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Zefeng Zhu NatureGeorge

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Still have lots more to work on.
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NatureGeorge / How_to_Install_Theseus.md
Created November 18, 2022 03:00
The way to install Theseus on Linux. 
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
NatureGeorge / cif2dataframe.py
Created September 23, 2022 08:41
Convert mmCIF file to pandas.Dataframe.
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
NatureGeorge / 2aw3_version_update.cif
Created June 16, 2021 07:25
This file has been truncated, but you can view the full file.
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
NatureGeorge / pdb-profiling_README.md
Created November 2, 2020 05:33
README of pdb-profiling
@NatureGeorge
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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@NatureGeorge
NatureGeorge / graphviz_demo.md
Last active September 8, 2020 05:54
graphviz demo 
```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
NatureGeorge / PDBe_API_Issue.md
Last active September 5, 2020 12:48
📝Record for PDBe API Issue
title author date categories tags
Record for PDBe API Issues
Zefeng Zhu
2020-09-04 17:39:51 +0800
Notes
Research
pdbe

Basic Information

@NatureGeorge
NatureGeorge / pdbe-kb.md
Last active August 30, 2020 09:28 — forked from PawelSzczerbiak/pdbe-kb.md

PDBe-KB

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.

Why graph DB?

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: