conda install -c conda-forge theseus
conda install -c bioconda muscle
sudo ln -s /home/your_name/miniconda3/bin/muscle /usr/local/bin/muscle
sudo ln -s /home/your_name/miniconda3/bin/theseus /usr/local/bin/theseus
NatureGeorge
/ How_to_Install_Theseus.md
Created
November 18, 2022 03:00
The way to install Theseus on Linux.
NatureGeorge
/ cif2dataframe.py
Created
September 23, 2022 08:41
Convert mmCIF file to pandas.Dataframe.
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| import gemmi | |
| import pandas as pd | |
| cif_doc_block = gemmi.cif.read('1ug6.cif.gz')[0] | |
| keys = ( | |
| '_atom_site.id', | |
| '_atom_site.label_atom_id', | |
| '_atom_site.label_comp_id', | |
| '_atom_site.label_asym_id', |
NatureGeorge
/ 2aw3_version_update.cif
Created
June 16, 2021 07:25
This file has been truncated, but you can view the full file.
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| data_2AW3 | |
| # | |
| _entry.id 2AW3 | |
| # | |
| _audit_conform.dict_name mmcif_pdbx.dic | |
| _audit_conform.dict_version 5.329 | |
| _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic | |
| # | |
| loop_ | |
| _database_2.database_id |
NatureGeorge
/ github_dark_issue_demo.ipynb
Created
September 22, 2020 16:35
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NatureGeorge
/ ResetIndexUsage.ipynb
Last active
September 23, 2020 04:31
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NatureGeorge
/ SuperImposed_RMSD_Radius.ipynb
Created
September 18, 2020 14:36
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```viz
digraph flowchart_4 {
# rankdir=LR;
fontname="Courier New";
size="6,5"; ratio = fill;
node [style="filled,setlinewidth(3)", color="#8383cc", fontname="Courier New", shape="Mrecord",fixedsize=true,width=2.5,fillcolor="#d9e7ee"];
edge [color="0.635 0.707 0.707", fontname="Courier New"];
label="从头预测与结构建模";
# step1[label="数据准备"];
NatureGeorge
/ pdbe-kb.md
Last active
August 30, 2020 09:28
— forked from PawelSzczerbiak/pdbe-kb.md
Note: this gist is heavily based on materials provided by organizers of the Mining PDBe and PDBe-KB Using a Graph Database workshop.
Note: this gist is foke from PawelSzczerbiak/pdbe-kb.md.
Graph DBs are much more useful for representing unstructured, sparse data and relationships than conventional relational DBs.
Graph is a structure that models pairwise relations between objects:
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