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cpdb's Introduction

Hi there ๐Ÿ‘‹

  • ๐Ÿ”ญ Iโ€™m a PhD student at the University of Cambridge. I work on deep learning applied to structural biology and drug discovery.

  • I'm currently doing things with proteins at Genentech / Roche / Prescient Design

  • Previously, I was a visiting researcher at EPFL and MILA, AI Resident at X - The Moonshot Factory (formerly Google X) and an ML Consultant at Relation Therapeutics.

  • ๐ŸŒฑ Iโ€™m currently developing Graphein, a data processing library for geometric deep learning in biology.

    • Graphein supports construction and featurisation of:
      • Protein structure graphs
      • Protein meshes
      • Small molecule graphs
      • RNA structure graphs
      • Protein-protein interaction graphs
      • Gene regulatory interaction graphs
  • ๐Ÿ“ซ How to reach me:

cpdb's People

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cpdb's Issues

installation failed

Macbook pro 2021 M1 pro
Ststem: Mac OS 14.3.1 (23D60)
Python 3.8.19
numpy 1.24.3

Error:
Building wheels for collected packages: cpdb-protein
Building wheel for cpdb-protein (pyproject.toml) ... error
error: subprocess-exited-with-error

ร— Building wheel for cpdb-protein (pyproject.toml) did not run successfully.
โ”‚ exit code: 1
โ•ฐโ”€> [17 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11.1-arm64-cpython-38
creating build/lib.macosx-11.1-arm64-cpython-38/cpdb
copying cpdb/init.py -> build/lib.macosx-11.1-arm64-cpython-38/cpdb
running build_ext
building 'cpdb.parser' extension
creating build/temp.macosx-11.1-arm64-cpython-38
creating build/temp.macosx-11.1-arm64-cpython-38/cpdb
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/homebrew/anaconda3/envs/pytorch/include -arch arm64 -I/opt/homebrew/anaconda3/envs/pytorch/include -arch arm64 -I</opt/homebrew/opt/portaudio>/include/ -I/opt/homebrew/anaconda3/envs/pytorch/include/python3.8 -c cpdb/parser.c -o build/temp.macosx-11.1-arm64-cpython-38/cpdb/parser.o
cpdb/parser.c:1240:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]

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