0.00      66/207566      Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00   69152/207566      MarkHetatm(Atoms*) [72]
                0.00    0.00   69152/207566      GetCoordList(Protein*) [73]
                0.00    0.00   69174/207566      GetResidues(Protein*) [20]
[32]     0.0    0.00    0.00  207566         Atoms::size() [32]
-----------------------------------------------
                0.00    0.00   69175/199671      Atom::parsePDBAtom(char const*) [15]
                0.00    0.00  130496/199671      Atoms::addAtom(Atom*, bool) [35]
[33]     0.0    0.00    0.00  199671         Atom::Atom() [33]
-----------------------------------------------
                0.00    0.00  130496/130496      Atoms::addAtom(Atom*, bool) [35]
[34]     0.0    0.00    0.00  130496         Atom::operator=(Atom&) [34]
-----------------------------------------------
                0.00    0.00    7764/130496      Protein::parseHetAtom(char const*) [25]
                0.00    0.00   61366/130496      Atoms::extractMarkedAtoms(int) [75]
                0.00    0.00   61366/130496      Protein::parseAtom(char const*) [7]
[35]     0.0    0.00    0.00  130496         Atoms::addAtom(Atom*, bool) [35]
                0.00    0.00  130496/199671      Atom::Atom() [33]
                0.00    0.00  130496/130496      Atom::operator=(Atom&) [34]
                0.00    0.00     566/1065        std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [64]
-----------------------------------------------
                0.00    0.00   87047/87047       Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float) [11]
[36]     0.0    0.00    0.00   87047         std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&) [36]
-----------------------------------------------
                0.00    0.00   69175/69175       Atom::parsePDBAtom(char const*) [15]
[37]     0.0    0.00    0.00   69175         Atom::setResidueFullSequence(Atom*) [37]
-----------------------------------------------
                0.00    0.00   61377/61377       Protein::parseDSSPLine(char const*) [8]
[38]     0.0    0.00    0.00   61377         Atom::setSecondaryStructure(char) [38]
-----------------------------------------------
                0.00    0.00   61366/61366       assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[39]     0.0    0.00    0.00   61366         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&) [39]
-----------------------------------------------
                0.00    0.00   14986/59944       Atom::getChainDistance() [18]
                0.00    0.00   14986/59944       Atom::getAmide() [56]
                0.00    0.00   14986/59944       Atom::getHydrophobicity() [55]
                0.00    0.00   14986/59944       AtomProperties::setPeptide(Atom*) [42]
[40]     0.0    0.00    0.00   59944         Atom::isBackbone() [40]
-----------------------------------------------
                0.00    0.00    7830/59276       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&) [60]
                0.00    0.00   51446/59276       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&) [17]
[41]     0.0    0.00    0.00   59276         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&) [41]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[42]     0.0    0.00    0.00   14986         AtomProperties::setPeptide(Atom*) [42]
                0.00    0.00   14986/59944       Atom::isBackbone() [40]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[43]     0.0    0.00    0.00   14986         AtomProperties::setRingSystem(Atom*) [43]
                0.00    0.00   14986/14986       Atom::isRingSystem() [54]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[44]     0.0    0.00    0.00   14986         AtomProperties::setResidueName(Atom*) [44]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[45]     0.0    0.00    0.00   14986         AtomProperties::setPartialCharge(Atom*) [45]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[46]     0.0    0.00    0.00   14986         AtomProperties::setResidueClass1(Atom*) [46]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[47]     0.0    0.00    0.00   14986         AtomProperties::setResidueClass2(Atom*) [47]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[48]     0.0    0.00    0.00   14986         AtomProperties::setSecondaryStructure1(Atom*) [48]
-----------------------------------------------
                0.00    0.00   14986/14986       Featurize::RunPointEnvironmentMode() [2]
[49]     0.0    0.00    0.00   14986         AtomProperties::setSecondaryStructure2(Atom*) [49]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[50]     0.0    0.00    0.00   14986         AtomProperties::setName(Atom*) [50]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[51]     0.0    0.00    0.00   14986         AtomProperties::setType(Atom*) [51]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[52]     0.0    0.00    0.00   14986         Atom::getCarbonyl() [52]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[53]     0.0    0.00    0.00   14986         Atom::getHydroxyl() [53]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::setRingSystem(Atom*) [43]
[54]     0.0    0.00    0.00   14986         Atom::isRingSystem() [54]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[55]     0.0    0.00    0.00   14986         Atom::getHydrophobicity() [55]
                0.00    0.00   14986/59944       Atom::isBackbone() [40]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[56]     0.0    0.00    0.00   14986         Atom::getAmide() [56]
                0.00    0.00   14986/59944       Atom::isBackbone() [40]
-----------------------------------------------
                0.00    0.00   14986/14986       AtomProperties::calculateAtomProperties(Atom*) [10]
[57]     0.0    0.00    0.00   14986         Atom::getAmine() [57]
-----------------------------------------------
                0.00    0.00   10560/10560       PrintEnvironment(Properties&, _IO_FILE*) [68]
[58]     0.0    0.00    0.00   10560         Properties::get(int) [58]
-----------------------------------------------
                               61366             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*>*) [59]
                0.00    0.00    8039/8039        assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[59]     0.0    0.00    0.00    8039+61366   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*>*) [59]
                               61366             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*>*) [59]
-----------------------------------------------
                0.00    0.00    7830/7830        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&) [17]
[60]     0.0    0.00    0.00    7830         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&) [60]
                0.00    0.00    7830/59276       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&) [41]
-----------------------------------------------
                               59276             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> >*) [61]
                0.00    0.00    7830/7830        assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[61]     0.0    0.00    0.00    7830+59276   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> >*) [61]
                               59276             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> >*) [61]
-----------------------------------------------
                0.00    0.00    7764/7764        MarkHetatm(Atoms*) [72]
[62]     0.0    0.00    0.00    7764         Atoms::decrementAtomMark(int) [62]
-----------------------------------------------
                0.00    0.00    1881/1881        Featurize::RunPointEnvironmentMode() [2]
[63]     0.0    0.00    0.00    1881         Properties::include(AtomProperties*) [63]
-----------------------------------------------
                0.00    0.00     219/1065        Protein::parseHetAtom(char const*) [25]
                0.00    0.00     280/1065        Protein::parseAtom(char const*) [7]
                0.00    0.00     566/1065        Atoms::addAtom(Atom*, bool) [35]
[64]     0.0    0.00    0.00    1065         std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&) [64]
-----------------------------------------------
                0.00    0.00     573/573         assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[65]     0.0    0.00    0.00     573         InSameResidue(Atom*, Atom*) [65]
-----------------------------------------------
                0.00    0.00     280/566         Featurize::RunPointEnvironmentMode() [2]
                0.00    0.00     286/566         GetCoordList(Protein*) [73]
[66]     0.0    0.00    0.00     566         std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [66]
-----------------------------------------------
                0.00    0.00     238/238         GetResidues(Protein*) [20]
[67]     0.0    0.00    0.00     238         std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&) [67]
-----------------------------------------------
                0.00    0.00     132/132         Featurize::RunPointEnvironmentMode() [2]
[68]     0.0    0.00    0.00     132         PrintEnvironment(Properties&, _IO_FILE*) [68]
                0.00    0.00   10560/10560       Properties::get(int) [58]
-----------------------------------------------
                0.00    0.00     132/132         Featurize::RunPointEnvironmentMode() [2]
[69]     0.0    0.00    0.00     132         Properties::Properties() [69]
-----------------------------------------------
                0.00    0.00     132/132         Featurize::RunPointEnvironmentMode() [2]
[70]     0.0    0.00    0.00     132         Properties::~Properties() [70]
-----------------------------------------------
                0.00    0.00      45/45          Protein::parseAtom(char const*) [7]
[71]     0.0    0.00    0.00      45         Atom::~Atom() [71]
-----------------------------------------------
                0.00    0.00      22/22          GetNonExcludedResidues(Atoms*, Strings&) [74]
[72]     0.0    0.00    0.00      22         MarkHetatm(Atoms*) [72]
                0.00    0.00   69152/207566      Atoms::size() [32]
                0.00    0.00   69130/429429      Atoms::getAtom(int) [30]
                0.00    0.00   69130/429429      Atoms::operator[](int) [31]
                0.00    0.00    7764/7764        Atoms::decrementAtomMark(int) [62]
-----------------------------------------------
                0.00    0.00      22/22          assign_types(Protein*, ForceFieldParametersSet*, char const*) [13]
[73]     0.0    0.00    0.00      22         GetCoordList(Protein*) [73]
                0.00    0.00   69152/207566      Atoms::size() [32]
                0.00    0.00   69130/429429      Atoms::getAtom(int) [30]
                0.00    0.00   69130/429429      Atoms::operator[](int) [31]
                0.00    0.00     286/566         std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&) [66]
-----------------------------------------------
                0.00    0.00      22/22          Featurize::RunPointEnvironmentMode() [2]
[74]     0.0    0.00    0.00      22         GetNonExcludedResidues(Atoms*, Strings&) [74]
                0.00    0.00      22/22          MarkHetatm(Atoms*) [72]
-----------------------------------------------
                0.00    0.00      22/22          Featurize::RunPointEnvironmentMode() [2]
[75]     0.0    0.00    0.00      22         Atoms::extractMarkedAtoms(int) [75]
                0.00    0.00   61366/130496      Atoms::addAtom(Atom*, bool) [35]
-----------------------------------------------
                0.00    0.00      22/22          Featurize::RunPointEnvironmentMode() [2]
[76]     0.0    0.00    0.00      22         Atoms::~Atoms() [76]
-----------------------------------------------
                0.00    0.00      22/22          Protein::~Protein() [78]
[77]     0.0    0.00    0.00      22         Atoms::~Atoms() [77]
-----------------------------------------------
                0.00    0.00      22/22          Featurize::RunPointEnvironmentMode() [2]
[78]     0.0    0.00    0.00      22         Protein::~Protein() [78]
                0.00    0.00      22/22          Atoms::~Atoms() [77]
-----------------------------------------------
                0.00    0.00       7/7           Featurize::main(int, char**) [3]
[79]     0.0    0.00    0.00       7         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&) [79]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[80]     0.0    0.00    0.00       1         global constructors keyed to DEFAULT_VERBOSITY [80]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[81]     0.0    0.00    0.00       1         global constructors keyed to IsFullName(Atom&, void*) [81]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[82]     0.0    0.00    0.00       1         global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*) [82]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[83]     0.0    0.00    0.00       1         global constructors keyed to InSameResidue(Atom*, Atom*) [83]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[84]     0.0    0.00    0.00       1         global constructors keyed to Properties::Properties() [84]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[85]     0.0    0.00    0.00       1         global constructors keyed to Environment::Environment(int) [85]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[86]     0.0    0.00    0.00       1         global constructors keyed to AtomProperties::setName(Atom*) [86]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[87]     0.0    0.00    0.00       1         global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double) [87]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[88]     0.0    0.00    0.00       1         global constructors keyed to Atom::operator=(Atom&) [88]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[89]     0.0    0.00    0.00       1         global constructors keyed to Protein::Protein() [89]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[90]     0.0    0.00    0.00       1         global constructors keyed to Property::Property(std::string const&) [90]
-----------------------------------------------
                0.00    0.00       1/1           __do_global_ctors_aux [566]
[91]     0.0    0.00    0.00       1         global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double) [91]
-----------------------------------------------

 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

  [80] global constructors keyed to DEFAULT_VERBOSITY (featurize.cc) [44] AtomProperties::setResidueName(Atom*) [35] Atoms::addAtom(Atom*, bool)
  [81] global constructors keyed to IsFullName(Atom&, void*) (Atoms.cc) [14] AtomProperties::setChargeWithHis(Atom*) [30] Atoms::getAtom(int)
  [82] global constructors keyed to assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc) [45] AtomProperties::setPartialCharge(Atom*) [76] Atoms::~Atoms()
  [83] global constructors keyed to InSameResidue(Atom*, Atom*) (ResidueHelper.cc) [46] AtomProperties::setResidueClass1(Atom*) [77] Atoms::~Atoms()
  [84] global constructors keyed to Properties::Properties() (Properties.cc) [47] AtomProperties::setResidueClass2(Atom*) [31] Atoms::operator[](int)
  [85] global constructors keyed to Environment::Environment(int) (Environments.cc) [48] AtomProperties::setSecondaryStructure1(Atom*) [4] Protein::readPDBFile(char const*)
  [86] global constructors keyed to AtomProperties::setName(Atom*) (AtomProperties.cc) [49] AtomProperties::setSecondaryStructure2(Atom*) [25] Protein::parseHetAtom(char const*)
  [87] global constructors keyed to StatisticsFile::StatisticsFile(std::string const&, std::string const&, double) (StatisticsFile.cc) [10] AtomProperties::calculateAtomProperties(Atom*) [6] Protein::parsePDBLine(char const*)
  [88] global constructors keyed to Atom::operator=(Atom&) (Atom.cc) [50] AtomProperties::setName(Atom*) [9] Protein::readDSSPFile(char const*)
  [89] global constructors keyed to Protein::Protein() (Protein.cc) [51] AtomProperties::setType(Atom*) [8] Protein::parseDSSPLine(char const*)
  [90] global constructors keyed to Property::Property(std::string const&) (Property.cc) [40] Atom::isBackbone() [7] Protein::parseAtom(char const*)
  [91] global constructors keyed to ModelFile::ModelFile(std::string const&, std::string const&, double) (ModelFile.cc) [52] Atom::getCarbonyl() [5] Protein::Protein(char const*)
  [72] MarkHetatm(Atoms*)     [53] Atom::getHydroxyl()    [78] Protein::~Protein()
  [20] GetResidues(Protein*)  [54] Atom::isRingSystem()   [11] Neighbor::Neighbor(std::vector<Point3D*, std::allocator<Point3D*> > const*, float)
  [73] GetCoordList(Protein*) [15] Atom::parsePDBAtom(char const*) [22] Neighbor::~Neighbor()
  [13] assign_types(Protein*, ForceFieldParametersSet*, char const*) [18] Atom::getChainDistance() [2] Featurize::RunPointEnvironmentMode()
  [65] InSameResidue(Atom*, Atom*) [55] Atom::getHydrophobicity() [3] Featurize::main(int, char**)
  [68] PrintEnvironment(Properties&, _IO_FILE*) [38] Atom::setSecondaryStructure(char) [67] std::vector<SResidueIndices*, std::allocator<SResidueIndices*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<SResidueIndices**, std::vector<SResidueIndices*, std::allocator<SResidueIndices*> > >, SResidueIndices* const&)
  [74] GetNonExcludedResidues(Atoms*, Strings&) [37] Atom::setResidueFullSequence(Atom*) [64] std::vector<Atom*, std::allocator<Atom*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Atom**, std::vector<Atom*, std::allocator<Atom*> > >, Atom* const&)
  [21] LispParser::GetLine(std::string&) [56] Atom::getAmide() [66] std::vector<Point3D*, std::allocator<Point3D*> >::_M_insert_aux(__gnu_cxx::__normal_iterator<Point3D**, std::vector<Point3D*, std::allocator<Point3D*> > >, Point3D* const&)
  [58] Properties::get(int)   [57] Atom::getAmine()       [79] 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&)
  [63] Properties::include(AtomProperties*) [16] Atom::getCharge() [36] std::vector<int, std::allocator<int> >::_M_insert_aux(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&)
  [69] Properties::Properties() [19] Atom::getRadius()    [39] 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&)
  [70] Properties::~Properties() [33] Atom::Atom()        [59] 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*>*)
  [42] AtomProperties::setPeptide(Atom*) [71] Atom::~Atom() [41] 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&)
  [23] AtomProperties::setNegCharge(Atom*) [34] Atom::operator=(Atom&) [60] 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&)
  [24] AtomProperties::setPosCharge(Atom*) [62] Atoms::decrementAtomMark(int) [17] 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&)
  [12] AtomProperties::setVDWVolume(Atom*) [75] Atoms::extractMarkedAtoms(int) [61] 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> >*)
  [43] AtomProperties::setRingSystem(Atom*) [32] Atoms::size()