Memcheck, a memory error detector
Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
Using Valgrind-3.6.0.SVN-Debian and LibVEX; rerun with -h for copyright info
Command: featurize -P trypsin_ser_og.pos.ptf

Invalid read of size 1
   at 0x4C296D2: __GI_strlen (mc_replace_strmem.c:284)
   by 0x42C81E: tostring(Strings const&) (char_traits.h:263)
   by 0x406DC4: Featurize::main(int, char**) (featurize.cc:443)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bc0168 is not stack'd, malloc'd or (recently) free'd

Invalid read of size 1
   at 0x4C296E4: __GI_strlen (mc_replace_strmem.c:284)
   by 0x42C81E: tostring(Strings const&) (char_traits.h:263)
   by 0x406DC4: Featurize::main(int, char**) (featurize.cc:443)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bc0169 is not stack'd, malloc'd or (recently) free'd

Invalid read of size 1
   at 0x50EE520: std::string::append(char const*, unsigned long) (in /usr/lib/libstdc++.so.6.0.13)
   by 0x42C82C: tostring(Strings const&) (basic_string.h:866)
   by 0x406DC4: Featurize::main(int, char**) (featurize.cc:443)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bc0168 is not stack'd, malloc'd or (recently) free'd

Invalid read of size 1
   at 0x4C296D2: __GI_strlen (mc_replace_strmem.c:284)
   by 0x42C81E: tostring(Strings const&) (char_traits.h:263)
   by 0x406DF0: Featurize::main(int, char**) (featurize.cc:444)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bbf5a8 is not stack'd, malloc'd or (recently) free'd

Invalid read of size 1
   at 0x4C296E4: __GI_strlen (mc_replace_strmem.c:284)
   by 0x42C81E: tostring(Strings const&) (char_traits.h:263)
   by 0x406DF0: Featurize::main(int, char**) (featurize.cc:444)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bbf5a9 is not stack'd, malloc'd or (recently) free'd

Invalid read of size 1
   at 0x50EE520: std::string::append(char const*, unsigned long) (in /usr/lib/libstdc++.so.6.0.13)
   by 0x42C82C: tostring(Strings const&) (basic_string.h:866)
   by 0x406DF0: Featurize::main(int, char**) (featurize.cc:444)
   by 0x405368: main (featurize.cc:616)
 Address 0x5bbf5a8 is not stack'd, malloc'd or (recently) free'd


FILE DESCRIPTORS: 3 open at exit.
Open file descriptor 2: /home/teague/Business/clients/simtk.org/feature/trunk/examples/serprot/valgrind-output-pos
   <inherited from parent>

Open file descriptor 1: /home/teague/Business/clients/simtk.org/feature/trunk/examples/serprot/trypsin_ser_og.pos.ff
   <inherited from parent>

Open file descriptor 0: /dev/pts/0
   <inherited from parent>


HEAP SUMMARY:
    in use at exit: 29,163,071 bytes in 206,216 blocks
  total heap usage: 563,262 allocs, 357,046 frees, 129,332,244 bytes allocated

4 bytes in 1 blocks are still reachable in loss record 1 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58B474A: create_cd_newstate (regex_internal.c:1020)
   by 0x58C2C9A: re_compile_internal (regex_internal.c:1531)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

4 bytes in 1 blocks are still reachable in loss record 2 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58B1613: register_state (regex_internal.c:960)
   by 0x58B48F0: create_cd_newstate (regex_internal.c:1707)
   by 0x58C2C9A: re_compile_internal (regex_internal.c:1531)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

16 bytes in 1 blocks are still reachable in loss record 3 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x4C28522: realloc (vg_replace_malloc.c:525)
   by 0x58B1702: register_state (regex_internal.c:1565)
   by 0x58B48F0: create_cd_newstate (regex_internal.c:1707)
   by 0x58C2C9A: re_compile_internal (regex_internal.c:1531)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

16 bytes in 4 blocks are still reachable in loss record 4 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58B474A: create_cd_newstate (regex_internal.c:1020)
   by 0x58B5594: build_trtable (regex_internal.c:1531)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

16 bytes in 4 blocks are still reachable in loss record 5 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58B1613: register_state (regex_internal.c:960)
   by 0x58B48F0: create_cd_newstate (regex_internal.c:1707)
   by 0x58B5594: build_trtable (regex_internal.c:1531)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

20 bytes in 5 blocks are still reachable in loss record 6 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58B1D9A: calc_eclosure_iter (regex_internal.c:960)
   by 0x58C2866: re_compile_internal (regcomp.c:1636)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

32 bytes in 1 blocks are still reachable in loss record 7 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B8D9A: parse_bracket_exp (regcomp.c:3042)
   by 0x58C1228: parse_expression (regcomp.c:2231)
   by 0x58C190D: parse_reg_exp (regcomp.c:2157)
   by 0x58C2193: re_compile_internal (regcomp.c:2085)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

32 bytes in 1 blocks are still reachable in loss record 8 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B8D9A: parse_bracket_exp (regcomp.c:3042)
   by 0x58C1228: parse_expression (regcomp.c:2231)
   by 0x58C1966: parse_reg_exp (regcomp.c:2164)
   by 0x58C2193: re_compile_internal (regcomp.c:2085)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

64 bytes in 4 blocks are still reachable in loss record 9 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x4C28522: realloc (vg_replace_malloc.c:525)
   by 0x58B1702: register_state (regex_internal.c:1565)
   by 0x58B48F0: create_cd_newstate (regex_internal.c:1707)
   by 0x58B5594: build_trtable (regex_internal.c:1531)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

80 bytes in 1 blocks are still reachable in loss record 10 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58C2337: re_compile_internal (regcomp.c:1127)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

88 bytes in 1 blocks are still reachable in loss record 11 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B4709: create_cd_newstate (regex_internal.c:1654)
   by 0x58C2C9A: re_compile_internal (regex_internal.c:1531)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

110 bytes in 22 blocks are definitely lost in loss record 12 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x418738: PointFile::getPdbids(char const***, int*) (Points.cc:180)
   by 0x406CBA: Featurize::main(int, char**) (featurize.cc:423)
   by 0x405368: main (featurize.cc:616)

144 bytes in 1 blocks are still reachable in loss record 13 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x4082EE: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

144 bytes in 1 blocks are still reachable in loss record 14 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x4082AF: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

144 bytes in 3 blocks are still reachable in loss record 15 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x425D72: std::_Rb_tree<char const*, std::pair<char const* const, ResidueTemplate*>, std::_Select1st<std::pair<char const* const, ResidueTemplate*> >, compare_cstring, std::allocator<std::pair<char const* const, ResidueTemplate*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, ResidueTemplate*> const&) (new_allocator.h:89)
   by 0x425E9F: std::_Rb_tree<char const*, std::pair<char const* const, ResidueTemplate*>, std::_Select1st<std::pair<char const* const, ResidueTemplate*> >, compare_cstring, std::allocator<std::pair<char const* const, ResidueTemplate*> > >::_M_insert_unique(std::pair<char const* const, ResidueTemplate*> const&) (stl_tree.h:1182)
   by 0x4260C1: std::_Rb_tree<char const*, std::pair<char const* const, ResidueTemplate*>, std::_Select1st<std::pair<char const* const, ResidueTemplate*> >, compare_cstring, std::allocator<std::pair<char const* const, ResidueTemplate*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, ResidueTemplate*> >, std::pair<char const* const, ResidueTemplate*> const&) (stl_tree.h:1254)
   by 0x425942: ResidueTemplateSet::LoadFile(char const*) (stl_map.h:540)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

144 bytes in 1 blocks are possibly lost in loss record 16 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40B13E: Atom::parsePDBAtom(char const*) (Atom.cc:94)
   by 0x4209F0: Protein::parseAtom(char const*) (Protein.cc:86)
   by 0x420FAA: Protein::parsePDBLine(char const*) (Protein.cc:155)
   by 0x42106C: Protein::readPDBFile(char const*) (Protein.cc:178)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

144 bytes in 1 blocks are possibly lost in loss record 17 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40C139: Atoms::addAtom(Atom*, bool) (Atoms.cc:52)
   by 0x40C260: Atoms::extractMarkedAtoms(int) (Atoms.cc:132)
   by 0x405E35: Featurize::RunPointEnvironmentMode() (featurize.cc:521)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

168 bytes in 3 blocks are still reachable in loss record 18 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40FFE2: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (new_allocator.h:89)
   by 0x41016F: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_unique(std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (stl_tree.h:1182)
   by 0x410289: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (stl_tree.h:1236)
   by 0x40FB52: ForceFieldParametersSet::LoadFile(char const*) (stl_map.h:540)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

224 bytes in 1 blocks are still reachable in loss record 19 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x4C28522: realloc (vg_replace_malloc.c:525)
   by 0x58C34F3: re_compile_internal (regcomp.c:760)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

256 bytes in 1 blocks are still reachable in loss record 20 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58C381C: regcomp (regcomp.c:487)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

312 bytes in 78 blocks are still reachable in loss record 21 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x4256F1: ResidueTemplateSet::LoadFile(char const*) (ResidueTemplate.cc:65)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

320 bytes in 1 blocks are still reachable in loss record 22 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58C1F07: re_compile_internal (regcomp.c:852)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

320 bytes in 1 blocks are still reachable in loss record 23 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58C2359: re_compile_internal (regcomp.c:1129)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

320 bytes in 1 blocks are still reachable in loss record 24 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x58C236A: re_compile_internal (regcomp.c:1130)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

352 bytes in 4 blocks are still reachable in loss record 25 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B4709: create_cd_newstate (regex_internal.c:1654)
   by 0x58B5594: build_trtable (regex_internal.c:1531)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

512 bytes in 1 blocks are still reachable in loss record 26 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58C1F35: re_compile_internal (regcomp.c:859)
   by 0x58C387E: regcomp (regcomp.c:506)
   by 0x42B715: getPotentialId(char*, char*) (Utilities.cc:52)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

1,298 bytes in 22 blocks are definitely lost in loss record 27 of 48
   at 0x4C28939: operator new[](unsigned long) (vg_replace_malloc.c:305)
   by 0x4179CB: Parser::Parser(std::string const&) (Parser.cc:25)
   by 0x417B6E: LispParser::LispParser(std::string const&) (Parser.cc:121)
   by 0x420FFE: Protein::readPDBFile(char const*) (Protein.cc:171)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

1,658 bytes in 621 blocks are still reachable in loss record 28 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x40F952: ForceFieldParametersSet::LoadFile(char const*) (ForceFieldParameters.cc:102)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

1,815 bytes in 621 blocks are still reachable in loss record 29 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x40F964: ForceFieldParametersSet::LoadFile(char const*) (ForceFieldParameters.cc:99)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

2,048 bytes in 1 blocks are still reachable in loss record 30 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B5C78: build_trtable (regexec.c:3334)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

2,484 bytes in 621 blocks are still reachable in loss record 31 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x40F97C: ForceFieldParametersSet::LoadFile(char const*) (ForceFieldParameters.cc:95)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

3,600 bytes in 75 blocks are still reachable in loss record 32 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x425D72: std::_Rb_tree<char const*, std::pair<char const* const, ResidueTemplate*>, std::_Select1st<std::pair<char const* const, ResidueTemplate*> >, compare_cstring, std::allocator<std::pair<char const* const, ResidueTemplate*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, ResidueTemplate*> const&) (new_allocator.h:89)
   by 0x426133: std::_Rb_tree<char const*, std::pair<char const* const, ResidueTemplate*>, std::_Select1st<std::pair<char const* const, ResidueTemplate*> >, compare_cstring, std::allocator<std::pair<char const* const, ResidueTemplate*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, ResidueTemplate*> >, std::pair<char const* const, ResidueTemplate*> const&) (stl_tree.h:1249)
   by 0x425942: ResidueTemplateSet::LoadFile(char const*) (stl_map.h:540)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

3,744 bytes in 78 blocks are still reachable in loss record 33 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x4256BC: ResidueTemplateSet::LoadFile(char const*) (ResidueTemplate.cc:64)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

3,744 bytes in 78 blocks are still reachable in loss record 34 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x425EF2: std::_Rb_tree<char const*, std::pair<char const* const, char const*>, std::_Select1st<std::pair<char const* const, char const*> >, compare_cstring, std::allocator<std::pair<char const* const, char const*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, char const*> const&) (new_allocator.h:89)
   by 0x42601F: std::_Rb_tree<char const*, std::pair<char const* const, char const*>, std::_Select1st<std::pair<char const* const, char const*> >, compare_cstring, std::allocator<std::pair<char const* const, char const*> > >::_M_insert_unique(std::pair<char const* const, char const*> const&) (stl_tree.h:1182)
   by 0x426241: std::_Rb_tree<char const*, std::pair<char const* const, char const*>, std::_Select1st<std::pair<char const* const, char const*> >, compare_cstring, std::allocator<std::pair<char const* const, char const*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, char const*> >, std::pair<char const* const, char const*> const&) (stl_tree.h:1254)
   by 0x425911: ResidueTemplateSet::LoadFile(char const*) (stl_map.h:540)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

4,044 bytes in 1,055 blocks are still reachable in loss record 35 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x42569C: ResidueTemplateSet::LoadFile(char const*) (ResidueTemplate.cc:73)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

4,094 bytes in 1,055 blocks are still reachable in loss record 36 of 48
   at 0x4C284A8: malloc (vg_replace_malloc.c:236)
   by 0x5875D51: strdup (strdup.c:43)
   by 0x425608: ResidueTemplateSet::LoadFile(char const*) (ResidueTemplate.cc:83)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

8,192 bytes in 4 blocks are still reachable in loss record 37 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58B5637: build_trtable (regexec.c:3421)
   by 0x58BF659: re_search_internal (regexec.c:2279)
   by 0x58BFB72: regexec@@GLIBC_2.3.4 (regexec.c:253)
   by 0x42B73C: getPotentialId(char*, char*) (Utilities.cc:64)
   by 0x42B939: getPdbIdFromFilename(char*, char const*) (Utilities.cc:88)
   by 0x405DCD: Featurize::RunPointEnvironmentMode() (featurize.cc:508)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

9,936 bytes in 621 blocks are still reachable in loss record 38 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40FA5D: ForceFieldParametersSet::LoadFile(char const*) (ForceFieldParameters.cc:106)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

10,192 bytes in 182 blocks are still reachable in loss record 39 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40FFE2: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (new_allocator.h:89)
   by 0x410347: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (stl_tree.h:1230)
   by 0x40FB52: ForceFieldParametersSet::LoadFile(char const*) (stl_map.h:540)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

11,312 bytes in 202 blocks are still reachable in loss record 40 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40FFE2: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (new_allocator.h:89)
   by 0x4102D1: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (stl_tree.h:1215)
   by 0x40FB52: ForceFieldParametersSet::LoadFile(char const*) (stl_map.h:540)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

13,104 bytes in 234 blocks are still reachable in loss record 41 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40FFE2: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (new_allocator.h:89)
   by 0x41026E: std::_Rb_tree<ForceFieldAtom, std::pair<ForceFieldAtom const, ForceFieldParameters*>, std::_Select1st<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, ForceFieldAtom::compare, std::allocator<std::pair<ForceFieldAtom const, ForceFieldParameters*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<ForceFieldAtom const, ForceFieldParameters*> >, std::pair<ForceFieldAtom const, ForceFieldParameters*> const&) (stl_tree.h:1233)
   by 0x40FB52: ForceFieldParametersSet::LoadFile(char const*) (stl_map.h:540)
   by 0x40FD6C: ForceFieldParametersSet::ForceFieldParametersSet(char const*) (ForceFieldParameters.cc:47)
   by 0x408307: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:40)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

46,896 bytes in 977 blocks are still reachable in loss record 42 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x425EF2: std::_Rb_tree<char const*, std::pair<char const* const, char const*>, std::_Select1st<std::pair<char const* const, char const*> >, compare_cstring, std::allocator<std::pair<char const* const, char const*> > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair<char const* const, char const*> const&) (new_allocator.h:89)
   by 0x4262B3: std::_Rb_tree<char const*, std::pair<char const* const, char const*>, std::_Select1st<std::pair<char const* const, char const*> >, compare_cstring, std::allocator<std::pair<char const* const, char const*> > >::_M_insert_unique_(std::_Rb_tree_const_iterator<std::pair<char const* const, char const*> >, std::pair<char const* const, char const*> const&) (stl_tree.h:1249)
   by 0x425911: ResidueTemplateSet::LoadFile(char const*) (stl_map.h:540)
   by 0x425B1C: ResidueTemplateSet::ResidueTemplateSet(char const*) (ResidueTemplate.cc:13)
   by 0x4082C1: assign_types(Protein*, ForceFieldParametersSet*, char const*) (AssignAtomType.cc:45)
   by 0x421099: Protein::readPDBFile(char const*) (Protein.cc:181)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

285,068 bytes in 1 blocks are still reachable in loss record 43 of 48
   at 0x4C277CC: calloc (vg_replace_malloc.c:467)
   by 0x58DC462: monstartup (gmon.c:136)
   by 0x404360: __gmon_start__ (in /home/teague/Business/clients/simtk.org/feature/trunk/featurize)
   by 0x4C27141: ??? (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
   by 0x7FF000280: ???
   by 0x79727400502D0064: ???
   by 0x7265735F6E69736F: ???
   by 0x2E736F702E676F5E: ???
   by 0x5353454C0066746F: ???
   by 0x2F207C3D4E45504E: ???
   by 0x2F6E69622F727374: ???
   by 0x657069707373656B: ???
   by 0x5F4D44470073251F: ???
   by 0x4452414F4259454A: ???
   by 0x3D54554F59414C5E: ???
   by 0x454D4F4E47007374: ???
   by 0x474E495259454B5E: ???
   by 0x3134323D4449505E: ???
   by 0x743D52455355002F: ???
   by 0x5344006575676164: ???

1,118,016 bytes in 7,764 blocks are definitely lost in loss record 44 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40B13E: Atom::parsePDBAtom(char const*) (Atom.cc:94)
   by 0x420958: Protein::parseHetAtom(char const*) (Protein.cc:113)
   by 0x420F6C: Protein::parsePDBLine(char const*) (Protein.cc:156)
   by 0x42106C: Protein::readPDBFile(char const*) (Protein.cc:178)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

1,118,016 bytes in 7,764 blocks are definitely lost in loss record 45 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40C139: Atoms::addAtom(Atom*, bool) (Atoms.cc:52)
   by 0x4209AC: Protein::parseHetAtom(char const*) (Protein.cc:118)
   by 0x420F6C: Protein::parsePDBLine(char const*) (Protein.cc:156)
   by 0x42106C: Protein::readPDBFile(char const*) (Protein.cc:178)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

8,836,560 bytes in 61,365 blocks are definitely lost in loss record 46 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40B13E: Atom::parsePDBAtom(char const*) (Atom.cc:94)
   by 0x4209F0: Protein::parseAtom(char const*) (Protein.cc:86)
   by 0x420FAA: Protein::parsePDBLine(char const*) (Protein.cc:155)
   by 0x42106C: Protein::readPDBFile(char const*) (Protein.cc:178)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

8,836,560 bytes in 61,365 blocks are definitely lost in loss record 47 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40C139: Atoms::addAtom(Atom*, bool) (Atoms.cc:52)
   by 0x40C260: Atoms::extractMarkedAtoms(int) (Atoms.cc:132)
   by 0x405E35: Featurize::RunPointEnvironmentMode() (featurize.cc:521)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

8,836,704 bytes in 61,366 blocks are definitely lost in loss record 48 of 48
   at 0x4C28CC1: operator new(unsigned long) (vg_replace_malloc.c:261)
   by 0x40C139: Atoms::addAtom(Atom*, bool) (Atoms.cc:52)
   by 0x420AE8: Protein::parseAtom(char const*) (Protein.cc:105)
   by 0x420FAA: Protein::parsePDBLine(char const*) (Protein.cc:155)
   by 0x42106C: Protein::readPDBFile(char const*) (Protein.cc:178)
   by 0x421833: Protein::Protein(char const*) (Protein.cc:25)
   by 0x405DA0: Featurize::RunPointEnvironmentMode() (featurize.cc:506)
   by 0x406E1F: Featurize::main(int, char**) (featurize.cc:608)
   by 0x405368: main (featurize.cc:616)

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

For counts of detected and suppressed errors, rerun with: -v
ERROR SUMMARY: 78 errors from 15 contexts (suppressed: 4 from 4)

Profiling timer expired

real	0m20.547s
user	0m19.910s
sys	0m0.440s