├── Articles ├── 20200328-抽提微信聊天记录并绘制词云 │ └── README.md ├── 20200616-蛋白配体gromacs模拟预处理 │ └── README.md ├── 20200617-蛋白配体gromacs模拟分析 │ └── README.md ├── 20200620-PLIP │ └── README.md ├── 20200818-蛋白配体模拟-配体使用amber的GAFF力场 │ └── README.md ├── 20200825-蛋白配体模拟-利用AmberTools构建体系 │ └── README.md ├── 20200926-蛋白配体模拟-混用力场参数 │ └── README.md ├── 20201106-docsify │ └── README.md ├── 20210314-GMX-insert-molecules │ ├── 1.png │ ├── 2.png │ ├── 3.png │ ├── README.md │ ├── complex.gro │ ├── lig.pdb │ ├── out.gro │ └── protein.gro ├── 20210524-xpm2gpl │ ├── README.md │ ├── ss.png │ └── xpm2all-fancy.png ├── 20210611-DSSP-do_dssp │ ├── README.md │ ├── WeChat Image_20210612162523.png │ ├── WeChat Image_20210612200052.png │ ├── WeChat Photo Editor_20210612144857.jpg │ ├── WeChat Photo Editor_20210612145849.jpg │ ├── WeChat Photo Editor_20210612151339.jpg │ ├── WeChat Photo Editor_20210612151534.jpg │ ├── WeChat Screenshot_20210612094418.png │ ├── WeChat Screenshot_20210612110614.png │ ├── blueFlamingo_logo.png │ ├── dsspsc.png │ └── ss.png ├── 20210807-xpm2png │ ├── README.md │ ├── covapic.png │ ├── covapic.xpm │ ├── dssp.png │ ├── dssp.xpm │ ├── gibbs.png │ ├── gibbs.xpm │ ├── gibbs_noip.png │ ├── ss.xpm │ ├── xpm2png.exe │ ├── xpm2png.go │ ├── xpm2png.png │ └── xpm2png.py ├── 20210811-脂双层构建 │ ├── 1.png │ ├── 2.png │ ├── 3.png │ ├── 4.png │ ├── 5.png │ ├── 6.png │ ├── 7.png │ ├── 8.png │ ├── 9.png │ ├── README.md │ ├── box.gro │ ├── box_down.gro │ ├── box_up.gro │ ├── command.log │ ├── dppc.pdb │ ├── dppc_box.gro │ ├── mem_down.gro │ ├── mem_up.gro │ ├── spc216.gro │ ├── true_box.gro │ ├── water_box.gro │ ├── water_box_down.gro │ ├── water_box_up.gro │ ├── water_down.gro │ └── water_up.gro ├── 20210922-自由能形貌图 │ ├── README.md │ ├── corr.png │ ├── fel_1.png │ ├── fel_2.png │ ├── fel_show.jpg │ └── pca.png ├── 20211118-轨迹周期性校正 │ ├── README.md │ └── find_center.py ├── 20211121-蛋白配体能量计算 │ ├── LJ.png │ ├── LJ_graph.png │ └── README.md ├── 20211201-计算苯环间距和角度 │ ├── README.md │ ├── example.gro │ ├── index.ndx │ ├── output.xvg │ ├── pic.png │ ├── pic2.png │ ├── pic3.png │ └── pipi_dist_ang.py ├── 20211214-PeptideBuilder │ └── README.md ├── 20211216-多肽构建-tLEaP和rdkit │ └── README.md ├── 20211220-PeptideConstructor │ ├── 2.png │ ├── README.md │ ├── cover_1.png │ └── cover_2.png ├── 20211222-Tinker-多肽和核酸的构建 │ ├── 1.png │ ├── 2.png │ ├── 3.png │ ├── 4.png │ ├── 5.png │ ├── 6.png │ ├── 7.png │ ├── 8.png │ ├── 9.png │ ├── README.md │ └── chi.jpg ├── 20220204-xpm_show │ ├── 1.png │ ├── 2.png │ ├── 3d.png │ ├── README.md │ ├── combine.png │ ├── dssp.png │ ├── dssp_1.png │ ├── test_3.png │ └── xpm_show.py ├── 20220218-RamachandranPlot │ ├── Figure_1.png │ ├── README.md │ ├── fig_0.png │ ├── md.tpr │ ├── mda.py │ ├── pro.gro │ ├── rama.log │ ├── rama.py │ ├── rama.xvg │ └── test.xtc ├── 20220227_dPCA │ ├── 2.png │ ├── README.md │ ├── R_1.png │ ├── R_2.png │ ├── gibbs.png │ ├── gibbs2.png │ └── pic1.jpg ├── 20220310-DIT │ ├── README.md │ ├── xpm_show.png │ ├── xpm_show_2.png │ ├── xvg_ave_bar.png │ ├── xvg_box.png │ ├── xvg_compare.png │ ├── xvg_compare_2.png │ ├── xvg_rama.png │ ├── xvg_show.png │ ├── xvg_show_distribution.png │ └── xvg_show_stack.png ├── 20220430_RMSD │ ├── README.md │ ├── mdanalysis.png │ ├── mdtraj.png │ ├── rmsd_defination.png │ ├── rmsd_matrix.png │ └── rmsd_pro.png ├── 20220727-Hbond-DIT │ ├── 1.png │ ├── 2.png │ ├── 3.png │ └── README.md ├── 20220909-DCCM │ ├── README.md │ ├── coor2corr.py │ ├── coor2corr_fit2ref_offset2ave.png │ ├── corr.png │ ├── correlation-correlation-vs-distance.png │ ├── correlation-overall.png │ ├── correlation_pymol.png │ ├── correlation_pymol2.png │ ├── cov2corr.py │ ├── covar.png │ ├── cover.png │ ├── diff-map-overall-difference.png │ ├── fig_0.png │ ├── fig_1.png │ ├── mdtask_res.png │ ├── pca_corr.png │ └── self_corr.png ├── 20221006-CONAN │ ├── MDcons.png │ ├── README.md │ ├── conan_0.jpg │ ├── cross-correlate.png │ ├── gr2.jpg │ ├── interaction_lifetime.domains.png │ ├── interaction_types.png │ ├── local_interactions.domains.png │ ├── mdmat.png │ ├── pearson_inter_residue.png │ ├── pearson_time.domains.png │ ├── rmsd_contact_map_initial.png │ ├── rmsd_formula.png │ ├── rmsd_interframe.png │ └── rmsf_old_new.png ├── 20230410-lightdock │ ├── README.md │ └── README.txt ├── 20230412-PLIP绘图 │ ├── 2.png │ ├── 3.png │ ├── Figure_1.png │ ├── README.md │ ├── WeChat Image_20230409220316.png │ ├── show.png │ ├── show.py │ ├── show2.py │ └── show3.py ├── 20230905-ShiftX2及其RMSD的计算 │ ├── 0.png │ ├── 1.png │ ├── README.md │ └── ins6.png ├── 20240229-DuIvyProcedures │ ├── Distance_Average.png │ ├── PiStacking_Distances.png │ ├── PiStacking_Existence_Map.png │ ├── PiStacking_Type_Map.png │ ├── RDCM_Residues_dendrogram.png │ ├── REDAME.md │ ├── SaltBridge_Existence_Map.png │ ├── Scatter_FEL.png │ ├── correlation_matrix.png │ ├── dpc12_scatter.png │ ├── dssp_Protein.png │ ├── gibbs.png │ ├── hbdistall.png │ ├── hbnum.png │ ├── pc12_scatter.png │ └── top_hbmap.png └── README.md ├── DuIvy.png ├── README.md └── sources ├── LICENSE ├── MovingAverage ├── ReadMe.md ├── energy.xvg ├── energy2.xvg ├── energy_results_.xvg └── xvg_movingaverage.py ├── README.md ├── dccm ├── coor2corr.py └── cov2corr.py ├── dssp ├── README.md ├── ss.gpl ├── ss.png ├── ss.xpm ├── ss_gpl.png ├── xpm2gpl.exe ├── xpm2gpl.go ├── xpm2gpl │ ├── README.md │ ├── xpm2gpl.exe │ └── xpm2gpl.go ├── xpm2gpl_CS.go ├── xpm2gpl_noCS.go ├── xpm_xshrink1000.exe ├── xpm_xshrink1000.go ├── xvg_xshrink.exe └── xvg_xshrink.go ├── energy_compute ├── README.md ├── energy_compute.py ├── energy_results_.xvg ├── lig.xvg ├── pro.xvg └── prolig.xvg ├── other ├── Dock │ ├── README.md │ ├── analysis_deep.py │ ├── analysis_donor_count.py │ ├── average_perAA.py │ ├── generate_ligand_list.py │ ├── ligand_pdbFromDlg.py │ ├── ligand_pdbFromDlg_split.py │ ├── ligand_pdbqt_to_config.py │ └── roc.py ├── FELmap2.py ├── PCA_FEL │ ├── PCA_analysis.R │ ├── pc_combine.py │ ├── pca_command.sh │ ├── pepend_identify.py │ ├── xpm2png.py │ └── xtc2dcd.sh ├── find_center.py ├── gmx_shell.log.sh ├── pbc.sh └── show_me_energy.sh ├── pipi_dist_ang ├── README.md ├── example.gro ├── index.ndx ├── output.xvg ├── pic.png ├── pic2.png ├── pic3.png ├── pipi_dist_ang.py └── pipi_distang_vec.py ├── xpm_show ├── README.md ├── covapic.png ├── covapic.xpm ├── dssp.png ├── dssp.xpm ├── gibbs.png ├── gibbs.xpm ├── hbmap.png ├── hbmap.xpm ├── xpm2png.exe ├── xpm2png.go ├── xpm2png.png ├── xpm2png.py └── xpm_show.py ├── xvg_average ├── README.md ├── pro.xvg ├── rdf.xvg ├── resveratrol.xvg ├── rmsd.xvg └── xvg_average.py ├── xvg_compare ├── README.md ├── brazilin.xvg ├── hematoxylin.xvg ├── resveratrol.xvg ├── xvg_compare.png ├── xvg_compare.py ├── xvgcompare.jl └── xvgcompare.py ├── xvg_show ├── README.md ├── pro_SR.xvg ├── xvg_show.py ├── xvgshow.jl ├── xvgshow.png └── xvgshow.py └── xvgformat ├── README.md ├── energy.xvg ├── energy_formatted.xvg ├── pro.xvg ├── pro_formatted.csv ├── pro_formatted.xvg ├── rdf.xvg ├── 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