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platinhom / gfwlist.action
Created August 16, 2021 00:34
gfwlist.action
# Generated by gfwlist2privoxy at 2021-08-16 08:25:41
{+forward-override{forward-socks5 127.0.0.1:1080 .}}
14.102.250.18
14.102.250.19
50.7.31.230:8898
67.220.91.15
67.220.91.18
67.220.91.23
69.65.19.160
72.52.81.22
@platinhom
platinhom / gout2gjf.sh
Created May 31, 2018 06:20
网上一个gout到gjf的脚本
#!/bin/bash
#
# 目的：从高斯输出文件中提取坐标信息生成xyz文件和输入文件
# 用法： gout2gjf xxxx.out 后面为高斯输出文件名作为参数
#
# ChemiAndy, 2014.03.11
#
# get the prefix of the gaussian output file
NAME=`echo $1|sed "s/\..*$//"`
@platinhom
platinhom / G09TestDetails.txt
Created January 31, 2018 10:17
Gaussian09 Test Examples
Test0000: Water with archiving
# SP, RHF/STO-3G punch=archive trakio scf=conventional
Test0001: SINGLET DELTA STO-3G//STO-3G DIOXYGEN
#P TEST STO-3G COMPLEX pop=full scf=tight
Test0002: METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE, using L506 direct, mixed ints
#p gvb(0)/4-31g test force scf=noincore iop(5/29=3)
Test0003: STEEPEST DESCENT SCF 3-21G//3-21G ETHYLENE
@platinhom
platinhom / 0-EndnoteProcess.md
Last active November 28, 2023 07:32
DOI-endnote-process

Scripts for endnote librart processing.

  • modifyXML.py: To deal with nonsense chars in "Notes" column, reserve Time Cited information; modify improper doi format (remove DOI:, litter case)
  • prepareDOI.py: To pre-process doi number for getPDF.py script.
  • getPDF.py: Search PDF for endnote XML DOI records based on scihub.
    Save the doi number in a file (one doi per line) and use the file as script input.
    Each file save as "10.1021_ci111111a.pdf" in current directory. You have to move the valid file to "Done" Directory and use addPDF.py.
  • addPDF.py: Put found PDF in "Done" Directory, Some pdf don't want to search anymore in "Accept".
    Give a endnote XML as input. Move the PDF to a directory based on doi-paper number. A new xml file will be generated.
    Move all the directories in "Done" to "Endnote library.Data/PDF" and import the new xml file. You may delete old records firstly.
@platinhom
platinhom / 0-Github-scripts.md
Last active December 19, 2015 20:01
Some scripts for github page blog

Some scripts for github page blog

  • newblog.sh: Generate a new post blog with title, time, category, tag.
  • hourlater.sh: Generate new post blog with title, time, category, tag. Can delay the published time.
  • getlink4index.sh: Generate index.md containing directory and pdf links.
  • gitsubmit.sh: Submit the revision by git.
  • gitsubmit-general.sh: Submit the revision by git, use for many repositories.
  • gitall.sh: Git pull/push several repositories.
  • changeRSA.sh: Exchange the ssh-key for exchange user submitting git.
  • init-changeUser.sh: Initial a repository by another user information. Need to setup the second github host(such as two.github.com)
@platinhom
platinhom / 0-GetDataOnline.md
Last active November 26, 2015 20:57
Get some data directly from internet.

Get some data directly from internet.

Need wget/python.

  • getPubChemSDF.sh: Get Pubchem 3D sdf file from a file saving Pubchem CID. You can use echo 123 | ./getPubChemSDF.sh
  • getEMDMap.sh: Get EMD file from a EMD number.
@platinhom
platinhom / 0-PQR-related-process.md
Last active March 15, 2016 20:33
To deal with pqr/pqra/pqrta
@platinhom
platinhom / 0-AmberScripts.md
Last active February 8, 2024 02:24
Some scripts for Amber

This gist contains some scripts for Amber.

  • anteligand.sh: Use antechamber to prepare a ligand for Amber
  • complex_tleap.sh: Use tleap to prepare a ligand-protein complex input parameter file (Amber14)
  • checkPDBID_MDprep.sh: After running many preparation jobs for PDB ligand-protein complexes, you should check whether the preparation is done.
  • rename_water.py: rename water to HOH O,H1,H2 for PDB/PQR

Maybe need some other tools installed, such as pdb2pqr and g09 and so on.