03-Transform and Export¶
This example demonstrates a real parse-and-export workflow and ensures output paths are stably printed relative to the repository root.
In [1]:
Copied!
from pathlib import Path
import shutil
from molop.io import AutoParser
def find_repo_root(start: Path) -> Path:
for candidate in [start, *start.parents]:
if (candidate / "pyproject.toml").exists():
return candidate
raise RuntimeError("Could not find repository root containing pyproject.toml")
repo_root = find_repo_root(Path.cwd().resolve())
from pathlib import Path
import shutil
from molop.io import AutoParser
def find_repo_root(start: Path) -> Path:
for candidate in [start, *start.parents]:
if (candidate / "pyproject.toml").exists():
return candidate
raise RuntimeError("Could not find repository root containing pyproject.toml")
repo_root = find_repo_root(Path.cwd().resolve())
Transform to an SDF file¶
In [2]:
Copied!
log_batch = AutoParser((repo_root / "tests/test_files/g16log/*.log").as_posix())
log_batch[:10].format_transform(format="sdf", output_dir="/tmp", frameID=-1, n_jobs=-1)
log_batch = AutoParser((repo_root / "tests/test_files/g16log/*.log").as_posix())
log_batch[:10].format_transform(format="sdf", output_dir="/tmp", frameID=-1, n_jobs=-1)
INFO - Using 10 processes for 137 tasks.
MolOP parsing with 10 processes: 0%| | 0/137 [00:00<?, ?it/s]
MolOP processing sdf format with -1 jobs: 0%| | 0/10 [00:00<?, ?it/s]
Out[2]:
{'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/0-1a-Opt.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 28 29 0 0 0 0 0 0 0 0999 V2000\n 3.4629 -2.3005 0.0150 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7989 -1.0087 0.3487 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8652 0.0483 0.1953 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5564 -0.2523 -0.3009 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2413 -1.5900 -0.6535 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1757 -2.5887 -0.4967 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1817 1.6195 0.8846 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1860 -3.1012 0.1353 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.7887 -0.7755 0.7309 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1886 1.3944 0.5066 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.6428 0.8271 -0.4337 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2652 -1.8145 -1.0621 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.9243 -3.6081 -0.7727 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9648 2.1417 -0.1683 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.2743 2.4013 0.3189 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5430 3.4293 0.5427 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0078 3.2735 -0.3659 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5252 4.1906 -0.6298 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7270 3.0533 -1.1584 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5749 3.4630 0.5510 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.6317 0.5148 -0.9613 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.9614 0.5874 0.0020 S 0 0 0 0 0 6 0 0 0 0 0 0\n -3.0437 1.0649 -0.8375 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6377 1.1629 1.2966 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2526 -1.2362 0.2753 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.4476 -1.3826 0.8422 F 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3112 -1.7256 1.0782 F 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2278 -1.8808 -0.8924 F 0 0 0 0 0 0 0 0 0 0 0 0\n 1 8 1 0\n 1 2 2 0\n 2 9 1 0\n 3 2 1 0\n 3 10 2 0\n 4 3 1 0\n 5 6 2 0\n 5 4 1 0\n 6 1 1 0\n 10 7 1 0\n 11 4 2 0\n 11 14 1 0\n 12 5 1 0\n 13 6 1 0\n 14 15 2 0\n 15 10 1 0\n 15 16 1 0\n 17 14 1 0\n 17 20 1 0\n 18 17 1 0\n 19 17 1 0\n 21 11 1 0\n 21 22 1 0\n 22 25 1 0\n 22 24 2 0\n 23 22 2 0\n 25 26 1 0\n 25 27 1 0\n 28 25 1 0\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/0-1a-Sp.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 28 29 0 0 0 0 0 0 0 0999 V2000\n 3.4528 -2.3146 0.0096 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7952 -1.0254 0.3467 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8666 0.0367 0.1960 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5564 -0.2561 -0.3011 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2348 -1.5914 -0.6571 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1642 -2.5951 -0.5028 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1909 1.5995 0.8895 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.1719 -3.1191 0.1279 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.7860 -0.7980 0.7296 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1968 1.3803 0.5109 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.6482 0.8281 -0.4310 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2576 -1.8100 -1.0664 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.9078 -3.6125 -0.7815 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9767 2.1403 -0.1622 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.2874 2.3922 0.3257 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5612 3.4183 0.5522 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0097 3.2775 -0.3569 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5473 4.1926 -0.6184 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7105 3.0629 -1.1500 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5565 3.4674 0.5605 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.6278 0.5234 -0.9595 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.9571 0.6001 0.0039 S 0 0 0 0 0 6 0 0 0 0 0 0\n -3.0371 1.0851 -0.8344 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6307 1.1706 1.3000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2574 -1.2228 0.2724 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.4531 -1.3647 0.8389 F 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3185 -1.7189 1.0741 F 0 0 0 0 0 0 0 0 0 0 0 0\n -2.2357 -1.8644 -0.8969 F 0 0 0 0 0 0 0 0 0 0 0 0\n 1 8 1 0\n 1 2 2 0\n 2 9 1 0\n 3 2 1 0\n 3 10 2 0\n 4 3 1 0\n 5 6 2 0\n 5 4 1 0\n 6 1 1 0\n 10 7 1 0\n 11 4 2 0\n 11 14 1 0\n 12 5 1 0\n 13 6 1 0\n 14 15 2 0\n 15 10 1 0\n 15 16 1 0\n 17 14 1 0\n 17 20 1 0\n 18 17 1 0\n 19 17 1 0\n 21 11 1 0\n 21 22 1 0\n 22 25 1 0\n 22 24 2 0\n 23 22 2 0\n 25 26 1 0\n 25 27 1 0\n 28 25 1 0\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/02209_00862_00000_0000.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 16 14 0 0 0 0 0 0 0 0999 V2000\n 0.4498 -1.4337 0.4949 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3178 -0.7024 -0.2920 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3165 0.7049 -0.2919 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4472 1.4345 0.4951 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.1265 -1.0575 1.4583 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.3934 -2.5137 0.3879 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8581 -1.2124 -1.0877 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.8559 1.2159 -1.0875 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.1247 1.0575 1.4585 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.3890 2.5144 0.3882 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5733 -0.6933 -0.2303 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5746 0.6905 -0.2302 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.0699 -1.2380 0.5670 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4583 -1.2369 -1.1608 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4605 1.2344 -1.1606 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.0721 1.2342 0.5672 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 5 1 0\n 2 3 1 0\n 2 1 2 0\n 3 4 2 0\n 4 9 1 0\n 6 1 1 0\n 7 2 1 0\n 8 3 1 0\n 10 4 1 0\n 11 12 2 0\n 11 13 1 0\n 12 16 1 0\n 14 11 1 0\n 15 12 1 0\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/1-INT1-Opt.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 0 0 0 0 0 0 0 0 0 0999 V3000\nM V30 BEGIN CTAB\nM V30 COUNTS 101 106 0 0 1\nM V30 BEGIN ATOM\nM V30 1 C -2.846200 0.839800 -0.496100 0\nM V30 2 O -1.589700 -1.047300 -2.488400 0\nM V30 3 P 0.904100 1.346300 0.575000 0\nM V30 4 O -0.698600 -1.314500 0.645600 0\nM V30 5 C 2.447600 -1.031400 0.863500 0 CFG=2\nM V30 6 C 2.540800 0.461600 0.492200 0\nM V30 7 H 1.834200 -1.105200 1.763300 0\nM V30 8 H 2.947100 0.582700 -0.509900 0\nM V30 9 H 3.232700 0.945500 1.186600 0\nM V30 10 C 1.421200 3.049000 0.122100 0\nM V30 11 C 0.971900 4.158900 0.852800 0\nM V30 12 C 2.178700 3.266000 -1.039400 0\nM V30 13 C 1.274300 5.453800 0.431500 0\nM V30 14 H 0.378700 4.007200 1.747200 0\nM V30 15 C 2.483400 4.561500 -1.455600 0\nM V30 16 H 2.523100 2.427400 -1.632300 0\nM V30 17 C 2.030100 5.660400 -0.723600 0\nM V30 18 H 0.918200 6.302500 1.008300 0\nM V30 19 H 3.078200 4.710000 -2.352400 0\nM V30 20 H 2.265800 6.669200 -1.049200 0\nM V30 21 C 0.697400 1.437900 2.406300 0\nM V30 22 C -0.478500 0.935600 2.979300 0\nM V30 23 C 1.684700 1.977800 3.245500 0\nM V30 24 C -0.667600 0.973900 4.361600 0\nM V30 25 H -1.248100 0.523400 2.338600 0\nM V30 26 C 1.499300 2.011100 4.626200 0\nM V30 27 H 2.592200 2.394400 2.818200 0\nM V30 28 C 0.321500 1.508100 5.186800 0\nM V30 29 H -1.595100 0.596800 4.781200 0\nM V30 30 H 2.269300 2.434500 5.264700 0\nM V30 31 H 0.176400 1.540300 6.262800 0\nM V30 32 S 0.167500 -2.400700 -0.004600 0 CHG=-1 VAL=5\nM V30 33 C 3.825800 -1.599100 1.185600 0\nM V30 34 C 4.938500 -1.303800 0.385300 0\nM V30 35 C 4.014700 -2.420700 2.303000 0\nM V30 36 C 6.191600 -1.842900 0.673800 0\nM V30 37 H 4.828700 -0.640600 -0.464800 0\nM V30 38 C 5.268000 -2.957900 2.599200 0\nM V30 39 H 3.179300 -2.634300 2.960500 0\nM V30 40 C 6.360800 -2.676800 1.779900 0\nM V30 41 H 7.038400 -1.603500 0.037400 0\nM V30 42 H 5.389600 -3.588500 3.474800 0\nM V30 43 H 7.337100 -3.093700 2.007000 0\nM V30 44 C 0.178200 -3.715300 1.356200 0\nM V30 45 C 1.351200 -4.650100 1.067300 0\nM V30 46 H 2.312200 -4.143900 1.171700 0\nM V30 47 H 1.325100 -5.489300 1.770400 0\nM V30 48 H 1.288800 -5.065900 0.055600 0\nM V30 49 C -1.163400 -4.438100 1.158800 0\nM V30 50 H -1.207500 -5.294300 1.839900 0\nM V30 51 H -2.002700 -3.777100 1.381500 0\nM V30 52 H -1.278800 -4.812100 0.136700 0\nM V30 53 C 0.223100 -3.081500 2.744300 0\nM V30 54 H -0.508200 -2.274600 2.821800 0\nM V30 55 H -0.014300 -3.844600 3.493400 0\nM V30 56 H 1.205500 -2.677300 2.986700 0\nM V30 57 N 1.755800 -1.852600 -0.161900 0 CHG=1\nM V30 58 C 2.385900 -2.135100 -1.462700 0\nM V30 59 H 1.765400 -2.895200 -1.947900 0\nM V30 60 H 3.361600 -2.597600 -1.284500 0\nM V30 61 C 2.536600 -0.944600 -2.389100 0\nM V30 62 C 3.777500 -0.612900 -2.936200 0\nM V30 63 C 1.424900 -0.162000 -2.726000 0\nM V30 64 C 3.914400 0.495700 -3.776900 0\nM V30 65 H 4.648600 -1.219100 -2.701000 0\nM V30 66 C 1.562500 0.933600 -3.570100 0\nM V30 67 H 0.449000 -0.399400 -2.323700 0\nM V30 68 C 2.811200 1.289500 -4.103100 0\nM V30 69 H 4.892100 0.746100 -4.180100 0\nM V30 70 H 0.688300 1.533400 -3.804300 0\nM V30 71 C 2.943200 2.499200 -4.994000 0\nM V30 72 H 2.491000 3.381000 -4.527000 0\nM V30 73 H 3.990600 2.726800 -5.209500 0\nM V30 74 H 2.430400 2.345200 -5.950500 0\nM V30 75 C -4.802800 0.794400 3.317800 0\nM V30 76 C -4.038500 1.882900 2.927700 0\nM V30 77 C -3.432600 1.936100 1.656800 0\nM V30 78 C -3.582900 0.829100 0.768800 0\nM V30 79 C -4.404300 -0.242400 1.166200 0\nM V30 80 C -4.998100 -0.266200 2.420400 0\nM V30 81 H -2.635500 3.945200 1.908200 0\nM V30 82 H -5.262200 0.771800 4.301600 0\nM V30 83 H -3.901900 2.726200 3.599900 0\nM V30 84 C -2.685300 3.093900 1.234900 0\nM V30 85 H -4.574300 -1.062700 0.484100 0\nM V30 86 H -5.616600 -1.112700 2.704600 0\nM V30 87 C -2.067100 2.006900 -0.894600 0\nM V30 88 C -2.077800 3.134900 0.022200 0\nM V30 89 H -1.555600 4.033900 -0.292400 0\nM V30 90 C -1.807200 2.330400 -2.354400 0\nM V30 91 H -0.969800 3.032000 -2.426400 0\nM V30 92 H -1.549400 1.447700 -2.940700 0\nM V30 93 H -2.682900 2.799700 -2.823000 0\nM V30 94 S -3.046400 -0.955200 -2.527700 0 VAL=6\nM V30 95 O -3.764500 -0.857400 -3.786700 0\nM V30 96 O -3.631500 0.168400 -1.561500 0\nM V30 97 C -3.649000 -2.515000 -1.711000 0\nM V30 98 F -4.974400 -2.486700 -1.570400 0\nM V30 99 F -3.084100 -2.655100 -0.506800 0\nM V30 100 F -3.303000 -3.554600 -2.473600 0\nM V30 101 Ni -0.971500 0.544500 -0.212900 0 VAL=2\nM V30 END ATOM\nM V30 BEGIN BOND\nM V30 1 2 1 78\nM V30 2 1 3 21\nM V30 3 1 5 33\nM V30 4 1 5 7 CFG=1\nM V30 5 1 6 3\nM V30 6 1 6 5\nM V30 7 1 6 9\nM V30 8 1 8 6\nM V30 9 1 10 3\nM V30 10 2 10 11\nM V30 11 1 11 14\nM V30 12 1 12 10\nM V30 13 1 13 11\nM V30 14 1 13 18\nM V30 15 2 15 12\nM V30 16 1 15 17\nM V30 17 1 16 12\nM V30 18 2 17 13\nM V30 19 1 19 15\nM V30 20 1 20 17\nM V30 21 2 21 22\nM V30 22 1 21 23\nM V30 23 1 22 24\nM V30 24 2 23 26\nM V30 25 1 24 29\nM V30 26 2 24 28\nM V30 27 1 25 22\nM V30 28 1 26 28\nM V30 29 1 26 30\nM V30 30 1 27 23\nM V30 31 1 28 31\nM V30 32 2 32 4\nM V30 33 1 32 44\nM V30 34 2 33 35\nM V30 35 2 34 36\nM V30 36 1 34 33\nM V30 37 1 35 38\nM V30 38 1 35 39\nM V30 39 1 36 40\nM V30 40 1 37 34\nM V30 41 1 38 42\nM V30 42 1 40 43\nM V30 43 2 40 38\nM V30 44 1 41 36\nM V30 45 1 44 53\nM V30 46 1 45 46\nM V30 47 1 45 44\nM V30 48 1 45 47\nM V30 49 1 48 45\nM V30 50 1 49 44\nM V30 51 1 49 51\nM V30 52 1 49 50\nM V30 53 1 52 49\nM V30 54 1 53 54\nM V30 55 1 53 56\nM V30 56 1 53 55\nM V30 57 2 57 32\nM V30 58 1 57 5\nM V30 59 1 58 60\nM V30 60 1 58 57\nM V30 61 1 59 58\nM V30 62 1 61 58\nM V30 63 1 62 65\nM V30 64 2 62 61\nM V30 65 1 63 61\nM V30 66 1 63 67\nM V30 67 1 64 62\nM V30 68 2 66 63\nM V30 69 2 68 64\nM V30 70 1 68 66\nM V30 71 1 69 64\nM V30 72 1 70 66\nM V30 73 1 71 72\nM V30 74 1 71 68\nM V30 75 1 73 71\nM V30 76 1 74 71\nM V30 77 1 75 82\nM V30 78 2 76 75\nM V30 79 1 76 83\nM V30 80 1 77 76\nM V30 81 1 78 79\nM V30 82 1 78 77\nM V30 83 2 79 80\nM V30 84 1 80 86\nM V30 85 1 80 75\nM V30 86 2 84 77\nM V30 87 1 84 81\nM V30 88 1 85 79\nM V30 89 1 87 1\nM V30 90 2 87 88\nM V30 91 1 88 84\nM V30 92 1 89 88\nM V30 93 1 90 87\nM V30 94 1 91 90\nM V30 95 1 92 90\nM V30 96 1 93 90\nM V30 97 2 94 2\nM V30 98 1 94 97\nM V30 99 1 94 96\nM V30 100 2 95 94\nM V30 101 1 96 1\nM V30 102 1 97 98\nM V30 103 1 97 99\nM V30 104 1 100 97\nM V30 105 9 3 101\nM V30 106 9 4 101\nM V30 END BOND\nM V30 END CTAB\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/1-INT1-Sp.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 0 0 0 0 0 0 0 0 0 0999 V3000\nM V30 BEGIN CTAB\nM V30 COUNTS 101 106 0 0 1\nM V30 BEGIN ATOM\nM V30 1 C -2.841100 0.947000 -0.323300 0\nM V30 2 O -1.667900 -0.726900 -2.543800 0\nM V30 3 P 0.942100 1.269800 0.701900 0\nM V30 4 O -0.708900 -1.355800 0.517700 0\nM V30 5 C 2.446300 -1.150200 0.685800 0 CFG=2\nM V30 6 C 2.559200 0.373200 0.480000 0\nM V30 7 H 1.852800 -1.313600 1.587100 0\nM V30 8 H 2.944200 0.598400 -0.512400 0\nM V30 9 H 3.276300 0.765400 1.206000 0\nM V30 10 C 1.480900 3.003700 0.427500 0\nM V30 11 C 1.070000 4.032600 1.288000 0\nM V30 12 C 2.214900 3.336100 -0.721600 0\nM V30 13 C 1.387100 5.361200 1.005200 0\nM V30 14 H 0.495100 3.791900 2.174800 0\nM V30 15 C 2.534500 4.664800 -0.999100 0\nM V30 16 H 2.529400 2.563200 -1.412300 0\nM V30 17 C 2.119500 5.682700 -0.138600 0\nM V30 18 H 1.060900 6.146100 1.681500 0\nM V30 19 H 3.110800 4.902400 -1.888700 0\nM V30 20 H 2.366700 6.717400 -0.356200 0\nM V30 21 C 0.780100 1.160300 2.536600 0\nM V30 22 C -0.391500 0.616700 3.080100 0\nM V30 23 C 1.796900 1.587300 3.405200 0\nM V30 24 C -0.547400 0.504000 4.462500 0\nM V30 25 H -1.183500 0.291000 2.417500 0\nM V30 26 C 1.644500 1.469700 4.785400 0\nM V30 27 H 2.702000 2.034000 3.003900 0\nM V30 28 C 0.470700 0.926800 5.316500 0\nM V30 29 H -1.471900 0.097800 4.861100 0\nM V30 30 H 2.437100 1.806800 5.447200 0\nM V30 31 H 0.351500 0.841400 6.392800 0\nM V30 32 S 0.120900 -2.376900 -0.270700 0 CHG=-1 VAL=5\nM V30 33 C 3.820600 -1.772600 0.907900 0\nM V30 34 C 4.919700 -1.408400 0.117200 0\nM V30 35 C 4.019900 -2.716500 1.922100 0\nM V30 36 C 6.168700 -1.996600 0.312400 0\nM V30 37 H 4.802700 -0.653000 -0.651000 0\nM V30 38 C 5.269300 -3.303700 2.125100 0\nM V30 39 H 3.196200 -2.988200 2.572900 0\nM V30 40 C 6.347800 -2.951100 1.314500 0\nM V30 41 H 7.004800 -1.701800 -0.314900 0\nM V30 42 H 5.399300 -4.029700 2.922000 0\nM V30 43 H 7.321100 -3.406600 1.469200 0\nM V30 44 C 0.138300 -3.834800 0.935300 0\nM V30 45 C 1.286100 -4.750600 0.514800 0\nM V30 46 H 2.258900 -4.275000 0.650300 0\nM V30 47 H 1.260500 -5.662300 1.121100 0\nM V30 48 H 1.192200 -5.050200 -0.534800 0\nM V30 49 C -1.221100 -4.509100 0.693000 0\nM V30 50 H -1.265600 -5.434900 1.275900 0\nM V30 51 H -2.042100 -3.863300 1.008900 0\nM V30 52 H -1.367400 -4.765000 -0.360900 0\nM V30 53 C 0.227800 -3.360100 2.383500 0\nM V30 54 H -0.486000 -2.555100 2.568500 0\nM V30 55 H -0.006500 -4.197900 3.049200 0\nM V30 56 H 1.223100 -3.001600 2.644300 0\nM V30 57 N 1.715200 -1.840800 -0.406500 0 CHG=1\nM V30 58 C 2.309100 -1.986900 -1.746100 0\nM V30 59 H 1.663100 -2.678100 -2.296800 0\nM V30 60 H 3.279800 -2.482300 -1.645100 0\nM V30 61 C 2.460900 -0.703400 -2.538400 0\nM V30 62 C 3.694800 -0.333200 -3.076600 0\nM V30 63 C 1.356700 0.129900 -2.758200 0\nM V30 64 C 3.833100 0.859800 -3.792500 0\nM V30 65 H 4.559400 -0.976000 -2.932300 0\nM V30 66 C 1.495400 1.310300 -3.478800 0\nM V30 67 H 0.386200 -0.134800 -2.360000 0\nM V30 68 C 2.737800 1.702800 -4.000500 0\nM V30 69 H 4.805700 1.137500 -4.190100 0\nM V30 70 H 0.627600 1.946600 -3.622800 0\nM V30 71 C 2.872000 3.001900 -4.754900 0\nM V30 72 H 2.447700 3.833500 -4.181700 0\nM V30 73 H 3.918200 3.234900 -4.970400 0\nM V30 74 H 2.334200 2.963600 -5.709200 0\nM V30 75 C -4.708500 0.509500 3.510400 0\nM V30 76 C -3.933000 1.621900 3.224200 0\nM V30 77 C -3.356100 1.806300 1.952100 0\nM V30 78 C -3.548200 0.807700 0.950900 0\nM V30 79 C -4.380300 -0.287800 1.247800 0\nM V30 80 C -4.945000 -0.441300 2.506300 0\nM V30 81 H -2.515100 3.761700 2.404300 0\nM V30 82 H -5.145100 0.385000 4.497000 0\nM V30 83 H -3.764600 2.382900 3.982100 0\nM V30 84 C -2.596900 2.991600 1.642300 0\nM V30 85 H -4.581900 -1.024200 0.483500 0\nM V30 86 H -5.572700 -1.304000 2.710400 0\nM V30 87 C -2.049500 2.138400 -0.609600 0\nM V30 88 C -2.017300 3.157300 0.426600 0\nM V30 89 H -1.485500 4.077100 0.200400 0\nM V30 90 C -1.817700 2.618100 -2.030700 0\nM V30 91 H -0.969000 3.309500 -2.045700 0\nM V30 92 H -1.590600 1.801900 -2.717500 0\nM V30 93 H -2.695000 3.150800 -2.422000 0\nM V30 94 S -3.123000 -0.607200 -2.535700 0 VAL=6\nM V30 95 O -3.868400 -0.358100 -3.757400 0\nM V30 96 O -3.663800 0.411300 -1.436300 0\nM V30 97 C -3.736000 -2.238100 -1.881900 0\nM V30 98 F -5.057000 -2.204000 -1.705500 0\nM V30 99 F -3.145900 -2.520600 -0.715400 0\nM V30 100 F -3.427800 -3.191900 -2.763600 0\nM V30 101 Ni -0.966300 0.591500 -0.122200 0 VAL=2\nM V30 END ATOM\nM V30 BEGIN BOND\nM V30 1 2 1 78\nM V30 2 2 2 94\nM V30 3 1 3 21\nM V30 4 1 5 33\nM V30 5 1 5 7 CFG=1\nM V30 6 1 6 5\nM V30 7 1 6 3\nM V30 8 1 6 9\nM V30 9 1 8 6\nM V30 10 1 10 3\nM V30 11 2 10 11\nM V30 12 1 11 14\nM V30 13 1 12 10\nM V30 14 1 13 11\nM V30 15 1 13 18\nM V30 16 2 15 12\nM V30 17 1 15 17\nM V30 18 1 16 12\nM V30 19 2 17 13\nM V30 20 1 19 15\nM V30 21 1 20 17\nM V30 22 2 21 22\nM V30 23 1 21 23\nM V30 24 1 22 24\nM V30 25 2 23 26\nM V30 26 1 24 29\nM V30 27 2 24 28\nM V30 28 1 25 22\nM V30 29 1 26 28\nM V30 30 1 26 30\nM V30 31 1 27 23\nM V30 32 1 28 31\nM V30 33 2 32 4\nM V30 34 1 32 44\nM V30 35 2 33 35\nM V30 36 2 34 36\nM V30 37 1 34 33\nM V30 38 1 35 38\nM V30 39 1 35 39\nM V30 40 1 36 40\nM V30 41 1 37 34\nM V30 42 1 38 42\nM V30 43 1 40 43\nM V30 44 2 40 38\nM V30 45 1 41 36\nM V30 46 1 44 53\nM V30 47 1 45 46\nM V30 48 1 45 44\nM V30 49 1 45 47\nM V30 50 1 48 45\nM V30 51 1 49 44\nM V30 52 1 49 51\nM V30 53 1 49 50\nM V30 54 1 52 49\nM V30 55 1 53 54\nM V30 56 1 53 56\nM V30 57 1 53 55\nM V30 58 2 57 32\nM V30 59 1 57 5\nM V30 60 1 58 60\nM V30 61 1 58 57\nM V30 62 1 59 58\nM V30 63 1 61 58\nM V30 64 1 62 65\nM V30 65 2 62 61\nM V30 66 1 63 61\nM V30 67 1 63 67\nM V30 68 1 64 62\nM V30 69 2 66 63\nM V30 70 2 68 64\nM V30 71 1 68 66\nM V30 72 1 69 64\nM V30 73 1 70 66\nM V30 74 1 71 72\nM V30 75 1 71 68\nM V30 76 1 73 71\nM V30 77 1 74 71\nM V30 78 1 75 82\nM V30 79 2 76 75\nM V30 80 1 76 83\nM V30 81 1 77 76\nM V30 82 1 78 79\nM V30 83 1 78 77\nM V30 84 2 79 80\nM V30 85 1 80 86\nM V30 86 1 80 75\nM V30 87 2 84 77\nM V30 88 1 84 81\nM V30 89 1 85 79\nM V30 90 1 87 1\nM V30 91 2 87 88\nM V30 92 1 88 84\nM V30 93 1 89 88\nM V30 94 1 90 87\nM V30 95 1 91 90\nM V30 96 1 92 90\nM V30 97 1 93 90\nM V30 98 1 94 97\nM V30 99 1 94 96\nM V30 100 2 95 94\nM V30 101 1 96 1\nM V30 102 1 97 98\nM V30 103 1 97 99\nM V30 104 1 100 97\nM V30 105 9 3 101\nM V30 106 9 4 101\nM V30 END BOND\nM V30 END CTAB\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/1-N_radical_Opt.log': 'charge 0 multiplicity 2\n RDKit 3D\n\n 12 11 0 0 0 0 0 0 0 0999 V2000\n 0.0009 1.4295 0.1113 C 0 0 0 0 0 3 0 0 0 0 0 0\n -0.9288 1.9628 -0.0631 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9313 1.9616 -0.0633 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0000 0.0811 -0.2291 N 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2196 -0.6602 0.0386 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2008 -1.6105 -0.5056 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3564 -0.8757 1.1124 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.0809 -0.0806 -0.3070 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2188 -0.6616 0.0386 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.1986 -1.6122 -0.5051 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.0808 -0.0833 -0.3075 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.3556 -0.8767 1.1124 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 1 0\n 3 1 1 0\n 4 5 1 0\n 4 9 1 0\n 4 1 1 0\n 5 7 1 0\n 6 5 1 0\n 8 5 1 0\n 9 12 1 0\n 10 9 1 0\n 11 9 1 0\nM RAD 1 1 2\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/1-isoquin_anion_Opt.log': 'charge -1 multiplicity 1\n RDKit 3D\n\n 19 20 0 0 0 0 0 0 0 0999 V2000\n -1.9077 2.0873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2548 2.9530 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.4492 0.7973 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0023 0.4512 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0143 1.4212 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.3870 -0.9336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.9534 -1.4859 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3705 1.0933 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7331 2.4708 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7737 -1.2465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.6284 -1.9211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.7451 -2.2467 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.7450 -0.2592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.1249 1.8776 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.0627 -2.2973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.3767 -2.9792 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 3.7995 -0.5351 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9785 2.2627 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3900 -0.2347 -0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1 18 1 0\n 1 2 1 0\n 3 4 2 0\n 3 1 1 0\n 4 6 1 0\n 5 8 2 0\n 5 4 1 0\n 6 11 2 0\n 6 10 1 0\n 7 19 2 0\n 7 11 1 0\n 8 14 1 0\n 8 13 1 0\n 9 5 1 0\n 10 15 1 0\n 11 16 1 0\n 12 7 1 0\n 13 10 2 0\n 13 17 1 0\n 19 3 1 0\nM CHG 1 1 -1\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/1.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 3.4382 0.6833 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.6952 0.6833 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/10-2a-Opt.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 37 40 0 0 0 0 0 0 0 0999 V2000\n -2.7877 -0.8655 0.0415 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.1250 -1.3310 -1.2076 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1942 -1.2668 -2.2774 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8956 -0.7075 -2.0438 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5710 -0.2192 -0.7388 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5078 -0.3099 0.2729 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.5014 -2.1668 -3.7453 H 0 0 0 0 0 0 0 0 0 0 0 0\n -3.5021 -0.9191 0.8575 H 0 0 0 0 0 0 0 0 0 0 0 0\n -4.1073 -1.7566 -1.3939 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5143 -1.7451 -3.5758 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0302 -0.6610 -3.1208 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.2507 0.0571 1.2619 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.3124 -1.1330 -4.3676 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5976 -1.6793 -4.5995 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0170 -0.2487 -2.9398 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4074 -1.0904 -5.1795 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.8556 -2.0484 -5.5875 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.6133 -2.4996 1.0462 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6021 -1.7652 0.4697 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7933 -0.3968 0.1323 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0691 0.1979 0.3984 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.0894 -0.5867 0.9982 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8697 -1.9064 1.3174 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4483 -3.5438 1.2945 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.6423 -2.2248 0.2629 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7642 0.3924 -0.4706 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.2758 1.5557 0.0491 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.0514 -0.1221 1.1983 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.6579 -2.4971 1.7743 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.2723 2.2877 -0.5379 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0005 1.7193 -0.8097 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.2422 2.0093 0.2521 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4436 3.3278 -0.8012 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0669 2.5585 -1.4697 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.2269 3.6107 -1.5043 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.2519 2.2251 -2.4973 H 0 0 0 0 0 0 0 0 0 0 0 0\n -1.0202 2.4820 -0.9389 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 6 2 0\n 1 8 1 0\n 2 1 1 0\n 3 4 1 0\n 3 2 2 0\n 4 5 2 0\n 5 26 1 0\n 5 6 1 0\n 6 12 1 0\n 7 10 1 0\n 9 2 1 0\n 10 3 1 0\n 11 15 1 0\n 11 4 1 0\n 13 11 2 0\n 14 13 1 0\n 14 10 2 0\n 16 13 1 0\n 17 14 1 0\n 18 24 1 0\n 18 23 2 0\n 19 18 1 0\n 20 21 1 0\n 20 19 2 0\n 21 22 2 0\n 22 28 1 0\n 22 23 1 0\n 23 29 1 0\n 25 19 1 0\n 26 20 1 0\n 27 32 1 0\n 27 21 1 0\n 30 27 2 0\n 31 30 1 0\n 31 26 2 0\n 33 30 1 0\n 34 37 1 0\n 34 31 1 0\n 35 34 1 0\n 36 34 1 0\nM END\n',
'/Users/tmj/Documents/proj/MolOP/tests/test_files/g16log/10-2a-Sp.log': 'charge 0 multiplicity 1\n RDKit 3D\n\n 37 40 0 0 0 0 0 0 0 0999 V2000\n -2.1638 -0.9952 2.4233 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.1895 -1.0135 1.5077 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9883 -0.5293 0.1886 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.7022 -0.0164 -0.1811 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.6532 0.0030 0.7916 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8949 -0.4861 2.0611 C 0 0 0 0 0 0 0 0 0 0 0 0\n -5.0012 -0.9308 -0.4902 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3216 -1.3692 3.4303 H 0 0 0 0 0 0 0 0 0 0 0 0\n -4.1679 -1.4004 1.7791 H 0 0 0 0 0 0 0 0 0 0 0 0\n -4.0284 -0.5413 -0.7784 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5117 0.4535 -1.5085 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.0912 -0.4736 2.7912 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.5416 0.4281 -2.4214 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8137 -0.0725 -2.0538 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.5345 0.8302 -1.7907 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3787 0.7905 -3.4319 H 0 0 0 0 0 0 0 0 0 0 0 0\n -4.6179 -0.0872 -2.7832 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5964 -2.5788 -0.3487 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5608 -1.7460 0.0093 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7462 -0.3376 0.0794 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0364 0.1959 -0.2414 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.0845 -0.6916 -0.6025 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8731 -2.0496 -0.6552 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.4342 -3.6515 -0.3985 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5847 -2.1564 0.2416 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.6899 0.5547 0.4446 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.2265 1.5994 -0.1924 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.0595 -0.2741 -0.8397 H 0 0 0 0 0 0 0 0 0 0 0 0\n 4.6816 -2.7185 -0.9343 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1912 2.4340 0.1525 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9053 1.9274 0.4750 C 0 0 0 0 0 0 0 0 0 0 0 0\n 4.2052 2.0057 -0.4333 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3500 3.5084 0.1860 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.2059 2.8843 0.8338 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.1796 3.8969 0.9778 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.9656 2.9207 0.0447 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.7191 2.5754 1.7491 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 8 1 0\n 2 9 1 0\n 2 1 2 0\n 3 2 1 0\n 4 3 2 0\n 4 5 1 0\n 5 6 2 0\n 6 1 1 0\n 6 12 1 0\n 10 7 1 0\n 10 3 1 0\n 11 4 1 0\n 13 14 1 0\n 13 11 2 0\n 14 10 2 0\n 15 11 1 0\n 16 13 1 0\n 17 14 1 0\n 18 19 2 0\n 19 20 1 0\n 19 25 1 0\n 20 26 2 0\n 21 27 2 0\n 21 20 1 0\n 22 21 1 0\n 23 22 2 0\n 23 18 1 0\n 24 18 1 0\n 26 31 1 0\n 26 5 1 0\n 27 30 1 0\n 28 22 1 0\n 29 23 1 0\n 30 33 1 0\n 30 31 2 0\n 31 34 1 0\n 32 27 1 0\n 34 35 1 0\n 34 37 1 0\n 36 34 1 0\nM END\n'}
Transform to a GJF input file with a specified method¶
In [3]:
Copied!
log_batch[:10].format_transform(format="gjf", output_dir="/tmp", frameID=-1, n_jobs=-1, options="%MEM=10GB", route="#p PBE1PBE/def2svp opt")
log_batch[:10].format_transform(format="gjf", output_dir="/tmp", frameID=-1, n_jobs=-1, options="%MEM=10GB", route="#p PBE1PBE/def2svp opt")
MolOP processing gjf format with -1 jobs: 0%| | 0/10 [00:00<?, ?it/s]
Out[3]:
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