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pymolshortcuts4rnaUpdated.py
15840 lines (12878 loc) · 492 KB
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pymolshortcuts4rnaUpdated.py
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# -*- coding: utf-8 -*-
'''
DESCRIPTION
Loads functions that enable faster work in PyMOL.
When sourced in the pymolrc file by including the line 'run pymolshortcuts.py,
this script defines a number of Python functions upon the startup of PyMOL.
These functions are called shortcuts becasue they are invoked with
shortnames in analogy to keyborad shortcuts. Unlike keyboard shortcuts,
their names consist only of the home keys for faster entry.
The shortcuts are designed to save time and address some shortcommings
of PyMOL that are annoying like no version control for output files.
The variant of this file called pymolshortcutsNobs4.py does not depend
on Python module beuafitulsoup4 which does not come with PyMOL.
INSTALLATION
Source this file from your .pymolrc file on the mac or linux or
from your pymolrc.pml file on Windows by adding the command
below (adjust the file path as appropriate) on a separate line:
run ~/Scripts/PyMOLscripts/pymolshortcuts.py
Enter "SC" to print to the command history window a list of shortcuts.
You will need to edit the paths to your installation of several external applications.
See the section "PATHS to Applications" below.
REQUIREMENTS
Should work for PyMOL running with Python 2.7 and 3.7 interpreters.
Incentive PyMOL built with Anaconda Python3.7 is ideal but not essential.
To use the functions that submit searches to multiple websites from within PyMOL.
install the following packages:
bs4>=4.8.0
requests>=2.22.0
Note that bs4 == beautifulsoup4
With the incentive PyMOL that uses the Anaconda Python as its Python interpreter,
enter the following command on the upper command line in PyMOL:
conda install beautifulsoup4 requests
For the Open Source PyMOL, use the software manager for the Python used to
build PyMOL. E.g., with macports, use "sudo port install py37-bs4 &&
sudo port install py37-requests"
Alternatively, use pip with the python used to install PyMOL:
/opt/local/bin/python3.7 -m pip install --upgrade bs4
/opt/local/bin/python3.7 -m pip install --upgrade requests
The above procedure should work for older versions of Open Source PyMOL.
PLAN B -- BS4FREE VERSION
For older incentrive versions of PyMOL, the installation of external modules is not easy
and it may simpler to forgo the functions that depend on beautiful soup.
For these versions of PyMOL, download pymolshortcutsnobs4.py.
This script lacks the bs4 and request dependent functions.
Source this file from your .pymolrc file on the mac or linux or
from your pymolrc.pml file on Windows by adding the command
below (adjust the file path as appropriate) on a separate line:
run ~/Scripts/PyMOLscripts/pymolshortcutsNobs4.py
HELP
To see the documentation for shortcut, enter at the PyMOL prompt:
help <ShortCutName>
e.g.,
help AO
The documentation for a shortcut includes a 1) description of the shortcut,
2) one or more examples of its usage, 3) the corresponding PyMOL Macro
Language codeas vertical script, 4) the same as a horizontal script to ease
copying and pasting the code on the command line,
and 5) the corresponding Python code.
Copyright Notice
================
Copyright (c) 2019 Board of Regents for the University of Oklahoma
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Blaine Mooers , PhD
blaine@ouhsc.edu
975 NE 10th St, BRC 466
Department of Biochemistry and Molecular Biology
College of Medicine
Stephenson Cancer Center
University of Oklahoma Health Sciences Center,
Oklahoma City, OK, USA 73104
'''
from __future__ import division, print_function
import subprocess
from math import cos, sin, radians, sqrt
import datetime, time, webbrowser, random, glob
import os, os.path
from pymol import cmd, stored, math, cgo, xray
import numpy
__author__ = "Blaine Mooers"
__copyright__ = "2019 Board of Regents for the University of Oklahoma"
__license__ = "MIT Licencse"
__version__ = "1.0.0"
# Versioning follows follows MAJOR.MINOR[.PATCH] where major releases are not backward compatable.
__credits__ = ["Miriam Shakir", "Safra Shakir"]
# Credits are for people who tested the code, reported bug fixes, made suggestions, etc.
__date__ = "2 October 2019"
__maintainer__ = "Blaine Mooers"
__email__ = "blaine-mooers@ouhsc.edu"
__status__ = "Production"
cmd.set('ray_opaque_background','on')
################################## Edit PATHS to local directories of files ###############################################
# $HOME/ is the user's main directory: /Users/username or /home/username. r'$HOME' is equivalent to ~.
localPDBfilePath = r'$HOME/pdbFiles/'
localEMAPfilePath = r'$HOME/emapFiles/'
localHKLfilePath = r'$HOME/hklFiles/'
AppPaths='''You may have to edit the file paths to your applications around line 477 in pymolshortcut.py.'''
print(AppPaths)
################################## Edit PATHS to Applications ###############################################
#
# Find your operating system from the three sets of paths or commands below.
# The default OS is Mac.
# If your computer is not a Mac, comment out the Mac set and uncomment the set for your operating system.
# Comment out the paths to the applications that you lack.
#
# The paths are for my Mac OS 10.14 with some applications stored in /usr/local
# and some in /opt/local/bin thanks to macports.
# Some paths can be found by entering "which <program>" in a terminal window.
#
# You can replace the file path with a command to open the application.
# For example, you can use the command "open -a bbedit" on the Mac.
# This approach is the preferred one: it avoids the spinning ball.
# The analogous command is "start" on Windows.
#
################################## Mac Open Commands and PATHS to Applications ###############################################
# Data analysis
DBBrowserSQLiteOpen = ['open','-a','DBBrowserForSQLite']
DBBrowserSQLitePath = '/Applications/DBBrowserForSQLite.app/Contents/MacOS/DB\ Browser\ for\ SQLite'
excelOpen = ['open','-a','Microsoft Excel']
excelPath = r'/Applications/Microsoft\ Excel.app/Contents/MacOS/Microsoft\ Excel'
JabRefOpen = ['open','-a','JabRef.app']
JabRefPath = r'/Applications/JabRef.app/Contents/MacOS/JavaApplicationStub'
jaspOpen = ['open','-a','JASP.app']
jaspPath = r'Applications/JASP.app/Contents/MacOS/JASP'
jmpOpen = ['open','-a','JMP Pro 14.app']
jmpPath = r'/Applications/JMP\ Pro\ 14.app/Contents/MacOS/JMP'
juliaOpen = ['open','-a','Julia-1.2.app']
juliaPath = r'/Applications/Julia-1.2.app/Contents/MacOS/applet'
juliaproOpen = ['open','-a','JuliaPro-1.2.0-1.app']
juliaproPath = r'/Applications/JuliaPro-1.2.0-1.app/Contents/MacOS/applet'
jupyterPath = r'/opt/local/Library/Frameworks/Python.framework/Versions/3.7/bin/jupyter-notebook'
octaveCommand = '/Applications/MacPorts/Octave.app/Contents/MacOS/Octave'
octaveOpen = ['open', '-n','-a','/Applications/MacPorts/Octave.app/Contents/MacOS/Octave']
octavePath = '/Applications/MacPorts/Octave.app/Contents/MacOS/Octave'
Rpath = r'/usr/local/bin/R'
ROpen = ['open','-a','R']
RStudioOpen = ['open','-a','RStudio']
RStudioPath = r'/Applications/RStudio.app/Contents/MacOS/Rstudio'
# Image manipulation programs
gimpOpen=['/opt/local/bin/gimp','-n']
gimpPath = r'/opt/local/bin/gimp'
inkscapeCommand = ['/opt/local/bin/inkscape','--file=','fileName']
inkscapeOpen = ['/opt/local/bin/inkscape']
inkscapePath = '/opt/local/bin/inkscape'
pptOpen = ['open','-a','Microsoft PowerPoint']
pptPath = r'/Applications/Microsoft\ Excel.app/Contents/MacOS/Microsoft\ PowerPoint'
# Molecular graphics programs
ccp4mgCommand = ['/Applications/ccp4-7.0/QtMG.app/Contents/MacOS/QtMG','shell=True']
ccp4mgOpen = ['open','-n','-a','QtMG.app']
ccp4mgPath = r'/Applications/ccp4-7.0/QtMG.app/Contents/MacOS/QtMG'
chimeraOpen = ['open','-a','Chimera.app']
chimeraPath = r'/Applications/Chimera.app/Contents/MacOS/chimera'
cootOpen =['open','-a','coot.app']
cootPath = '/usr/local/bin/coot'
jmolCommand = 'java -jar /Applications/jars/jmol-14.29.54/Jmol.jar'
jmolOpen = ['java','-jar','/Applications/jars/jmol-14.29.54/Jmol.jar']
jmolPath = '/Applications/jars/jmol-14.29.54/Jmol.jar'
yasaraOpen = ['open','-a','YASARA.app']
yasaraPath = r'/Applications/YASARA.app/Contents/MacOS/yasara.app'
vmdOpen = ['open','-a','VMD194.app']
vmdPath = r'/Applications/VMD194.app/Contents/MacOS/startup.command'
# Text editors
atomOpen = ['open','-a','atom']
atomPath = r'/usr/local/bin/atom'
atomStart = ['start','atom']
bbeditOpen = ['open','-a','bbedit']
bbeditPath = r'/usr/local/bin/bbedit'
codeOpen = ['/usr/local/bin/code']
codePath = r'/usr/local/bin/code'
emacsCommand = ['open','-a','Emacs.app', '"$@"']
emacsOpen = ['open','-a','Emacs.app']
emacsPath = r'/opt/local/bin/emacs'
geditOpen = ['open','-a','gedit2.30.2.app']
geditPath = r'/Applications/gedit2.30.2.app/Contents/MacOS/gedit'
jeditOpen = ['open','-a','jEdit.app']
jeditPath = r'/Applications/jEdit.app/Contents/MacOS/jedit'
neovimPath = r'/Users/blaine/software/nvim-osx64/bin/nvim'
neovimOpen = ['open','-n','-a','/Users/blaine/software/nvim-osx64/bin/nvim']
nppOpen = ['open','-a','Notepad++.app']
nppPath = r'/Applications/Notepad++.app/Contents/MacOS/startwine'
oniOpen = ['open','-a','Oni.app']
oniPath = r'/Applications/Oni.app/Contents/MacOS/Oni'
pdbeditorOpen = ['java','-jar','/Applications/jars/PDB_Editor_FIX090203.jar']
pdbeditorPath = r'/Applications/jars/PDB_Editor_FIX090203.jar'
sublimeText3Open = ['/usr/local/bin/subl','test.pml']
sublimeText3Path = r'/usr/local/bin/subl'
textmatePath = r'/usr/local/bin/mate'
textMateOpen = ['open','-a','TextMate']
vimPath = r'/opt/local/bin/vim'
vimOpen = ['open','-a','MacVim.app']
#Terminals
itermOpen = ['open','-n','-a','iTerm.app']
terminalOpen = ['open','-n','-a','Terminal.app']
xquartzOpen = ['open','-n','-a','XQuartz.app']
x11Open = ['open','-n','-a','X11.app']
# Web sites
gcalURL = 'https://calendar.google.com/calendar/r'
gmailURL = 'https://mail.google.com/mail/u/0/#inbox'
webmailURL = 'https://webmail.ouhsc.edu/owa/auth/logon.aspx?replaceCurrent=1&url=http%3a%2f%2fwebmail.ouhsc.edu%2fowa%2f'
weatherServiceRadarURL = 'https://radar.weather.gov/radar.php?rid=TLX'
# Web static sites
atsasURL = 'https://www.embl-hamburg.de/biosaxs/download.html'
scatterURL = 'http://www.bioisis.net/tutorial/9'
bioxtasrawURL = 'https://bioxtas-raw.readthedocs.io/en/latest/manual/Introduction_to_RAW_and_this_documentation.html'
acaURL = 'http://www.amercrystalassn.org'
alsURL = 'https://als.lbl.gov/'
apsURL = 'https://www.aps.anl.gov/'
biocatURL = 'https://www.bio.aps.anl.gov/pages/links.html'
sasbdbURL = 'https://www.sasbdb.org/'
chimeriaURL = 'https://www.cgl.ucsf.edu/chimera/'
chessURL = 'https://www.chess.cornell.edu'
emdbURL = 'https://www.ebi.ac.uk/pdbe/emdb/'
epURL = 'https://github.com/MooersLab/EasyPyMOL'
jmURL = 'http://wiki.jmol.org/index.php/Main_Page'
lbsfURL = 'https://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx'
ouMCLURL = 'http://structuralbiology.ou.edu/mcl'
molgrURL = 'https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html'
molgrwikiURL = 'https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems'
nslsIIURL = 'https://www.bnl.gov/ps/'
ndbURL = 'http://ndbserver.rutgers.edu'
ppcURL = 'http://www.ou.edu/cas/chemistry/research/research-support-services/protein-production-core'
psURL = 'https://www.proteinsociety.org/'
rsURL = 'https://www.rnasociety.org/'
saxsURL = 'https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0'
saxierURL = 'https://www.saxier.org/forum/'
ssrlbl42URL = 'https://www-ssrl.slac.stanford.edu/~saxs/'
sbgridURL= 'https://www.youtube.com/user/SBGridTV/videos'
ssrlsmbURL = 'http://smb.slac.stanford.edu'
ssurfURL = 'http://www.ssurf.org'
scipyURL = 'https://www.scipy2019.scipy.org'
#### Web search sites
# Send search term to Amazon.com
abURL = 'https://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Dstripbooks&field-keywords='
anacondaURL = 'https://anaconda.org/search?q='
# Send search term to arxiv
axURL = 'https://arxiv.org/search/?query='
# Send search term to Biorxiv
bxURL = 'https://www.biorxiv.org/search/'
gbURL = 'https://www.google.com/search?tbm=bks&q='
ghURL = 'https://www.github.com/search?q='
# Send search terms to Google.com.
goURL = 'http://www.google.com/search?btnG=1&q='
# Had to use Sweden's Google Scholar.
gsURL = 'https://scholar.google.se/scholar?hl=en&q='
gsnURL = 'https://scholar.google.se/scholar?hl=en&q='
# Send search terms to Google Videos.
gvURL = 'https://www.google.com/videohp/search?btnG=1&q='
# Send search terms to PubMed.
ipmURL = 'https://www.ncbi.nlm.nih.gov/pubmed/?term='
iucrURL = 'https://journals.iucr.org/'
stackoverflowURL = 'https://stackoverflow.com/search?q='
spnURL = 'https://www.springer.com/gp/search?query='
spURL = 'https://www.springer.com/gp/search?query='
scienceDirectURL1 = 'https://www.sciencedirect.com/search/advanced?qs='
scienceDirectURL2 = '&show=100&sortBy=relevance'
rgnURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
rgURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
pwURL = 'https://pymolwiki.org/index.php/'
pmlURL = 'https://sourceforge.net/p/pymol/mailman/search/?q='
pmlnURL = 'https://sourceforge.net/p/pymol/mailman/search/?q='
pmURL = 'https://www.ncbi.nlm.nih.gov/pubmed/?term='
pdbURL = 'https://www.rcsb.org/structure/'
pdbnURL = 'https://www.rcsb.org/structure/'
pymolURL = 'https://pymolwiki.org/index.php/'
researchGateURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
scienceDirectURL1 = 'https://www.sciencedirect.com/search/advanced?qs='
scienceDirectURL2 = '&show=100&sortBy=relevance'
sourceForgeURL = "https://sourceforge.net/directory/os:mac/?q="
springerBooksURL1 = 'https://www.springer.com/gp/search?query='
springerBooksURL2 = '&submit=Submit+Query'
#wordProcessor
wordOpen = ['open','-a','Microsoft Word.app']
# Optional local mirror of the PDB
local_mirror_divided = '/mnt/bio/db/pdb.divided'
# ################################## Linux run commands and PATHS to Applications ###############################################
#
# # Data analysis
# DBBrowserSQLiteStart = ['DBBrowserForSQLite']
# DBBrowserSQLitePath = '/Applications/DBBrowserForSQLite/Contents/MacOS/DB\ Browser\ for\ SQLite'
# excelOpen = ['Microsoft Excel']
# excelPath = '/Applications/Microsoft\ Excel/Contents/MacOS/Microsoft\ Excel'
# jabrefOpen = ['JabRef'] '/Applications/JabRef/Contents/MacOS/JavaApplicationStub'
# jabrefPath = '/Applications/JabRef/Contents/MacOS/JavaApplicationStub'
# jaspOpen = ['JASP']
# jaspPath = 'Applications/JASP/Contents/MacOS/JASP'
# jmpOpen = ['JMP Pro 14']
# jmpPath = '/Applications/JMP\ Pro\ 14/Contents/MacOS/JMP'
# juliaOpen = ['Julia-1.2']
# juliaPath = '/Applications/Julia-1.2/Contents/MacOS/applet'
# jupyterPath = '/opt/local/Library/Frameworks/Python.framework/Versions/3.7/bin/jupyter-notebook'
# RstudioPathOpen = ['RStudio']
# RstudioPath = '/Applications/RStudio/Contents/MacOS/Rstudio'
#
#
# # Local files
# localPDBfilePath = '$HOME/pdbFiles/'
# localEMAPfilePath = '$HOME/emapFiles/'
# localHKLfilePath = '$HOME/hklFiles/'
#
# # Image manipulation programs
# gimp = '/usr/local/bin/gimp'
# inkscapePath = '/opt/local/bin/inkscape'
# pptOpen = ['Microsoft PowerPoint']
# pptPath = '/Applications/Microsoft\ Excel/Contents/MacOS/Microsoft\ PowerPoint'
#
#
# # Molecular graphics programs
# ccp4mgPath = '/Applications/ccp4-7.0/ccp4i2/Contents/MacOS/ccp4mg'
# chimeraOpen = ['Chimera']
# chimeraPath = '/Applications/Chimera/Contents/MacOS/chimera'
# cootPath = '/usr/local/bin/coot'
# jmolPath = 'java -jar /Applications/jars/jmol-14.29.52/Jmol.jar'
# yasaraOpen = ['YASARA']
# yasaraPath = '/Applications/YASARA/Contents/MacOS/yasara'
# vmdOpen = ['VMD194']
# vmdPath = '/Applications/VMD194/Contents/MacOS/startup.command'
#
#
# # Text editors
# atomOpen = ['atom']
# atomPath = '/usr/local/bin/atom'
# atomStart = ['start','atom']
# codeOpen = ['code']
# codePath = '/usr/local/bin/code'
# emacsOpen = ['emacs']
# emacsPath = '/opt/local/bin/emacs'
# geditOpen = ['gedit2.30.2']
# geditPath = '/Applications/gedit2.30.2/Contents/MacOS/gedit'
# jeditOpen = ['jEdit']
# jeditPath = '/usr/local/bin/jEdit'
# neovimPath = '$HOME/software/nvim-osx64/bin/nvim'
# nppOpen = ['Notepad++']
# nppPath = '/usr/local//Notepad++/Contents/MacOS/startwine'
# oniOpen = ['Oni']
# oniPath = '/Applications/Oni/Contents/MacOS/Oni'
# pdbedPath = 'java -jar /Applications/jars/PDB_Editor_FIX090203.jar'
# sublOpen = ['subl']
# sublimeText3Path = '/usr/local/bin/subl'
# textmatePath = '/usr/local/bin/mate'
# textmateOpen = ['mate']
# vimPath = '/usr/local/bin/vim'
#
#
# #Terminals
# itermOpen = ['iTerm','-n','"`pwd`"']
# terminalOpen = ['Terminal','-n','"`pwd`"']
# x11termOpen = ['XQuartz','-n','"`pwd`"']
#
#
# # Web sites
# gcalPath = 'firefox https://calendar.google.com/calendar/r'
# gmailPath = 'firefox https://mail.google.com/mail/u/0/#inbox'
# webmailPath = 'firefox https://webmail.ouhsc.edu'
# weatherServicePath = 'firefox https://radar.weather.gov/radar.php?rid=TLX'
#
#
# wordProcessor
# wordOpen = ['open','-a','Microsoft Word']
#
# # Optional local mirror of the PDB
# local_mirror_divided = '/mnt/bio/db/pdb.divided'
# ###################### Windows Start Commands and PATHS to Applications###########################
#
# # Data analysis
# DBBrowserSQLiteStart = ['start','DBBrowserForSQLite']
# DBBrowserSQLitePath = '/Applications/DBBrowserForSQLite.exe/Contents/MacOS/DB\ Browser\ for\ SQLite'
# excelStart = ['start','Microsoft Excel']
# excelPath = '/Applications/Microsoft\ Excel.exe/Contents/MacOS/Microsoft\ Excel'
# jabrefStart = ['start','JabRef.exe'] '/Applications/JabRef.exe/Contents/MacOS/JavaApplicationStub'
# jabrefPath = '/Applications/JabRef.exe/Contents/MacOS/JavaApplicationStub'
# jaspStart = ['start','JASP.exe']
# jaspPath = 'Applications/JASP.exe/Contents/MacOS/JASP'
# jmpStart = ['start','JMP Pro 14.exe']
# jmpPath = '/Applications/JMP\ Pro\ 14.exe/Contents/MacOS/JMP'
# juliaStart = ['start','Julia-1.2.exe']
# juliaPath = '/Applications/Julia-1.2.exe/Contents/MacOS/applet'
# jupyterPath = '/opt/local/Library/Frameworks/Python.framework/Versions/3.7/bin/jupyter-notebook'
# RstudioPathStart = ['start','RStudio']
# RstudioPath = '/Applications/RStudio.exe/Contents/MacOS/Rstudio'
#
#
# # Local files
# localPDBfilePath = '$HOME/pdbFiles/'
# localEMAPfilePath = '$HOME/emapFiles/'
# localHKLfilePath = '$HOME/hklFiles/'
#
# # Image manipulation programs
# gimp = '/usr/local/bin/gimp'
# inkscapePath = '/opt/local/bin/inkscape'
# pptStart = ['start','Microsoft PowerPoint']
# pptPath = '/Applications/Microsoft\ Excel.exe/Contents/MacOS/Microsoft\ PowerPoint'
#
#
# # Molecular graphics programs
# ccp4mgPath = '/Applications/ccp4-7.0/ccp4i2.exe/Contents/MacOS/ccp4mg'
# chimeraStart = ['start','Chimera.exe']
# chimeraPath = '/Applications/Chimera.exe/Contents/MacOS/chimera'
# cootPath = '/usr/local/bin/coot'
# jmolPath = 'java -jar /Applications/jars/jmol-14.29.52/Jmol.jar'
# yasaraStart = ['start','YASARA.exe']
# yasaraPath = '/Applications/YASARA.exe/Contents/MacOS/yasara.exe'
# vmdStart = ['start','VMD194.exe']
# vmdPath = '/Applications/VMD194.exe/Contents/MacOS/startup.command'
#
# # Text editors
# atomStart = ['start','atom']
# atomPath = '/usr/local/bin/atom'
# atomStart = ['start','atom']
# codeStart = ['start','code']
# codePath = '/usr/local/bin/code'
# codeStart = ['start','code']
# emacsStart = ['start','emacs']
# emacsPath = '/opt/local/bin/emacs'
# geditStart = ['start','gedit2.30.2.exe']
# geditPath = '/Applications/gedit2.30.2.exe/Contents/MacOS/gedit'
# jeditStart = ['start','jEdit.exe']
# jeditPath = '/Applications/jEdit.exe/Contents/MacOS/jedit'
# neovimPath = '/Users/blaine/software/nvim-osx64/bin/nvim'
# nppStart = ['start','Notepad++.exe']
# nppPath = '/Applications/Notepad++.exe/Contents/MacOS/startwine'
# oniStart = ['start','Oni.exe']
# oniPath = '/Applications/Oni.exe/Contents/MacOS/Oni'
# pdbedPath = 'java -jar /Applications/jars/PDB_Editor_FIX090203.jar'
# sublStart = ['start','subl']
# sublimeText3Path = '/usr/local/bin/subl'
# textmatePath = '/usr/local/bin/mate'
# textmateStart = ['start','mate']
# vimPath = '/opt/local/bin/vim'
#
#
# #Terminals
# itermStart = ['start','iTerm.exe','-n','"`pwd`"']
# terminalStart = ['start','Terminal','-n','"`pwd`"']
# x11termStart = ['start','XQuartz','-n','"`pwd`"']
#
# # Web sites
# gcalPath = 'open -a Safari.exe https://calendar.google.com/calendar/r'
# gmailPath = 'open -a Safari.exe https://mail.google.com/mail/u/0/#inbox'
# webmailPath = 'open -a Safari.exe https://webmail.ouhsc.edu'
# weatherServicePath = 'open -a Safari.exe https://radar.weather.gov/radar.php?rid=TLX'
#
# #wordProcessor
# wordStart = ['start','Microsoft Word.exe']
# # Optional local mirror of the PDB
# local_mirror_divided = '/mnt/bio/db/pdb.divided'
########################################################################################################
def AB(searchTerm="pymol"):
'''
DESCRIPTION:
Send search term or phrase to Amazon.com Books in default browser.
USAGE:
AB
ARGUMENTS:
searchTerm
EXAMPLE:
AB
MORE DETAILS:
Send search term or phrase to Amazon.com Books in default browser.
The search phrase does not need to be enclosed in quotes.
The second argument is the number of hits to return.
The default web browser is used.
VERTICAL PML SCRIPT:
url = 'https://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Dstripbooks&field-keywords=';
webbrowser.open(url+searchTerm)
HORIZONTAL PML SCRIPT:
url = 'https://www.amazon.com/s/ref=nb_sb_noss_2?url=search-alias%3Dstripbooks&field-keywords=';webbrowser.open(url+searchTerm)
PYTHON CODE:
def AB(searchTerm="pymol"):
url = abURL
try:
print("Sending", searchTerm, " to Amazon.com Books in default browser.");
# URL must be in single quotes
webbrowser.open_new_tab(url+searchTerm)
print("Sent ", searchTerm, "to Amazon.com Books in default browser.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('AB',AB)
'''
url = abURL
try:
print("Sending", searchTerm, " to Amazon.com Books in default browser.");
# URL must be in single quotes
webbrowser.open_new_tab(url+searchTerm)
print("Sent ", searchTerm, "to Amazon.com Books in default browser.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('AB',AB)
def AC(searchTerm='pymol'):
'''
DESCRIPTION:
Send search term to Anaconda Cloud.
USAGE:
AC
ARGUMENTS:
NA
EXAMPLE:
AC
MORE DETAILS:
Send search term to Anaconda Cloud.
May have to login first on default browser.
VERTICAL PML SCRIPT:
NA
HORIZONTAL PML SCRIPT:
NA
PYTHON CODE:
def AC(searchTerm='pymol'):
url=anacondaURL
try:
print("Sending ", searchTerm, " to the Anaconda Cloud webpage in default browser. May have to register and login in first.");
webbrowser.open_new_tab(url+searchTerm)
print("Sent ", searchTerm, " to Anaconda Cloud in default browser.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('AC',AC)
'''
url=anacondaURL
try:
print("Sending ", searchTerm, " to the Anaconda Cloud webpage in default browser. May have to register and login in first.");
webbrowser.open_new_tab(url+searchTerm)
print("Sent ", searchTerm, " to Anaconda Cloud in default browser.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('AC',AC)
def ACA():
'''
DESCRIPTION:
Open the American Crystallographic Association Annual Meeting webpage.
USAGE:
ACA
ARGUMENTS:
NA
EXAMPLE:
ACA
MORE DETAILS:
Open the American Crystallographic Association Annual Meeting webpage.
VERTICAL PML SCRIPT:
NA
HORIZONTAL PML SCRIPT:
NA
PYTHON CODE:
def ACA():
url=acaURL
try:
print("Trying to open American Crystallographic Association (ACA) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening ACA homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('ACA',ACA)
'''
url=acaURL
try:
print("Trying to open American Crystallographic Association (ACA) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening ACA homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('ACA',ACA)
def ALS():
'''
DESCRIPTION:
Open website of the Advanced Light Source.
USAGE:
ALS
ARGUMENTS:
NA
EXAMPLE:
ALS
MORE DETAILS:
Open website of the Advanced Light Source.
VERTICAL PML SCRIPT:
NA
HORIZONTAL PML SCRIPT:
NA
PYTHON CODE:
def ALS():
url=alsURL
try:
print("Trying to open Advanced Light Source (ALS) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening ALS homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('ALS',ALS)
'''
url=alsURL
try:
print("Trying to open Advanced Light Source (ALS) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening ALS homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('ALS',ALS)
def AO():
'''
DESCRIPTION:
Commands to make ambient occlusion image like those in Qutemole.
USAGE:
AO
ARGUMENTS:
None
EXAMPLE:
AO
MORE DETAILS:
Commands to make ambient occlusion image like those in Qutemole.
Works only with the command line immediately under the command
history window at the top of the gui.
VERTICAL PML SCRIPT:
set_color oxygen, [1.0,0.4,0.4];
set_color nitrogen, [0.5,0.5,1.0];
remove solvent;
as spheres;
util.cbaw;
bg white;
set light_count,10;
set spec_count,1;
set shininess, 10;
set specular,0.25;
set ambient,0;
set direct,0;
set reflect,1.5;
set ray_shadow_decay_factor, 0.1;
set ray_shadow_decay_range, 2;
set depth_cue, 0;
ray
HORIZONTAL PML SCRIPT:
set_color oxygen, [1.0,0.4,0.4];set_color nitrogen, [0.5,0.5,1.0];remove solvent;as spheres;util.cbaw;bg white;set light_count,8;set spec_count,1;set shininess, 10;set specular,0.25;set ambient,0;set direct,0;set reflect,1.5;set ray_shadow_decay_factor, 0.1;set ray_shadow_decay_range, 2;set depth_cue,0;color gray20, symbol c;ray
PYTHON CODE:
def AO():
cmd.set_color("oxygen", "[1.0,0.4,0.4]")
cmd.set_color("nitrogen", "[0.5,0.5,1.0]")
cmd.remove("solvent")
cmd.show_as("spheres")
cmd.util.cbaw()
cmd.bg_color("white")
cmd.set("light_count", "8")
cmd.set("spec_count", "1")
cmd.set("shininess", "10")
cmd.set("specular", "0.25")
cmd.set("ambient", "0")
cmd.set("direct", "0")
cmd.set("reflect", "1.5")
cmd.set("ray_shadow_decay_factor", "0.1")
cmd.set("ray_shadow_decay_range", "2")
cmd.set("depth_cue","0")
cmd.set("ray_opaque_background","on")
cmd.ray()
cmd.extend('AO',AO)
'''
cmd.set_color("oxygen", "[1.0,0.4,0.4]")
cmd.set_color("nitrogen", "[0.5,0.5,1.0]")
cmd.remove("solvent")
cmd.show_as("spheres")
cmd.util.cbaw()
cmd.bg_color("white")
cmd.set("light_count", "8")
cmd.set("spec_count", "1")
cmd.set("shininess", "10")
cmd.set("specular", "0.25")
cmd.set("ambient", "0")
cmd.set("direct", "0")
cmd.set("reflect", "1.5")
cmd.set("ray_shadow_decay_factor", "0.1")
cmd.set("ray_shadow_decay_range", "2")
cmd.set("depth_cue","0")
cmd.set("ray_opaque_background","on")
cmd.ray()
cmd.extend('AO',AO)
def AOD():
'''
DESCRIPTION:
Make ambient occlusion image of any with dark carbon atoms.
USAGE:
AOD
ARGUMENTS:
None
EXAMPLE:
AOD
MORE DETAILS:
Type "help AOD" to see this documentation printed to the command history window.
Select from the command history individual lines of code to build a new script.
Select the hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the comand line below. Works only
with the command line immediately under the command history window at
the top of the gui.
VERTICAL PML SCRIPT:
set_color oxygen, [1.0,0.4,0.4];
set_color nitrogen, [0.5,0.5,1.0];
remove solvent;
as spheres;
util.cbaw;
bg white;
set light_count,8;
set spec_count,1;
set shininess, 10;
set specular,0.25;
set ambient,0;
set direct,0;
set reflect,1.5;
set ray_shadow_decay_factor, 0.1;
set ray_shadow_decay_range, 2;
set depth_cue, 0;
color gray20, symbol c
color gray90, symbol h
ray
HORIZONTAL PML SCRIPT:
set_color oxygen, [1.0,0.4,0.4];set_color nitrogen, [0.5,0.5,1.0];remove solvent;as spheres;util.cbaw;bg white;set light_count,8;set spec_count,1;set shininess, 10;set specular,0.25;set ambient,0;set direct,0;set reflect,1.5;set ray_shadow_decay_factor, 0.1;set ray_shadow_decay_range, 2;set depth_cue,0;color gray20, symbol c;color gray70, symbol h;ray
PYTHON CODE:
def AOD():
cmd.set_color("oxygen", "[1.0,0.4,0.4]")
cmd.set_color("nitrogen", "[0.5,0.5,1.0]")
cmd.remove("solvent")
cmd.show_as("spheres")
cmd.util.cbaw()
cmd.set_color("carbon", "[0.00 , 0.00 , 0.0]")
cmd.bg_color("white")
cmd.set("light_count","8")
cmd.set("spec_count", "1")
cmd.set("shininess", "10")
cmd.set("specular", "0.25")
cmd.set("ambient", "0")
cmd.set("direct", "0")
cmd.set("reflect", "1.5")
cmd.set("ray_shadow_decay_factor", "0.1")
cmd.set("ray_shadow_decay_range", "2")
cmd.set("depth_cue","0")
cmd.color("gray20", "symbol c")
cmd.color("gray90", "symbol h")
cmd.set("ray_opaque_background","on")
cmd.ray()
cmd.extend("AOD",AOD)
'''
cmd.set_color("oxygen", "[1.0,0.4,0.4]")
cmd.set_color("nitrogen", "[0.5,0.5,1.0]")
cmd.remove("solvent")
cmd.show_as("spheres")
cmd.util.cbaw()
cmd.set_color("carbon", "[0.00 , 0.00 , 0.0]")
cmd.bg_color("white")
cmd.set("light_count","8")
cmd.set("spec_count", "1")
cmd.set("shininess", "10")
cmd.set("specular", "0.25")
cmd.set("ambient", "0")
cmd.set("direct", "0")
cmd.set("reflect", "1.5")
cmd.set("ray_shadow_decay_factor", "0.1")
cmd.set("ray_shadow_decay_range", "2")
cmd.set("depth_cue","0")
cmd.color("gray20", "symbol c")
cmd.color("gray90", "symbol h")
cmd.set("ray_opaque_background","on")
cmd.ray()
cmd.extend("AOD",AOD)
def APS():
'''
DESCRIPTION:
Open website of the Advanced Photon Source.
USAGE:
APS
ARGUMENTS:
NA
EXAMPLE:
APS
MORE DETAILS:
Open website of the Advanced Photon Source.
VERTICAL PML SCRIPT:
NA
HORIZONTAL PML SCRIPT:
NA
PYTHON CODE:
def APS():
url=apsURL
try:
print("Trying to open Advanced Photon Source (APS) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening APS homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('APS',APS)
'''
url=apsURL
try:
print("Trying to open Advanced Photon Source (APS) homepage.");
# URL must be in single quotes
webbrowser.open_new_tab(url)
print("Success opening APS homepage.")
except Exception as e:
print("Webbrowser error: " % e) # prints error if browser is not found
cmd.extend('APS',APS)
def AX(searchTerm="pymol"):
'''
DESCRIPTION:
Send search term or phrase to arXiv.
USAGE:
AX
ARGUMENTS:
searchTerm
EXAMPLE:
AX
MORE DETAILS:
Send search term or phrase to arXiv.
The search phrase does not need to be enclosed in quotes.
The default web browser is used.