Flat profile:

Each sample counts as 0.01 seconds.
  %   cumulative   self              self     total           
 time   seconds   seconds    calls   s/call   s/call  name    
 92.88     91.81    91.81  6555425     0.00     0.00  get_neighbors
  5.17     96.92     5.11      757     0.01     0.13  is_ringpath
  1.73     98.63     1.71  6607342     0.00     0.00  path_pos
  0.10     98.73     0.10  6545856     0.00     0.00  path_length
  0.05     98.78     0.05    45399     0.00     0.00  get_bond
  0.04     98.82     0.04                             memset
  0.02     98.84     0.02        1     0.02     0.07  update_atypes
  0.01     98.85     0.01     3480     0.00     0.00  get_nextneighbors
  0.00     98.85     0.00     6304     0.00     0.00  strsub
  0.00     98.85     0.00     4839     0.00     0.00  strpos2
  0.00     98.85     0.00     3249     0.00     0.00  is_oxo_C
  0.00     98.85     0.00     2025     0.00     0.00  is_aryl
  0.00     98.85     0.00     1978     0.00     0.00  is_thioxo_C
  0.00     98.85     0.00     1858     0.00     0.00  hetbond_count
  0.00     98.85     0.00     1511     0.00     0.00  is_alkyl
  0.00     98.85     0.00     1428     0.00     0.00  is_amino
  0.00     98.85     0.00     1063     0.00     0.00  is_true_alkyl
  0.00     98.85     0.00     1025     0.00     0.00  find_exocyclic_methylene_C
  0.00     98.85     0.00      735     0.00     0.00  is_alkynyl
  0.00     98.85     0.00      730     0.00     0.00  is_hydroxy
  0.00     98.85     0.00      674     0.00     0.00  get_nvalences
  0.00     98.85     0.00      674     0.00     0.00  is_heavyatom
  0.00     98.85     0.00      674     0.00     0.00  is_metal
  0.00     98.85     0.00      618     0.00     0.00  is_alkylamino
  0.00     98.85     0.00      618     0.00     0.00  is_arylamino
  0.00     98.85     0.00      585     0.00     0.00  is_alkenyl
  0.00     98.85     0.00      555     0.00     0.00  chk_single
  0.00     98.85     0.00      471     0.00     0.00  is_diarylamino
  0.00     98.85     0.00      413     0.00     0.00  is_acyl_gen
  0.00     98.85     0.00      357     0.00     0.00  is_alkylarylamino
  0.00     98.85     0.00      357     0.00     0.00  is_dialkylamino
  0.00     98.85     0.00      357     0.00     0.00  is_subst_amino
  0.00     98.85     0.00      338     0.00     0.00  is_hydrazino
  0.00     98.85     0.00      327     0.00     0.00  is_C_disubst_amino
  0.00     98.85     0.00      327     0.00     0.00  is_C_monosubst_amino
  0.00     98.85     0.00      221     0.00     0.00  is_azido
  0.00     98.85     0.00      221     0.00     0.00  is_hydroxylamino
  0.00     98.85     0.00      220     0.00     0.00  swap_atoms
  0.00     98.85     0.00      214     0.00     0.00  is_subst_acylamino
  0.00     98.85     0.00      141     0.00     0.00  chk_double
  0.00     98.85     0.00      119     0.00     0.00  is_true_imino_C
  0.00     98.85     0.00      117     0.00     0.00  is_acyl
  0.00     98.85     0.00      114     0.00     0.00  chk_carboxyl_deriv
  0.00     98.85     0.00      114     0.00     0.00  is_diazonium
  0.00     98.85     0.00      114     0.00     0.00  is_nitro
  0.00     98.85     0.00      114     0.00     0.00  is_true_alkylamino
  0.00     98.85     0.00      114     0.00     0.00  is_true_dialkylamino
  0.00     98.85     0.00      113     0.00     0.00  is_carbamoyl
  0.00     98.85     0.00       99     0.00     0.00  chk_imide
  0.00     98.85     0.00       93     0.00     0.00  is_arene
  0.00     98.85     0.00       49     0.00     0.00  chk_arom_fg
  0.00     98.85     0.00       46     0.00     0.00  is_aryloxy
  0.00     98.85     0.00       37     0.00     0.00  is_heterocycle
  0.00     98.85     0.00       31     0.00     0.00  chk_oxo_thioxo_imino_hetarene
  0.00     98.85     0.00       27     0.00     0.00  is_acylamino
  0.00     98.85     0.00       27     0.00     0.00  is_alkoxy
  0.00     98.85     0.00       26     0.00     0.00  is_alkynyloxy
  0.00     98.85     0.00       19     0.00     0.00  is_true_alkoxy
  0.00     98.85     0.00       10     0.00     0.00  is_arylsulfanyl
  0.00     98.85     0.00       10     0.00     0.00  is_sulfanyl
  0.00     98.85     0.00       10     0.00     0.00  is_true_alkylsulfanyl
  0.00     98.85     0.00        7     0.00     0.00  is_alkenyloxy
  0.00     98.85     0.00        5     0.00     0.00  chk_x_y_single
  0.00     98.85     0.00        4     0.00     0.00  safe_calloc
  0.00     98.85     0.00        1     0.00     0.06  chk_arom
  0.00     98.85     0.00        1     0.00     0.10  chk_functionalgroups
  0.00     98.85     0.00        1     0.00    98.56  chk_ringbonds
  0.00     98.85     0.00        1     0.00     0.00  count_neighbors
  0.00     98.85     0.00        1     0.00     0.00  file_exists
  0.00     98.85     0.00        1     0.00     0.00  get_filetype
  0.00     98.85     0.00        1     0.00     0.01  get_molstat
  0.00     98.85     0.00        1     0.00     0.00  normalize_ionic_bonds
  0.00     98.85     0.00        1     0.00     0.00  read_MDLmolfile
  0.00     98.85     0.00        1     0.00     0.00  readinputfile
  0.00     98.85     0.00        1     0.00     0.00  safe_malloc
  0.00     98.85     0.00        1     0.00     0.01  update_Htotal
  0.00     98.85     0.00        1     0.00     0.00  update_ringcount
  0.00     98.85     0.00        1     0.00     0.00  write_fg_text
  0.00     98.85     0.00        1     0.00     0.00  zap_molecule

 %         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 4 byte(s) for 0.01% of 98.85 seconds

index % time    self  children    called     name
                                                 <spontaneous>
[1]    100.0    0.00   98.81                 main [1]
                0.00   98.56       1/1           chk_ringbonds [2]
                0.00    0.10       1/1           chk_functionalgroups [7]
                0.02    0.05       1/1           update_atypes [8]
                0.00    0.06       1/1           chk_arom [9]
                0.00    0.01       1/1           update_Htotal [19]
                0.00    0.01       1/1           get_molstat [23]
                0.00    0.00       1/1           update_ringcount [50]
                0.00    0.00       1/1           safe_malloc [80]
                0.00    0.00       1/1           file_exists [75]
                0.00    0.00       1/1           readinputfile [79]
                0.00    0.00       1/1           get_filetype [76]
                0.00    0.00       1/1           count_neighbors [74]
                0.00    0.00       1/1           zap_molecule [82]
                0.00    0.00       1/1           read_MDLmolfile [78]
                0.00    0.00       1/4839        strpos2 [66]
                0.00    0.00       1/1           normalize_ionic_bonds [77]
                0.00    0.00       1/1           write_fg_text [81]
-----------------------------------------------
                0.00   98.56       1/1           main [1]
[2]     99.7    0.00   98.56       1         chk_ringbonds [2]
                5.11   93.44     757/757         is_ringpath [3]
                0.01    0.00     696/6555425     get_neighbors [4]
-----------------------------------------------
                             6542898             is_ringpath [3]
                5.11   93.44     757/757         chk_ringbonds [2]
[3]     99.7    5.11   93.44     757+6542898 is_ringpath [3]
               91.63    0.00 6542570/6555425     get_neighbors [4]
                0.10    1.69 6545856/6545856     path_length [5]
                0.02    0.00   61486/6607342     path_pos [6]
                             6542898             is_ringpath [3]
-----------------------------------------------
                0.00    0.00       2/6555425     chk_arom_fg [41]
                0.00    0.00       5/6555425     chk_double [16]
                0.00    0.00      69/6555425     chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00      99/6555425     chk_imide [22]
                0.00    0.00     124/6555425     is_true_imino_C [34]
                0.00    0.00     254/6555425     chk_single [14]
                0.00    0.00     342/6555425     chk_carboxyl_deriv [17]
                0.01    0.00     392/6555425     get_molstat [23]
                0.01    0.00     674/6555425     update_Htotal [19]
                0.01    0.00     674/6555425     update_atypes [8]
                0.01    0.00     674/6555425     chk_functionalgroups [7]
                0.01    0.00     696/6555425     chk_ringbonds [2]
                0.01    0.00     740/6555425     chk_arom [9]
                0.01    0.00    1025/6555425     find_exocyclic_methylene_C [18]
                0.03    0.00    1858/6555425     hetbond_count [13]
                0.03    0.00    1978/6555425     is_thioxo_C [15]
                0.05    0.00    3249/6555425     is_oxo_C [10]
               91.63    0.00 6542570/6555425     is_ringpath [3]
[4]     92.9   91.81    0.00 6555425         get_neighbors [4]
-----------------------------------------------
                0.10    1.69 6545856/6545856     is_ringpath [3]
[5]      1.8    0.10    1.69 6545856         path_length [5]
                1.69    0.00 6545856/6607342     path_pos [6]
-----------------------------------------------
                0.02    0.00   61486/6607342     is_ringpath [3]
                1.69    0.00 6545856/6607342     path_length [5]
[6]      1.7    1.71    0.00 6607342         path_pos [6]
-----------------------------------------------
                0.00    0.10       1/1           main [1]
[7]      0.1    0.00    0.10       1         chk_functionalgroups [7]
                0.00    0.03     555/555         chk_single [14]
                0.00    0.03     141/141         chk_double [16]
                0.00    0.02    1074/1858        hetbond_count [13]
                0.01    0.00     674/6555425     get_neighbors [4]
                0.00    0.01      99/99          chk_imide [22]
                0.00    0.00      31/31          chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00      31/93          is_arene [28]
                0.00    0.00      49/49          chk_arom_fg [41]
                0.00    0.00     220/220         swap_atoms [70]
                0.00    0.00      31/37          is_heterocycle [71]
-----------------------------------------------
                0.02    0.05       1/1           main [1]
[8]      0.1    0.02    0.05       1         update_atypes [8]
                0.00    0.02    1392/3249        is_oxo_C [10]
                0.00    0.02    1050/1978        is_thioxo_C [15]
                0.01    0.00     674/6555425     get_neighbors [4]
                0.00    0.00    1392/45399       get_bond [11]
-----------------------------------------------
                0.00    0.06       1/1           main [1]
[9]      0.1    0.00    0.06       1         chk_arom [9]
                0.00    0.02    1016/3249        is_oxo_C [10]
                0.00    0.02    1025/1025        find_exocyclic_methylene_C [18]
                0.00    0.01     740/1978        is_thioxo_C [15]
                0.01    0.00     740/6555425     get_neighbors [4]
                0.00    0.00    4382/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       5/3249        chk_double [16]
                0.00    0.00      69/3249        chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00     113/3249        is_carbamoyl [35]
                0.00    0.00     114/3249        chk_carboxyl_deriv [17]
                0.00    0.00     127/3249        is_acyl [29]
                0.00    0.01     413/3249        is_acyl_gen [21]
                0.00    0.02    1016/3249        chk_arom [9]
                0.00    0.02    1392/3249        update_atypes [8]
[10]     0.1    0.00    0.05    3249         is_oxo_C [10]
                0.05    0.00    3249/6555425     get_neighbors [4]
                0.01    0.00    6883/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       5/45399       chk_arom_fg [41]
                0.00    0.00       7/45399       is_alkenyloxy [62]
                0.00    0.00      10/45399       is_sulfanyl [61]
                0.00    0.00      10/45399       is_true_alkylsulfanyl [54]
                0.00    0.00      10/45399       is_arylsulfanyl [55]
                0.00    0.00      19/45399       is_true_alkoxy [60]
                0.00    0.00      26/45399       is_alkynyloxy [59]
                0.00    0.00      27/45399       is_alkoxy [58]
                0.00    0.00      27/45399       is_acylamino [57]
                0.00    0.00      36/45399       chk_single [14]
                0.00    0.00      46/45399       is_aryloxy [56]
                0.00    0.00     113/45399       is_carbamoyl [35]
                0.00    0.00     114/45399       is_true_alkylamino [52]
                0.00    0.00     114/45399       is_true_dialkylamino [53]
                0.00    0.00     114/45399       is_diazonium [49]
                0.00    0.00     127/45399       is_acyl [29]
                0.00    0.00     149/45399       chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00     171/45399       chk_double [16]
                0.00    0.00     186/45399       is_nitro [51]
                0.00    0.00     214/45399       is_subst_acylamino [26]
                0.00    0.00     221/45399       is_hydroxylamino [40]
                0.00    0.00     221/45399       is_azido [44]
                0.00    0.00     311/45399       update_ringcount [50]
                0.00    0.00     327/45399       is_C_monosubst_amino [39]
                0.00    0.00     327/45399       is_C_disubst_amino [46]
                0.00    0.00     338/45399       is_hydrazino [25]
                0.00    0.00     357/45399       is_true_imino_C [34]
                0.00    0.00     357/45399       is_dialkylamino [48]
                0.00    0.00     357/45399       is_alkylarylamino [47]
                0.00    0.00     471/45399       is_diarylamino [45]
                0.00    0.00     585/45399       is_alkenyl [32]
                0.00    0.00     618/45399       is_alkylamino [37]
                0.00    0.00     618/45399       is_arylamino [38]
                0.00    0.00     730/45399       is_hydroxy [43]
                0.00    0.00     735/45399       is_alkynyl [42]
                0.00    0.00    1063/45399       is_true_alkyl [31]
                0.00    0.00    1392/45399       update_Htotal [19]
                0.00    0.00    1392/45399       update_atypes [8]
                0.00    0.00    1428/45399       is_amino [36]
                0.00    0.00    1482/45399       chk_carboxyl_deriv [17]
                0.00    0.00    1511/45399       is_alkyl [27]
                0.00    0.00    1916/45399       find_exocyclic_methylene_C [18]
                0.00    0.00    2025/45399       is_aryl [33]
                0.00    0.00    3172/45399       is_thioxo_C [15]
                0.00    0.00    3255/45399       is_arene [28]
                0.00    0.00    4382/45399       chk_arom [9]
                0.01    0.00    6883/45399       is_oxo_C [10]
                0.01    0.00    7400/45399       hetbond_count [13]
[11]     0.1    0.05    0.00   45399         get_bond [11]
-----------------------------------------------
                                                 <spontaneous>
[12]     0.0    0.04    0.00                 memset [12]
-----------------------------------------------
                0.00    0.00      56/1858        chk_arom_fg [41]
                0.00    0.01     357/1858        chk_double [16]
                0.00    0.01     371/1858        chk_single [14]
                0.00    0.02    1074/1858        chk_functionalgroups [7]
[13]     0.0    0.00    0.03    1858         hetbond_count [13]
                0.03    0.00    1858/6555425     get_neighbors [4]
                0.01    0.00    7400/45399       get_bond [11]
-----------------------------------------------
                0.00    0.03     555/555         chk_functionalgroups [7]
[14]     0.0    0.00    0.03     555         chk_single [14]
                0.00    0.01     371/1858        hetbond_count [13]
                0.00    0.00     254/6555425     get_neighbors [4]
                0.00    0.00     117/117         is_acyl [29]
                0.00    0.00     221/338         is_hydrazino [25]
                0.00    0.00    1185/1511        is_alkyl [27]
                0.00    0.00    1048/1063        is_true_alkyl [31]
                0.00    0.00     585/585         is_alkenyl [32]
                0.00    0.00    1867/2025        is_aryl [33]
                0.00    0.00     735/735         is_alkynyl [42]
                0.00    0.00     220/327         is_C_monosubst_amino [39]
                0.00    0.00     627/1428        is_amino [36]
                0.00    0.00     114/221         is_hydroxylamino [40]
                0.00    0.00     491/730         is_hydroxy [43]
                0.00    0.00     261/618         is_alkylamino [37]
                0.00    0.00     261/618         is_arylamino [38]
                0.00    0.00     114/221         is_azido [44]
                0.00    0.00     114/114         is_diazonium [49]
                0.00    0.00     220/327         is_C_disubst_amino [46]
                0.00    0.00     114/114         is_nitro [51]
                0.00    0.00      20/357         is_subst_amino [30]
                0.00    0.00     114/114         is_true_alkylamino [52]
                0.00    0.00     114/471         is_diarylamino [45]
                0.00    0.00     114/114         is_true_dialkylamino [53]
                0.00    0.00      10/10          is_true_alkylsulfanyl [54]
                0.00    0.00      10/10          is_arylsulfanyl [55]
                0.00    0.00      39/46          is_aryloxy [56]
                0.00    0.00      36/45399       get_bond [11]
                0.00    0.00      27/27          is_acylamino [57]
                0.00    0.00      20/27          is_alkoxy [58]
                0.00    0.00      19/26          is_alkynyloxy [59]
                0.00    0.00      19/19          is_true_alkoxy [60]
                0.00    0.00      10/10          is_sulfanyl [61]
                0.00    0.00       5/5           chk_x_y_single [72]
-----------------------------------------------
                0.00    0.00       5/1978        chk_double [16]
                0.00    0.00      69/1978        chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00     114/1978        chk_carboxyl_deriv [17]
                0.00    0.01     740/1978        chk_arom [9]
                0.00    0.02    1050/1978        update_atypes [8]
[15]     0.0    0.00    0.03    1978         is_thioxo_C [15]
                0.03    0.00    1978/6555425     get_neighbors [4]
                0.00    0.00    3172/45399       get_bond [11]
-----------------------------------------------
                0.00    0.03     141/141         chk_functionalgroups [7]
[16]     0.0    0.00    0.03     141         chk_double [16]
                0.00    0.02     114/114         chk_carboxyl_deriv [17]
                0.00    0.01     357/1858        hetbond_count [13]
                0.00    0.00     171/45399       get_bond [11]
                0.00    0.00      10/338         is_hydrazino [25]
                0.00    0.00       5/119         is_true_imino_C [34]
                0.00    0.00       5/3249        is_oxo_C [10]
                0.00    0.00       5/1978        is_thioxo_C [15]
                0.00    0.00       5/6555425     get_neighbors [4]
                0.00    0.00       5/3480        get_nextneighbors [20]
-----------------------------------------------
                0.00    0.02     114/114         chk_double [16]
[17]     0.0    0.00    0.02     114         chk_carboxyl_deriv [17]
                0.00    0.00     342/6555425     get_neighbors [4]
                0.00    0.00     214/214         is_subst_acylamino [26]
                0.00    0.00     114/119         is_true_imino_C [34]
                0.00    0.00     114/3249        is_oxo_C [10]
                0.00    0.00     114/1978        is_thioxo_C [15]
                0.00    0.00    1482/45399       get_bond [11]
                0.00    0.00     107/338         is_hydrazino [25]
                0.00    0.00     107/221         is_hydroxylamino [40]
                0.00    0.00     107/327         is_C_monosubst_amino [39]
                0.00    0.00     107/221         is_azido [44]
                0.00    0.00     107/327         is_C_disubst_amino [46]
                0.00    0.00     107/1428        is_amino [36]
                0.00    0.00       7/730         is_hydroxy [43]
                0.00    0.00       7/27          is_alkoxy [58]
                0.00    0.00       7/46          is_aryloxy [56]
                0.00    0.00       7/7           is_alkenyloxy [62]
                0.00    0.00       7/26          is_alkynyloxy [59]
-----------------------------------------------
                0.00    0.02    1025/1025        chk_arom [9]
[18]     0.0    0.00    0.02    1025         find_exocyclic_methylene_C [18]
                0.01    0.00    1025/6555425     get_neighbors [4]
                0.00    0.00    1916/45399       get_bond [11]
-----------------------------------------------
                0.00    0.01       1/1           main [1]
[19]     0.0    0.00    0.01       1         update_Htotal [19]
                0.01    0.00     674/6555425     get_neighbors [4]
                0.00    0.00    1392/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       5/3480        is_true_alkylamino [52]
                0.00    0.00       5/3480        chk_double [16]
                0.00    0.00      10/3480        is_true_alkylsulfanyl [54]
                0.00    0.00      10/3480        is_arylsulfanyl [55]
                0.00    0.00      18/3480        is_diarylamino [45]
                0.00    0.00      18/3480        is_nitro [51]
                0.00    0.00      36/3480        is_C_disubst_amino [46]
                0.00    0.00      90/3480        is_diazonium [49]
                0.00    0.00     107/3480        is_acyl [29]
                0.00    0.00     112/3480        is_alkylamino [37]
                0.00    0.00     112/3480        is_arylamino [38]
                0.00    0.00     175/3480        is_azido [44]
                0.00    0.00     188/3480        is_subst_acylamino [26]
                0.00    0.00     202/3480        is_hydroxylamino [40]
                0.00    0.00     265/3480        is_C_monosubst_amino [39]
                0.00    0.00     301/3480        is_hydrazino [25]
                0.00    0.00     544/3480        is_true_alkyl [31]
                0.00    0.00     585/3480        is_alkenyl [32]
                0.00    0.00     697/3480        is_alkyl [27]
[20]     0.0    0.01    0.00    3480         get_nextneighbors [20]
-----------------------------------------------
                0.00    0.00     206/413         is_subst_acylamino [26]
                0.00    0.00     207/413         chk_imide [22]
[21]     0.0    0.00    0.01     413         is_acyl_gen [21]
                0.00    0.01     413/3249        is_oxo_C [10]
-----------------------------------------------
                0.00    0.01      99/99          chk_functionalgroups [7]
[22]     0.0    0.00    0.01      99         chk_imide [22]
                0.00    0.00     207/413         is_acyl_gen [21]
                0.00    0.00     113/113         is_carbamoyl [35]
                0.00    0.00      99/6555425     get_neighbors [4]
-----------------------------------------------
                0.00    0.01       1/1           main [1]
[23]     0.0    0.00    0.01       1         get_molstat [23]
                0.01    0.00     392/6555425     get_neighbors [4]
                0.00    0.00      31/93          is_arene [28]
                0.00    0.00       6/37          is_heterocycle [71]
-----------------------------------------------
                0.00    0.00      31/31          chk_functionalgroups [7]
[24]     0.0    0.00    0.00      31         chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00      31/93          is_arene [28]
                0.00    0.00      69/3249        is_oxo_C [10]
                0.00    0.00      69/1978        is_thioxo_C [15]
                0.00    0.00      69/6555425     get_neighbors [4]
                0.00    0.00     149/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      10/338         chk_double [16]
                0.00    0.00     107/338         chk_carboxyl_deriv [17]
                0.00    0.00     221/338         chk_single [14]
[25]     0.0    0.00    0.00     338         is_hydrazino [25]
                0.00    0.00     337/357         is_subst_amino [30]
                0.00    0.00     301/3480        get_nextneighbors [20]
                0.00    0.00     338/45399       get_bond [11]
                0.00    0.00     337/1428        is_amino [36]
-----------------------------------------------
                0.00    0.00     214/214         chk_carboxyl_deriv [17]
[26]     0.0    0.00    0.00     214         is_subst_acylamino [26]
                0.00    0.00     206/413         is_acyl_gen [21]
                0.00    0.00     188/3480        get_nextneighbors [20]
                0.00    0.00     214/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     112/1511        is_alkylamino [37]
                0.00    0.00     214/1511        is_acyl [29]
                0.00    0.00    1185/1511        chk_single [14]
[27]     0.0    0.00    0.00    1511         is_alkyl [27]
                0.00    0.00     697/3480        get_nextneighbors [20]
                0.00    0.00    1511/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      31/93          chk_oxo_thioxo_imino_hetarene [24]
                0.00    0.00      31/93          chk_functionalgroups [7]
                0.00    0.00      31/93          get_molstat [23]
[28]     0.0    0.00    0.00      93         is_arene [28]
                0.00    0.00    3255/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     117/117         chk_single [14]
[29]     0.0    0.00    0.00     117         is_acyl [29]
                0.00    0.00     127/3249        is_oxo_C [10]
                0.00    0.00     214/1511        is_alkyl [27]
                0.00    0.00     107/3480        get_nextneighbors [20]
                0.00    0.00     127/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      20/357         chk_single [14]
                0.00    0.00     337/357         is_hydrazino [25]
[30]     0.0    0.00    0.00     357         is_subst_amino [30]
                0.00    0.00     357/618         is_alkylamino [37]
                0.00    0.00     357/618         is_arylamino [38]
                0.00    0.00     357/471         is_diarylamino [45]
                0.00    0.00     357/1428        is_amino [36]
                0.00    0.00     357/357         is_dialkylamino [48]
                0.00    0.00     357/357         is_alkylarylamino [47]
-----------------------------------------------
                0.00    0.00       5/1063        is_true_alkylamino [52]
                0.00    0.00      10/1063        is_true_alkylsulfanyl [54]
                0.00    0.00    1048/1063        chk_single [14]
[31]     0.0    0.00    0.00    1063         is_true_alkyl [31]
                0.00    0.00     544/3480        get_nextneighbors [20]
                0.00    0.00    1063/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     585/585         chk_single [14]
[32]     0.0    0.00    0.00     585         is_alkenyl [32]
                0.00    0.00     585/3480        get_nextneighbors [20]
                0.00    0.00     585/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      10/2025        is_arylsulfanyl [55]
                0.00    0.00      36/2025        is_diarylamino [45]
                0.00    0.00     112/2025        is_arylamino [38]
                0.00    0.00    1867/2025        chk_single [14]
[33]     0.0    0.00    0.00    2025         is_aryl [33]
                0.00    0.00    2025/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       5/119         chk_double [16]
                0.00    0.00     114/119         chk_carboxyl_deriv [17]
[34]     0.0    0.00    0.00     119         is_true_imino_C [34]
                0.00    0.00     124/6555425     get_neighbors [4]
                0.00    0.00     357/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     113/113         chk_imide [22]
[35]     0.0    0.00    0.00     113         is_carbamoyl [35]
                0.00    0.00     113/3249        is_oxo_C [10]
                0.00    0.00     113/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     107/1428        chk_carboxyl_deriv [17]
                0.00    0.00     337/1428        is_hydrazino [25]
                0.00    0.00     357/1428        is_subst_amino [30]
                0.00    0.00     627/1428        chk_single [14]
[36]     0.0    0.00    0.00    1428         is_amino [36]
                0.00    0.00    1428/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     261/618         chk_single [14]
                0.00    0.00     357/618         is_subst_amino [30]
[37]     0.0    0.00    0.00     618         is_alkylamino [37]
                0.00    0.00     618/45399       get_bond [11]
                0.00    0.00     112/3480        get_nextneighbors [20]
                0.00    0.00     112/1511        is_alkyl [27]
-----------------------------------------------
                0.00    0.00     261/618         chk_single [14]
                0.00    0.00     357/618         is_subst_amino [30]
[38]     0.0    0.00    0.00     618         is_arylamino [38]
                0.00    0.00     618/45399       get_bond [11]
                0.00    0.00     112/3480        get_nextneighbors [20]
                0.00    0.00     112/2025        is_aryl [33]
-----------------------------------------------
                0.00    0.00     107/327         chk_carboxyl_deriv [17]
                0.00    0.00     220/327         chk_single [14]
[39]     0.0    0.00    0.00     327         is_C_monosubst_amino [39]
                0.00    0.00     265/3480        get_nextneighbors [20]
                0.00    0.00     327/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     107/221         chk_carboxyl_deriv [17]
                0.00    0.00     114/221         chk_single [14]
[40]     0.0    0.00    0.00     221         is_hydroxylamino [40]
                0.00    0.00     202/3480        get_nextneighbors [20]
                0.00    0.00     229/730         is_hydroxy [43]
                0.00    0.00     221/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      49/49          chk_functionalgroups [7]
[41]     0.0    0.00    0.00      49         chk_arom_fg [41]
                0.00    0.00      56/1858        hetbond_count [13]
                0.00    0.00       2/6555425     get_neighbors [4]
                0.00    0.00       5/45399       get_bond [11]
                0.00    0.00       3/730         is_hydroxy [43]
-----------------------------------------------
                0.00    0.00     735/735         chk_single [14]
[42]     0.0    0.00    0.00     735         is_alkynyl [42]
                0.00    0.00     735/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       3/730         chk_arom_fg [41]
                0.00    0.00       7/730         chk_carboxyl_deriv [17]
                0.00    0.00     229/730         is_hydroxylamino [40]
                0.00    0.00     491/730         chk_single [14]
[43]     0.0    0.00    0.00     730         is_hydroxy [43]
                0.00    0.00     730/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     107/221         chk_carboxyl_deriv [17]
                0.00    0.00     114/221         chk_single [14]
[44]     0.0    0.00    0.00     221         is_azido [44]
                0.00    0.00     175/3480        get_nextneighbors [20]
                0.00    0.00     221/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     114/471         chk_single [14]
                0.00    0.00     357/471         is_subst_amino [30]
[45]     0.0    0.00    0.00     471         is_diarylamino [45]
                0.00    0.00     471/45399       get_bond [11]
                0.00    0.00      18/3480        get_nextneighbors [20]
                0.00    0.00      36/2025        is_aryl [33]
-----------------------------------------------
                0.00    0.00     107/327         chk_carboxyl_deriv [17]
                0.00    0.00     220/327         chk_single [14]
[46]     0.0    0.00    0.00     327         is_C_disubst_amino [46]
                0.00    0.00     327/45399       get_bond [11]
                0.00    0.00      36/3480        get_nextneighbors [20]
-----------------------------------------------
                0.00    0.00     357/357         is_subst_amino [30]
[47]     0.0    0.00    0.00     357         is_alkylarylamino [47]
                0.00    0.00     357/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     357/357         is_subst_amino [30]
[48]     0.0    0.00    0.00     357         is_dialkylamino [48]
                0.00    0.00     357/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     114/114         chk_single [14]
[49]     0.0    0.00    0.00     114         is_diazonium [49]
                0.00    0.00      90/3480        get_nextneighbors [20]
                0.00    0.00     114/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[50]     0.0    0.00    0.00       1         update_ringcount [50]
                0.00    0.00     311/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00     114/114         chk_single [14]
[51]     0.0    0.00    0.00     114         is_nitro [51]
                0.00    0.00     186/45399       get_bond [11]
                0.00    0.00      18/3480        get_nextneighbors [20]
-----------------------------------------------
                0.00    0.00     114/114         chk_single [14]
[52]     0.0    0.00    0.00     114         is_true_alkylamino [52]
                0.00    0.00     114/45399       get_bond [11]
                0.00    0.00       5/3480        get_nextneighbors [20]
                0.00    0.00       5/1063        is_true_alkyl [31]
-----------------------------------------------
                0.00    0.00     114/114         chk_single [14]
[53]     0.0    0.00    0.00     114         is_true_dialkylamino [53]
                0.00    0.00     114/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      10/10          chk_single [14]
[54]     0.0    0.00    0.00      10         is_true_alkylsulfanyl [54]
                0.00    0.00      10/3480        get_nextneighbors [20]
                0.00    0.00      10/1063        is_true_alkyl [31]
                0.00    0.00      10/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      10/10          chk_single [14]
[55]     0.0    0.00    0.00      10         is_arylsulfanyl [55]
                0.00    0.00      10/3480        get_nextneighbors [20]
                0.00    0.00      10/45399       get_bond [11]
                0.00    0.00      10/2025        is_aryl [33]
-----------------------------------------------
                0.00    0.00       7/46          chk_carboxyl_deriv [17]
                0.00    0.00      39/46          chk_single [14]
[56]     0.0    0.00    0.00      46         is_aryloxy [56]
                0.00    0.00      46/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      27/27          chk_single [14]
[57]     0.0    0.00    0.00      27         is_acylamino [57]
                0.00    0.00      27/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       7/27          chk_carboxyl_deriv [17]
                0.00    0.00      20/27          chk_single [14]
[58]     0.0    0.00    0.00      27         is_alkoxy [58]
                0.00    0.00      27/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       7/26          chk_carboxyl_deriv [17]
                0.00    0.00      19/26          chk_single [14]
[59]     0.0    0.00    0.00      26         is_alkynyloxy [59]
                0.00    0.00      26/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      19/19          chk_single [14]
[60]     0.0    0.00    0.00      19         is_true_alkoxy [60]
                0.00    0.00      19/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00      10/10          chk_single [14]
[61]     0.0    0.00    0.00      10         is_sulfanyl [61]
                0.00    0.00      10/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       7/7           chk_carboxyl_deriv [17]
[62]     0.0    0.00    0.00       7         is_alkenyloxy [62]
                0.00    0.00       7/45399       get_bond [11]
-----------------------------------------------
                0.00    0.00       6/6304        get_filetype [76]
                0.00    0.00    6298/6304        read_MDLmolfile [78]
[65]     0.0    0.00    0.00    6304         strsub [65]
-----------------------------------------------
                0.00    0.00       1/4839        main [1]
                0.00    0.00     710/4839        read_MDLmolfile [78]
                0.00    0.00    4128/4839        get_filetype [76]
[66]     0.0    0.00    0.00    4839         strpos2 [66]
-----------------------------------------------
                0.00    0.00     674/674         read_MDLmolfile [78]
[67]     0.0    0.00    0.00     674         get_nvalences [67]
-----------------------------------------------
                0.00    0.00     674/674         read_MDLmolfile [78]
[68]     0.0    0.00    0.00     674         is_heavyatom [68]
-----------------------------------------------
                0.00    0.00     674/674         read_MDLmolfile [78]
[69]     0.0    0.00    0.00     674         is_metal [69]
-----------------------------------------------
                0.00    0.00     220/220         chk_functionalgroups [7]
[70]     0.0    0.00    0.00     220         swap_atoms [70]
-----------------------------------------------
                0.00    0.00       6/37          get_molstat [23]
                0.00    0.00      31/37          chk_functionalgroups [7]
[71]     0.0    0.00    0.00      37         is_heterocycle [71]
-----------------------------------------------
                0.00    0.00       5/5           chk_single [14]
[72]     0.0    0.00    0.00       5         chk_x_y_single [72]
-----------------------------------------------
                0.00    0.00       4/4           read_MDLmolfile [78]
[73]     0.0    0.00    0.00       4         safe_calloc [73]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[74]     0.0    0.00    0.00       1         count_neighbors [74]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[75]     0.0    0.00    0.00       1         file_exists [75]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[76]     0.0    0.00    0.00       1         get_filetype [76]
                0.00    0.00    4128/4839        strpos2 [66]
                0.00    0.00       6/6304        strsub [65]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[77]     0.0    0.00    0.00       1         normalize_ionic_bonds [77]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[78]     0.0    0.00    0.00       1         read_MDLmolfile [78]
                0.00    0.00    6298/6304        strsub [65]
                0.00    0.00     710/4839        strpos2 [66]
                0.00    0.00     674/674         is_heavyatom [68]
                0.00    0.00     674/674         get_nvalences [67]
                0.00    0.00     674/674         is_metal [69]
                0.00    0.00       4/4           safe_calloc [73]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[79]     0.0    0.00    0.00       1         readinputfile [79]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[80]     0.0    0.00    0.00       1         safe_malloc [80]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[81]     0.0    0.00    0.00       1         write_fg_text [81]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[82]     0.0    0.00    0.00       1         zap_molecule [82]
-----------------------------------------------

 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

   [9] chk_arom (gcrt0.c)     [58] is_alkoxy (gcrt0.c)    [30] is_subst_amino (gcrt0.c)
  [41] chk_arom_fg (gcrt0.c)  [27] is_alkyl (gcrt0.c)     [61] is_sulfanyl (gcrt0.c)
  [17] chk_carboxyl_deriv (gcrt0.c) [37] is_alkylamino (gcrt0.c) [15] is_thioxo_C (gcrt0.c)
  [16] chk_double (gcrt0.c)   [47] is_alkylarylamino (gcrt0.c) [60] is_true_alkoxy (gcrt0.c)
   [7] chk_functionalgroups (gcrt0.c) [42] is_alkynyl (gcrt0.c) [31] is_true_alkyl (gcrt0.c)
  [22] chk_imide (gcrt0.c)    [59] is_alkynyloxy (gcrt0.c) [52] is_true_alkylamino (gcrt0.c)
  [24] chk_oxo_thioxo_imino_hetarene (gcrt0.c) [36] is_amino (gcrt0.c) [54] is_true_alkylsulfanyl (gcrt0.c)
   [2] chk_ringbonds (gcrt0.c) [28] is_arene (gcrt0.c)    [53] is_true_dialkylamino (gcrt0.c)
  [14] chk_single (gcrt0.c)   [33] is_aryl (gcrt0.c)      [34] is_true_imino_C (gcrt0.c)
  [72] chk_x_y_single (gcrt0.c) [38] is_arylamino (gcrt0.c) [12] memset
  [74] count_neighbors (gcrt0.c) [56] is_aryloxy (gcrt0.c) [77] normalize_ionic_bonds (gcrt0.c)
  [75] file_exists (gcrt0.c)  [55] is_arylsulfanyl (gcrt0.c) [5] path_length (gcrt0.c)
  [18] find_exocyclic_methylene_C (gcrt0.c) [44] is_azido (gcrt0.c) [6] path_pos (gcrt0.c)
  [11] get_bond (gcrt0.c)     [35] is_carbamoyl (gcrt0.c) [78] read_MDLmolfile (gcrt0.c)
  [76] get_filetype (gcrt0.c) [48] is_dialkylamino (gcrt0.c) [79] readinputfile (gcrt0.c)
  [23] get_molstat (gcrt0.c)  [45] is_diarylamino (gcrt0.c) [73] safe_calloc
   [4] get_neighbors (gcrt0.c) [49] is_diazonium (gcrt0.c) [80] safe_malloc
  [20] get_nextneighbors (gcrt0.c) [68] is_heavyatom (gcrt0.c) [66] strpos2 (gcrt0.c)
  [67] get_nvalences (gcrt0.c) [71] is_heterocycle (gcrt0.c) [65] strsub (gcrt0.c)
  [13] hetbond_count (gcrt0.c) [25] is_hydrazino (gcrt0.c) [70] swap_atoms (gcrt0.c)
  [46] is_C_disubst_amino (gcrt0.c) [43] is_hydroxy (gcrt0.c) [19] update_Htotal (gcrt0.c)
  [39] is_C_monosubst_amino (gcrt0.c) [40] is_hydroxylamino (gcrt0.c) [8] update_atypes (gcrt0.c)
  [29] is_acyl (gcrt0.c)      [69] is_metal (gcrt0.c)     [50] update_ringcount (gcrt0.c)
  [21] is_acyl_gen (gcrt0.c)  [51] is_nitro (gcrt0.c)     [81] write_fg_text (gcrt0.c)
  [57] is_acylamino (gcrt0.c) [10] is_oxo_C (gcrt0.c)     [82] zap_molecule (gcrt0.c)
  [32] is_alkenyl (gcrt0.c)    [3] is_ringpath (gcrt0.c)
  [62] is_alkenyloxy (gcrt0.c) [26] is_subst_acylamino (gcrt0.c)
