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tutorials | 8 months ago | |
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RELEASE.md | 1 year ago | |
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build.sh | 10 months ago | |
requirements.txt | 8 months ago | |
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ENGLISH | 简体中文
MindSpore SPONGE(Simulation Package tOwards Next GEneration molecular modelling) is a toolkit for Computational Biology based on AI framework MindSpore,which supports MD, folding and so on. It aims to provide efficient AI computational biology software for a wide range of scientific researchers, staff, teachers and students.
Top
open source internship task has been released! Everyone is welcome to claim it~2023.1.31
MindSPONGE version 1.0.0-alpha is released. The documents are available on Scientific Computing MindSPONGE module on MindSpore website2022.8.23
Paper "Few-Shot Learning of Accurate Folding Landscape for Protein Structure Prediction" is preprinted in arxiv, Please refer to Paper2022.8.11—2022.8.15
MindSpore SPONGE SIG Summer School, replay2022.07.18
Paper "SPONGE: A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms"is published in Chinese Journal of Chemistry. Please refer to paper and codes2022.07.09
MEGA-Assessment wins CAMEO-QE monthly 1st2022.06.27
Paper "PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction" is preprinted in arxiv. Please refer to Paper and codes.2022.04.21
MEGA-Fold wins CAMEO-3D monthly 1st. Related Newsimport os
import stat
import pickle
from mindsponge import PipeLine
from mindsponge.common.protein import to_pdb_v2, from_prediction_v2
cmd = "wget https://download.mindspore.cn/mindscience/mindsponge/Multimer/examples/6T36.pkl"
os.system(cmd)
pipe = PipeLine(name="Multimer")
pipe.set_device_id(0)
pipe.initialize("predict_256")
pipe.model.from_pretrained()
f = open("./6T36.pkl", "rb")
raw_feature = pickle.load(f)
f.close()
final_atom_positions, final_atom_mask, confidence, b_factors = pipe.predict(raw_feature)
unrelaxed_protein = from_prediction_v2(final_atom_positions,
final_atom_mask,
raw_feature["aatype"],
raw_feature["residue_index"],
b_factors,
raw_feature["asym_id"],
False)
pdb_file = to_pdb_v2(unrelaxed_protein)
os.makedirs('./result/', exist_ok=True)
os_flags = os.O_RDWR | os.O_CREAT
os_modes = stat.S_IRWXU
pdb_path = './result/unrelaxed_6T36.pdb'
with os.fdopen(os.open(pdb_path, os_flags, os_modes), 'w') as fout:
fout.write(pdb_file)
print("confidence:", confidence)
import numpy as np
from mindspore import context
from mindsponge import Sponge
from mindsponge import Molecule
from mindsponge import ForceFieldBase
from mindsponge import DynamicUpdater
from mindsponge.potential import BondEnergy, AngleEnergy
from mindsponge.callback import WriteH5MD, RunInfo
from mindsponge.function import VelocityGenerator
from mindsponge.control import LeapFrog
context.set_context(mode=context.GRAPH_MODE, device_target="GPU")
system = Molecule(
atoms=['O', 'H', 'H'],
coordinate=[[0, 0, 0], [0.1, 0, 0], [-0.0333, 0.0943, 0]],
bond=[[[0, 1], [0, 2]]],
)
bond_energy = BondEnergy(
index=system.bond,
force_constant=[[345000, 345000]],
bond_length=[[0.1, 0.1]],
)
angle_energy = AngleEnergy(
index=[[1, 0, 2]],
force_constant=[[383]],
bond_angle=[[109.47 / 180 * np.pi]],
)
energy = ForceFieldBase(energy=[bond_energy, angle_energy])
velocity_generator = VelocityGenerator(300)
velocity = velocity_generator(system.coordinate.shape, system.atom_mass)
opt = DynamicUpdater(
system,
integrator=LeapFrog(system),
time_step=1e-3,
velocity=velocity,
)
md = Sponge(system, energy, opt)
run_info = RunInfo(10)
cb_h5md = WriteH5MD(system, 'test.h5md', save_freq=10, write_velocity=True, write_force=True)
md.run(1000, callbacks=[run_info, cb_h5md])
More Cases:👀
Due to the dependency between MindSPONGE and MindSpore, please follow the table below and install the corresponding MindSpore version from MindSpore download page.
MindSPONGE Version | Branch | MindSpore Version | Python Version |
---|---|---|---|
1.0.0 | master | >=2.0.0-alpha | >=3.7 |
pip install -r requirements.txt
Hardware | OS | Status |
---|---|---|
Ascend 910 | Ubuntu-x86 | ✔️ |
Ubuntu-aarch64 | ✔️ | |
EulerOS-aarch64 | ✔️ | |
CentOS-x86 | ✔️ | |
CentOS-aarch64 | ✔️ | |
GPU CUDA 10.1 | Ubuntu-x86 | ✔️ |
pip install mindsponge-[gpu|ascend]
The version of mindsponge installed by pip corresponds to the r0.2.0-alpha branch code. The code can be downloaded using the following instruct.
git clone -b r0.2.0-alpha https://gitee.com/mindspore/mindscience.git
git clone https://gitee.com/mindspore/mindscience.git
cd {PATH}/mindscience/MindSPONGE
bash build.sh -e ascend
Enable c
if you want to use Cybertron.
Enable t
if you want to use traditional MD.
export CUDA_PATH={your_cuda_path}
bash build.sh -e gpu -j32 -t on -c on
cd {PATH}/mindscience/MindSPONGE/output
pip install mindsponge_ascend*.whl # Ascend
pip install mindsponge-gpu*.whl # GPU
pip install cybertron*.whl # if "-c on" is used
For details about MindSPONGE APIs, please refer to API pages.
MindSpore SPONGE SIG (Special Interesting Group) is a team composed of a group of people who are interested and have a mission to make achievements in the field of AI × biological computing.
MindSpore SPONGE SIG group provides efficient and easy-to-use AI computational biology software for researchers, teachers and students, and provides a platform for people with strong abilities or strong interests in this field to communicate and cooperate together.
At present, the SIG group has six core teachers. After members joining the SIG group, our teachers will lead the team to carry out scientific research and develop the software function development. Of course, members are also welcome to do research on their own topics using MindSPONGE.
In the SIG group, we will hold various activities, including summer school, public lecture, technology communication meeting and other large-scale activities. Small-scale activities like weekly meetings, blogs writing will also be held in the group. By joining the activities, there will be lots of chances to communicate with our experts. During the summer school program ended on August 15th, we invited 13 teachers to have a five-day lecture mainly including three themes of MindSpore basics, molecular dynamics and advanced AI × Science courses. You can get the replay here.
In the SIG group, we will also release the public intelligence task and open source internship task, welcome everyone to claim it.
If you want to join us and become a member of our group, please send your resume to dingyahao@huawei.com, we are always looking forward to your arrival.
MindScience is scientific computing kits for various industries based on the converged MindSpore framework.
Jupyter Notebook Python Unity3D Asset Pickle nesC other
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