Olamide Isreal
f971fd0e21
- Nextflow pipeline using chai1 Docker image from Harbor - S3-based input/output paths (s3://omic/eureka/chai-lab/) - GPU-accelerated protein folding with MSA support Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
38 lines
861 B
Python
Executable File
38 lines
861 B
Python
Executable File
# Copyright (c) 2024 Chai Discovery, Inc.
|
|
|
|
# Licensed under the Apache License, Version 2.0.
|
|
# See the LICENSE file for details.
|
|
|
|
example_ligands = [
|
|
"C",
|
|
"O",
|
|
"C(C1C(C(C(C(O1)O)O)O)O)O",
|
|
"[O-]S(=O)(=O)[O-]",
|
|
"CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C",
|
|
"CCC1=C(c2cc3c(c(c4n3[Mg]56[n+]2c1cc7n5c8c(c9[n+]6c(c4)C(C9CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C)[C@H](C(=O)c8c7C)C(=O)OC)C)C=C)C=O",
|
|
r"C=CC1=C(C)/C2=C/c3c(C)c(CCC(=O)O)c4n3[Fe@TB16]35<-N2=C1/C=c1/c(C)c(C=C)/c(n13)=C/C1=N->5/C(=C\4)C(CCC(=O)O)=C1C",
|
|
# different ions
|
|
"[Mg+2]",
|
|
"[Na+]",
|
|
"[Cl-]",
|
|
]
|
|
|
|
example_proteins = [
|
|
"AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVR",
|
|
"(KCJ)(SEP)(PPN)(B3S)(BAL)(PPN)K(NH2)",
|
|
"XDHPX",
|
|
]
|
|
|
|
|
|
example_rna = [
|
|
"AGUGGCUA",
|
|
"AAAAAA",
|
|
"AGUC",
|
|
]
|
|
|
|
example_dna = [
|
|
"AGTGGCTA",
|
|
"AAAAAA",
|
|
"AGTC",
|
|
]
|