ViewDock - Revision history

Jwagsta: /* Keyboard shortcuts */

2020-04-16T16:58:34Z

Keyboard shortcuts

← Older revision		Revision as of 16:58, 16 April 2020
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	== Keyboard shortcuts ==		== Keyboard shortcuts ==

	Using ViewDock requires a fair amount of clicking and mouse movement. To reduce these you can use this [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script], mostly written by Tom Goddard ([http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-March/016642.html Chimera user list discussion]):		Using ViewDock requires a fair amount of clicking and mouse movement. To reduce these you can use this [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators] script, mostly written by Tom Goddard ([http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-March/016642.html Chimera user list discussion]):

	<nowiki>		<nowiki>

Jwagsta at 15:20, 30 March 2020

2020-03-30T15:20:14Z

← Older revision		Revision as of 15:20, 30 March 2020
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	add_accelerator('cn', 'Move to next View Dock compound', vdock_next)		add_accelerator('cn', 'Move to next View Dock compound', vdock_next)
	add_accelerator('cp', 'Move to next View Dock compound', vdock_previous)		add_accelerator('cp', 'Move to next View Dock compound', vdock_previous)
	add_accelerator('ct', 'Print ~~vdock~~ totals', vdock_totals)		add_accelerator('ct', 'Print ViewDock totals to Reply Log', vdock_totals)

	def vdock_delete():		def vdock_delete():

Jwagsta at 15:19, 30 March 2020

2020-03-30T15:19:18Z

← Older revision		Revision as of 15:19, 30 March 2020
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	[https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html ViewDock] is a [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera] extension for viewing ~~outputs~~ from several docking software packages. There is a [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html tutorial] on the Chimera web pages.		[https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html ViewDock] is a [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera] extension for viewing output poses from several docking software packages. There is a [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html tutorial] on the Chimera web pages.

	== Keyboard shortcuts ==		== Keyboard shortcuts ==

Jwagsta: /* Keyboard shortcuts */

2020-03-30T15:18:11Z

Keyboard shortcuts

Show changes

Jwagsta: /* Keyboard shortcuts */

2020-03-30T13:53:40Z

Keyboard shortcuts

← Older revision		Revision as of 13:53, 30 March 2020
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	== Keyboard shortcuts ==		== Keyboard shortcuts ==

	Using ViewDock requires a fair amount of clicking and mouse movement. To reduce these you can use this [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script], written by Tom Goddard ([http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-March/016642.html~~] Chimer~~ user list discussion):		Using ViewDock requires a fair amount of clicking and mouse movement. To reduce these you can use this [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script], written by Tom Goddard ([http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-March/016642.html Chimera user list discussion]):

	def register_accelerators():		def register_accelerators():
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	Accelerators "cv" (Viable), "cd" (Delete), "cx" (Purge), work like clicking the radio buttons in the ViewDock dialog box - they change the status of the selected compound. Accelerators "cn" and "cp"		Accelerators "cv" (Viable), "cd" (Delete), "cx" (Purge), work like clicking the radio buttons in the ViewDock dialog box - they change the status of the selected compound. Accelerators "cn" and "cp"

			== ChimeraX/ViewDockX ==

			There is an equivalent tool [https://www.cgl.ucsf.edu/chimerax/docs/user/tools/viewdockx.html ViewDockX] in the next generation visualisation tool [https://www.cgl.ucsf.edu/chimerax/ ChimeraX].

Jwagsta: updated code

2020-03-30T13:51:28Z

updated code

Show changes

Jwagsta at 14:03, 27 March 2020

2020-03-27T14:03:02Z

← Older revision		Revision as of 14:03, 27 March 2020
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	== Keyboard shortcuts ==		== Keyboard shortcuts ==

	Using ViewDock as designed requires a fair amount of clicking and mouse movement. To reduce these one option is to do the following:		Using ViewDock as designed requires a fair amount of clicking and mouse movement. To reduce these one option is to do the following.

	Create a [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script] containing this code, originally written by Tom Goddard:		Create a [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script] containing this code, originally written by Tom Goddard:

Jwagsta at 14:02, 27 March 2020

2020-03-27T14:02:26Z

← Older revision		Revision as of 14:02, 27 March 2020
Line 5:		Line 5:
	Using ViewDock as designed requires a fair amount of clicking and mouse movement. To reduce these one option is to do the following:		Using ViewDock as designed requires a fair amount of clicking and mouse movement. To reduce these one option is to do the following:

	Create a [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script] containing:		Create a [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script] containing this code, originally written by Tom Goddard:

	def register_accelerators():		def register_accelerators():

Jwagsta: Created page with "[https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html ViewDock] is a [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera] extension for viewing outputs ..."

2020-03-27T12:56:48Z

Created page with "[https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html ViewDock] is a [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera] extension for viewing outputs ..."

New page

[https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html ViewDock] is a [https://www.cgl.ucsf.edu/chimera/ UCSF Chimera] extension for viewing outputs from several docking software packages. There is a [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html tutorial] on the Chimera web pages.

== Keyboard shortcuts ==

Using ViewDock as designed requires a fair amount of clicking and mouse movement. To reduce these one option is to do the following:

Create a [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#adding Chimera accelerators script] containing:

def register_accelerators():
from Accelerators import standard_accelerators
standard_accelerators.register_accelerators()

from Accelerators import add_accelerator
add_accelerator('cd', 'Mark current View Dock compound deleted', vdock_delete)
add_accelerator('cx', 'Mark current View Dock compound purged', vdock_purged)
add_accelerator('cv', 'Mark current View Dock compound viable', vdock_viable)

def vdock_delete():
from ViewDock.Compound import Compound
vdock_set_state(Compound.Deleted)

def vdock_purged():
from ViewDock.Compound import Compound
vdock_set_state(Compound.Purged)

def vdock_viable():
from ViewDock.Compound import Compound
vdock_set_state(Compound.Viable)

def vdock_set_state(state):
vd = vdock_dialog()
if vd:
vd.results.setSelectedState(state)
vd._reloadCompounds()

def vdock_dialog():
from ViewDock import ViewDock
from chimera import extension
for vd in extension.manager.instances:
if isinstance(vd, ViewDock):
return vd
return None

Then [https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/accelerators.html#dialog enable Chimera keyboard shortcuts] and load the new file.

When looking at your compounds, initially assign them all status "Deleted" and show only "Deleted" compounds by choosing Compounds > List Deleted in the compound table dialog. Use accelerators "cv"and "cx" to reassign "Purged", and "Viable" statuses.