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pymolshortcutsNoDateTime.py
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pymolshortcutsNoDateTime.py
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# -*- coding: utf-8 -*-
'''
DESCRIPTION
Loads functions that enable faster work in PyMOL.
To source this script on startup of PyMOL, include the
following line:
run pymolshortcuts.py
This script defines a number of Python functions or shortcts.
These functions are called shortcuts becasue they are invoked with
shortnames in analogy to keyborad shortcuts. Unlike keyboard
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 pymolshortcuts.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.
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
__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__ = "6 November 2019"
__maintainer__ = "Blaine Mooers"
__email__ = "blaine-mooers@ouhsc.edu"
__status__ = "Production"
from pymol import cmd, stored, math, cgo, xray
from math import cos, sin, radians, sqrt
import time
import webbrowser
import random
import glob
import os
import os.path
import numpy
import subprocess
# Set the background to opaque white.
cmd.set('ray_opaque_background','on')
# ################ Edit PATHS to local directories of files #########
# $HOME/ is the user's main directory:
# /Users/username on Mac OS
# /home/username on Linux
# $HOME is equivalent to ~.
localPDBfilePath = r'$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']
excelOpen = ['open','-a','Microsoft Excel']
JabRefOpen = ['open','-a','JabRef.app']
jaspOpen = ['open','-a','JASP.app']
jmpOpen = ['open','-a','JMP Pro 14.app']
juliaOpen = ['open','-a','Julia-1.2.app']
juliaproOpen = ['open','-a','JuliaPro-1.2.0-1.app']
octaveOpen = ['open',
'-n',
'-a',
'/Applications/MacPorts/Octave.app/Contents/MacOS/Octave']
ROpen = ['open','-a','R']
RStudioOpen = ['open','-a','RStudio']
# Image manipulation programs
gimpOpen=['/opt/local/bin/gimp','-n']
inkscapeCommand = ['/opt/local/bin/inkscape','--file=','fileName']
inkscapeOpen = ['/opt/local/bin/inkscape']
pptOpen = ['open','-a','Microsoft PowerPoint']
# Molecular graphics programs
ccp4mgOpen = ['open','-n','-a','QtMG.app']
chimeraOpen = ['open','-a','Chimera.app']
cootOpen =['open','-a','coot.app']
jmolOpen = ['java','-jar','/Applications/jars/jmol-14.29.54/Jmol.jar']
yasaraOpen = ['open','-a','YASARA.app']
vmdOpen = ['open','-a','VMD194.app']
# Text editors
atomOpen = ['open','-a','atom']
atomStart = ['start','atom']
bbeditOpen = ['open','-a','bbedit']
codeOpen = ['/usr/local/bin/code']
emacsCommand = ['open','-a','Emacs.app', '"$@"']
emacsOpen = ['open','-a','Emacs.app']
geditOpen = ['open','-a','gedit2.30.2.app']
jeditOpen = ['open','-a','jEdit.app']
neovimOpen = ['open',
'-n',
'-a',
'/Users/blaine/software/nvim-osx64/bin/nvim']
nppOpen = ['open','-a','Notepad++.app']
oniOpen = ['open','-a','Oni.app']
pdbeditorOpen = ['java',
'-jar',
'/Applications/jars/PDB_Editor_FIX090203.jar']
sublimeText3Open = ['/usr/local/bin/subl','test.pml']
textMateOpen = ['open','-a','TextMate']
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='
# Send search terms to anaconda
anacondaURL = 'https://anaconda.org/search?q='
# Send search terms to ArXiv
axURL = 'https://arxiv.org/search/?query='
# Send search terms to BioRxiv
bxURL = 'https://www.biorxiv.org/search/'
# Send search terms to Google Books
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='
# 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/'
# Send search terms to Stackoverflow.
stackoverflowURL = 'https://stackoverflow.com/search?q='
# Send search terms to Springer.
spnURL = 'https://www.springer.com/gp/search?query='
spURL = 'https://www.springer.com/gp/search?query='
# Send search terms to Science Direct.
scienceDirectURL1 = 'https://www.sciencedirect.com/search/advanced?qs='
scienceDirectURL2 = '&show=100&sortBy=relevance'
# Send search terms to Research Gate.
rgnURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
rgURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
# Send search terms to PyMOLWiki
pwURL = 'https://pymolwiki.org/index.php/'
pymolURL = 'https://pymolwiki.org/index.php/'
# Send search terms to PyMOL mailing list
pmlURL = 'https://sourceforge.net/p/pymol/mailman/search/?q='
pmlnURL = 'https://sourceforge.net/p/pymol/mailman/search/?q='
# Send search terms to PubMed
pmURL = 'https://www.ncbi.nlm.nih.gov/pubmed/?term='
# Send search terms to RCSB
pdbURL = 'https://www.rcsb.org/structure/'
pdbnURL = 'https://www.rcsb.org/structure/'
# Send search terms to Research Gate
researchGateURL = 'https://www.researchgate.net/search.Search.html?type=researcher&query='
# Send search terms to Science Direct
scienceDirectURL1 = 'https://www.sciencedirect.com/search/advanced?qs='
scienceDirectURL2 = '&show=100&sortBy=relevance'
# Send search terms to SourceForge
sourceForgeURL = "https://sourceforge.net/directory/os:mac/?q="
# Send search terms to Springer Books
springerBooksURL1 = 'https://www.springer.com/gp/search?query='
springerBooksURL2 = '&submit=Submit+Query'
#wordProcessors
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 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 AOBW():
'''
DESCRIPTION:
Commands to make ambient occlusion image like those in Qutemole but coloring with grayscale.
USAGE:
AOBW
ARGUMENTS:
None
EXAMPLE:
AOBW
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;
gscale
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;gscale;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 AOBW():
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")
gscale()
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('AOBW',AOBW)
'''
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")
gscale()
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('AOBW',AOBW)
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 AODBW():
'''
DESCRIPTION:
Make ambient occlusion image of any with dark carbon atoms in grayscale.
USAGE:
AODBW
ARGUMENTS:
None
EXAMPLE:
AODBW
MORE DETAILS:
Type "help AODBW" 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;
gscale;
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 AODBW():
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]")
gscale()
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('AODBW',AODBW)
'''
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]")
gscale()
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('AODBW',AODBW)
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