The shell being used is:  /bin/zsh
Running pipeline...
Running the pipeline with manual routes.
Elaborating compound: Cn1ncc(NC(=O)CC#N)c1NC(=O)C1CCCO1
┌──────────────────────────────────────────────────────────────────────────────┐
│                                 PyRosetta-4                                  │
│              Created in JHU by Sergey Lyskov and PyRosetta Team              │
│              (C) Copyright Rosetta Commons Member Institutions               │
│                                                                              │
│ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │
│         See LICENSE.PyRosetta.md or email license@uw.edu for details         │
└──────────────────────────────────────────────────────────────────────────────┘
PyRosetta-4 2024 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python312.Release 2024.16+release.bc4dfa1b240a4138da057c7de791d08506956c8d 2024-04-16T10:39:11] retrieved from: http://www.pyrosetta.org
Step 1 in this route using Amidation
Looking for analogue library .pkl.gz if already created...
Running superstructure search for O=C(O)C1CCCO1. Only searching for building blocks.
Found 790 for O=C(O)C1CCCO1 before filtering.
Found 790 before filtering.
Removing repeat analogues...
Removed 516 molecules (65.32%) by simple filters.
Removing chirality from analogues...
Removing repeat analogues...
Removed 0 invalid or repeated molecules (0.0%) of r1 analogues.
Checking if analogues contain SMARTS pattern of original reactant...
Checking if analogues contain SMARTS pattern of other reactant...
Saving r1 analogue library to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_r1_1of3.pkl.gz 

Looking for analogue library .pkl.gz if already created...
Running superstructure search for Cn1ncc(NC(=O)OC(C)(C)C)c1N. Only searching for building blocks.
Found 15 for Cn1ncc(NC(=O)OC(C)(C)C)c1N before filtering.
Found 15 before filtering.
Removing repeat analogues...
Removed 5 molecules (33.33%) by simple filters.
Removing chirality from analogues...
Removing repeat analogues...
Removed 0 invalid or repeated molecules (0.0%) of r2 analogues.
Checking if analogues contain SMARTS pattern of original reactant...
Checking if analogues contain SMARTS pattern of other reactant...
Saving r2 analogue library to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_r2_1of3.pkl.gz 

Filtering analogues of reactants on SMARTS...
Filtered 100 rows (36.5%) from r1 dataframe.
Ordering analogues of r1 before finding products...
Filtering analogues of reactants on SMARTS...
Filtered 2 rows (20.0%) from r2 dataframe.
Ordering analogues of r2 before finding products...
Adding metadata to products...
Since these products are not the final products they will be saved in the /extra folder. 

Saving products to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_products_1of3.pkl.gz 

Step 2 in this route using N-Boc_deprotection
Since this is an internal or final step looking for the products .pkl from previous step...
Found /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_products_1of3.pkl.gz as the products .pkl from previous step.
Removing chirality from analogues...
Removing repeat analogues...
Removed 0 invalid or repeated molecules (0.0%) of r1 analogues.
Checking if analogues contain SMARTS pattern of original reactant...
Saving r1 analogue library to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_N-Boc_deprotection_r1_2of3.pkl.gz 

Filtering analogues of reactants on SMARTS...
Filtered 0 rows (0.0%) from r1 dataframe.
Ordering analogues of r1 before finding products...
Adding metadata to products...
Found 1448 unique products.
Since these products are not the final products they will be saved in the /extra folder. 

Saving products to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_N-Boc_deprotection_products_2of3.pkl.gz 

Step 3 in this route using Amidation
Since this is an internal or final step looking for the products .pkl from previous step...
Running superstructure search for N#CCC(=O)O. Only searching for building blocks.
Found 1266 for N#CCC(=O)O before filtering.
Found 1266 before filtering.
Removing repeat analogues...
Removed 473 molecules (37.36%) by simple filters.
Removing chirality from analogues...
Removing repeat analogues...
Removed 0 invalid or repeated molecules (0.0%) of r1 analogues.
Checking if analogues contain SMARTS pattern of original reactant...
Checking if analogues contain SMARTS pattern of other reactant...
Saving r1 analogue library to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_r1_3of3.pkl.gz 

Since this is an internal or final step looking for the products .pkl from previous step...
Found /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_N-Boc_deprotection_products_2of3.pkl.gz as the products .pkl from previous step.
Removing chirality from analogues...
Removing repeat analogues...
Removed 0 invalid or repeated molecules (0.0%) of r2 analogues.
Checking if analogues contain SMARTS pattern of original reactant...
Checking if analogues contain SMARTS pattern of other reactant...
Saving r2 analogue library to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/extra/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_r2_3of3.pkl.gz 

Filtering analogues of reactants on SMARTS...
Filtered 588 rows (74.15%) from r1 dataframe.
Ordering analogues of r1 before finding products...
Filtering analogues of reactants on SMARTS...
Filtered 128 rows (8.84%) from r2 dataframe.
Ordering analogues of r2 before finding products...
Too many analogues for both reactants.
Cutting 105 analogues from r1 dataframe.
Cutting 1220 analogues from r2 dataframe.
Adding metadata to products...
Enumerating stereoisomers since this is the final step...
Found 52023 unique products.
Saving final products to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_products_3of3.pkl.gz 

Saving final products to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/LXINEYASRREWNB-UHFFFAOYSA-N_Amidation_products_3of3.csv 

Fitting products, warning: it is expected that the base compound has already passed minimisation and intramolecular checks.

Cutting products with number of atoms difference greater than 10.
Kept 34356 (65.99%) unique analogues out of 52059 analogues.
Even after cutting products, the number of products is over 100. Only placing the top 100 products.
Placing 100 (0.19%) unique analogues out of 52059 analogues.
┌──────────────────────────────────────────────────────────────────────────────┐
│                                 PyRosetta-4                                  │
│              Created in JHU by Sergey Lyskov and PyRosetta Team              │
│              (C) Copyright Rosetta Commons Member Institutions               │
│                                                                              │
│ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │
│         See LICENSE.PyRosetta.md or email license@uw.edu for details         │
└──────────────────────────────────────────────────────────────────────────────┘
PyRosetta-4 2024 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python312.Release 2024.16+release.bc4dfa1b240a4138da057c7de791d08506956c8d 2024-04-16T10:39:11] retrieved from: http://www.pyrosetta.org
Placing 100 run time: 0:00:52.976726
Mol could not pass internal clash checks.
Mol could not pass internal clash checks.
Mol could not pass internal clash checks.
99 (99.0%) successful placements where ∆∆G < -1 and RMSD < 2 Å.

Saved HIPPO output to /Users/kate_fieseler/PycharmProjects/syndirella/syndirella/tests/profiling/outputs/LXINEYASRREWNB-UHFFFAOYSA-N/LXINEYASRREWNB-UHFFFAOYSA-N_g2Sr6V_to_hippo.pkl.gz
Cleaning up placement directory...
Finished elaborating compound Cn1ncc(NC(=O)CC#N)c1NC(=O)C1CCCO1 after 0:11:38.378324

Pipeline complete.
Done!
         176686606 function calls (174363088 primitive calls) in 698.391 seconds

   Ordered by: internal time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
 38849/50  429.768    0.011    0.001    0.000 {method 'acquire' of '_thread.lock' objects}
 55106140  117.521    0.000  117.521    0.000 __init__.py:33(FingerprintSimilarity)
  1165/58   24.014    0.021    0.005    0.000 {built-in method time.sleep}
  740/737   14.944    0.020   67.463    0.092 {method 'poll' of 'select.poll' objects}
   617422   10.520    0.000   10.775    0.000 generic.py:6284(__getattr__)
8874/8799    7.696    0.001  840.393    0.096 threading.py:323(wait)
   480383    7.640    0.000    8.530    0.000 base.py:3777(get_loc)
   557793    6.336    0.000   14.418    0.000 generic.py:6301(__setattr__)
    10000    6.099    0.001    6.982    0.001 EnumerateStereoisomers.py:81(_getFlippers)
   191865    4.608    0.000    4.632    0.000 cast.py:551(maybe_promote)
    62059    3.749    0.000   11.713    0.000 EnumerateStereoisomers.py:165(EnumerateStereoisomers)
   391263    3.618    0.000    7.648    0.000 series.py:734(name)
25654274/25484299    2.649    0.000    4.171    0.000 {built-in method builtins.isinstance}
   102051    2.482    0.000    9.135    0.000 indexing.py:1452(_convert_to_indexer)
    10000    2.434    0.000   14.082    0.001 SlipperSynthesizer.py:545(find_stereoisomers)
   303530    2.271    0.000    2.271    0.000 config.py:649(_get_deprecated_option)
    90809    1.652    0.000    1.731    0.000 warnings.py:182(_add_filter)
   180409    1.416    0.000   47.017    0.000 series.py:1261(__setitem__)
    11392    1.326    0.000   18.060    0.002 SlipperSynthesizer.py:336(apply_reaction)
       52    1.294    0.025    1.294    0.025 {method 'read' of '_ssl._SSLSocket' objects}
      517    1.193    0.002    1.193    0.002 {method 'compress' of 'zlib.Compress' objects}
       26    1.125    0.043    1.125    0.043 {method 'connect' of '_socket.socket' objects}
   180409    1.087    0.000    4.123    0.000 series.py:1369(_set_with_engine)
9008273/6944699    1.069    0.000    1.995    0.000 {built-in method builtins.len}
       26    0.995    0.038    0.995    0.038 {method 'do_handshake' of '_ssl._SSLSocket' objects}
205347/204931    0.950    0.000   18.575    0.000 series.py:389(__init__)
11570/6509    0.901    0.000 1019.514    0.157 queue.py:154(get)
   329564    0.880    0.000    3.658    0.000 construction.py:517(sanitize_array)
    12896    0.820    0.000    0.828    0.000 SlipperSynthesizer.py:419(<lambda>)
    76291    0.816    0.000   26.231    0.000 indexing.py:2221(_setitem_with_indexer_missing)
   638905    0.707    0.000    0.773    0.000 inference.py:334(is_hashable)
   276673    0.699    0.000    1.176    0.000 cast.py:1157(maybe_infer_to_datetimelike)
    12928    0.677    0.000    0.677    0.000 SlipperSynthesizer.py:376(can_be_sanitized)
    28053    0.629    0.000    0.737    0.000 __init__.py:298(__init__)
       63    0.597    0.009    0.597    0.009 {method 'recv' of '_socket.socket' objects}
       33    0.592    0.018    0.679    0.021 csvs.py:315(_save_chunk)
  2985816    0.546    0.000    1.256    0.000 generic.py:42(_instancecheck)
  2985844    0.470    0.000    0.696    0.000 generic.py:37(_check)
   123600    0.452    0.000    3.137    0.000 base.py:475(__new__)
   173873    0.441    0.000    4.853    0.000 base.py:3820(get_indexer)
4631183/4631155    0.437    0.000    2.011    0.000 {built-in method builtins.getattr}
   180664    0.427    0.000    5.165    0.000 take.py:120(_take_nd_ndarray)
   348100    0.426    0.000    0.506    0.000 generic.py:278(__init__)
    77688    0.424    0.000    0.954    0.000 function_base.py:5369(insert)
   420946    0.390    0.000    0.613    0.000 numeric.py:274(full)
   181857    0.377    0.000    0.535    0.000 generic.py:6236(__finalize__)
    12896    0.371    0.000    0.779    0.000 SlipperSynthesizer.py:421(<lambda>)
   185288    0.366    0.000    0.601    0.000 base.py:2744(inferred_type)
   726383    0.323    0.000    0.323    0.000 __init__.py:90(_getRDKitItem)
  1366275    0.319    0.000    1.733    0.000 __init__.py:65(__getitem__)
   289145    0.314    0.000    1.245    0.000 base.py:5552(equals)
77789/77688    0.310    0.000    3.930    0.000 base.py:6956(insert)
       26    0.307    0.012    0.307    0.012 {method 'load_verify_locations' of '_ssl._SSLContext' objects}
   288749    0.302    0.000    0.424    0.000 base.py:649(_simple_new)
    89171    0.299    0.000   40.777    0.000 indexing.py:882(__setitem__)
   220023    0.297    0.000    0.297    0.000 {method 'reduce' of 'numpy.ufunc' objects}
   145907    0.296    0.000    0.718    0.000 common.py:231(asarray_tuplesafe)
   121713    0.294    0.000    0.637    0.000 base.py:3955(_get_indexer)
   639892    0.282    0.000    0.282    0.000 __init__.py:99(_getRDKitItem)
  2563862    0.276    0.000    0.416    0.000 base.py:3809(<genexpr>)
     3172    0.265    0.000    0.499    0.000 inchi.py:94(MolToInchiAndAuxInfo)
   751055    0.263    0.000    0.555    0.000 common.py:1434(_is_dtype_type)
   371668    0.262    0.000    0.910    0.000 {built-in method builtins.any}
   204931    0.252    0.000    0.892    0.000 managers.py:1863(from_array)
   576671    0.242    0.000    0.724    0.000 common.py:137(is_object_dtype)
  1413634    0.241    0.000    0.627    0.000 __init__.py:60(__len__)
     1448    0.241    0.000    1.333    0.001 SlipperSynthesizer.py:299(apply_reaction_single)
1200756/1174455    0.230    0.000    1.446    0.000 {built-in method numpy.asarray}
   780889    0.226    0.000    0.226    0.000 __init__.py:87(_sizeCalc)
    77716    0.224    0.000    2.459    0.000 base.py:674(_with_infer)
   793489    0.219    0.000    0.219    0.000 {built-in method numpy.empty}
    89171    0.210    0.000   29.055    0.000 indexing.py:1785(_setitem_with_indexer)
  1413013    0.208    0.000    1.976    0.000 __init__.py:78(__iter__)
      101    0.204    0.002    7.046    0.070 intra_geometry.py:67(check_geometry)
   513931    0.195    0.000    0.368    0.000 indexing.py:2765(check_dict_or_set_indexers)
  1440756    0.195    0.000    0.291    0.000 base.py:909(__len__)
    66231    0.179    0.000    0.388    0.000 cast.py:124(maybe_convert_platform)
   211476    0.179    0.000    0.287    0.000 _dtype.py:346(_name_get)
  1096831    0.179    0.000    4.191    0.000 {built-in method builtins.hasattr}
   680104    0.178    0.000    0.178    0.000 __init__.py:96(_sizeCalc)
   169059    0.171    0.000    0.171    0.000 {built-in method numpy.array}
    13195    0.168    0.000    0.358    0.000 managers.py:958(fast_xs)
    76317    0.168    0.000    0.192    0.000 concat.py:52(concat_compat)
   254619    0.168    0.000    2.603    0.000 config.py:127(_get_single_key)
   402945    0.167    0.000    0.208    0.000 generic.py:586(_get_axis)
   218864    0.161    0.000    0.292    0.000 blocks.py:2716(new_block)
   128312    0.160    0.000    5.687    0.000 series.py:1095(__getitem__)
   2278/7    0.157    0.000    0.001    0.000 threading.py:637(wait)
    91488    0.155    0.000    0.732    0.000 managers.py:317(apply)
     2272    0.152    0.000    0.437    0.000 pydevd.py:801(process_internal_commands)
       11    0.151    0.014    1.286    0.117 {built-in method _pickle.dump}
   155378    0.150    0.000    0.201    0.000 numeric.py:1330(normalize_axis_tuple)
    89171    0.149    0.000    9.483    0.000 indexing.py:744(_get_setitem_indexer)
   180664    0.149    0.000    5.490    0.000 take.py:59(take_nd)
    77688    0.148    0.000    0.417    0.000 numeric.py:1393(moveaxis)
   174332    0.145    0.000    0.467    0.000 common.py:1081(is_numeric_dtype)
   590800    0.143    0.000    0.164    0.000 managers.py:2004(internal_values)
   232247    0.142    0.000    0.447    0.000 series.py:784(name)
  1211878    0.141    0.000    0.141    0.000 __init__.py:34(using_copy_on_write)
        5    0.141    0.028    0.252    0.050 Library.py:88(process_analogues)
  1795718    0.141    0.000    0.141    0.000 {built-in method builtins.issubclass}
   926316    0.138    0.000    0.279    0.000 <frozen abc>:117(__instancecheck__)
   926316    0.137    0.000    0.141    0.000 {built-in method _abc._abc_instancecheck}
   253983    0.134    0.000    2.901    0.000 config.py:145(_get_option)
   173883    0.133    0.000    1.395    0.000 base.py:6394(_should_compare)
        7    0.130    0.019    0.149    0.021 {built-in method _pickle.load}
   207877    0.130    0.000    0.256    0.000 blocks.py:2645(maybe_coerce_values)
   329328    0.127    0.000    0.270    0.000 construction.py:696(_sanitize_ndim)
   186662    0.126    0.000    0.372    0.000 base.py:5170(_get_engine_target)
     1586    0.125    0.000    0.626    0.000 Slipper.py:141(calculate_inchi_similarity)
   205745    0.124    0.000    0.469    0.000 generic.py:807(_set_axis)
   254619    0.124    0.000    0.178    0.000 config.py:635(_get_root)
   411248    0.124    0.000    0.149    0.000 construction.py:481(ensure_wrapped_if_datetimelike)
   180664    0.123    0.000    4.579    0.000 take.py:564(_take_preprocess_indexer_and_fill_value)
   173878    0.123    0.000    0.455    0.000 base.py:6324(_maybe_downcast_for_indexing)
   218130    0.122    0.000    0.122    0.000 intra_geometry.py:134(<genexpr>)
   554243    0.119    0.000    1.259    0.000 base.py:7593(ensure_index)
    64943    0.119    0.000    0.333    0.000 base.py:842(_engine)
   180409    0.114    0.000    1.666    0.000 series.py:1484(_check_is_chained_assignment_possible)
   328969    0.114    0.000    0.381    0.000 base.py:7688(maybe_extract_name)
   590800    0.113    0.000    0.277    0.000 series.py:831(_values)
       25    0.111    0.004    0.111    0.004 {built-in method _posixsubprocess.fork_exec}
   129795    0.111    0.000    0.111    0.000 missing.py:564(_array_equivalent_object)
       26    0.110    0.004    0.110    0.004 {built-in method _socket.getaddrinfo}
   132000    0.109    0.000    0.109    0.000 intra_geometry.py:258(_is_hydrogen)
   128540    0.109    0.000    4.029    0.000 blocks.py:1287(take_nd)
   510097    0.108    0.000    0.108    0.000 {built-in method __new__ of type object at 0x1027af2b8}
   335051    0.107    0.000    0.131    0.000 managers.py:1993(dtype)
   236716    0.107    0.000    0.124    0.000 warnings.py:482(__enter__)
    77691    0.106    0.000    1.678    0.000 warnings.py:131(filterwarnings)
      101    0.104    0.001    0.104    0.001 _base.py:142(<lambda>)
290097/277253    0.104    0.000    0.718    0.000 {built-in method builtins.all}
   408624    0.101    0.000    0.171    0.000 construction.py:416(extract_array)
        3    0.100    0.033   13.353    4.451 SlipperSynthesizer.py:480(assign_names_based_on_groups)
    28860    0.097    0.000    0.097    0.000 {method 'astype' of 'numpy.ndarray' objects}
    36118    0.096    0.000    4.265    0.000 managers.py:623(reindex_indexer)
    78126    0.096    0.000    0.758    0.000 managers.py:557(copy)
   236716    0.093    0.000    0.108    0.000 warnings.py:503(__exit__)
  237/229    0.092    0.000    0.092    0.000 {built-in method posix.write}
    22683    0.091    0.000    4.719    0.000 series.py:1155(_get_with)
   226202    0.089    0.000    0.236    0.000 common.py:1375(_is_dtype)
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   528340    0.089    0.000    0.126    0.000 common.py:372(apply_if_callable)
   232362    0.088    0.000    0.305    0.000 common.py:1571(validate_all_hashable)
   117014    0.088    0.000    0.191    0.000 base.py:341(setitem_inplace)
   117014    0.087    0.000    0.304    0.000 managers.py:2021(setitem_inplace)
    78104    0.087    0.000    2.593    0.000 generic.py:6662(copy)
   100238    0.085    0.000    0.134    0.000 cast.py:1580(construct_1d_object_array_from_listlike)
   173883    0.084    0.000    0.124    0.000 base.py:7723(_unpack_nested_dtype)
       52    0.082    0.002  272.222    5.235 socket.py:693(readinto)
   221350    0.082    0.000    0.133    0.000 blocks.py:2674(get_block_type)
  1245473    0.081    0.000    0.081    0.000 base.py:5144(_values)
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