class Form extends Group implements FormInterface
Form.
Properties
| array | $fields | Fields. |
Methods
|
__construct(string $name = null, array $options = array(), Request $request = null, array $fields = array())
Constructor. |
||
| ValidatorInterface |
createValidator()
Create a validator. |
|
| TranslatorInterface |
getTranslator()
Get the translator. |
|
| Request |
getRequest()
Get the request from group or a parent. |
|
| string |
name()
Return the name. |
from Group |
|
setName(string $name)
Set the name. |
from Group | |
| integer |
size()
Return the number of fields. |
from Group |
| boolean |
hasFile()
Check if group has a file. |
from Group |
| WidgetManagerInterface |
getWidgetManager()
Return the widgets manager. |
from Group |
|
setWidgetManager(WidgetManager $WidgetManager)
Set the widgets manager. |
from Group | |
| Widget |
render(string|callable $render_callback, Field $field, array $options = array())
Render a field. |
from Group |
| boolean |
isValid($validationGroups = array())
Check if group is valid. |
|
| boolean |
sent()
Check if group's form was sent. |
|
| Report |
errors($validationGroups = array())
Return errors. |
from Group |
|
remove(string $name)
Remove a field. |
from Group | |
| Field|Group |
get(string $name)
Return a field. |
from Group |
|
add(Field|GroupInterface $field, string $name = null)
Add a field. |
from Group | |
| boolean |
has(string $field_name)
Check if has a field. |
from Group |
| GroupInterface |
resetFields()
Reset fields. |
from Group |
| array |
fields()
Return all fields. |
from Group |
|
addFields(array $fields)
Add fields. |
from Group | |
| GroupInterface |
reset()
Reset data. |
from Group |
|
setData(array $data)
Set data. |
from Group | |
| array |
data()
Return data. |
from Group |
|
offsetSet(string $offset, mixed $value)
Array set implementation. |
from Group | |
| boolean |
offsetExists(string $offset)
Array exists implementation. |
from Group |
|
offsetUnset(string $offset)
Array unset implementation. |
from Group | |
| mixed |
offsetGet(string $offset)
Array get implementation. |
from Group |
| boolean |
valid()
Iterator valid implementation. |
from Group |
|
rewind()
Iterator rewind implementation. |
from Group | |
| integer |
current()
Iterator current implementation. |
from Group |
| string |
key()
Iterator key implementation. |
from Group |
| mixed |
next()
Iterator next implementation. |
from Group |
| GroupInterface |
setParent(GroupInterface $parent)
Set parent. |
|
| FormInterface |
getTopForm()
Get top parent form. |
from Group |
|
setFields(array $fields)
Set fields. |
from Group | |
| array |
getParents()
Get all parents. |
from Group |
|
doSave()
Actually perform the group saving. |
||
| Widget |
doRender(string|callable $render_callback, Group|Field $field, array $options)
Pass the doRender call to the parent group/form. |
|
|
setValidatorFactory(ValidatorFactoryInterface $validatorFactory)
Set validator factory dependency. |
||
|
setTranslator(TranslatorInterface $translator)
Set the translator. |
||
|
setRequest(Request $request)
Set the request. |
||
|
setMethod(string $method)
Set the HTTP method. |
||
| string |
getMethod()
Get the HTTP method. |
|
|
setOption(string $option, mixed $value)
Set an option. |
||
| mixed |
getOption(string $option)
Get an option. |
|
| FormInterface |
csrf(boolean $active = true)
Activate CSRF protection. |
|
|
setSaveCallback(callable $saveCallback)
Set the save callback. |
||
|
setPreSaveCallback(callable $preSaveCallback)
Set the pre-save callback. |
||
| boolean |
save($validationGroups = array())
Save the form and its children. |
|
| array |
getGeneralErrors()
Get errors not belonging to a specific field or hidden ones. |
|
| boolean |
uploadSuccess()
Check if content was uploaded successfully. |
|
| string |
open(array $options = array())
Return the opening form tag. |
|
| string |
close()
Return the closing form tag. |
|
| string |
submit(mixed $value, array $options = array())
Return the submit button. |
|
| FormInterface |
fetch()
Fetch data. |
|
| Widget |
getWidget(string|callable $widget, string $name, mixed $value, array $options = array())
Return a new widget instance. |
Details
at line 54
public
__construct(string $name = null, array $options = array(), Request $request = null, array $fields = array())
Constructor.
at line 80
public ValidatorInterface
createValidator()
Create a validator.
at line 100
public TranslatorInterface
getTranslator()
Get the translator.
at line 121
public Request
getRequest()
Get the request from group or a parent.
in Group at line 96
public string
name()
Return the name.
in Group at line 103
public
setName(string $name)
Set the name.
in Group at line 110
public integer
size()
Return the number of fields.
in Group at line 117
public boolean
hasFile()
Check if group has a file.
in Group at line 135
public WidgetManagerInterface
getWidgetManager()
Return the widgets manager.
in Group at line 147
public
setWidgetManager(WidgetManager $WidgetManager)
Set the widgets manager.
in Group at line 155
public Widget
render(string|callable $render_callback, Field $field, array $options = array())
Render a field.
at line 267
public boolean
isValid($validationGroups = array())
Check if group is valid.
at line 218
public boolean
sent()
Check if group's form was sent.
in Group at line 179
public Report
errors($validationGroups = array())
Return errors.
in Group at line 201
public
remove(string $name)
Remove a field.
in Group at line 208
public Field|Group
get(string $name)
Return a field.
in Group at line 215
public
add(Field|GroupInterface $field, string $name = null)
Add a field.
in Group at line 227
public boolean
has(string $field_name)
Check if has a field.
in Group at line 234
public GroupInterface
resetFields()
Reset fields.
in Group at line 242
public array
fields()
Return all fields.
in Group at line 249
public
addFields(array $fields)
Add fields.
in Group at line 258
public GroupInterface
reset()
Reset data.
in Group at line 266
public
setData(array $data)
Set data.
in Group at line 275
public array
data()
Return data.
in Group at line 296
public
offsetSet(string $offset, mixed $value)
Array set implementation.
in Group at line 308
public boolean
offsetExists(string $offset)
Array exists implementation.
in Group at line 316
public
offsetUnset(string $offset)
Array unset implementation.
in Group at line 325
public mixed
offsetGet(string $offset)
Array get implementation.
in Group at line 333
public boolean
valid()
Iterator valid implementation.
in Group at line 341
public
rewind()
Iterator rewind implementation.
in Group at line 349
public integer
current()
Iterator current implementation.
in Group at line 357
public string
key()
Iterator key implementation.
in Group at line 365
public mixed
next()
Iterator next implementation.
at line 319
public GroupInterface
setParent(GroupInterface $parent)
Set parent.
in Group at line 380
public FormInterface
getTopForm()
Get top parent form.
in Group at line 390
public
setFields(array $fields)
Set fields.
in Group at line 398
public array
getParents()
Get all parents.
at line 210
public
doSave()
Actually perform the group saving.
Empty by default but can be overriden.
at line 363
public Widget
doRender(string|callable $render_callback, Group|Field $field, array $options)
Pass the doRender call to the parent group/form.
at line 72
public
setValidatorFactory(ValidatorFactoryInterface $validatorFactory)
Set validator factory dependency.
at line 92
public
setTranslator(TranslatorInterface $translator)
Set the translator.
at line 112
public
setRequest(Request $request)
Set the request.
at line 131
public
setMethod(string $method)
Set the HTTP method.
at line 140
public string
getMethod()
Get the HTTP method.
at line 147
public
setOption(string $option, mixed $value)
Set an option.
at line 155
public mixed
getOption(string $option)
Get an option.
at line 164
public FormInterface
csrf(boolean $active = true)
Activate CSRF protection.
at line 175
public
setSaveCallback(callable $saveCallback)
Set the save callback.
at line 183
public
setPreSaveCallback(callable $preSaveCallback)
Set the pre-save callback.
at line 191
public boolean
save($validationGroups = array())
Save the form and its children.
at line 253
public array
getGeneralErrors()
Get errors not belonging to a specific field or hidden ones.
at line 274
public boolean
uploadSuccess()
Check if content was uploaded successfully.
at line 281
public string
open(array $options = array())
Return the opening form tag.
at line 297
public string
close()
Return the closing form tag.
at line 309
public string
submit(mixed $value, array $options = array())
Return the submit button.
at line 328
public FormInterface
fetch()
Fetch data.
at line 388
public Widget
getWidget(string|callable $widget, string $name, mixed $value, array $options = array())
Return a new widget instance.


I am a full stack web developer looking for opportunites to build something amazing.
I am passionate about the creative process that brings the web to life. I am a graduate of the Awesome Inc. web developer bootcamp where I learned a full stack of technologies that range from front-end to back-end development. Below are some examples of my personal and professional work.
My hobbies and interests range from music to the great outdoors. I have played music for most of my life. I enjoy picking up a guitar or sitting down at a piano whenever I get a chance. My idea of a relaxing weekend would be hiking into the woods, fishing for my dinner, and then cooking it over a fire before heading to the tent for the night.
 Uses Vuex and Vue Router.
My bootcamp final project built with Laravel. Includes product ratings and reviews, quick search, a shopping cart and the ability to view past orders.
A freelance WordPress theme that I designed and developed. Includes a custom JavaScript and PHP solution for adding new Google map pins from the dashboard.
My rendition of a cellular automaton devised by the British mathematician John Horton Conway in 1970. Highlights VUE.js.
Custom WordPress theme. Using PHP and MYSQL, I created a login protected file uploader as well as a feature that pulls data from an API for horse statistics.
ADDY award winning Custom WordPress theme that includes a sophisticated PHP sorting algorithm for ordering stallion progeny.
A custom WordPress Theme for the leading consignor of horses in North America.
Custom WordPress theme for central Kentucky's leading home builder
859-753-6767


Copyright (c) Pedro Sena 1994
FILM TITLE: MY TWENTIETH CENTURY DIRECTOR: ENYEDI ILDIKO COUNTRY: HUNGARY ( 1991 ) SUPER FEATURES: SURREALISTIC FILM. MUSIC: Vidovszky Loszlo ( Nice classical passages ) CAST: Dorotha Segda ( both sisters ); Oleg Jankovskiy; Paulus Marker; Andorai Peter; Mate Gabor.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
There aren't many films made today that have a sense of wonder, of, what is all this about anyway?, and that keep you wondering what is all this leading to.
My Twentieth Century is one of those films. The best way I can explain it, is that it reminds me ( A LOT, too ) of Luis Bunuel's style of film making, which was surrealistic, and bounced from the person's mind to external action without any reason, or idea, but all based on the whimsical nature of the character, or characters, involved. Or the director's of course.
The only real theme, this enchanting and very curious film appears to have, is a small subplot, related to Thomas Edison, who is trying, nervously and once again, to prove to people that his telegraph is not a joke, and neither is it a ghost, or trickery, which, is very likely to have happened to him, by people who feared modern discoveries, or the unknown. This film plods along, never explaining anything, although it does have a story of sorts. There is a birth of two girls, twins, Lili and Dora, and they grow up to be separated after they were orphaned, and one has become a spinster and high class prostitute, while the other is a revolutionary ideologist. And a man, whose talents lie in writing, or studying the psychological behavior of people, through his observation of animals, happens to have had an affair with one of them. Along the way, he accidentally bumps into the other sister, whom he thinks is the original, and gets even with her by taking her to bed ( he was robbed before ), ... but in the end there is a sequence full of mirrors, where he gets a look at the two girls, while a voice talks, the seer of his thoughts, perhaps, or is it an alien form which has talked from the start, and plays with the stars, animals, the girls, and him.
And the film, shot in black & white, has an aura of wonder, like the films around the turn of the century did, which makes it really nice. The film floats, easily along, while you wonder what is happening. Amidst all the visual scenes and events, you end up thinking things like this: 1. If this were a film around the beginning of the 20th century, then you would think you were seeing something which was alien. 2. The 20th century was the time when psychology took hold. ( A sociology professor delivers a lecture to women on sexuality and psychology of. ) 3. Do we like seeing 'floating' fantasies, instead of politics, or serious and meaningful faire .? One of the sisters almost drops a bomb on a political figure, but she freezes at the last moment and keeps running off with the bomb in her hand. The fuse ends. The bomb never explodes. 4. And finally, if we are going to see something, give them something which they can never explain. Which was the main theme which led Salvador Dali, Luis Bunuel and Andre Bretton to create the surrealistic movement of art, starting with a manifesto, and a film, which had sequences which may or may not have matched to anything. It defied convention, and your ability to decipher any meaningful understanding, except that it lived, on its own.
This film does.
The fun part of seeing this film is that you can not tell if it is being funny, weird, off the wall, or just plain serious. And it carries you all the way to the end, because it never goes back to explain anything, although it repeats three visual sequences that have each person 'listening' to the stars talk to them, much like people may have thought the telegraph would have done. In fact, this is the only real link it has, the only thread which makes any sense, and it also is the catchy theme, which makes this work, although it is a bit odd. We would have to be transplanted to that time to 'feel' what the wonder was all about.
Nice film. A bit too artsy for those that like entertainment and a good escape or romance. This film is for the free thinkers of the world, and the real appreciators of the fine dialect of film, ... by a Hungarian artist with a surreal boot on his hand.
4 GIBLOONS out of 5
The review above was posted to the
rec.arts.movies.reviews newsgroup (de.rec.film.kritiken for German reviews).
The Internet Movie Database accepts no responsibility for the contents of the
review and has no editorial control. Unless stated otherwise, the copyright
belongs to the author.
Please direct comments/criticisms of the review to relevant newsgroups.
Broken URLs inthe reviews are the responsibility of the author.
The formatting of the review is likely to differ from the original due
to ASCII to HTML conversion.
Related links: index of all rec.arts.movies.reviews reviews


Bill.com files for IPO
Business payments platform Bill.com has filed for an IPO on the New York Stock Exchange in a bid to raise $100 million in capital.
Bill.com hit the $1 billion valuation mark in April thanks to an $88 million funding round led by Franklin Templeton with participation from Mastercard and Fidelity Investments Canada.
Bill.com targets the small and midsize business segment that is still heavily reliant on cheques and, the firm argues, is ripe for disruption.
It has built up a network of more than three million members paying and getting paid with its technology and manages more than $60 billion in annual payment volume.
In its SEC filing, the company said that it had over 81,000 customers using its platform.
Underwriters for its planned offering include Goldman Sachs, BofA Securities, Jeffries and William Blair, among others. Pricing terms have not yet been disclosed. It will trade on the New York Stock Exchange under the ticker symbol “BILL.”


In POSIX sh, /dev/{tcp,udp} is undefined.
(or "In dash, ... is not supported." when using dash
)
echo foo > /dev/tcp/myhost/1234
Rewrite using a tool like netcat (nc
):
echo foo | nc myhost 1234
/dev/tcp/$host/$port
and /dev/udp/$host/$port
are recognized in redirections by bash and ksh, and a socket connection is made instead of opening a file. They do not physically exist in /dev
.
POSIX sh and dash do not support this, so any such code should be rewritten to use a socket tool explicitly. The obvious candidate is netcat aka nc
.
None


Hi Gary.
I turned on ECCE_RCOM_LOGMODE and managed to sort out the scp problem and with that got things running.
Thank you so much for pointing me in the right direction! It turns out that you made ECCE a bit too smart...
The original problems were
1. I can't copy the files to remote site/node and
2. No remote xterm opens
SCP problem: Turns out scp wants upper-case P and doesn't accept lower-case p. ssh of course want lower-case p and doesn't accept upper-case P.
This is from a succesful run on a local node using port 22
arg 0: scp
arg 1: -r
arg 2: /tmp/ecce_andy/jobs/water__8PsJsN/nwch.nw
arg 3: /tmp/ecce_andy/jobs/water__8PsJsN/submit__water
arg 4: /tmp/ecce_andy/jobs/water__8PsJsN/eccejobmonitor.conf
arg 5: /tmp/ecce_andy/jobs/water__8PsJsN/nwchem.desc
arg 6: /home/andy/.ecce/ecce-6.3/apps/scripts/eccejobmonitor
arg 7: andy@borax:/home/andy/mine/testing/old/water
end remote copy command
This is an unsuccesful run using a node via localhost -p 9999
with this in the ecce-6.3/apps/siteconfig/remote_shells.site file
ssh_p9999: ssh -p 9999
and this is what happens:
arg 0: scp
arg 1: -p
arg 2: 9999
arg 3: /tmp/ecce_andy/jobs/water__bLmRNx/nwch.nw
arg 4: /tmp/ecce_andy/jobs/water__bLmRNx/submit__water
arg 5: /tmp/ecce_andy/jobs/water__bLmRNx/eccejobmonitor.conf
arg 6: /tmp/ecce_andy/jobs/water__bLmRNx/nwchem.desc
arg 7: /home/andy/.ecce/ecce-6.3/apps/scripts/eccejobmonitor
arg 8: andy@localhost:/home/andy/jobs/testing/old/water
Forgetting about the -r switch for a second here, the latter command fails when I try:
scp -p 9999 /tmp/ecce_andy/jobs/water__bLmRNx/nwch.nw andy@localhost:/home/andy/jobs/testing/old/water
scp: /home/andy/jobs/testing/old/water: No such file or directory
which is true, there isn't on localhost (but should be on localhost -p 9999). That directory structure is on the remote node (runtime: /home/andy/jobs + testing/old/water) but for some reason the -p switch is completely ignored by scp (the files on the ecce workstation is on ~/.ecce/ecce-6.3/server/data/Ecce/users/andy/testing/old/water/).
However,
scp -P 9999 /tmp/ecce_andy/jobs/water__bLmRNx/nwch.nw andy@localhost:/home/andy/jobs/testing/old/water
nwch.nw 100% 476 0.5KB/s 00:00
works.
The solution is thus to change to:
ssh_p9999: ssh -p 9999|scp -P 9999
I can now submit jobs to the remote debian node (p 9999)!
Getting the remote site to work for submission took a little longer and boiled down to a silly little thing (in addition to the -P issue):
I had qsub in the path name like this:
NWChem: /opt/sw/nwchem-6.1/bin/nwchem
Gaussian-03: /usr/local/bin/G09
perlPath: /usr/bin/perl
qmgrPath: /opt/n1ge62/bin/lx24-amd64/qsub
while it should really be
NWChem: /opt/sw/nwchem-6.1/bin/nwchem
Gaussian-03: /usr/local/bin/G09
perlPath: /usr/bin
qmgrPath: /opt/n1ge62/bin/lx24-amd64
On a related note, I'm not sure what corresponding lines I'm to look for when parsing the logging output from using "singleConnect: check", but it's not quite as relevant anymore.
See here for the full setup using port redirection:
[blog http://verahill.blogspot.com.au/2012/05/port-redirection-with-eccenwchem.html]
Remaining problem:
This really isn't that important anymore since I'm more concerned with launching jobs.
However, here it is for completeness:
I still can't open any remote terminals, and I've also tried with e.g.
' ssh_p9999: ssh -XC -p 9999|scp -P 9999
I'm not sure why, as running
xterm -title "oxygen" -bg "#b7b8ba" -fg "#000000" -sb -e csh -c "cd ~ && $SHELL"
opens a window as it is supposed to.
Creating remote shell:
machine (localhost)
remote shell (ssh_p9999)
local shell (csh)
user name (andy)
password is 0 characters
Remote shell command:
arg 0: ssh
arg 1: -XC
arg 2: -p
arg 3: 9999
arg 4: -v
arg 5: -o
arg 6: ForwardX11=yes
arg 7: -l
arg 8: andy
arg 9: localhost
arg 10: echo
arg 11: +hi+
arg 12: &&
arg 13: csh
arg 14: -i
End remote shell command
OpenSSH_5.9p1 Debian-5, OpenSSL 1.0.1c 10 May 2012
Authenticated to localhost ([<IP_ADDRESS>]:9999).
unalias precmd; set prompt=+go+; unset echo
+hi+
% Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
+go+unalias *
+go+date; echo CMDSTAT=$status
Wed May 30 20:06:23 PDT 2012
CMDSTAT=0
+go+exit; echo GOODBYE
GOODBYE
+go+exit
Transferred: sent 2952, received 2576 bytes, in 1.1 seconds
Bytes per second: sent 2622.8, received 2288.7
Creating remote shell:
machine (localhost)
remote shell (ssh_p9999)
local shell (csh)
user name (andy)
password is 0 characters
Remote shell command:
arg 0: ssh
arg 1: -XC
arg 2: -p
arg 3: 9999
arg 4: -v
arg 5: -o
arg 6: ForwardX11=yes
arg 7: -l
arg 8: andy
arg 9: localhost
arg 10: echo
arg 11: +hi+
arg 12: &&
arg 13: csh
arg 14: -i
End remote shell command
OpenSSH_5.9p1 Debian-5, OpenSSL 1.0.1c 10 May 2012
Authenticated to localhost ([<IP_ADDRESS>]:9999).
unalias precmd; set prompt=+go+; unset echo
+hi+
% Warning: no access to tty (Bad file descriptor).

Creating remote shell:
machine (localhost)
remote shell (ssh_p9999)
local shell (csh)
user name (andy)
password is 0 characters
Remote shell command:
arg 0: ssh
arg 1: -XC
arg 2: -p
arg 3: 9999
arg 4: -v
arg 5: -o
arg 6: ForwardX11=yes
arg 7: -l
arg 8: andy
arg 9: localhost
arg 10: echo
arg 11: +hi+
arg 12: &&
arg 13: csh
arg 14: -i
End remote shell command
OpenSSH_5.9p1 Debian-5, OpenSSL 1.0.1c 10 May 2012
Authenticated to localhost ([<IP_ADDRESS>]:9999).
unalias precmd; set prompt=+go+; unset echo
+hi+
% Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
+go+unalias *
+go+date; echo CMDSTAT=$status
Wed May 30 20:07:17 PDT 2012
CMDSTAT=0
+go+exit; echo GOODBYE
GOODBYE
+go+exit
Transferred: sent 2952, received 2592 bytes, in 1.1 seconds
Bytes per second: sent 2626.2, received 2305.9
Creating remote shell:
machine (localhost)
remote shell (ssh_p9999)
local shell (csh)
user name (andy)
password is 0 characters
Remote shell command:
arg 0: ssh
arg 1: -XC
arg 2: -p
arg 3: 9999
arg 4: -v
arg 5: -o
arg 6: ForwardX11=yes
arg 7: -l
arg 8: andy
arg 9: localhost
arg 10: echo
arg 11: +hi+
arg 12: &&
arg 13: csh
arg 14: -i
End remote shell command
|


--- layout: archive title: Zulip Chat Archive permalink: /stream/116395-maths/topic/category_theory.2Fgroupoid.20and.20category_theory.2FGroupoid.html ---
The files category_theory/groupoid
and category_theory/Groupoid
differ by the case of one character. This is apparently a problem on older macs, which are case insensitive. I guess this needs to be changed.
This didn't cause problems on windows? It's also case-insensitive
Did you ever checkout that commit? It was only like that for half a day.
Oh no, I was just wondering where else it could be problematic.
{% endraw %}Last updated: Apr 24 2020 at 19:02 UTC


Overview User interface Main window Command line ↑ | ↓
In the following, commands are listed alphabetically.
Attaches the 3D model window as the model panel to the main window. If the 3D model is already displayed in the main window, the command has no effect. The command can be undone by detach
.
Changes the background color of the model window or model panel. Possible arguments are grey
(default), white
(enforced with depth cueing or for copying to the clipboard) and black
.
Example:
bckg white
Computes beacon (reference) residue sets in an ordered domain for localization of a spin-labelled residue in a disordered domain. Arguments are the address of the last residue in the ordered domain that precedes the disordered domain (anchor residue), the spin label type, the number of beacons (4-6), and, optionally, a minimum and maximum distance [nm] from a beacon to the anchor residue. Furthermore, a maximum number of beacon sets can be specified. This is based on a spin labeling site scan and computation of the position dilution of precision (see G. Jeschke, Proteins 2016, 84, 544-560.). The list of beacon sets with their figure of merit is displayed in the report editor and can be saved from there.
Examples:
beacons 164 MTSL 4 1.5 5 25
% for a loop after residue 164, compute the 25 best sets of 4 MTSL beacons in the distance range from 1.5 to 5 nm
The minimum and maximum distance default to 2.5 and 3.5 nm, respectively, the maximum number of sets defaults to 20. The minimum distance cannot be shorter than 0.3 nm (lower values are automatically corrected).
Sets a defined camera up vector (rotation about viewing direction).
If called with one argument, the camera up direction can be x|-x|y|-y|z|-z
, whereas +x|+y|+z
are accepted for x|y|z
. If called with three arguments, the three numbers define the camera up vector. Note that +z or 0 0 1 is the default camera up vector. The current camera up vector is displayed in the View
panel (dark green numbers). This command resets the camera zoom so that all displayed graphics is seen.
camup -z
% topple the model upside down w.r.t. normal viewing direction
camup 0 0.707 0.707
% turn the camera up vector to an arbitrary, but well defined direction
Changes the color of objects, such as chains, residues, atoms, or atom locations. The objects can be selected via their systematic address or the color of all currently selected objects (address
Examples:
Color changes can be taken back by issuing an undo command (multiple undo possible).
Applies a colorscheme to objects, such as chains, residues, atoms, or atom locations. The objects can be selected via their systematic address or the colorscheme of all currently selected objects (address
Color scheme
Color scheme
Color scheme
Color scheme
Color scheme
Color scheme
Color scheme
Color scheme
Color scheme
Compacts an ensemble model by r.m.s.d. superposition of all ensemble members onto the one that has the smallest mean-square deviation from all others (central conformation). Individual conformations are rotated and translated so that the ensemble looks most compact (see G. Jeschke, Proteins 2016, 84, 544-560).
Arguments are an address (only structure or chain) and either *
) can be changed. The color argument can be an SVG named color or an RGB triple (red, green, and blue fraction between 0 and 1).
color (B)123-138 limegreen
color "His" 0 1 1
color * blue
*
) can be changed. The second argument can be one of the following color schemes:
secondary
assigns standard metal colors to secondary structure elements in ribbon plots (helices: copper, sheets: steelblue, loops: gold).
chain
assigns rainbow colors from blue to red to the chains starting from chain A to the last chain.
sequence
assigns rainbow colors from blue to red within a chain starting from the N terminus to the C terminus.
Bfactor
assigns rainbow colors from blue to red according to the B factor, with the blue end corresponding to a coordinate r.m.s.d. of about 0.45 Å (B factor 16) and the red end to about 1.5 Å (B factor 169). Color grade is proportional to the r.m.s.d., i.e. to the square root of the B factor.
Bfactor_tight
assigns rainbow colors from blue to red according to the B factor, with the blue end corresponding to the minimum B factor and the red end to the maximum B factor in the structure. Color grade is proportional to the r.m.s.d., i.e. to the square root of the B factor.
charge
assigns rainbow colors from blue to red according to charge. Dark blue: +2, blue +1, grey 0, red: -1, dark red: -2.
hydropathy
assigns rainbow colors from blue to red according to hydropathy, with the blue end corresponding to the most hydrophilic and the red end to the most hydrophobic residues.
helix_propensity
assigns rainbow colors from blue to red according to helix propensity, with the blue end corresponding to residues that tend to form and alpha helix and the red end to helix-breaking residues (Pro). Color grade is proportional to the square root of helix propensity.
ensemble
assigns rainbow colors from blue to red according to per residue Cα r.m.s.d. of individual structures from the mean structure of an ensemble (PDB structures with several models, such as NMR structures, or ensembles generated by elastic network model based fitting from a template). The blue end corresponds to the minimum r.m.s.d. and the red end to the maximum r.m.s.d. of any residue the structure. Color grade is proportional to the r.m.s.d. Note that relative variability within the structure is visualized by color, absolute variability has to be visualaized by superimposing all structures. This colorscheme applies only at residue level to ribbon, coil, Cα stick and Cα wire models.
colorscheme (:) Bfactor
'all'
for an all-atom computation (default) or 'backbone'
for considering only backbone atoms for compaction. The central conformation (representative model) is listed in the message board with its mean r.m.s.d. to all other conformations. Likewise, the conformation that is on average most remote from all the others is listed. The final orientation is in the eigenframe of the inertia tensor of the representative model.
compact backbone
% compact the ensemble considering only the N,CA, and C atoms in the backbone
Ensemble compaction cannot be undone.
Copies the current visualization in the detached model window to the clipboard. If the 3D model is attached, use the command sequence detach,
The copy format is determined in Matlab general preferences, accessible via the
Deletes an object together with the underlying data. Use the hide command to delete (or hide) only the graphical representation of the object.
Currently, this is supported only for surfaces. Future versions will allow to delete structures, coordinate sets, chains, residues, atoms, or atom locations.
Example:
Detaches the 3D model panel as a separate model window. If the 3D model is already detached, the command has no effect. The command can be undone by the attach command. Loading a new PDB structure or model automatically reattaches the model window.
Predicts the distance between spin labels attached to two residues and its standard deviation. If several rotamer libraries of the same type exist, a measure for the uncertainty of the prediction is given. The results can be written to a file, otherwise they are output to the message board.
Syntax:
Defines a set of residues or whole secondary structure elements (helices, sheets, loops) as a domain. If the domain already exists, the command can be used with the
Syntax:
Any other command can then use copy
, attach.
File/Preferences...
menu item of the Matlab main window. In the left list, go to the Figure Copy Template
item and the Copy Options
subitem. For MS Windows we recommend Preserve information (metafile if possible)
and in all cases we recommend Force white background
. We also recommend to activate the Match figure screen size
checkbox.
delete $SAS:SAS_1
% deletes the solvent accessible surface with tag SAS_1
distance addr1 addr2 label [file name]
distance 72 131 IA-Proxyl
% prediction for iodoacetamido-Proxyl attached to residues 72 and 131
+
modifier to add residues or secondary structure elements to a domain. A domain is associated with a structure, not a chain, hence it can contain residues and cofactors from different chains. Individual atoms or whole chains cannot be added to a domain.
domain (+) address domain_name
|domain_name|
as a valid address.
domain 12-40,83-97 translocation
% defines residues 12-40 and 83-97 in the current structure as a domain with name "translocation"
domain [NhaA]<H.IVp> substrate-binding
% defines helix IVp in structure NhaA as substrate binding domain
domain + [NhaA]<H.IVc> substrate-binding
% adds helix IVc in structure NhaA to the substrate binding domain
color [NhaA]|substrate-binding| crimson
% changes color of the substrate binding domain ins structure NhaA
The command cannot be undone and does not need to be undone. You can always redefine a domain by using domain
without the +
mode.
Download structure from PDB web server. The structure is not displayed, but display is initialized if it was not before. Internet access is required. A valid PDB identifier (case insensitive) must be provided.
Usage:
download pdb_identifier
Reassigns secondary structure according to DSSP information, if present.
Such information is created when reading a PDB file, if DSSP is installed.
This requires application of unlock
before and lock
after, as secondary structure information is protected.
Usage:
dssp address
where address may pertain to a whole structure, to a chain, one model of a chain or a range of residues.
Displays the text argument in the Message Board of the Main Window. This is mainly intended for scripts to inform the script user of performed actions.
Defines a stretch of residues as a helix and assigns a name to this helix. The first argument specifies the structure and chain, the second argument the name, the third and fourth argument the range of residues. As an optional argument, the fifth argument specifies a special helix type. Currently, the only special type is TM (transmembrane).
This command is mainly intended for initialization scripts (see Scripting). MMM does not check for consistency of secondary structure definitions and does not update the display after redefinition. By default, secondary structure definitions are locked (see commands lock and unlock) and an ERROR message is displayed when the
The hierarchy window is automatically closed, as current display becomes invalid.
Example:
The command cannot be undone. Use undefine to undefine all helices.
Without an argument,
Hides (deletes) the graphics of objects, such as chains, residues, atoms, or atom locations. The objects can be selected via their systematic address or all currently selected objects (address
Example:
The
Transforms all models (conformations) in an ensemble to the eigenframes of their respective inertia tensor. If you are not sure that you want this, use compact instead.
Attaches precomputed rotamers for a spin label at a given site (or sites). No undo is available. In many cases you might rather want to use the Site scan and Attach precomputed labels items of the
Usage:
where address must be provided and must address a residue or several residues. The other arguments are optional.
Labeled residues are annotated with the keyword "spin label attached".
Please use command rotamers with the same arguments for computing the rotamers, unless this was done before in a Site scan.
Example:
Systematic comparison of spin label position predictions by two different rotamer libraries, which can be used for comparing alternative libraries for the same label or for comparing different label types.
Usage:
where
A text output file can be specified by the optional argument
Arguments can also be specified in an input file. In this case, usage is:
followed by one or more lines of MMM addresses for residues. It must finish with a line
Currently provided test data sets are for MTSL only and are named
Currently available rotamer libraries are of the form
Locks the secondary structure definitions (this is the default state of MMM). The lock can be released by the command unlock.
Defines a stretch of residues as a loop and assigns a name to this loop. The first argument specifies the structure and chain, the second argument the name, the third and fourth argument the range of residues.
This command is mainly intended for initialization scripts (see Scripting). MMM does not check for consistency of secondary structure definitions and does not update the display after redefinition. By default, secondary structure definitions are locked (see commands lock and unlock) and an ERROR message is displayed when the
The hierarchy window is automatically closed, as current display becomes invalid.
Example:
The command cannot be undone. Use undefine to undefine all loops.
Displays the mass of the addressed object in the message board. For structures, chains, and chain models water molecules are not counted into the mass. Use option
Examples:
For a pair of structures that are related by a structural transition, display a pale green coil model of the first structure and crimson conical arrwos that point to the second structure.
Usage:
where adr1 is the address of the moving structure and adr2 the address of the target.
Note that the structures are actually superimposed and that this cannot be undone. Note also that the whole structure is superiomposed and moved, even if the addresses are addresses of chains.
The conical arrows are associated with the moving structure. To remove them from the display, the moving structure must be hidden. Alternatively, any object can be selected and the Graphics mode toolbutton be clicked to access the Graphics window. In this window the motion arrows can be selected from a popup menu and deactivated by unchecking the corresponding checkbox.
Changes the projection mode for the 3D model to orthographic (the default). Can be undone by command persp.
Load structure in PDB format from local disk. The structure is not displayed, but display is initialized if it was not before. The file must be on the current Matlab path, which is automatically the case, if it is stored in an MMM subdirectory (the subdirectory must have existed before starting MMM).
Usage:
We advise to provide a filename with extension. Otherwise MMM tries to find a file with extension
Changes the projection mode for the 3D model to perspective. Can be undone by command ortho.
Plots a line connecting two atoms that are specified by addresses
Examples:
Computes the radius of gyration, which is particularly useful for an ensemble of conformations.
Usage:
Redoes the last undone command. This may or may not work (as in most programs). It should work certainly for simple things like color and transparency changes, it works approximately for moderately complex things as selections and graphics display and it does not work for complex things like secondary structure definitions.
Computes the r.m.s.d. of conformations with respect to a reference conformation.
helix
command is issued.
unlock
% unlocks secondary structure definition, unnecessary in initalization scripts
undefine
% deletes previous secondary structure definitions
helix (A) H1 10 30
% in chain A assign residues 10-30 as helix H1
helix (A) TM1 45 66 TM
% in chain A assign residues 45-66 as transmembrane helix TM1
help
displays the list of available commands in the message board. With a valid command as an argument, the command help page is opened at the corresponding line. With any other argument, an error message is displayed in the message board.
*
) can be hidden.
hide [2BHW](B)123-138
% hides residues 123-138 in chain B of structure 2BHW
hide
command does not hide spin label graphics (spheres for midpoint of the N-O bond and molecular frame). Use show (C)147 label_hide
to hide label graphics for residue 147 in chain C (sorry for the nonsensical syntax, see show).
EPR
menu. Mainly intended for scripts.
label address type temperature
type
specifies the label and can be MTSL
or IA-PROXYL
with allowed synonyms MTSSL and R1A for MTSL and IA1 and IAP for IA-PROXYL. This argument defaults to MTSL
. temperature
can be cryo
(175 K) or ambient
(298 K) or any number specifying a temperature in Kelvin. It defaults to cryo
. If you want to specify the temperature, you must specify the label.
label (A)123 IA-PROXYL ambient
% label residue 123 in chain A by iodoacetamido-PROXYL to simulate room temperature experiments
libcomp address library1 library2 >output_file
address
is a mandatory argument and specifies the structure, chain, chain model, or residues for which the libraries are to be compared. Mandatory arguments library1 and library2 specify the libraries to be compared.
The libraries must be present on the current Matlab path, usually they should be stored in MMM subdirectory \rotamer_libraries
.
>output_file
. If this argument is missing, output is directed to the message board and stored in the log file.
libcomp <input_file >output_file
#LIBCOMP library1 library2
#END
libtest testdata_298K.dat test_xray_298K.dat R1A_298K_xray.mat
% this may take half an hour or so
testdata_298K.dat
, outliers.dat
, and rotamer_test.dat
. The format is given in comment lines of these text (ASCII) files.
They are found in subdirectory rotamer_libraries
. The corresponding PDB files are found in subdirectory tests
.
R1A_T_type.mat
, where T
is either 175K
or 298K
and type
is 090619
(original MMM libraries for MTSL), culled
(all rotamers with respect to chi1 and chi2
removed that were never observed in crystal structures), xray
(chi1, chi2 probabilities as in the set of all reliable
x-ray structures), flat
(equal probabilities for all rotamers), sezer12
(chi1, chi2 probabilities as in
the MD computations of D. Sezer, J. H. Freed, B. Roux 2008 J. Phys. Chem. B 122:5755-5767, Table 10), or warsh
(chi1, chi2 probabilities as in D. T. Warshaviak, L. Serbulea, K. N. Houk, W. L. Hubbell 2011 J. Phys. Chem. B 115:397-405).
For more information, see G. Jeschke 2013 Progr. Nucl. Magn. Reson. submitted.
loop
command is issued.
unlock
% unlocks secondary structure definition, unnecessary in initalization scripts
undefine
% deletes previous secondary structure definitions
loop (A) L1-2 31 35
% in chain A assign residues 10-30 as loop L1-2
-water
to include water.
mass (A)
% displays mass of chain A
mass (A) -water
% displays mass of chain A, including water molecules.
motion adr1 adr2
pdbload filename
.pdb
and, if this cannot be found, a file with extension .ent
. We also advise against using the "single-chain" files with extensions .pdb1 etc. that can be found on the PDB Web server as "Biological Assembly 1" etc.
adr1
and adr2
.
plot adr1 adr2 [[width] color]
plot 123.CA 325.CA
radgyr adr [mode]
adr
denotes the address of a structure or chain and mode
is all
for an all-atom computation or backbone
for a backbone-only computations and defaults to all
.
refrmsd adr refadr [mode]
adr
denotes the address of a structure or chain (can be an ensemble) and refadr
the address of the reference conformation. The number and type of atoms must agree. Furthermore, mode
is all
for an all-atom computation or backbone
for a backbone-only computations and defaults to all
.
Repacks (or creates) sidechains of native amino acids in a structure. Hetero amino acids will have missing sidechains and even backbone atoms may be lost. Consider applying the replace
command before to substitute them by corresponding native amino acids.
This requires that SCWRL4 from the Dunbrack lab is installed and on the Matlab path.
Usage:
repack address
repack address crystal
where address is an MMM object address of a structure. The current version does nothing if lower-level objects are addressed. The optional argument crystal
selects the -#
option of SCWRL4, which calculates side-chain cobforamtions within the crystal environment. This can be used to detect packing effects. The option requires that the original PDB file
has a CRYST1 record.
Replaces non-standard residues such as selenocysteine or selenomethionine as well as spin-labels by their native amino acid equivalents (cysteine or methionine).
Only the first location is kept (leading rotamer in case of spin labels).
The command will hide replaced residues in the 3D plot (if they were displayed before). The user needs to redisplay them if required.
Usage:
where address is an MMM object address of a structure. When lower-level objects are addressed, only addressed residues are replaced. The address must correspond to residues in only one structure.
The argument hettype specifies which residue type(s) are to be replaced. Residue types are three-character identifiers specified by PDB and the non-standrad identifier
Examples:
replace address hettype
IA1
for iodoacetamido-PROXYL.
In a list of residue type, the individual types need to be separated by colons (:). Only a colon in place of hettype leads to replacement of all non-standard residues defined in MMM.
replace [3K2R] V1A
% replaces the two imidazole-type spin labels in T4 lysozyme structure 3K2R by cysteins
replace [2X79] MSE:R1A
% replaces in structure 2X79 all selenomethionines by methionines and removes all MTS-spin labels attached before (replaced by cysteine)
replace [2X79]20-100 :
% replace all non-standard residues known to MMM among residues 20 to 100 of structure 2X79
Writes information on spin-labels and distance distributions to a report file. If the file exists, the information is appended. Useful mainly in command scripts.
Usage:
where filename is the name of the report file (plain text) that will be written to the current Matlab directory (unless a pathname is provided) and information specifies the type of information to be reported. Additional arguments depend on the type of information requested:
Examples:
Computes the r.m.s.d. of conformations in an ensemble from the "mean" conformation.
report filename information [...]
report filename label address extent
where address is an MMM residue address and extent is an optional argument that is either brief
(default) or full
. In brief
mode, only mean position and r.m.s.d. are reported.
report filename distance address1 address2 extent
where address1 and address2 are MMM residue addresses and extent is an optional argument that is either brief
(default) or full
. In brief
mode, only mean distance and r.m.s.d. are reported, in full mode the whole distribution is written out.
report LHCII_labels.txt label [2BHW]123
% writes mean position and r.m.s.d of the label at residue 123 of structure [2BHW] to the file LHCII_labels.txt. The label must have been computed with rotamers
, but not necessarily attached. The labels must have been computed with rotamers
, but not necessarily attached.
rmsd adr [mode]
adr
denotes the address of a structure or chain (must be an ensemble) and mode
is all
for an all-atom computation or backbone
for a backbone-only computations and defaults to all
.
Compute rotamers for a spin label at a given site (or sites). In many cases you might rather want to use the Site scan items of the EPR
menu, which allows for more input and output options. Mainly intended for scripts.
Usage:
rotamers address type temperature
where address must be provided and must address a residue or several residues. The other arguments are optional. type
specifies the label and can be MTSL
or IA-PROXYL
with allowed synonyms MTSSL and R1A for MTSL and IA1 and IAP for IA-PROXYL. This argument defaults to MTSL
. temperature
can be cryo
(175 K) or ambient
(298 K) or any number specifying a temperature in Kelvin. It defaults to ambient
. If you want to specify the temperature, you must specify the label.
Basic rotamer statistics information (number of significantly populated rotamers, partition function, r.m.s.d. of N-O midpoint coordinates) is stored in the residue annotations with the keyword "rotamers computed". The Site scan menu item allows for more complete analysis.
The spin labels are only computed, not immediately attached. Please use the command label with the same arguments to actually attach them.
Example:
rotamers (A)123 IA-PROXYL ambient
% label residue 123 in chain A by iodoacetamido-PROXYL to simulate room temperature experiments
Creates and displays the solvent accessible surface for a single object, which must be a structure, chain, coordinate set of a chain, or residue. This requires that MSMS by Michel Sanner is installed.
Usage:
where address is an MMM object address, tag is the tag by which the surface can be accessed later, and radius is an optional probe radius in units of Å. The probe radius defaults to 1.5 Å, which is Sanner's suggested value for water.
The surface is originally displayed with aquamarine color and 50% transparency.
Usage:
Note that a surface address always begins with
Makes a copy of a structure with a new structure tag. The copied structure becomes the current structure.
Usage:
where address is an MMM object address of a structure and tag is the tag by which the new structure can be accessed later.
Selects objects, such as structures, chains, domains, secondary structure elements, residues, atoms, or atom locations via their systematic address.
Examples:
Selections of already selected objects are ignored, a warning is issued in the message board. Selections can be taken back by issuing an unselect command to the same objects. Note that undo of a selection may have unintended consequences after a double selection- the previously doubly selected object will also be unselected.
The command
Defines a stretch of residues as a strand (part of a sheet) and assigns a name to this strand. The first argument specifies the structure and chain, the second argument the name, the third and fourth argument the range of residues. As an optional argument, the fifth argument specifies a special strand type. Currently, the only special type is TM (transmembrane).
This command is mainly intended for initialization scripts (see Scripting). MMM does not check for consistency of secondary structure definitions and does not update the display after redefinition. By default, secondary structure definitions are locked (see commands lock and unlock) and an ERROR message is displayed when the
The hierarchy window is automatically closed, as current display becomes invalid.
Example:
The command cannot be undone. Use undefine to undefine all sheets.
Displays graphics for objects, such as chains, residues, atoms, or atom locations. The objects can be selected via their systematic address or graphics can be shown for all currently selected objects (address
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
Graphics mode
The following graphics modes exist only if spin labels are defined and apply to residues:
Graphics mode
Graphics mode
Graphics mode
Examples:
Graphics are first displayed in a default color scheme, atoms and locations by element color ribbons by the secondary structure color scheme and other graphics by their uniform color. Use command color to change color afterwards. If there are alternative locations for an atom, transparency is assigned by population. Use command transparency to change transparency.
Checks whether selected objects define a symmetry or pseudosymmetry axis.
If so, transforms the structure to a frame where this axis is the z axis
and where the center of the structure is on this axis.
The number of selected objects determines the multiplicity of the axis. All selected objects must belong to the same structure, this structure is transformed. All selected objects must have the same number of atoms (sorry).
This command cannot be undone and it hides the transformed structure. To preserve the display properties of the structure, please use the Edit/Symmetry menu item, which cares about automatic redisplay. The command version is mainly intended for scripts.
Assigns a synonym to a structure or chain name. The first argument is a structure or chain address, the second argument the synonym for the structure or chain name.
Example:
Assigns a transparency value to objects, such as chains, residues, atoms, or atom locations. The objects can be selected via their systematic address or transparency can be assigned to all currently selected objects (address
Examples:
Undoes the last issued command. This may or may not work (as in most programs). It should work certainly for simple things like color and transparency changes, it works approximately for moderately complex things as selections and graphics display and it does not work for complex things like secondary structure definitions.
This command is mainly intended for initialization scripts (see Scripting). Undefines secondary structure assignments (helix, strand/sheet, and loop definitions).
Without argument, the command operates on the current chain, as indicated in the title of the main window. If a structure address is given as argument, the command operates on all chains of this structure. If a chain address is given, it operates on this chain.
The
Unlocks the secondary structure definitions, which are locked by default in MMM. The lock can be imposed again by the command lock. Use
Unselects objects, such as structures, chains, domains, secondary structure elements, residues, atoms, or atom locations via their systematic address, if they were previously selected.
Example:
If the addressed objects were not selected, the command has no effect. No warning is issued.
Sets a defined viewing direction.
If called with one argument, the viewing direction can be
Write out the sequence for a selection of residues. The sequence in single-letter code is displayed in a report editor window, so that it can easily be copied for use in other programs or with webservers.
SAS address tag (radius)
SAS ! native
% water accessible surface with tag "native" for the current structure (!)
color $SAS:native cornflowerblue
% change color to cornflowerblue
$
, followed by the surface type (here SAS
).
scopy address tag
select [2BHW](B)123,145,217
% select residues 123, 145, and 217 in chain B of structure 2BHW
select "His"
% select all histidine residues in the current structure and chain
select (A)
% select the helix with name H3 in chain A of the current structure
select *
*
stands for all objects that are currently selected. However, it is useful for displaying the current selection in the message board.
sheet
command is issued.
unlock
% unlocks secondary structure definition, unnecessary in initalization scripts
undefine
% deletes previous secondary structure definitions
sheet (A) SI 36 49
% in chain A assign residues 36-49 as strand SI
sheet (A) TMS1 58 76 TM
% in chain A assign residues 58-76 as a transmembrane strand TMS1
*
) at once. The second argument can be one of the following graphics modes:
wire
applies to atoms and locations and displays a wire plot with lines for the bonds and dots for the atoms.
stick
applies to atoms and locations and displays a stick plot with cylinders for bonds and spheres with the same radius for atoms.
ball&stick
applies to atoms and locations and displays sticks for the bonds and slightly larger spheres for atoms.
space-filling
applies to atoms and locations and displays a space-filling model (spheres with the van-der-Waals radius).
CaWire
applies to chains and residues and displays a wire model of the Cα trace. Cofactors are shown in wire
mode. For DNA and RNA chains, the wire model connects the midpoints of the C3'-C4' bond of the ribose or desoxyribose.
CaStick
applies to chains and residues and displays a stick model of the Cα trace. Cofactors are shown in stick
mode. For DNA and RNA chains, the stick model connects the midpoints of the C3'-C4' bond of the ribose or desoxyribose.
ribbon
applies to chains and residues and displays a ribbon model of amino acid residues. Cofactors are not shown. For DNA or RNA, the backbones are shown as ribbons, the connection between each midpoint of the C3'-C4' bond of the ribose/desoxyribose and the atom of the base bound to the sugar is shown as a tube, and the plane of the base as a filled polygon. Nucleotides are color-coded: G is lightgreen, C is lightcoral, T/U is gold, and A is mediumpurple.
coil
applies to chains and residues and displays a coil model of the backbone. Individual residues can be selected by clicking in coil mode. Cofactors are not shown. Coil mode also applies to DNA/RNA.
string
looks similar as coil
, but creates a single graphics object per chain. This allows for selecting chains by a single click, but does not allow for selecting residues by clicking into the graphics. Cofactors are not shown. String mode also applies to DNA/RNA.
water
displays water molecules, which are suppressed in all other graphics modes.
label
shows the midpoint of the N-O bonds of all label rotamers as small spheres. Relative sphere volume corresponds to relative label population, the total sphere volume is selected so that both very narrow and very broad rotamer distributions can be well seen. If a single rotamer makes up at least 99.5% of the total population, its sphere radius corresponds to the half of the sum of the van-der-Waals-radii of nitrogen and oxygen plus the N-O bond length (full extension of the N-O group). In all other cases spheres are smaller.
label_frame
shows the midpoint of the N-O bonds of all label rotamers as spheres and the molecular frame with a red x axis, green y axis, and a blue z axis. This gives an impression on orientational distribution.
label_hide
hides label graphics without affecting other graphics of this residue.
show (A)123-136 ball&stick
% displays residues 123-136 in ball & stick mode
show (A) coil
% displays a coil model of chain A
show (A)"Gly" space-filling
% displays all glycine residues of chain A in space-filling mode
synonym [2BHW] LHCII
show [LHCII] coil
% displays a coil model of structure 2BHW
*
) at once. The second argument is the opaqueness between 0 (fully transparent) and 1 (fully opaque). A negative value is interpreted as request to assign transparency according to population of alternate locations (the default mode).
transparency (C)147 0.5
% makes residue 147 in chain C semi-transparent
transparency (A)"Asn" -1
% assigns default transparency (by population of alternate locations) to all asparagine residues in chain (A)
undefine
command is usually blocked (error is displayed in the message board), since secondary structure definitions are locked by default. Use the unlock command before, if you must do that outside an initialization script, and do not forget to lock again. Only the list of helices, strands, and loops is deleted, secondary structure assignment of residues is kept. The hierarchy window is automatically closed, as current display becomes invalid.
unlock
only if you understand the consequences of modifying secondary structure definitions in the current state of the model. Make a backup copy of the model ( save button) before you do that.
The same function unlocks the protection against using alternative rotamer libraries or alternative parameters in elastic network modeling of structural transitions.
unselect [2BHW](B)145
% unselects residue 145 in chain B of structure 2BHW
x|-x|y|-y|z|-z
, whereas +x|+y|+z
are accepted for x|y|z
. If called with three arguments, the three numbers define a viewing vector. If called with six arguments, the six numbers define a viewing vector and a camera up vector. Note that the current viewing vector (dark blue numbers) and camera up vector (dark green numbers) are displayed in the View
panel. This command resets the camera zoom so that all displayed graphics is seen.
view -z
% look at the model from the -z direction
view 0.5 0.5 0.707
% view at the model from an arbitrary, but well defined direction
view 0.5 0.5 0.707 0 0 -1
% view at the model from an arbitrary, but well defined direction and upside down compared to usual camera up vector
wrseq [2LZM]72-131
% write out the sequence for residues 72-131 of T4 lysozyme (structure must be loaded)
Zooms in to selected objects or zooms out to display the whole model.
Examples:
zoom in
% define the camera view so that the select objects fill the model window
zoom out
% define the camera view so that all displayed graphics is shown
The zoom in
command may produce funny results if the 3D model is shown in the model panel (attached state), as graphics is not clipped to the panel.


Anything your heart desires. Weather it is laying on a beach, snorkling in the ocean, or even playing hide and seek in the forest. The possiblities are endless!


##
### Features
- Tile and popup fade animation
- Very nice default design for markers, popups and map controls
- Retina resolution support
- Customization Features
- Performance Features
- Map Controls
- Browser Support
- Mobile
- Lightweight
- No external dependencies
### Usage
#### For this project
This project is using leaflet.js in combination with Open Street Maps to create maps and to drop markers on the map
#### General usage
Map is the central class of the API — it is used to create a map on a page and manipulate it.
Usage example
// initialize the map on the "map" div with a given center and zoom
var map = L.map('map', {
center: [51.505, -0.09], zoom: 13
});
Factory |Description|
---------------- | ---------------- |
`L.map( id,


We’ll see you and your friend tomorrow! Make sure to come to both services > 10:00 and 11:30 < to see all the winners and claim your awesome prizes!


EXPLAIN [ ( option [, ...] ) ] statement
EXPLAIN [ ANALYZE ] [ VERBOSE ] statement
where option can be one of:
ANALYZE [ boolean ]
VERBOSE [ boolean ]
COSTS [ boolean ]
BUFFERS [ boolean ]
TIMING [ boolean ]
FORMAT { TEXT | XML | JSON | YAML }
This command displays the execution plan that the PostgreSQL planner generates for the supplied statement. The execution plan shows how the table(s) referenced by the statement will be scanned — by plain sequential scan, index scan, etc. — and if multiple tables are referenced, what join algorithms will be used to bring together the required rows from each input table.
The most critical part of the display is the estimated statement execution cost, which is the planner's guess at how long it will take to run the statement (measured in cost units that are arbitrary, but conventionally mean disk page fetches). Actually two numbers are shown: the start-up cost before the first row can be returned, and the total cost to return all the rows. For most queries the total cost is what matters, but in contexts such as a subquery in EXISTS, the planner will choose the smallest start-up cost instead of the smallest total cost (since the executor will stop after getting one row, anyway). Also, if you limit the number of rows to return with a LIMIT clause, the planner makes an appropriate interpolation between the endpoint costs to estimate which plan is really the cheapest.
The ANALYZE option causes the statement to be actually executed, not only planned. Then actual run time statistics are added to the display, including the total elapsed time expended within each plan node (in milliseconds) and the total number of rows it actually returned. This is useful for seeing whether the planner's estimates are close to reality.
Important: Keep in mind that the statement is actually executed when the ANALYZE option is used. Although EXPLAIN will discard any output that a SELECT would return, other side effects of the statement will happen as usual. If you wish to use EXPLAIN ANALYZE on an INSERT, UPDATE, DELETE, CREATE TABLE AS, or EXECUTE statement without letting the command affect your data, use this approach:
BEGIN; EXPLAIN ANALYZE ...; ROLLBACK;
Only the ANALYZE and VERBOSE options can be specified, and only in that order, without surrounding the option list in parentheses. Prior to PostgreSQL 9.0, the unparenthesized syntax was the only one supported. It is expected that all new options will be supported only in the parenthesized syntax.
Carry out the command and show actual run times and other statistics. This parameter defaults to FALSE.
Display additional information regarding the plan. Specifically, include the output column list for each node in the plan tree, schema-qualify table and function names, always label variables in expressions with their range table alias, and always print the name of each trigger for which statistics are displayed. This parameter defaults to FALSE.
Include information on the estimated startup and total cost of each plan node, as well as the estimated number of rows and the estimated width of each row. This parameter defaults to TRUE.
Include information on buffer usage. Specifically, include the number of shared blocks hit, read, dirtied, and written, the number of local blocks hit, read, dirtied, and written, and the number of temp blocks read and written. A hit means that a read was avoided because the block was found already in cache when needed. Shared blocks contain data from regular tables and indexes; local blocks contain data from temporary tables and indexes; while temp blocks contain short-term working data used in sorts, hashes, Materialize plan nodes, and similar cases. The number of blocks dirtied indicates the number of previously unmodified blocks that were changed by this query; while the number of blocks written indicates the number of previously-dirtied blocks evicted from cache by this backend during query processing. The number of blocks shown for an upper-level node includes those used by all its child nodes. In text format, only non-zero values are printed. This parameter may only be used when ANALYZE is also enabled. It defaults to FALSE.
Include actual startup time and time spent in each node in the output. The overhead of repeatedly reading the system clock can slow down the query significantly on some systems, so it may be useful to set this parameter to FALSE when only actual row counts, and not exact times, are needed.  This parameter may only be used when ANALYZE is also enabled. It defaults to TRUE.
Specify the output format, which can be TEXT, XML, JSON, or YAML. Non-text output contains the same information as the text output format, but is easier for programs to parse. This parameter defaults to TEXT.
Specifies whether the selected option should be turned on or off. You can write TRUE, ON, or 1 to enable the option, and FALSE, OFF, or 0 to disable it. The boolean value can also be omitted, in which case TRUE is assumed.
Any SELECT, INSERT, UPDATE, DELETE, VALUES, EXECUTE, DECLARE, or CREATE TABLE AS statement, whose execution plan you wish to see.
The command's result is a textual description of the plan selected for the statement, optionally annotated with execution statistics. Section 14.1 describes the information provided.
In order to allow the PostgreSQL query planner to make reasonably informed decisions when optimizing queries, the pg_statistic data should be up-to-date for all tables used in the query. Normally the autovacuum daemon will take care of that automatically. But if a table has recently had substantial changes in its contents, you might need to do a manual ANALYZE rather than wait for autovacuum to catch up with the changes.
In order to measure the run-time cost of each node in the execution plan, the current implementation of EXPLAIN ANALYZE adds profiling overhead to query execution. As a result, running EXPLAIN ANALYZE on a query can sometimes take significantly longer than executing the query normally. The amount of overhead depends on the nature of the query, as well as the platform being used. The worst case occurs for plan nodes that in themselves require very little time per execution, and on machines that have relatively slow operating system calls for obtaining the time of day.
To show the plan for a simple query on a table with a single integer column and 10000 rows:
EXPLAIN SELECT * FROM foo; QUERY PLAN --------------------------------------------------------- Seq Scan on foo (cost=0.00..155.00 rows=10000 width=4) (1 row)
Here is the same query, with JSON output formatting:
EXPLAIN (FORMAT JSON) SELECT * FROM foo; QUERY PLAN -------------------------------- [ + { + "Plan": { + "Node Type": "Seq Scan",+ "Relation Name": "foo", + "Alias": "foo", + "Startup Cost": 0.00, + "Total Cost": 155.00, + "Plan Rows": 10000, + "Plan Width": 4 + } + } + ] (1 row)
If there is an index and we use a query with an indexable WHERE condition, EXPLAIN might show a different plan:
EXPLAIN SELECT * FROM foo WHERE i = 4; QUERY PLAN -------------------------------------------------------------- Index Scan using fi on foo (cost=0.00..5.98 rows=1 width=4) Index Cond: (i = 4) (2 rows)
Here is the same query, but in YAML format:
EXPLAIN (FORMAT YAML) SELECT * FROM foo WHERE i='4'; QUERY PLAN ------------------------------- - Plan: + Node Type: "Index Scan" + Scan Direction: "Forward"+ Index Name: "fi" + Relation Name: "foo" + Alias: "foo" + Startup Cost: 0.00 + Total Cost: 5.98 + Plan Rows: 1 + Plan Width: 4 + Index Cond: "(i = 4)" (1 row)
XML format is left as an exercise for the reader.
Here is the same plan with cost estimates suppressed:
EXPLAIN (COSTS FALSE) SELECT * FROM foo WHERE i = 4; QUERY PLAN ---------------------------- Index Scan using fi on foo Index Cond: (i = 4) (2 rows)
Here is an example of a query plan for a query using an aggregate function:
EXPLAIN SELECT sum(i) FROM foo WHERE i < 10; QUERY PLAN --------------------------------------------------------------------- Aggregate (cost=23.93..23.93 rows=1 width=4) -> Index Scan using fi on foo (cost=0.00..23.92 rows=6 width=4) Index Cond: (i < 10) (3 rows)
Here is an example of using EXPLAIN EXECUTE to display the execution plan for a prepared query:
PREPARE query(int, int) AS SELECT sum(bar) FROM test WHERE id > $1 AND id < $2 GROUP BY foo; EXPLAIN ANALYZE EXECUTE query(100, 200); QUERY PLAN ------------------------------------------------------------------------------------------------------------------------- HashAggregate (cost=39.53..39.53 rows=1 width=8) (actual time=0.661..0.672 rows=7 loops=1) -> Index Scan using test_pkey on test (cost=0.00..32.97 rows=1311 width=8) (actual time=0.050..0.395 rows=99 loops=1) Index Cond: ((id > $1) AND (id < $2)) Total runtime: 0.851 ms (4 rows)
Of course, the specific numbers shown here depend on the actual contents of the tables involved. Also note that the numbers, and even the selected query strategy, might vary between PostgreSQL releases due to planner improvements. In addition, the ANALYZE command uses random sampling to estimate data statistics; therefore, it is possible for cost estimates to change after a fresh run of ANALYZE, even if the actual distribution of data in the table has not changed.


--- layout: post authors: ["Greg Wilson"] title: "Scientific Coding vs. Software Engineering" date: 2015-02-08 time: "13:30:00" tags: ["Software Engineering", "Noticed"] ---
Daisie Huang recently wrote a great article for the Software Sustainability Institute's blog titled "Scientific coding and software engineering: what's the difference?". As a professional programmer who has become a scientist, rather than a scientist who's learned how to program, she has a fresh take on the differences between what those two groups do. Comments on her post would be very welcome.


float hypot ( float $x , float $y )
hypot() returns the length of the hypotenuse of a right-angle triangle with sides of length x and y, or the distance of the point (x, y) from the origin. This is equivalent to sqrt(x*x + y*y).
Calculated length of the hypotenuse


Uncheck "Loop" option to create one way route when you would like to create custom routes. This allows switching from "Source" to "Destination" but not backward.
Multiple destinations of the same source will shows as popup.


---
layout: concept
---
$$\begin{align*}
i\hbar\pdv{\Phi}{t}=-\frac{\hbar^2}{2m}\frac{\partial^2\Phi}{\partial x^2}+U(x)\Phi(x)
\end{align*}$$
Significance
Just like $F=ma$ and classical laws of motion describes how classical systems evolve, the schrodinger's equation describes how a quantum mechanical system evolves.
$$\begin{align*}
i\hbar\frac{d}{dt}|\psi(t)\rangle=H(t)|\psi(t)\rangle
\end{align*}$$
Derivation
The general wavefunction is $\Phi(x, t)=AE^{\frac{i}{\hbar}(p\hat{x}-Et)}$. Taking the derivative with respect to time gives us
$$\begin{align*}
\pdv{\Phi}{t}&=-\frac{i}{\hbar}E\Phi\\
\implies -\frac{\hbar}{i}\pdv{\Phi}{t}&=E\Phi
\end{align*}$$
Assuming we have a free particle, then $E=\frac{\hat{p}^2}{2m}$, and $p$ writing in the position basis is $\frac{\hbar}{i}\pdv{}{x}$
To be continued
Related Experiments
Coming soon
Associated Concepts
Coming soon
Related


CUSTOM GAME
FORGE
THEATER
| Menu Design & Functionality | Dynmap |
| Networking & Bug Fixes | Orion |
| Rcon & Direct Connect | SpartanCPP^DARKC0DE |
| Flags, Locks, & Bug Fixes | Limited |
| UI Sound Effects | Shad0wshayd3 |
| Halo Online Music | Khadazi |
| Loading Screens | Personality |
| Halo 3, ODST, & Reach Backgrounds | Lord Zedd |
| Lots of Suggestions | theTwister |
| ElDewrito Logo | AssaultCommand |
| Custom Edition Logo | WyvernZu |
| Dodger | FishPhd |


XDK Demo for AdMob Plugin
Banner
Standard:
SMART_BANNER
BANNER
IAB_MEDIUM_RECTANGLE
IAB_BANNER
IAB_LEADERBOARD
at top
overlap
create
remove banner
Interstitial
auto show when ready
Prepare
Show


Next: Semantics terms, Previous: An example tree, Up: Terms [Contents][Index]
We often want to “visit” all the nodes of a tree in a sequence,
or
traverse
the tree.
In the semantics phase,
it is often necessary to visit all the children of a node
before the node itself.
We can do this using a
postorder traversal
traversal.
Here is a recursive procedure for a postorder traversal
of the tree nd
:
If nd is not well-defined, return Traverse the children of nd, in order Visit nd
A postorder traversal is also often called a depth-first traversal, or a bottom-up traversal. A postorder traversal of our example tree (see An example tree) visits the nodes in the following order:
T U A B V C W X D Y Z E S


{% extends "skeleton.html" %} {% block content %}
Delete section {{story.title}}: {{chapter.title}} - {{section.num}}
{% include "section_description.html" %}


Plugin
annotationClass
.PluginManager
configured with internal dependencies for PluginContext
, AnnotationProcessor
and DependencyResolver
Permission
for the specified CodeSource
, given a
PluginClassLoader.permissionProperties
.URI
PluginSource
,
instantiating the objects, resolving any dependency and registering them
in the contextURLClassLoader
that is used to load Plugin
classes from Jar files.PluginClassLoader
from an single URL
PluginClassLoader
from an array of URL
Copyright © 2017–2018 PlugFace. All rights reserved.


Class DataValidationAttribute
Class DataValidationAttribute.
Inheritance
Implements
Inherited Members
Namespace: DotNetHelper_Contracts.Attribute
Assembly: DotNetHelper-Contracts.dll
Syntax
[AttributeUsage(AttributeTargets.Class | AttributeTargets.Property)]
public class DataValidationAttribute : Attribute, _Attribute
Properties
| Improve this Doc View SourceCanContainLetter
Gets or sets a value indicating whether this instance can contain letter.
Declaration
public bool? CanContainLetter { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<System.Boolean> |
|
CanContainNumbers
Gets or sets a value indicating whether this instance can contain numbers.
Declaration
public bool? CanContainNumbers { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<System.Boolean> |
|
DataType
Gets or sets the type of the data.
Declaration
public DataType? DataType { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<DataType> | The type of the data. |
Ignore
Gets or sets a value indicating whether this DataValidationAttribute is ignore.
Declaration
public bool? Ignore { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<System.Boolean> |
|
MaxLengthSize
Max Size Property Can Be
Declaration
public int? MaxLengthSize { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<System.Int32> | The maximum size of the length. |
RequireValue
Specifies whether the property is required.
Declaration
public bool? RequireValue { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Nullable<System.Boolean> |
|
SetCanContainLetter
Gets or sets a value indicating whether [set can contain letter].
Declaration
public bool SetCanContainLetter { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Boolean |
|
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo...
Declaration
public bool SetCanContainNumbers { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Boolean |
|
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo... Your Using DataValidationAttribute wrong You Must Set This Attribute Value Before Trying To Get It There IS NO SUCH THING AS NULL |
SetDataType
Gets or sets the type of the set data.
Declaration
public DataType SetDataType { get; set; }
Property Value
| Type | Description |
|---|---|
| DataType | The type of the set data. |
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo...
Declaration
public bool SetIgnore { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Boolean |
|
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo... Your Using DataValidationAttribute wrong You Must Set This Attribute Value Before Trying To Get It There IS NO SUCH THING AS NULL |
SetMaxLengthSize
Gets or sets the size of the set maximum length.
Declaration
public int SetMaxLengthSize { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Int32 | The size of the set maximum length. |
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo...
Declaration
public bool SetRequireValue { get; set; }
Property Value
| Type | Description |
|---|---|
| System.Boolean |
|
Exceptions
| Type | Condition |
|---|---|
| System.Exception | Nooo... Your Using DataValidationAttribute wrong You Must Set This Attribute Value Before Trying To Get It There IS NO SUCH THING AS NULL |


Temporary and permanent message queues for R. Built on top of 'SQLite' databases. 'SQLite' provides locking, and makes it possible to detect crashed consumers. Crashed jobs can be automatically marked as "failed", or put in the queue again, potentially a limited number of times.
| Version: | 1.0.1 |
| Imports: | assertthat, DBI, rappdirs, RSQLite |
| Suggests: | covr, testthat, withr |
| Published: | 2017-10-20 |
| Author: | Gábor Csárdi |
| Maintainer: | Gábor Csárdi <csardi.gabor at gmail.com> |
| BugReports: | https://github.com/r-lib/liteq/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/r-lib/liteq#readme |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| In views: | Databases |
| CRAN checks: | liteq results |
| Reference manual: | liteq.pdf |
| Package source: | liteq_1.0.1.tar.gz |
| Windows binaries: | r-devel: liteq_1.0.1.zip, r-release: liteq_1.0.1.zip, r-oldrel: liteq_1.0.1.zip |
| OS X binaries: | r-release: liteq_1.0.1.tgz, r-oldrel: liteq_1.0.1.tgz |
| Old sources: | liteq archive |
| Reverse imports: | BioInstaller, prrd |
Please use the canonical form https://CRAN.R-project.org/package=liteq to link to this page.


|
||||||||||
| PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |
See:
Description
| Interface Summary | |
| GroupIterator | A GroupIterator is an iterator that iterates over a sequence of groups. |
| NodeOrderComparer | A Comparer used for comparing nodes in document order |
| Sortable | A Sortable is an object that can be sorted using the QuickSort method. |
| Class Summary | |
| AtomicComparer | A Comparator used for comparing atomic values of arbitrary item types. |
| AtomicSortComparer | A Comparator used for comparing atomic values of arbitrary item types. |
| AtomicSortComparer.ComparisonKey | |
| CodepointCollator | A collating sequence that uses Unicode codepoint ordering |
| CollationFactory | CollationFactory allows a Collation to be created given a set of parameters, or a URI containing those parameters. |
| DescendingComparer | A Comparer used for comparing descending keys |
| DocumentOrderIterator | DocumentOrderIterator takes as input an iteration of nodes in any order, and returns as output an iteration of the same nodes in document order, eliminating any duplicates. |
| DocumentSorter | A DocumentSorter is an expression that sorts a sequence of nodes into document order. |
| FixedSortKeyDefinition | A FixedSortKeyDefinition is a SortKeyDefinition in which all aspects of the sort key definition (sort order, data type, etc,) are known. |
| GlobalOrderComparer | A Comparer used for comparing nodes in document order. |
| GroupAdjacentIterator | A GroupAdjacentIterator iterates over a sequence of groups defined by xsl:for-each-group group-adjacent="x". |
| GroupByIterator | A GroupByIterator iterates over a sequence of groups defined by xsl:for-each-group group-by="x". |
| GroupEndingIterator | A GroupEndingIterator iterates over a sequence of groups defined by xsl:for-each-group group-ending-with="x". |
| GroupStartingIterator | A GroupStartingIterator iterates over a sequence of groups defined by xsl:for-each-group group-starting-with="x". |
| LocalOrderComparer | A Comparer used for comparing nodes in document order. |
| LowercaseFirstComparer | A Comparer used for comparing keys |
| NumericComparer | A Comparer used for comparing sort keys when data-type="number". |
| QuickSort | This is a generic version of C.A.R Hoare's Quick Sort algorithm. |
| Reverser | A Reverser is an expression that reverses the order of a sequence of items. |
| SortedGroupIterator | A SortedGroupIterator is a modified SortedIterator. |
| SortedIterator | Class to do a sorted iteration |
| SortExpression | Expression equivalent to the imaginary syntax expr sortby (sort-key)+ |
| SortKeyDefinition | A SortKeyDefinition defines one component of a sort key. |
| TextComparer | A Comparer used for comparing sort keys when data-type="text". |
| TupleExpression | A tuple expression is an expression that returns a tuple. |
| TupleSorter | A TupleSorter is an expression that sorts a stream of tuples. |
| UppercaseFirstComparer | A Comparer used for comparing keys |
This package provides utility routines for sorting and grouping. Specifically, it contains a QuickSort implementation, and some Comparator objects that handle character and numeric comparisons, together with the important DocumentOrderIterator which iterates over a set of nodes in document order.
The package also contains the (unrelated) GroupedCollection class to support the XSLT 2.0 element xsl:for-each-group.
The HashMap
class is a legacy; it is used for lookup of element names by the
HTML serializer.
Michael H. Kay
25 April 2002
|
||||||||||
| PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |


Design (The What)
We specialize in information, user-interface and interaction design services. Our design process involves research, wireframing, prototyping and testing. We live for the complex problem solving that is inherent in web-applications, but we reserve a little love for websites too.
Development (The How)
Everything from the development of prototypes for testing and experimentation, to full, production-ready products can be fully realized by our team. Our focus is on the architecture, interface and interaction (behavior) of web-applications and content management systems (CMS). We are comfortable developing within client-only or client-server hybrid environments as well.
User-Experience (The Why)
User-neuropsychology is a special passion of ours. Knowledge of the human condition helps solve unique and complex problems while preserving an optimal user-experience. We're focus on driving goal-oriented behavior, capturing and sustaining attention, and ensuring a positive user-experience.


Compare two strings
Evaluate the protein dataset
About
This is an online tool that calculates the Edit Distance between two strings.
First text:
Second text:
Select your algorithm:
Recursive algorithm
Dynamic programming
K-stripe approach
Greedy approach
(Not always optimal)
Branch and bound algorithm
(No alignment)
Divide and conquer algorithm
Calculate ED


Grand Master Schule:
Since you've already completed your second class transfer, there is nothing further I can do.
Remember, when you chose the path of a Warrior, you swore to protect the weak and uphold the good! Sadly, the stronger Humans become, the easier they're tempted by the forces of evil. Never forget to stay true to your principles.


WIG OUT!
60s R&B, Garage, Soul Dance Party
Parties, Events, and Happenings
Hi everyone. Due to the state of the pandemic, and the wear and tear the last few months have put on us and our amazing staff, we are closed for the winter. We’ll be back better than ever some time early next year. Until then, please order merch and gift cards. And stock up on some beer, wine, or spirits for your home bar. Stay safe out there!


{% extends "layout.html" %} {% block pageTitle %} You have successfully updated your contact details {% endblock %} {% block header %} {{ govukHeader() }} {% endblock %} {% block beforeContent %} {% include ".././includes/phase.html" %} {{ govukBackLink({ text: "Back", href: "javascript:history.back()" }) }} {% endblock %} {% block content %}
This message was sent to you on 03 October 2018
Your new primary email address is {{data['emailAddress']}}


TLinearResampler implements a linear resampling algorithm. This algorithm is used only if the bounds of the destination bitmap is larger than the bounds of the source bitmap. Otherwise resampling is performed using the same method as in TKernelResampler.


The Harbingers
Battalion Detachment 0CP (Chaos - Death Guard) [53 PL, 5CP, 996pts]
Rules: Daemonic Ritual, Inexorable Advance, Malicious Volleys, Plague Host, Plague Weapon
Daemon Prince of Nurgle [8 PL, 160pts]: Putrescent Vitality, Shamblerot, Smite, The Epidemicyst Blade, Warlord
Malignant Plaguecaster [5 PL, 100pts]: Miasma of Pestilence, Blades of Putrefaction, Blight Grenades, Wormspitter, Corrupted staff, Krak grenades, Smite
5 Plague Marines [6 PL, 90pts]
- Plague Champion: Blight Grenades, Boltgun, Krak grenades, Plague knife
- 4x Plague Marine w/ boltgun: 4x Blight Grenades, 4x Boltgun, 4x Krak Grenades, 4x Plague knife
5 Plague Marines [6 PL, 90pts]
- Plague Champion: Blight Grenades, Boltgun, Krak grenades, Plague knife
- 4x Plague Marine w/ boltgun: 4x Blight Grenades, 4x Boltgun, 4x Krak Grenades, 4x Plague knife
5 Plague Marines [6 PL, 90pts]
- Plague Champion: Blight Grenades, Boltgun, Krak grenades, Plague knife
- 4x Plague Marine w/ boltgun: 4x Blight Grenades, 4x Boltgun, 4x Krak Grenades, 4x Plague knife
20 Poxwalkers [6 PL, 140pts]: 20x Improvised weapon
18 Poxwalkers [6 PL, 126pts]: 18x Improvised weapon
Myphitic Blight-hauler [5 PL, 100pts]: Bile spurt, Gnashing maw, Missile launcher - Frag missile, Missile launcher - Krak missile, Multi-melta
Myphitic Blight-hauler [5 PL, 100pts]: Bile spurt, Gnashing maw, Missile launcher - Frag missile, Missile launcher - Krak missile, Multi-melta
Total: [53 PL, 5CP, 996pts]
Roster Rules
- Inexorable Advance: If your Army is Battle-forged, all INFANTRY and HELBRUTE units in DEATH GUARD Detachments gain this ability. Such units do not suffer a penalty for moving and firing Heavy Weapons, or for Advancing and firing Assault weapons. In addition, a unit with this ability can fire twice with Rapid Fire weapons at a range of 18", instead of only being able to fire twice with them up to half the weapon's maximum range.
- Malicious Volleys: All DEATH GUARD units in Codex: Death Guard (excluding CHAOS CULTISTS units and POXWALKERS units) gain this ability:
Instead of following the normal rules for Rapid Fire weapons, Rapid Fire bolt weapons used by models in a unit with this ability make double the number of attacks if any of the following apply:
- The firing model’s target is within half the weapon’s maximum range.
- The firing model belongs to an INFANTRY unit and every model from that unit remained stationary in your
previous Movement phase.
- The firing model is a TERMINATOR , BIKER or HELBRUTE.
For the purposes of this ability, a Rapid Fire bolt weapon is any weapon with the Rapid Fire type whose profile includes the word ‘bolt’ (e.g. boltgun, combi-bolter, etc.)
- Plague Host: If your army is Battle-forged, all Troops units in DEATH GUARD Detachments gain this ability. Such a unit that is within range of an objective marker (as specified in the mission) controls that objective marker even if there are more enemy models within range of it. If an enemy unit within range of the same objective marker has a similar ability, then the objective marker is controlled by the player who has the most models within range as normal.
- Plague Weapon: You can re-roll wound rolls of 1 for a weapon with this ability.
Selection Rules
- Hateful Assault: If this unit makes a charge move, is charged or performs a Heroic Intervention, add 1 to the Attacks characteristic of models in this unit until the end of the turn.
Units
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
Wargear |
| Daemon Prince of Nurgle |
8" |
2+ |
2+ |
7 |
6 |
8 |
4 |
10 |
3+ |
The Epidemicyst Blade |
| Malignant Plaguecaster |
5" |
3+ |
3+ |
4 |
5 |
4 |
3 |
8 |
3+ |
Wormspitter, Blight Grenades, Corrupted staff, Krak grenades |
| Plague Champion |
5" |
3+ |
3+ |
4 |
5 |
1 |
2 |
8 |
3+ |
Blight Grenades, Boltgun, Krak grenades, Plague knife |
| Plague Marine |
5" |
3+ |
3+ |
4 |
5 |
1 |
1 |
7 |
3+ |
Blight Grenades, Boltgun, Krak grenades, Plague knife |
| Poxwalker |
4" |
5+ |
6+ |
3 |
3 |
1 |
2 |
4 |
7+ |
Improvised Weapon |
| Myphitic Blight-hauler |
10" |
4+ |
4+ |
6 |
7 |
8 |
3 |
8 |
3+ |
Bile spurt, Gnashing maw, Missile launcher - Frag missile, Missile launcher - Krak missile, Multi-melta |
Wargear
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| The Epidemicyst Blade |
Melee |
Melee |
+1 |
-2 |
3 |
Plague Weapon. Unmodified hit roll of 6 scores +1 hit. |
| Wormspitter |
15" |
Pistol 1 |
5 |
-2 |
1 |
Plague Weapon. When resolving an attack made with this weapon, if a hit is scored, the target is corroded until the end of the turn. When resolving an attack made with a weapon by a friendly DEATH GUARD model against a corroded unit, that weapon gains the Plague Weapon ability for that attack. |
| Blight Grenade |
6" |
Grenade D6 |
3 |
0 |
1 |
Plague Weapon. Blast. |
| Boltgun |
24" |
Rapid Fire 1 |
4 |
0 |
1 |
|
| Corrupted staff |
Melee |
Melee |
+2 |
-1 |
D3 |
|
| Krak grenades |
6" |
Grenade 1 |
6 |
-1 |
D3 |
|
| Plague knife |
Melee |
Melee |
User |
0 |
1 |
Plague Weapon |
| Bile spurt |
12" |
Assault D3 |
6 |
-1 |
1 |
Plague Weapon. Blast. |
| Gnashing maw |
Melee |
Melee |
User |
-2 |
1 |
Plague Weapon |
| Missile launcher, Frag missile |
48" |
Heavy D6 |
4 |
0 |
1 |
Blast. |
| Missile launcher, Krak missile |
48" |
Heavy 1 |
8 |
-2 |
D6 |
|
| Multi-melta |
24" |
Heavy 2 |
8 |
-4 |
D6 |
Half range damage is D6+2. |
Psychic Units
| Psycher |
Cast |
Deny |
Powers Known |
| Daemon Prince of Nurgle |
1 |
1 |
Smite, Putrescent Vitality |
| Malignant Plaguecaster |
2 |
1 |
Smite, Miasma of Pestilence, Blades of Putrefaction |
Psychic Powers
| Psychic |
Warp Charge |
Range |
Effect |
| Smite |
5/11 |
18" |
Closest visible enemy unit within 18" suffers D3 mortal wounds. If 11+ the target suffers D6 mortal wounds instead. |
| Miasma of Pestilence |
6 |
18" |
If manifested, select a visible friendly DEATH GUARD unit within 18" of the psyker. Until the start of your next Psychic phase, your opponent must subtract 1 from all hit rolls that target that unit. |
| Putrescent Vitality |
6 |
18" |
If manifested, select a visible friendly DEATH GUARD INFANTRY unit within 18" of the psyker. Until the start of your next Psychic phase, add 1 to that unit's Strength and Toughness characteristics. |
| Blades of Putrefaction |
5 |
18" |
If manifested, select a visible friendly DEATH GUARD unit within 18" of the psyker. Until the start of your next Psychic phase, add 1 to all wound rolls made by that unit in the Fight phase. Furthermore, any wound rolls of 7+ made for that unit in the Fight phase with a melee plague weapon (i.e. a plaguesword or any weapon with the Plague Weapon ability) inflict a mortal wound on the target in addition to any other damage. |
Daemon Prince of Nurgle [8 PL, 160pts]
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
| Daemon Prince of Nurgle |
8" |
2+ |
2+ |
7 |
6 |
8 |
4 |
10 |
3+ |
| Psycher |
Cast |
Deny |
Powers Known |
| Daemon Prince of Nurgle |
1 |
1 |
Smite, Putrescent Vitality |
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| The Epidemicyst Blade |
Melee |
Melee |
+1 |
-2 |
3 |
Plague Weapon. When resolving an attack made with this weapon, an unmodified hit roll of 6 scores one additional hit. |
| Psychic |
Warp Charge |
Range |
Effect |
| Smite |
5 |
18" |
Smite has a warp charge value of 5. If manifested, the closest visible enemy unit within 18" of the psyker suffers D3 mortal wounds (pg 181). If the result of the Psychic test was more than 11 the target suffers D6 mortal wounds instead. |
| Putrescent Vitality |
6 |
18" |
If manifested, select a visible friendly DEATH GUARD INFANTRY unit within 18" of the psyker. Until the start of your next Psychic phase, add 1 to that unit's Strength and Toughness characteristics. |
- Hateful Assault, Death to the False Emperor, Disgustingly Resilient
- Daemonic: This model has a 5+ invulnerable save.
- Prince of Chaos: You can re-roll hit rolls of 1 made for friendly DEATH GUARD and NURGLE DAEMON units within 6" of this model.
- Shamblerot: When an enemy INFANTRY model is destroyed as the result of an attack made with a melee weapon by this Warlord, add 1 model to a friendly HARBINGERS POXWALKERS unit within 7" of this Warlord. You must pay reinforcement points for each model that you add to that unit that would increase that unit above its starting strength.
Malignant Plaguecaster [5 PL, 100pts]
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
| Malignant Plaguecaster |
5" |
3+ |
3+ |
4 |
5 |
4 |
3 |
8 |
3+ |
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| Blight Grenade |
6" |
Grenade D6 |
3 |
0 |
1 |
Plague Weapon. Blast. |
| Wormspitter |
15" |
Pistol 1 |
5 |
-2 |
1 |
Plague Weapon. When resolving an attack made with this weapon, if a hit is scored, the target is corroded until the end of the turn. When resolving an attack made with a weapon by a friendly DEATH GUARD model against a corroded unit, that weapon gains the Plague Weapon ability for that attack. |
| Corrupted staff |
Melee |
Melee |
+2 |
-1 |
D3 |
|
| Krak grenades |
6" |
Grenade 1 |
6 |
-1 |
D3 |
|
| Psycher |
Cast |
Deny |
Powers Known |
| Malignant Plaguecaster |
1 |
1 |
Smite, Miasma of Pestilence, Blades of Putrefaction |
| Psychic |
Warp Charge |
Range |
Effect |
| Smite |
5 |
18" |
Smite has a warp charge value of 5. If manifested, the closest visible enemy unit within 18" of the psyker suffers D3 mortal wounds (pg 181). If the result of the Psychic test was more than 11 the target suffers D6 mortal wounds instead. |
| Miasma of Pestilence |
6 |
18" |
If manifested, select a visible friendly DEATH GUARD unit within 18" of the psyker. Until the start of your next Psychic phase, your opponent must subtract 1 from all hit rolls that target that unit. |
| Blades of Putrefaction |
5 |
18" |
If manifested, select a visible friendly DEATH GUARD unit within 18" of the psyker. Until the start of your next Psychic phase, add 1 to all wound rolls made by that unit in the Fight phase. Furthermore, any wound rolls of 7+ made for that unit in the Fight phase with a melee plague weapon (i.e. a plaguesword or any weapon with the Plague Weapon ability) inflict a mortal wound on the target in addition to any other damage. |
- Hateful Assault, Death to the False Emperor, Disgustingly Resilient
- Pestilential Fallout: Each time this model successfully manifests a psychic power with a Psychic test of 7 or more, the nearest enemy unit within 7" suffers a mortal wound after the effects of the psychic power have been resolved.
Plague Marines
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
| Plague Champion |
5" |
3+ |
3+ |
4 |
5 |
1 |
2 |
8 |
3+ |
| Plague Marine |
5" |
3+ |
3+ |
4 |
5 |
1 |
1 |
7 |
3+ |
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| Blight Grenade |
6" |
Grenade D6 |
3 |
0 |
1 |
Plague Weapon. Blast. |
| Boltgun |
24" |
Rapid Fire 1 |
4 |
0 |
1 |
|
| Krak grenades |
6" |
Grenade 1 |
6 |
-1 |
D3 |
|
| Plague knife |
Melee |
Melee |
User |
0 |
1 |
Plague Weapon |
- Hateful Assault, Death to the False Emperor, Disgustingly Resilient, Vectors of Death and Disease
Poxwalkers [6 PL, 112pts]
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
| Poxwalker |
4" |
5+ |
6+ |
3 |
3 |
1 |
2 |
4 |
7+ |
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| Improvised weapon |
Melee |
Melee |
User |
0 |
1 |
|
- Disgustingly Resilient
- Curse of the Walking Pox: Each time an enemy INFANTRY model is slain by a Poxwalker in the Fight phase, add one model to the Poxwalker's unit.
- Diseased Horde: You can add 1 to all hit rolls for this unit in the Fight phase if it contains more than 10 models.
- Mindless: This unit never has to take Morale tests.
Myphitic Blight-haulers [5 PL, 100pts]
| Unit |
M |
WS |
BS |
S |
T |
W |
A |
Ld |
Save |
| Myphitic Blight-hauler |
10" |
4+ |
4+ |
6 |
7 |
8 |
3 |
8 |
3+ |
| Weapon |
Range |
Type |
S |
AP |
D |
Abilities |
| Bile spurt |
12" |
Assault D3 |
6 |
-1 |
1 |
Plague Weapon. Blast. |
| Gnashing maw |
Melee |
Melee |
User |
-2 |
1 |
Plague Weapon |
| Missile launcher, Frag missile |
48" |
Heavy D6 |
4 |
0 |
1 |
Blast. |
| Missile launcher, Krak missile |
48" |
Heavy 1 |
8 |
-2 |
D6 |
|
| Multi-melta |
24" |
Heavy 2 |
8 |
-4 |
D6 |
Each time an attack made with this weapon targets a unit within half range, that attack has a Damage characteristic of D6+2. |
- Hateful Assault, Disgustingly Resilient
- Daemonic: This model has a 5+ invulnerable save.
- Foul Stench: Enemy units must subtract 1 from any hit rolls that target this unit in the Fight phase.
- Putrescent Fog: Friendly DEATH GUARD INFANTRY units that are entirely within 7" of a Mephitic Blight-hauler gain the benefit of cover when making armour saves.
- Putrid Explosion: If a Myphitic Blight-hauler is reduced to 0 Wounds, roll a dice before removing it from the battlefield, on a 4+ it explodes, and each unit within 7" suffers 1 mortal wound.