Internal:GPCD - Revision history

Nikos: Reverted edits by Spyridon97 (talk) to last revision by Angelos

2021-09-10T01:09:02Z

Reverted edits by Spyridon97 (talk) to last revision by Angelos

Spyridon97: /* (Spiros/Αngelos) Compute the Solvent Excluded Image */

2021-06-08T17:38:48Z

(Spiros/Αngelos) Compute the Solvent Excluded Image

← Older revision		Revision as of 13:38, 8 June 2021
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	### '''Note 2''': GPU parallelism can be employed [TODO]		### '''Note 2''': GPU parallelism can be employed [TODO]
	## (Spiros) Extract Solvent Excluded image from the EDT result by setting: [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		## (Spiros) Extract Solvent Excluded image from the EDT result by setting: [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	### All pixel values < probe-radius ~~- truncationError[atomType] - paddingDistance~~ = 0		### All pixel values < probe-radius = 0
	### All pixel values >= probe-radius ~~- truncationError[atomType] - paddingDistance~~ = 1		### All pixel values >= probe-radius = 1
	### '''Note 1''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		### '''Note 1''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	### '''Note 2''': GPU parallelism can be employed [TODO]		### '''Note 2''': GPU parallelism can be employed [TODO]
	# Challenges:		# Challenges:
	## (Spiros) Handle the calculation of ~~truncationError[atomType]~~ in a thread-safe way by sorting the atoms by radius in descending order ~~[<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]~~		## (Spiros) Handle the calculation of atom type with the greatest VDW radius in a thread-safe way by sorting the atoms by radius in descending order [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	~~### Truncation error is caused because of the spacing of the image.~~
	~~## (Spiros/Angelos) Select a paddingDistance value to help PODM3D produce an accurate surface~~ [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	## (Spiros) Close holes that should not exist using the distance of the pixel point vs the actual atom [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]		## (Spiros) Close holes that should not exist using the distance of the pixel point vs the actual atom [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]
	## (Spiros) Create smaller images using the concept that is described in the EDTSurf paper [<span style="color:orange">TODO</span>]		## (Spiros) Create smaller images using the concept that is described in the EDTSurf paper [<span style="color:orange">TODO</span>]

Spyridon97: /* Paper and Presenation */

2021-06-03T17:41:59Z

Paper and Presenation

← Older revision		Revision as of 13:41, 3 June 2021
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	== Paper and Presenation ==		== Paper and Presenation ==
	[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]		# [https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]
	[https://www.overleaf.com/3442949237tvggkctnjdbj Paper]		# [https://www.overleaf.com/3442949237tvggkctnjdbj Paper]

	== Resources ==		== Resources ==

Spyridon97: /* Paper and Presenation */

2021-06-03T17:41:51Z

Paper and Presenation

← Older revision		Revision as of 13:41, 3 June 2021
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	== Paper and Presenation ==		== Paper and Presenation ==
	[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]		[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]
			[https://www.overleaf.com/3442949237tvggkctnjdbj Paper]

	== Resources ==		== Resources ==

Spyridon97: /* Paper and Presenation */

2021-06-03T17:41:02Z

Paper and Presenation

← Older revision		Revision as of 13:41, 3 June 2021
Line 319:		Line 319:

	== Paper and Presenation ==		== Paper and Presenation ==
	[[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]]		[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]

	== Resources ==		== Resources ==

Spyridon97: /* Results */

2021-06-03T17:40:55Z

Results

← Older revision		Revision as of 13:40, 3 June 2021
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	\| style="background-color: red; color: white;" \| NO		\| style="background-color: red; color: white;" \| NO
	\|}		\|}

			== Paper and Presenation ==
			[[https://docs.google.com/presentation/d/1rYKfxhgCc9oUKI3xEZ0gLZQOapG64C2-6hNvoDtdpXY/edit?usp=sharing Presentation]]

	== Resources ==		== Resources ==

Spyridon97: /* (Angelos/Spiros) Cavity Detection */

2021-04-20T18:39:49Z

(Angelos/Spiros) Cavity Detection

← Older revision		Revision as of 14:39, 20 April 2021
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	## Tune the clustering parameters:		## Tune the clustering parameters:
	### (Spiros) Search-radius = 2 * minEdgeLength of the surface. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]		### (Spiros) Search-radius = 2 * minEdgeLength of the surface. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	### (Angelos) Esp = 5. [<span style="color:green">DONE</span>] [<span style="color:purple">~~Fall 2020~~</span>]		### (Angelos) Esp = 8. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	### (Spiros~~/Angelos~~) Min cavity size = cavityFactor * delta^-2.178. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]		### (Spiros) Min cavity size = cavityFactor * delta^-2.178. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	#### Default value of cavityFactor = 10.		#### Default value of cavityFactor = 20.
	## Limit the expansion of the cavity by using:		## Limit the expansion of the cavity by using:
	### (Spiros) A relative threshold for the difference an occlusion value from the average occlusion value of the cluster. [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]		### (Spiros) A relative threshold for the difference an occlusion value from the average occlusion value of the cluster. [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]

Spyridon97: /* (Angelos/Spiros) Cavity Detection */

2021-04-20T18:39:01Z

(Angelos/Spiros) Cavity Detection

← Older revision		Revision as of 14:39, 20 April 2021
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	# Challenges:		# Challenges:
	## Tune the clustering parameters:		## Tune the clustering parameters:
	### (Spiros) Search-radius = ~~maxEdgeLength~~ of the surface. [<span style="color:green">DONE</span>] [<span style="color:purple">~~Summer 2020~~</span>]		### (Spiros) Search-radius = 2 * minEdgeLength of the surface. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	### (Angelos) Esp = 5. [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]		### (Angelos) Esp = 5. [<span style="color:green">DONE</span>] [<span style="color:purple">Fall 2020</span>]
	### (Spiros/Angelos) Min cavity size = cavityFactor * delta^-2.178. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]		### (Spiros/Angelos) Min cavity size = cavityFactor * delta^-2.178. [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]

Spyridon97: /* (Spiros/Αngelos) Compute the Solvent Excluded Image */

2021-04-19T15:11:27Z

(Spiros/Αngelos) Compute the Solvent Excluded Image

← Older revision		Revision as of 11:11, 19 April 2021
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	# Output: Solvent Excluded Image of a chain		# Output: Solvent Excluded Image of a chain
	# Algorithmic steps:		# Algorithmic steps:
	## (Spiros) Calculate the optimal bounding box of the protein chain using CGAL's ~~algorithm~~ [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]		## (Spiros) Calculate the optimal bounding box of the protein chain using CGAL's implementation [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	## (Spiros/Angelos) Create the Solvent Accessible image by creating spheres for each atom that their radius is: Van der Waals radius + probe radius. [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		## (Spiros/Angelos) Create the Solvent Accessible image by creating spheres for each atom that their radius is: Van der Waals radius + probe radius. [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	### '''Note''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		### '''Note''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]

Spyridon97: /* (Spiros/Αngelos) Compute the Solvent Excluded Image */

2021-04-19T15:11:17Z

(Spiros/Αngelos) Compute the Solvent Excluded Image

← Older revision		Revision as of 11:11, 19 April 2021
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	# Output: Solvent Excluded Image of a chain		# Output: Solvent Excluded Image of a chain
	# Algorithmic steps:		# Algorithmic steps:
	## (Spiros) Calculate the ~~minimum~~ bounding box of the protein chain using CGAL's algorithm [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]		## (Spiros) Calculate the optimal bounding box of the protein chain using CGAL's algorithm [<span style="color:green">DONE</span>] [<span style="color:purple">Spring 2021</span>]
	## (Spiros/Angelos) Create the Solvent Accessible image by creating spheres for each atom that their radius is: Van der Waals radius + probe radius. [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		## (Spiros/Angelos) Create the Solvent Accessible image by creating spheres for each atom that their radius is: Van der Waals radius + probe radius. [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]
	### '''Note''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]		### '''Note''': Shared memory parallelism can be employed [<span style="color:green">DONE</span>] [<span style="color:purple">Summer 2020</span>]