Mol2db - Revision history

Khtang at 23:21, 4 January 2019

2019-01-04T23:21:20Z

← Older revision		Revision as of 23:21, 4 January 2019
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	[[Category:Software]]		[[Category:Software]]
	~~[[Category:ZINC]]~~
	[[Category:Formats]]		[[Category:Formats]]

Frodo at 04:18, 13 March 2014

2014-03-13T04:18:16Z

← Older revision		Revision as of 04:18, 13 March 2014
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	mol2db is a program developed to combine multimol2 files into the [[Flexibase Format]] read by [[DOCK]]. A standalone tool to decode the .db files produced is [[db2multipdb.py]].		mol2db is a program developed to combine multimol2 files into the [[Flexibase Format]] read by [[DOCK 3.6]]. A standalone tool to decode the .db files produced is [[db2multipdb.py]].

	The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.		The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.

Frodo at 04:17, 13 March 2014

2014-03-13T04:17:47Z

← Older revision		Revision as of 04:17, 13 March 2014
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	[[Category:Software]]		[[Category:Software]]
	~~[[Category:Databases]]~~
	[[Category:ZINC]]		[[Category:ZINC]]
			[[Category:Formats]]

Frodo at 17:36, 15 February 2014

2014-02-15T17:36:49Z

← Older revision		Revision as of 17:36, 15 February 2014
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	confhier.c puts the conformations into the hierarchy. the potential problem here is that only one atom in each conformation in used to determine if the conformation differs from a previous one. when there are some atoms in a conformation that are the same while others are different, the results will be random based on atom ordering in the mol2 files, and can be incorrect. This has been fixed so now each conformation when added checks against all atoms in the level, not just 1.		confhier.c puts the conformations into the hierarchy. the potential problem here is that only one atom in each conformation in used to determine if the conformation differs from a previous one. when there are some atoms in a conformation that are the same while others are different, the results will be random based on atom ordering in the mol2 files, and can be incorrect. This has been fixed so now each conformation when added checks against all atoms in the level, not just 1.

			[[Category:Software]]
			[[Category:Databases]]
			[[Category:ZINC]]

Therese: 16 revisions

2012-10-08T20:29:22Z

16 revisions

← Older revision

Revision as of 20:29, 8 October 2012

Rgc: clarifying mol2db changes

2010-01-07T02:07:37Z

clarifying mol2db changes

← Older revision		Revision as of 02:07, 7 January 2010
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	The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.		The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.

			NOTE: the requirement for 6 line headers of the input mol2 files is gone. asl.pl/etc are no longer necessary. Any number of lines is fine.

	ui.c reads the inhier parameter file and sets variables		ui.c reads the inhier parameter file and sets variables

	The proximal function in other.c figures out what coordinates are essentially the same. It uses a distance tolerance which is in thousandths of angstroms. Currently 7 is used, which amounts to 0.~~0007Å~~ differences in coordinates being called the same, the coordinates coming out of OMEGA do vary this much sometimes even for atoms in the same position.		The proximal function in other.c figures out what coordinates are essentially the same. It uses a distance tolerance which is in thousandths of angstroms. Currently 7 is used, which amounts to 0.007Å differences in coordinates being called the same, the coordinates coming out of OMEGA do vary this much sometimes even for atoms in the same position.

	hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:		hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:

Rgc: adding link to new decoder tool

2009-12-10T22:42:20Z

adding link to new decoder tool

← Older revision		Revision as of 22:42, 10 December 2009
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	mol2db is a program developed to combine multimol2 files into the [[Flexibase Format]] read by [[DOCK]].		mol2db is a program developed to combine multimol2 files into the [[Flexibase Format]] read by [[DOCK]]. A standalone tool to decode the .db files produced is [[db2multipdb.py]].

	The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.		The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.

Rgc: explaining distance tolerance

2009-12-09T20:04:43Z

explaining distance tolerance

← Older revision		Revision as of 20:04, 9 December 2009
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	ui.c reads the inhier parameter file and sets variables		ui.c reads the inhier parameter file and sets variables

			The proximal function in other.c figures out what coordinates are essentially the same. It uses a distance tolerance which is in thousandths of angstroms. Currently 7 is used, which amounts to 0.0007Å differences in coordinates being called the same, the coordinates coming out of OMEGA do vary this much sometimes even for atoms in the same position.

	hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:		hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:

Rgc: changing to reflect new bugfix

2009-11-24T21:28:05Z

changing to reflect new bugfix

← Older revision		Revision as of 21:28, 24 November 2009
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	hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:		hiergen.c uses the multiple conformations to construct the hierarchy data structure by the following algorithm:
	# find the ~~first atom in~~ the rigid component ~~as the first atom with only 1 unique position~~		# find the largest connected set of atoms that have only one unique position, call one of those atoms the beginning of the rigid component
	# expand through bonds to any atoms that have the same or fewer unique positions. bonded atoms with more unique positions are recursively added as branches		# expand through bonds to any atoms that have the same or fewer unique positions. bonded atoms with more unique positions are recursively added as branches
	# for each branch, repeat the examining of bonded atoms and examine unique positions		# for each branch, repeat the examining of bonded atoms and examine unique positions

Rgc: adding fix to multiple atom checks per level.

2009-11-18T17:12:16Z

adding fix to multiple atom checks per level.

← Older revision		Revision as of 17:12, 18 November 2009
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	this would appear to have flaws if the atom positions downstream overlap, especially since a distance tolerance is used to consider things overlapped.		this would appear to have flaws if the atom positions downstream overlap, especially since a distance tolerance is used to consider things overlapped.

	confhier.c puts the conformations into the hierarchy. the potential problem here is that only one atom in each conformation in used to determine if the conformation differs from a previous one. when there are some atoms in a conformation that are the same while others are different, the results will be random based on atom ordering in the mol2 files, and can be incorrect.		confhier.c puts the conformations into the hierarchy. the potential problem here is that only one atom in each conformation in used to determine if the conformation differs from a previous one. when there are some atoms in a conformation that are the same while others are different, the results will be random based on atom ordering in the mol2 files, and can be incorrect. This has been fixed so now each conformation when added checks against all atoms in the level, not just 1.