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Commit 694f8ba0 authored by zhuww's avatar zhuww
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modify version and add txt for relax

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openfold/resources/stereo_chemical_props.txt 0 → 100644
View file @ 694f8ba0
Bond Residue Mean StdDev
CA-CB ALA 1.520 0.021
N-CA ALA 1.459 0.020
CA-C ALA 1.525 0.026
C-O ALA 1.229 0.019
CA-CB ARG 1.535 0.022
CB-CG ARG 1.521 0.027
CG-CD ARG 1.515 0.025
CD-NE ARG 1.460 0.017
NE-CZ ARG 1.326 0.013
CZ-NH1 ARG 1.326 0.013
CZ-NH2 ARG 1.326 0.013
N-CA ARG 1.459 0.020
CA-C ARG 1.525 0.026
C-O ARG 1.229 0.019
CA-CB ASN 1.527 0.026
CB-CG ASN 1.506 0.023
CG-OD1 ASN 1.235 0.022
CG-ND2 ASN 1.324 0.025
N-CA ASN 1.459 0.020
CA-C ASN 1.525 0.026
C-O ASN 1.229 0.019
CA-CB ASP 1.535 0.022
CB-CG ASP 1.513 0.021
CG-OD1 ASP 1.249 0.023
CG-OD2 ASP 1.249 0.023
N-CA ASP 1.459 0.020
CA-C ASP 1.525 0.026
C-O ASP 1.229 0.019
CA-CB CYS 1.526 0.013
CB-SG CYS 1.812 0.016
N-CA CYS 1.459 0.020
CA-C CYS 1.525 0.026
C-O CYS 1.229 0.019
CA-CB GLU 1.535 0.022
CB-CG GLU 1.517 0.019
CG-CD GLU 1.515 0.015
CD-OE1 GLU 1.252 0.011
CD-OE2 GLU 1.252 0.011
N-CA GLU 1.459 0.020
CA-C GLU 1.525 0.026
C-O GLU 1.229 0.019
CA-CB GLN 1.535 0.022
CB-CG GLN 1.521 0.027
CG-CD GLN 1.506 0.023
CD-OE1 GLN 1.235 0.022
CD-NE2 GLN 1.324 0.025
N-CA GLN 1.459 0.020
CA-C GLN 1.525 0.026
C-O GLN 1.229 0.019
N-CA GLY 1.456 0.015
CA-C GLY 1.514 0.016
C-O GLY 1.232 0.016
CA-CB HIS 1.535 0.022
CB-CG HIS 1.492 0.016
CG-ND1 HIS 1.369 0.015
CG-CD2 HIS 1.353 0.017
ND1-CE1 HIS 1.343 0.025
CD2-NE2 HIS 1.415 0.021
CE1-NE2 HIS 1.322 0.023
N-CA HIS 1.459 0.020
CA-C HIS 1.525 0.026
C-O HIS 1.229 0.019
CA-CB ILE 1.544 0.023
CB-CG1 ILE 1.536 0.028
CB-CG2 ILE 1.524 0.031
CG1-CD1 ILE 1.500 0.069
N-CA ILE 1.459 0.020
CA-C ILE 1.525 0.026
C-O ILE 1.229 0.019
CA-CB LEU 1.533 0.023
CB-CG LEU 1.521 0.029
CG-CD1 LEU 1.514 0.037
CG-CD2 LEU 1.514 0.037
N-CA LEU 1.459 0.020
CA-C LEU 1.525 0.026
C-O LEU 1.229 0.019
CA-CB LYS 1.535 0.022
CB-CG LYS 1.521 0.027
CG-CD LYS 1.520 0.034
CD-CE LYS 1.508 0.025
CE-NZ LYS 1.486 0.025
N-CA LYS 1.459 0.020
CA-C LYS 1.525 0.026
C-O LYS 1.229 0.019
CA-CB MET 1.535 0.022
CB-CG MET 1.509 0.032
CG-SD MET 1.807 0.026
SD-CE MET 1.774 0.056
N-CA MET 1.459 0.020
CA-C MET 1.525 0.026
C-O MET 1.229 0.019
CA-CB PHE 1.535 0.022
CB-CG PHE 1.509 0.017
CG-CD1 PHE 1.383 0.015
CG-CD2 PHE 1.383 0.015
CD1-CE1 PHE 1.388 0.020
CD2-CE2 PHE 1.388 0.020
CE1-CZ PHE 1.369 0.019
CE2-CZ PHE 1.369 0.019
N-CA PHE 1.459 0.020
CA-C PHE 1.525 0.026
C-O PHE 1.229 0.019
CA-CB PRO 1.531 0.020
CB-CG PRO 1.495 0.050
CG-CD PRO 1.502 0.033
CD-N PRO 1.474 0.014
N-CA PRO 1.468 0.017
CA-C PRO 1.524 0.020
C-O PRO 1.228 0.020
CA-CB SER 1.525 0.015
CB-OG SER 1.418 0.013
N-CA SER 1.459 0.020
CA-C SER 1.525 0.026
C-O SER 1.229 0.019
CA-CB THR 1.529 0.026
CB-OG1 THR 1.428 0.020
CB-CG2 THR 1.519 0.033
N-CA THR 1.459 0.020
CA-C THR 1.525 0.026
C-O THR 1.229 0.019
CA-CB TRP 1.535 0.022
CB-CG TRP 1.498 0.018
CG-CD1 TRP 1.363 0.014
CG-CD2 TRP 1.432 0.017
CD1-NE1 TRP 1.375 0.017
NE1-CE2 TRP 1.371 0.013
CD2-CE2 TRP 1.409 0.012
CD2-CE3 TRP 1.399 0.015
CE2-CZ2 TRP 1.393 0.017
CE3-CZ3 TRP 1.380 0.017
CZ2-CH2 TRP 1.369 0.019
CZ3-CH2 TRP 1.396 0.016
N-CA TRP 1.459 0.020
CA-C TRP 1.525 0.026
C-O TRP 1.229 0.019
CA-CB TYR 1.535 0.022
CB-CG TYR 1.512 0.015
CG-CD1 TYR 1.387 0.013
CG-CD2 TYR 1.387 0.013
CD1-CE1 TYR 1.389 0.015
CD2-CE2 TYR 1.389 0.015
CE1-CZ TYR 1.381 0.013
CE2-CZ TYR 1.381 0.013
CZ-OH TYR 1.374 0.017
N-CA TYR 1.459 0.020
CA-C TYR 1.525 0.026
C-O TYR 1.229 0.019
CA-CB VAL 1.543 0.021
CB-CG1 VAL 1.524 0.021
CB-CG2 VAL 1.524 0.021
N-CA VAL 1.459 0.020
CA-C VAL 1.525 0.026
C-O VAL 1.229 0.019
-
Angle Residue Mean StdDev
N-CA-CB ALA 110.1 1.4
CB-CA-C ALA 110.1 1.5
N-CA-C ALA 111.0 2.7
CA-C-O ALA 120.1 2.1
N-CA-CB ARG 110.6 1.8
CB-CA-C ARG 110.4 2.0
CA-CB-CG ARG 113.4 2.2
CB-CG-CD ARG 111.6 2.6
CG-CD-NE ARG 111.8 2.1
CD-NE-CZ ARG 123.6 1.4
NE-CZ-NH1 ARG 120.3 0.5
NE-CZ-NH2 ARG 120.3 0.5
NH1-CZ-NH2 ARG 119.4 1.1
N-CA-C ARG 111.0 2.7
CA-C-O ARG 120.1 2.1
N-CA-CB ASN 110.6 1.8
CB-CA-C ASN 110.4 2.0
CA-CB-CG ASN 113.4 2.2
CB-CG-ND2 ASN 116.7 2.4
CB-CG-OD1 ASN 121.6 2.0
ND2-CG-OD1 ASN 121.9 2.3
N-CA-C ASN 111.0 2.7
CA-C-O ASN 120.1 2.1
N-CA-CB ASP 110.6 1.8
CB-CA-C ASP 110.4 2.0
CA-CB-CG ASP 113.4 2.2
CB-CG-OD1 ASP 118.3 0.9
CB-CG-OD2 ASP 118.3 0.9
OD1-CG-OD2 ASP 123.3 1.9
N-CA-C ASP 111.0 2.7
CA-C-O ASP 120.1 2.1
N-CA-CB CYS 110.8 1.5
CB-CA-C CYS 111.5 1.2
CA-CB-SG CYS 114.2 1.1
N-CA-C CYS 111.0 2.7
CA-C-O CYS 120.1 2.1
N-CA-CB GLU 110.6 1.8
CB-CA-C GLU 110.4 2.0
CA-CB-CG GLU 113.4 2.2
CB-CG-CD GLU 114.2 2.7
CG-CD-OE1 GLU 118.3 2.0
CG-CD-OE2 GLU 118.3 2.0
OE1-CD-OE2 GLU 123.3 1.2
N-CA-C GLU 111.0 2.7
CA-C-O GLU 120.1 2.1
N-CA-CB GLN 110.6 1.8
CB-CA-C GLN 110.4 2.0
CA-CB-CG GLN 113.4 2.2
CB-CG-CD GLN 111.6 2.6
CG-CD-OE1 GLN 121.6 2.0
CG-CD-NE2 GLN 116.7 2.4
OE1-CD-NE2 GLN 121.9 2.3
N-CA-C GLN 111.0 2.7
CA-C-O GLN 120.1 2.1
N-CA-C GLY 113.1 2.5
CA-C-O GLY 120.6 1.8
N-CA-CB HIS 110.6 1.8
CB-CA-C HIS 110.4 2.0
CA-CB-CG HIS 113.6 1.7
CB-CG-ND1 HIS 123.2 2.5
CB-CG-CD2 HIS 130.8 3.1
CG-ND1-CE1 HIS 108.2 1.4
ND1-CE1-NE2 HIS 109.9 2.2
CE1-NE2-CD2 HIS 106.6 2.5
NE2-CD2-CG HIS 109.2 1.9
CD2-CG-ND1 HIS 106.0 1.4
N-CA-C HIS 111.0 2.7
CA-C-O HIS 120.1 2.1
N-CA-CB ILE 110.8 2.3
CB-CA-C ILE 111.6 2.0
CA-CB-CG1 ILE 111.0 1.9
CB-CG1-CD1 ILE 113.9 2.8
CA-CB-CG2 ILE 110.9 2.0
CG1-CB-CG2 ILE 111.4 2.2
N-CA-C ILE 111.0 2.7
CA-C-O ILE 120.1 2.1
N-CA-CB LEU 110.4 2.0
CB-CA-C LEU 110.2 1.9
CA-CB-CG LEU 115.3 2.3
CB-CG-CD1 LEU 111.0 1.7
CB-CG-CD2 LEU 111.0 1.7
CD1-CG-CD2 LEU 110.5 3.0
N-CA-C LEU 111.0 2.7
CA-C-O LEU 120.1 2.1
N-CA-CB LYS 110.6 1.8
CB-CA-C LYS 110.4 2.0
CA-CB-CG LYS 113.4 2.2
CB-CG-CD LYS 111.6 2.6
CG-CD-CE LYS 111.9 3.0
CD-CE-NZ LYS 111.7 2.3
N-CA-C LYS 111.0 2.7
CA-C-O LYS 120.1 2.1
N-CA-CB MET 110.6 1.8
CB-CA-C MET 110.4 2.0
CA-CB-CG MET 113.3 1.7
CB-CG-SD MET 112.4 3.0
CG-SD-CE MET 100.2 1.6
N-CA-C MET 111.0 2.7
CA-C-O MET 120.1 2.1
N-CA-CB PHE 110.6 1.8
CB-CA-C PHE 110.4 2.0
CA-CB-CG PHE 113.9 2.4
CB-CG-CD1 PHE 120.8 0.7
CB-CG-CD2 PHE 120.8 0.7
CD1-CG-CD2 PHE 118.3 1.3
CG-CD1-CE1 PHE 120.8 1.1
CG-CD2-CE2 PHE 120.8 1.1
CD1-CE1-CZ PHE 120.1 1.2
CD2-CE2-CZ PHE 120.1 1.2
CE1-CZ-CE2 PHE 120.0 1.8
N-CA-C PHE 111.0 2.7
CA-C-O PHE 120.1 2.1
N-CA-CB PRO 103.3 1.2
CB-CA-C PRO 111.7 2.1
CA-CB-CG PRO 104.8 1.9
CB-CG-CD PRO 106.5 3.9
CG-CD-N PRO 103.2 1.5
CA-N-CD PRO 111.7 1.4
N-CA-C PRO 112.1 2.6
CA-C-O PRO 120.2 2.4
N-CA-CB SER 110.5 1.5
CB-CA-C SER 110.1 1.9
CA-CB-OG SER 111.2 2.7
N-CA-C SER 111.0 2.7
CA-C-O SER 120.1 2.1
N-CA-CB THR 110.3 1.9
CB-CA-C THR 111.6 2.7
CA-CB-OG1 THR 109.0 2.1
CA-CB-CG2 THR 112.4 1.4
OG1-CB-CG2 THR 110.0 2.3
N-CA-C THR 111.0 2.7
CA-C-O THR 120.1 2.1
N-CA-CB TRP 110.6 1.8
CB-CA-C TRP 110.4 2.0
CA-CB-CG TRP 113.7 1.9
CB-CG-CD1 TRP 127.0 1.3
CB-CG-CD2 TRP 126.6 1.3
CD1-CG-CD2 TRP 106.3 0.8
CG-CD1-NE1 TRP 110.1 1.0
CD1-NE1-CE2 TRP 109.0 0.9
NE1-CE2-CD2 TRP 107.3 1.0
CE2-CD2-CG TRP 107.3 0.8
CG-CD2-CE3 TRP 133.9 0.9
NE1-CE2-CZ2 TRP 130.4 1.1
CE3-CD2-CE2 TRP 118.7 1.2
CD2-CE2-CZ2 TRP 122.3 1.2
CE2-CZ2-CH2 TRP 117.4 1.0
CZ2-CH2-CZ3 TRP 121.6 1.2
CH2-CZ3-CE3 TRP 121.2 1.1
CZ3-CE3-CD2 TRP 118.8 1.3
N-CA-C TRP 111.0 2.7
CA-C-O TRP 120.1 2.1
N-CA-CB TYR 110.6 1.8
CB-CA-C TYR 110.4 2.0
CA-CB-CG TYR 113.4 1.9
CB-CG-CD1 TYR 121.0 0.6
CB-CG-CD2 TYR 121.0 0.6
CD1-CG-CD2 TYR 117.9 1.1
CG-CD1-CE1 TYR 121.3 0.8
CG-CD2-CE2 TYR 121.3 0.8
CD1-CE1-CZ TYR 119.8 0.9
CD2-CE2-CZ TYR 119.8 0.9
CE1-CZ-CE2 TYR 119.8 1.6
CE1-CZ-OH TYR 120.1 2.7
CE2-CZ-OH TYR 120.1 2.7
N-CA-C TYR 111.0 2.7
CA-C-O TYR 120.1 2.1
N-CA-CB VAL 111.5 2.2
CB-CA-C VAL 111.4 1.9
CA-CB-CG1 VAL 110.9 1.5
CA-CB-CG2 VAL 110.9 1.5
CG1-CB-CG2 VAL 110.9 1.6
N-CA-C VAL 111.0 2.7
CA-C-O VAL 120.1 2.1
-
Non-bonded distance Minimum Dist Tolerance
C-C 3.4 1.5
C-N 3.25 1.5
C-S 3.5 1.5
C-O 3.22 1.5
N-N 3.1 1.5
N-S 3.35 1.5
N-O 3.07 1.5
O-S 3.32 1.5
O-O 3.04 1.5
S-S 2.03 1.0
-
setup.py
View file @ 694f8ba0
...@@ -16,9 +16,11 @@ import os ...@@ -16,9 +16,11 @@ import os
from setuptools import setup, Extension, find_packages from setuptools import setup, Extension, find_packages
import subprocess import subprocess
from torch.utils.cpp_extension import BuildExtension, CUDAExtension, CUDA_HOME from torch.utils.cpp_extension import BuildExtension, CUDAExtension, ROCM_HOME
from scripts.utils import get_nvidia_cc from typing import Optional, Union
import subprocess
from pathlib import Path
version_dependent_macros = [ version_dependent_macros = [
...@@ -29,58 +31,60 @@ version_dependent_macros = [ ...@@ -29,58 +31,60 @@ version_dependent_macros = [
extra_cuda_flags = [ extra_cuda_flags = [
'-std=c++14', '-std=c++14',
'-maxrregcount=50', #'-maxrregcount=50',
'-U__CUDA_NO_HALF_OPERATORS__', #'-U__CUDA_NO_HALF_OPERATORS__',
'-U__CUDA_NO_HALF_CONVERSIONS__', #'-U__CUDA_NO_HALF_CONVERSIONS__',
'--expt-relaxed-constexpr', '--expt-relaxed-constexpr',
'--expt-extended-lambda' '--expt-extended-lambda'
] ]
def get_cuda_bare_metal_version(cuda_dir): cc_flag = ['-DAMDGPU_TARGETS', 'gfx900;gfx906']
raw_output = subprocess.check_output([cuda_dir + "/bin/nvcc", "-V"], universal_newlines=True)
output = raw_output.split()
release_idx = output.index("release") + 1
release = output[release_idx].split(".")
bare_metal_major = release[0]
bare_metal_minor = release[1][0]
return raw_output, bare_metal_major, bare_metal_minor
compute_capabilities = set([
(3, 7), # K80, e.g.
(5, 2), # Titan X
(6, 1), # GeForce 1000-series
])
compute_capabilities.add((7, 0))
_, bare_metal_major, _ = get_cuda_bare_metal_version(CUDA_HOME)
if int(bare_metal_major) >= 11:
compute_capabilities.add((8, 0))
compute_capability, _ = get_nvidia_cc()
if compute_capability is not None:
compute_capabilities = set([compute_capability])
cc_flag = []
for major, minor in list(compute_capabilities):
cc_flag.extend([
'-gencode',
f'arch=compute_{major}{minor},code=sm_{major}{minor}',
])
extra_cuda_flags += cc_flag extra_cuda_flags += cc_flag
def get_sha(pytorch_root: Union[str, Path]) -> str:
try:
return subprocess.check_output(['git', 'rev-parse', 'HEAD'], cwd=pytorch_root).decode('ascii').strip()
except Exception:
return 'Unknown'
def get_version_add(sha: Optional[str] = None) -> str:
add_version_path = "version.py"
if sha != 'Unknown':
if sha is None:
sha_path = os.getenv('OPENFOLD_DOWNLOAD_PATH', "")
sha = get_sha(sha_path)
version = 'git' + sha[:7]
if os.getenv('OPENFOLD_BUILD_VERSION'):
version_dtk = os.getenv('OPENFOLD_BUILD_VERSION', "")
version += "." + version_dtk
with open(add_version_path, encoding="utf-8", mode="w") as file:
file.write("__version__='1.0.1'+'+{}'\n".format(version))
file.close()
def get_version():
get_version_add()
version_file = 'version.py'
with open(version_file, encoding='utf-8') as f:
exec(compile(f.read(), version_file, 'exec'))
return locals()['__version__']
setup( setup(
name='openfold', name='openfold',
version='1.0.0', #version='1.0.1',
version=get_version,
description='A PyTorch reimplementation of DeepMind\'s AlphaFold 2', description='A PyTorch reimplementation of DeepMind\'s AlphaFold 2',
author='Gustaf Ahdritz & DeepMind', author='Gustaf Ahdritz & DeepMind',
author_email='gahdritz@gmail.com', author_email='gahdritz@gmail.com',
license='Apache License, Version 2.0', license='Apache License, Version 2.0',
url='https://github.com/aqlaboratory/openfold', url='https://github.com/aqlaboratory/openfold',
packages=find_packages(exclude=["tests", "scripts"]), packages=find_packages(exclude=["tests", "scripts"]),
include_package_data=True, include_package_data=False,
package_data={ package_data={
"openfold": ['utils/kernel/csrc/*'], "openfold": ['utils/kernel/csrc/*'],
"": ["resources/stereo_chemical_props.txt"] "": ["resources/stereo_chemical_props.txt"]
...@@ -99,7 +103,7 @@ setup( ...@@ -99,7 +103,7 @@ setup(
], ],
extra_compile_args={ extra_compile_args={
'cxx': ['-O3'] + version_dependent_macros, 'cxx': ['-O3'] + version_dependent_macros,
'nvcc': ( 'hipcc': (
['-O3', '--use_fast_math'] + ['-O3', '--use_fast_math'] +
version_dependent_macros + version_dependent_macros +
extra_cuda_flags extra_cuda_flags
......
version.py 0 → 100644
View file @ 694f8ba0
__version__ = "1.0.1"
\ No newline at end of file
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