MindSpore SPONGE Documents
===========================
MindSpore SPONGE is a computative biology suite based on MindSpore, supporting common functions such as molecular dynamics and protein folding.
The molecular simulation or modeling process has a high degree
of logic consistency with the AI model training/inferring process,
so the molecular simulation can in principle be unified with the
AI training/inferring mode. MindSpore SPONGE integrates molecular simulation
and AI training/inferring under the same programming structure.
The overall structure view is as follows:
.. figure:: ./intro/images/archi.png
:alt: MindSpore SPONGE Architecture
Different from traditional molecular simulation software,
AI molecular simulation library has completely new features, such as:
1. Instead of manual derivative programming, automatic differential
technology provides a unified programming paradigm for different
energy functions or the construction of complex scoring functions;
2. Fully compatible with neural network models, supporting AI inferring
within molecular simulation, or simulation as an engine for AI training;
3. The end-to-end differentiable modeling method can realize
the meta-optimization of the physical model;
4. Hierarchical code architecture, using efficient language operator
at the bottom; Provide users with object-oriented Python API
to facilitate user customization;
5. Automatic adaptation of multiple back-end. Users only need to write
a simple Python code to accelerate execution on multiple back-end,
such as GPU and NPU;
6. High-throughput simulation supported by automatic parallel. Users
do not need to distinguish between single or multi-machine execution
of code, can concurrently simulate multiple systems on a single
hardware unit, without special MPI programming.
Combined with these new features, the unified framework of molecular
simulation and AI can support a wide range of molecular modeling
and application scenarios, such as:
- Molecular simulation based on AI improved force field or enhanced sampling;
- Data-driven & physics-driven molecular docking;
- Protein structure prediction and force field optimization;
- High throughput molecular simulation;
- Molecular design, etc.
Code repository address: <https://gitee.com/mindspore/mindscience/tree/r0.5/MindSPONGE>
Installation
------------
Recommended Hardware
~~~~~~~~~~~~~~~~~~~~
+---------------+-----------------+--------+
| Hardware | os | Status |
+===============+=================+========+
| Ascend 910 | Ubuntu-x86 | ✔️ |
+---------------+-----------------+--------+
| | Ubuntu-aarch64 | ✔️ |
+---------------+-----------------+--------+
| | EulerOS-aarch64 | ✔️ |
+---------------+-----------------+--------+
| | CentOS-x86 | ✔️ |
+---------------+-----------------+--------+
| | CentOS-aarch64 | ✔️ |
+---------------+-----------------+--------+
| GPU CUDA 10.1 | Ubuntu-x86 | ✔️ |
+---------------+-----------------+--------+
Dependency
~~~~~~~~~~
- Python>=3.7
- MindSpore>=2.0
Please refer to `MindSpore installation
tutorial <https://www.mindspore.cn/install/en>`__.
source code install
~~~~~~~~~~~~~~~~~~~
.. code::
git clone https://gitee.com/mindspore/mindscience.git
cd mindscience/MindSPONGE
- dependency install
.. code::
pip install -r requirements.txt
- Ascend backend
Enable ``c`` if you want to use Cybertron.
.. code::
bash build.sh -e ascend -c on
- GPU backend
Enable ``c`` if you want to use Cybertron.
Enable ``t`` if you want to use traditional MD.
.. code::
export CUDA_PATH={your_cuda_path}
bash build.sh -e gpu -j32 -t on -c on
- Install whl package
.. code::
cd output/
pip install mindsponge*.whl
pip install cybertron*.whl # if "-c on" is used
SIG
---
CO-CHAIR
~~~~~~~~
- Shenzhen Bay Laboratory `Yi Isaac
Yang <https://gitee.com/helloyesterday>`__
- Chang Ping Laboratory `Jun Zhang <https://gitee.com/jz_90>`__
- Chang Ping Laboratory `Sirui Liu <https://gitee.com/sirui63>`__
Special Interesting Group
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
MindSpore SPONGE.
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 <https://www.bilibili.com/video/BV1pB4y167yS?spm_id_from=333.999.0.0&vd_source=94e532d8ff646603295d235e65ef1453>`__.
In the SIG group, we will also release the public intelligence task and
`open source internship
task <https://gitee.com/mindspore/community/issues/I561LI?from=project-issue>`__,
welcome everyone to claim it.
Core Contributor
~~~~~~~~~~~~~~~~
- `Yi Qin Gao Research Group <https://www.chem.pku.edu.cn/gaoyq/>`__:
`Yi Isaac Yang <https://gitee.com/helloyesterday>`__, `Jun
Zhang <https://gitee.com/jz_90>`__, `Sirui
Liu <https://gitee.com/sirui63>`__, `Yijie
Xia <https://gitee.com/xiayijie>`__, `Diqing
Chen <https://gitee.com/dechin>`__, `Yu-Peng
Huang <https://gitee.com/gao_hyp_xyj_admin>`__.
Contribution Guide
------------------
- Please click here to see how to contribute your code:\ `Contribution
Guide <https://gitee.com/mindspore/mindscience/blob/r0.5/CONTRIBUTION.md#>`__
.. toctree::
:glob:
:maxdepth: 1
:caption: Molecular Simulation Introduction
intro/physics_driven
intro/data_driven
intro/physics_plus_data_driven
.. toctree::
:glob:
:maxdepth: 1
:caption: User Guide
user/simulation
user/structure_prediction
user/property_prediction
user/design
user/basic
.. toctree::
:maxdepth: 1
:caption: API References
mindsponge.cell
mindsponge.common
mindsponge.data_transform
mindsponge.metrics
sponge.control
sponge.core
sponge.function
sponge.optimizer
sponge.potential
sponge.system
constant
.. toctree::
:glob:
:maxdepth: 1
:caption: RELEASE NOTES
RELEASE