anthropics/uplifting-biomolecular-modeling
File Size
The distribution of size of files (measured in lines of code).
File Size Overall
  • There are 3,636 files with 726,274 lines of code.
    • 89 very long files (128,597 lines of code)
    • 244 long files (165,343 lines of code)
    • 786 medium size files (247,476 lines of code)
    • 783 small files (113,616 lines of code)
    • 1,734 very small files (71,242 lines of code)
17% | 22% | 34% | 15% | 9%
Legend:
1001+
501-1000
201-500
101-200
1-100


explore: grouped by folders | grouped by size | sunburst | 3D view
File Size per Extension
1001+
501-1000
201-500
101-200
1-100
py17% | 22% | 34% | 15% | 9%
cuh52% | 24% | 14% | 3% | 5%
pt71% | 28% | 0% | 0% | 0%
cu0% | 60% | 29% | 7% | 2%
cc0% | 46% | 25% | 11% | 16%
toml0% | 0% | 98% | 0% | 1%
h0% | 0% | 0% | 64% | 35%
cpp0% | 0% | 0% | 92% | 7%
yaml0% | 0% | 0% | 13% | 86%
pyi0% | 0% | 0% | 0% | 100%
in0% | 0% | 0% | 0% | 100%
File Size per Logical Decomposition
primary
1001+
501-1000
201-500
101-200
1-100
opendde35% | 26% | 24% | 8% | 4%
common19% | 23% | 36% | 14% | 5%
esmfold229% | 26% | 29% | 9% | 4%
openfold3_ob014% | 21% | 38% | 15% | 10%
protenix_v215% | 28% | 34% | 16% | 5%
af3_jax24% | 17% | 28% | 16% | 14%
openfold312% | 22% | 38% | 15% | 11%
pxdesign17% | 32% | 31% | 13% | 5%
boltz219% | 29% | 33% | 12% | 5%
caliby31% | 25% | 29% | 4% | 8%
mosaic32% | 13% | 30% | 14% | 9%
colabfold34% | 15% | 25% | 13% | 10%
e134% | 0% | 29% | 14% | 21%
chrombpnet39% | 11% | 19% | 17% | 13%
proteinmpnn43% | 0% | 22% | 20% | 13%
protenix_v111% | 32% | 30% | 16% | 9%
boltzgen14% | 33% | 24% | 16% | 9%
af2ig19% | 9% | 34% | 23% | 13%
evo210% | 24% | 25% | 20% | 18%
ef2inv12% | 12% | 42% | 21% | 11%
af3_torch9% | 16% | 37% | 21% | 14%
colabdesign12% | 0% | 48% | 24% | 14%
rosettafold30% | 33% | 46% | 10% | 9%
atlasfold0% | 14% | 43% | 20% | 21%
chai10% | 19% | 35% | 24% | 19%
rfdiffusion30% | 38% | 35% | 17% | 8%
rfdiffusion10% | 26% | 27% | 33% | 12%
flashzoi0% | 39% | 20% | 20% | 18%
gpnstar0% | 46% | 28% | 8% | 15%
genie30% | 20% | 39% | 21% | 17%
esmc0% | 18% | 43% | 27% | 10%
complexa0% | 20% | 23% | 26% | 29%
progen20% | 0% | 54% | 31% | 13%
enformer0% | 0% | 61% | 22% | 15%
enformer_deepmind0% | 0% | 54% | 19% | 26%
borzoi0% | 0% | 41% | 36% | 21%
esm_if10% | 0% | 24% | 33% | 42%
Longest Files (Top 50)
File# lines# units
real_pairformer.py
in opendde/stock/src/opendde/distributed/foldcp
 5603 162
transformer.py
in opendde/stock/src/opendde/model/modules
 3187 86
__init__.py
in mosaic/stock/src/joltz/src/joltz
 3019 121
typing_extensions.py
in chrombpnet/opt/kit/torch/chrombpnet_k1/_vendor
 2610 214
pairformer.py
in opendde/stock/src/opendde/model/modules
 2180 72
parser.py
in protenix_v2/stock/src/protenix/data/core
 2097 60
modeling_esmfold2_common.py
in esmfold2/stock/src/transformers/src/transformers/models/esmfold2
 2075 109
pins.py
in e1/opt/forward/engines/e1/kits
 2018 20
structure.py
in af3_jax/stock/src/src/alphafold3/structure
 1992 132
template.py
in openfold3_ob0/stock/src/openfold3/core/data/pipelines/preprocessing
 1899 42
batch.py
in colabfold/stock/src/colabfold
 1875 26
constraint_featurizer.py
in protenix_v2/stock/src/protenix/data/constraint
 1846 55
opendde.py
in opendde/stock/src/opendde/model
 1845 55
constraint_featurizer.py
in pxdesign/stock/src/Protenix/protenix/data
 1814 55
triattn_sm90.cuh
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda/csrc
 1804 -
__init__.py
in common/opt_core/opt_core/kernels/trimul
 1699 99
template.py
in openfold3/stock/src/openfold3/core/data/pipelines/preprocessing
 1695 38
features.py
in af3_jax/stock/src/src/alphafold3/model
 1631 44
protpardelle_core_models.py
in caliby/opt/forward/xattempt_addon/fast
 1630 25
protpardelle_core_models.py
in caliby/opt/forward/xattempt_addon/stock
 1613 24
models.py
in caliby/stock/src/protpardelle-1c/src/protpardelle/core
 1613 24
parser.py
in pxdesign/stock/src/Protenix/protenix/data
 1559 46
inference.py
in opendde/stock/src/runner
 1538 58
parser.py
in pxdesign/stock/src/PXDesign/pxdesign/data
 1529 46
quality.py
in openfold3_ob0/stock/src/openfold3/core/metrics
 1489 29
quality.py
in openfold3/stock/src/openfold3/core/metrics
 1489 29
diffusion.py
in opendde/stock/src/opendde/model/modules
 1473 45
__init__.py
in common/opt_core/opt_core/kernels/transition
 1448 89
pt
a80_n400_s400_prefix.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1427 -
pt
a80_s400_none.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1426 -
dist.py
in common/opt_core/opt_core/mem/rowpair
 1424 173
__init__.py
in common/opt_core/opt_core/kernels/apb
 1406 73
modules.py
in colabfold/stock/src/alphafold/model
 1404 63
constants.py
in protenix_v2/stock/src/protenix/data
 1383 4
constants.py
in opendde/stock/src/opendde/data
 1383 4
tp.py
in protenix_v1/opt/protenix_v1_opt
 1364 81
lists.py
in openfold3_ob0/stock/src/openfold3/core/data/resources
 1339 -
lists.py
in openfold3/stock/src/openfold3/core/data/resources
 1339 -
pt
a80_s400_prefixvar.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1324 -
boltz.py
in boltzgen/stock/src/boltzgen/model/models
 1320 17
ptx_trunk2_levers.py
in protenix_v2/opt/forward/flashpairformer/src
 1302 49
tp.py
in opendde/opt/opendde_opt
 1302 92
triatt.py
in common/opt_core/opt_core/mem/rowpair
 1292 77
pair_fused.py
in common/opt_core/opt_core/attn
 1272 81
parsing.py
in af3_jax/stock/src/src/alphafold3/structure
 1269 31
modules.py
in af2ig/opt/forward/af2ig_kit/patches/patched_files/af2_initial_guess/alphafold/model
 1263 56
ef2_opt.py
in esmfold2/opt/forward/fast_inference/driver
 1255 65
run_alphafold.py
in af3_jax/opt/forward/fast_inference/patches/patched_files
 1248 35
structure.py
in openfold3_ob0/stock/src/openfold3/core/data/pipelines/preprocessing
 1209 34
batch_inference.py
in opendde/stock/src/runner
 1203 12
Files With Most Units (Top 50)
File# lines# units
typing_extensions.py
in chrombpnet/opt/kit/torch/chrombpnet_k1/_vendor
 2610 214
dist.py
in common/opt_core/opt_core/mem/rowpair
 1424 173
real_pairformer.py
in opendde/stock/src/opendde/distributed/foldcp
 5603 162
structure.py
in af3_jax/stock/src/src/alphafold3/structure
 1992 132
__init__.py
in mosaic/stock/src/joltz/src/joltz
 3019 121
modeling_esmfold2_common.py
in esmfold2/stock/src/transformers/src/transformers/models/esmfold2
 2075 109
__init__.py
in common/opt_core/opt_core/kernels/trimul
 1699 99
tp.py
in opendde/opt/opendde_opt
 1302 92
__init__.py
in common/opt_core/opt_core/kernels/transition
 1448 89
transformer.py
in opendde/stock/src/opendde/model/modules
 3187 86
census.py
in rfdiffusion3/opt/rfdiffusion3_opt
 980 83
pair_fused.py
in common/opt_core/opt_core/attn
 1272 81
trunk.py
in common/opt_core/opt_core/mem/rowpair
 843 81
tp.py
in protenix_v1/opt/protenix_v1_opt
 1364 81
graphs.py
in common/opt_core/opt_core/capture
 1099 80
confidence.py
in common/opt_core/opt_core/mem/rowpair
 1177 80
rowpair_xfold.py
in af3_torch/opt/af3_torch_opt
 1105 79
stack.py
in esmfold2/opt/esmfold2_opt
 1192 78
triatt.py
in common/opt_core/opt_core/mem/rowpair
 1292 77
affine3d.py
in esmfold2/stock/src/esm/utils/structure
 404 76
folding_input.py
in af3_jax/stock/src/src/alphafold3/common
 1170 75
rigid.py
in chai1/stock/src/chai_lab/tools
 692 74
__init__.py
in common/opt_core/opt_core/kernels/apb
 1406 73
pairformer.py
in opendde/stock/src/opendde/model/modules
 2180 72
offload.py
in common/opt_core/opt_core/mem
 750 71
alphafold.py
in common/opt_core/opt_core/mem/rowpair_jax
 1063 67
rigid_utils.py
in pxdesign/stock/src/Protenix/protenix/openfold_local/utils
 704 66
rowpair.py
in boltz2/opt/boltz2_opt
 1009 66
rigid_utils.py
in openfold3_ob0/stock/src/openfold3/core/utils
 658 66
rigid_utils.py
in openfold3/stock/src/openfold3/core/utils
 658 66
ef2_opt.py
in esmfold2/opt/forward/fast_inference/driver
 1255 65
experiment_runner.py
in openfold3_ob0/stock/src/openfold3/entry_points
 704 65
modules.py
in colabfold/stock/src/alphafold/model
 1404 63
stack.py
in openfold3_ob0/opt/openfold3_ob0_opt
 744 63
chunk.py
in common/opt_core/opt_core/mem
 806 62
bz_pairfuse.py
in boltz2/opt/forward/pairfuse
 742 62
stack.py
in colabfold/opt/colabfold_opt
 784 62
stack.py
in openfold3/opt/openfold3_opt
 761 62
ef2_dit.py
in esmfold2/opt/forward/fast_inference/driver
 1136 61
parser.py
in protenix_v2/stock/src/protenix/data/core
 2097 60
boltz_graph_trunk.py
in boltz2/opt/forward/graph
 799 60
cli.py
in openfold3_ob0/opt/openfold3_ob0_opt
 892 60
rowpair.py
in esmfold2/opt/esmfold2_opt
 1124 59
odde_offload.py
in opendde/opt/forward/fast_inference/levers/OFFLOAD
 780 59
experiment_runner.py
in openfold3/stock/src/openfold3/entry_points
 622 59
report.py
in esmfold2/opt/esmfold2_opt
 573 58
stack.py
in chai1/opt/chai1_opt
 736 58
launch.py
in common/opt_core/opt_core/kernels/trimul/native/pkg/v5/python/trimul_native
 382 58
inference.py
in opendde/stock/src/runner
 1538 58
big.py
in protenix_v1/opt/protenix_v1_opt
 974 58
Files With Long Lines (Top 50)

There are 1818 files with lines longer than 120 characters. In total, there are 35505 long lines.

File# lines# units# long lines
pt
a80_s400_none.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1426 - 594
pt
a80_n400_s400_prefix.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1427 - 588
pt
a80_s400_prefixvar.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 1324 - 587
pt
s256_prefix.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 836 - 387
registry.py
in opendde/opt/opendde_opt
 635 16 386
triattn_sm90.cuh
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda/csrc
 1804 - 367
pt
a80_d16_s512_prefix.ref_rows.pt
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/testvectors
 803 - 366
triattn_m1_sm90.cuh
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda_b/csrc/m1
 1114 - 341
tmn_kernels.cuh
in common/opt_core/opt_core/kernels/trimul/native/pkg/v5/csrc
 1055 - 249
triattn_b_sm90.cuh
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda_b/csrc
 1149 - 233
triattn_sm80.cuh
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda_80/csrc
 926 - 221
registry.py
in boltz2/opt/boltz2_opt
 245 1 199
triattn_mw.cu
in common/opt_core/opt_core/kernels/triattn/cuda_sm90a/csrc
 791 - 193
stack.py
in boltz2/opt/boltz2_opt
 1047 54 192
triattn_mw.cu
in common/opt_core/opt_core/kernels/triattn/triattn_native/pkg/v11/triattn_pkg/cuda_c/csrc
 818 - 189
tmn_kernels.cuh
in common/opt_core/opt_core/kernels/trimul_xla/pkg/v1/csrc
 918 - 189
__init__.py
in common/opt_core/opt_core/kernels/trimul
 1699 99 170
evidence.py
in ef2inv/opt/ef2inv_opt
 600 15 158
tp.py
in opendde/opt/opendde_opt
 1302 92 155
big.py
in protenix_v1/opt/protenix_v1_opt
 974 58 154
pins.py
in e1/opt/forward/engines/e1/kits
 2018 20 154
trimul_tx.cu
in common/opt_core/opt_core/kernels/trimul/tx_sm90a/csrc
 887 - 150
report.py
in boltz2/opt/boltz2_opt
 535 37 149
registry.py
in rosettafold3/opt/rosettafold3_opt
 262 1 147
cubin_launch.cc
in common/opt_core/opt_core/kernels/triattn_xla/csrc
 700 34 146
mpnn_worker2.py
in proteinmpnn/opt/forward/mpnn_exact_worker/addon
 1031 49 146
ptx_trunk2_levers.py
in protenix_v2/opt/forward/flashpairformer/src
 1302 49 145
flash_transition_sm90.cu
in common/opt_core/opt_core/kernels/transition/flash_sm90a/csrc
 471 - 137
rowpair.py
in esmfold2/opt/esmfold2_opt
 1124 59 131
modes.py
in openfold3_ob0/opt/openfold3_ob0_opt
 844 48 131
registry.py
in chai1/opt/chai1_opt
 246 - 130
tp.py
in protenix_v1/opt/protenix_v1_opt
 1364 81 130
modes.py
in openfold3/opt/openfold3_opt
 788 45 129
__init__.py
in common/opt_core/opt_core/kernels/apb
 1406 73 128
ef2_dit.py
in esmfold2/opt/forward/fast_inference/driver
 1136 61 124
constants.py
in protenix_v2/stock/src/protenix/data
 1383 4 123
constants.py
in opendde/stock/src/opendde/data
 1383 4 123
constants.py
in pxdesign/stock/src/PXDesign/pxdesign/data
 930 1 123
constants.py
in pxdesign/stock/src/Protenix/protenix/data
 889 1 123
__init__.py
in common/opt_core/opt_core/kernels/transition
 1448 89 119
math_sm80.cuh
in common/opt_core/opt_core/kernels/trimul/native/pkg/v5/csrc/sm80
 461 - 117
ef2_w4.py
in esmfold2/opt/forward/fast_inference/driver
 758 40 112
stack.py
in protenix_v2/opt/protenix_opt
 929 53 109
registry.py
in colabdesign/opt/colabdesign_opt
 206 4 108
__init__.py
in chrombpnet/opt/kit_ho/tf/chrombpnet_fastkit
 736 42 106
tmn_k3_wide.cuh
in common/opt_core/opt_core/kernels/trimul/native/pkg/v5/csrc
 520 - 105
modes.py
in af3_jax/opt/af3_jax_opt
 843 50 105
of3_offload.py
in openfold3/opt/forward/offload/of3o
 1169 44 105
template.py
in common/opt_core/opt_core/mem/rowpair
 861 56 104
cli.py
in openfold3_ob0/opt/openfold3_ob0_opt
 892 60 104
About This Analysis
  • File size measurements show the distribution of size of files.
  • Files are classified in four categories based on their size (lines of code): 1-100 (very small files), 101-200 (small files), 201-500 (medium size files), 501-1000 (long files), 1001+(very long files).
  • It is a good practice to keep files small. Long files may become "bloaters", code that have increased to such gargantuan proportions that they are hard to work with.
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