Mol2db2 Format 2 - Revision history

TBalius at 15:44, 23 October 2014

2014-10-23T15:44:20Z

← Older revision		Revision as of 15:44, 23 October 2014
Line 17:		Line 17:
	*per molecule pKa		*per molecule pKa
	*valence for each atom		*valence for each atom

			== Nomenclature Definitions ==

			* Conf - one set of atoms that moves together with a single position per atom.
			* Set - a group of conformations that completely defines one position for each atom in a ligand.
			* Cluster - Not yet implamented in DOCK3.7
			* Cloud - Not yet implamented in DOCK3.7

	= File Format =		= File Format =

Frodo at 02:34, 12 March 2014

2014-03-12T02:34:30Z

← Older revision		Revision as of 02:34, 12 March 2014
Line 179:		Line 179:
	!E does not get a format line		!E does not get a format line

	[[Category:~~Wishlists~~]]		[[Category:Formats]]

Therese: 70 revisions

2012-10-08T20:29:23Z

70 revisions

← Older revision

Revision as of 20:29, 8 October 2012

Rgc at 19:35, 11 July 2012

2012-07-11T19:35:47Z

← Older revision		Revision as of 19:35, 11 July 2012
Line 10:		Line 10:
	*arbitrary information to be written into output mol2 file (5th and above M lines) [x]		*arbitrary information to be written into output mol2 file (5th and above M lines) [x]

	== ~~planned~~ ==		== wished ==
	*Per-conformation per-atom partial charge & solvation information to support internal energies		*Per-conformation per-atom partial charge & solvation information to support internal energies
	*Aliphatic ring movements?		*Aliphatic ring movements?

Frodo at 02:10, 11 July 2012

2012-07-11T02:10:51Z

← Older revision		Revision as of 02:10, 11 July 2012
Line 1:		Line 1:
	This page is a wishlist for features that would be nice for a new version of the flexibase file format to support. mol2db2 format features that are actually implemented so far are marked [x]		This page is a wishlist for features that would be nice for a new version of the flexibase file format to support. mol2db2 format features that are actually implemented so far are marked [x]

			= New Features =
			== implemented ==
	*Real Atom Types and Bond Information [x]		*Real Atom Types and Bond Information [x]
	*Way to determine which mix-and-match conformations have clashes (and avoid trying them) [x]		*Way to determine which mix-and-match conformations have clashes (and avoid trying them) [x]
	*A place to store an internal energy for each possible conformation [x]		*A place to store an internal energy for each possible conformation [x]
	*Terminal hydrogen rotations?? [x]		*Terminal hydrogen rotations?? [x]
			*support for clusters of conformations [x]
			*arbitrary information to be written into output mol2 file (5th and above M lines) [x]

			== planned ==
	*Per-conformation per-atom partial charge & solvation information to support internal energies		*Per-conformation per-atom partial charge & solvation information to support internal energies
	*Aliphatic ring movements?		*Aliphatic ring movements?
	*support for clusters of conformations [x]
	*group tagging (needed for covalent docking) and basic set of covalent groups		*group tagging (needed for covalent docking) and basic set of covalent groups
	*specified rigid component override (and better rules for finding non-ring rigid components)		*specified rigid component override (and better rules for finding non-ring rigid components)
	*per molecule pKa		*per molecule pKa
	*valence for each atom		*valence for each atom
	*arbitrary information to be written into output mol2 file (5th and above M lines) [x]

	~~the following represents the~~ current plan for the file format		= File Format =
			==current plan for the file format ==
	*T type information (implicitly assumed)		*T type information (implicitly assumed)
	*M molecule (4 lines req'd, after that they are optional, 24 lines max)		*M molecule (4 lines req'd, after that they are optional, 24 lines max)

Rgc: another wishlist item

2012-07-09T18:09:25Z

another wishlist item

← Older revision		Revision as of 18:09, 9 July 2012
Line 11:		Line 11:
	*specified rigid component override (and better rules for finding non-ring rigid components)		*specified rigid component override (and better rules for finding non-ring rigid components)
	*per molecule pKa		*per molecule pKa
			*valence for each atom
	*arbitrary information to be written into output mol2 file (5th and above M lines) [x]		*arbitrary information to be written into output mol2 file (5th and above M lines) [x]

Rgc: Mol2db Format 2 moved to Mol2db2 Format 2

2012-02-14T18:51:23Z

Mol2db Format 2 moved to Mol2db2 Format 2

← Older revision

Revision as of 18:51, 14 February 2012

Rgc: adding f95 statements

2012-01-17T18:41:25Z

adding f95 statements

@@ Line 98: / Line 98: @@
   E\n
-The following are the fortran format statements
+The following are the fortran77 format statements
   !T ## namexxxx (implicitly assumed to be the standard 7)
@@ Line 130: / Line 130: @@
   !E
   !E does not get a format line
 [[Category:Wishlists]]

Rgc at 20:17, 9 January 2012

2012-01-09T20:17:23Z

← Older revision		Revision as of 20:17, 9 January 2012
Line 5:		Line 5:
	*A place to store an internal energy for each possible conformation [x]		*A place to store an internal energy for each possible conformation [x]
	*Terminal hydrogen rotations?? [x]		*Terminal hydrogen rotations?? [x]
			*Per-conformation per-atom partial charge & solvation information to support internal energies
	*Aliphatic ring movements?		*Aliphatic ring movements?
	*support for clusters of conformations		*support for clusters of conformations [x]
	*group tagging (needed for covalent docking) and basic set of covalent groups		*group tagging (needed for covalent docking) and basic set of covalent groups
	*specified rigid component override (and better rules for finding non-ring rigid components)		*specified rigid component override (and better rules for finding non-ring rigid components)

Rgc at 23:41, 8 June 2011

2011-06-08T23:41:33Z

← Older revision		Revision as of 23:41, 8 June 2011
Line 123:		Line 123:
	8100 format(2x,i6,1x,i6,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,		8100 format(2x,i6,1x,i6,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,
	& 1x,i6,1x,i6,1x,i6,1x,i6)		& 1x,i6,1x,i6,1x,i6,1x,i6)
	!D CLUSID STARTSETX ENDSETXXX ADD		!D CLUSID STARTSETX ENDSETXXX ADD MST MEN
	9000 format(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)		9000 format(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)
	!D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX		!D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX