All About DB2 Files - Revision history

Btingle at 19:05, 11 July 2023

2023-07-11T19:05:03Z

← Older revision		Revision as of 19:05, 11 July 2023
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	"A" and "B" lines define atoms and bonds for a molecule. These are practically identical to atom/bond lines in .mol2 files- not much else to say here		"A" and "B" lines define atoms and bonds for a molecule. These are practically identical to atom/bond lines in .mol2 files- not much else to say here

	"X" lines define the set of all coordinates for the entry- these will be referenced later on. coordinates are guaranteed to be "distinct", in the sense that no coordinate is within a threshold distance (typically 0.001A) of any other coordinate in the set of all coordinates		"X" lines define the set of all coordinates for the entry- these will be referenced later on. coordinates are guaranteed to be "distinct", in the sense that no atom coordinate is within a threshold distance (typically 0.001A) of any other coordinate for that same atom in the set of all coordinates

	"R" lines define the coordinates of the rigid component. this is the basis component of the molecule that does not move between rotomers, usually a benzene ring or the like. the choice of which structure should be the rigid component is arbitrary, and in fact usually a separate db2 entry is created for each possible rigid component (usually each ring system) in a molecule		"R" lines define the coordinates of the rigid component. this is the basis component of the molecule that does not move between rotomers, usually a benzene ring or the like. the choice of which structure should be the rigid component is arbitrary, and in fact usually a separate db2 entry is created for each possible rigid component (usually each ring system) in a molecule

Btingle: /* What is the deal with sets and confs? */

2023-06-14T00:33:41Z

What is the deal with sets and confs?

← Older revision		Revision as of 00:33, 14 June 2023
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	"D" lines are "clusters", and are a feature of older db2 files. The cluster lines were meant to group together similar rotomers, though the idea was scrapped and newer db2 files no longer have them, thus "D" may now stand for "deprecated"		"D" lines are "clusters", and are a feature of older db2 files. The cluster lines were meant to group together similar rotomers, though the idea was scrapped and newer db2 files no longer have them, thus "D" may now stand for "deprecated"

	== What is the deal with sets and confs? ==		=== What is the deal with sets and confs? ===

	First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation. "Set" is an annoyingly general term for something that is so specific. These are the terms we are stuck with though! If I could turn back time, I would probably rename set->conformation and conf->subconformation		First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation. "Set" is an annoyingly general term for something that is so specific. These are the terms we are stuck with though! If I could turn back time, I would probably rename set->conformation and conf->subconformation

Btingle: /* The nittier grittier */

2023-06-14T00:32:13Z

The nittier grittier

← Older revision		Revision as of 00:32, 14 June 2023
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	== The nittier grittier ==		== The nittier grittier ==

	Here is the specification of each type of line described before. Parts of the specification I don't understand the importance of are followed with a ?		Here is the specification of each type of line described before (as of 06/13/2023). Parts of the specification I don't understand the importance of are followed with a ?
	<nowiki>		<nowiki>
	M [name] [protname?] [# atoms] [# bonds] [# xyz] [# confs] [# sets] [# rigid] 5(?) [# clusters]		M [name] [protname?] [# atoms] [# bonds] [# xyz] [# confs] [# sets] [# rigid] 5(?) [# clusters]

Btingle: /* What is the deal with sets and confs? */

2023-06-14T00:31:32Z

What is the deal with sets and confs?

← Older revision		Revision as of 00:31, 14 June 2023
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	== What is the deal with sets and confs? ==		== What is the deal with sets and confs? ==

	First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation. "Set" is an annoyingly general term for something that is so specific. These are the terms we are stuck with though!		First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation. "Set" is an annoyingly general term for something that is so specific. These are the terms we are stuck with though! If I could turn back time, I would probably rename set->conformation and conf->subconformation

	Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.		Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.

Btingle: /* The nitty gritty */

2023-06-14T00:28:32Z

The nitty gritty

← Older revision		Revision as of 00:28, 14 June 2023
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	"A" and "B" lines define atoms and bonds for a molecule. These are practically identical to atom/bond lines in .mol2 files- not much else to say here		"A" and "B" lines define atoms and bonds for a molecule. These are practically identical to atom/bond lines in .mol2 files- not much else to say here

	"X" lines define the set of all coordinates for the entry- these will be referenced later on. coordinates are guaranteed to be "distinct", in the sense that no coordinate is within a threshold distance (typically 0.001A) of any other coordinate in the set		"X" lines define the set of all coordinates for the entry- these will be referenced later on. coordinates are guaranteed to be "distinct", in the sense that no coordinate is within a threshold distance (typically 0.001A) of any other coordinate in the set of all coordinates

	"R" lines define the coordinates of the rigid component. this is the basis component of the molecule that does not move between rotomers, usually a benzene ring or the like. the choice of which structure should be the rigid component is arbitrary, and in fact usually a separate db2 entry is created for each possible rigid component (usually each ring system) in a molecule		"R" lines define the coordinates of the rigid component. this is the basis component of the molecule that does not move between rotomers, usually a benzene ring or the like. the choice of which structure should be the rigid component is arbitrary, and in fact usually a separate db2 entry is created for each possible rigid component (usually each ring system) in a molecule

Btingle: /* What is the deal with sets and confs? */

2023-06-14T00:26:19Z

What is the deal with sets and confs?

← Older revision		Revision as of 00:26, 14 June 2023
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	== What is the deal with sets and confs? ==		== What is the deal with sets and confs? ==

	First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation.		First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation. "Set" is an annoyingly general term for something that is so specific. These are the terms we are stuck with though!

	Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.		Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.
	A single conf may be a part of one or more sets, thus confs can be used to define exactly where sets overlap.		A single conf may be a part of one or more sets, thus confs can be used to define exactly where sets overlap.

Btingle at 00:25, 14 June 2023

2023-06-14T00:25:20Z

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			The terms "rotomer", "conformation" and "set" may be used interchangeably in this text- unless "set" refers to the usual meaning of the word i.e a collection of objects.

	== The brass tacks ==		== The brass tacks ==

Btingle at 00:20, 14 June 2023

2023-06-14T00:20:14Z

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	~~The terms "set", "conformation", and "rotomer" will be used interchangeably in this text.~~

	== The brass tacks ==		== The brass tacks ==

Btingle at 00:19, 14 June 2023

2023-06-14T00:19:20Z

← Older revision		Revision as of 00:19, 14 June 2023
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			The terms "set", "conformation", and "rotomer" will be used interchangeably in this text.

	== The brass tacks ==		== The brass tacks ==

Btingle: /* What is the deal with sets and confs? */

2023-06-14T00:15:15Z

What is the deal with sets and confs?

← Older revision		Revision as of 00:15, 14 June 2023
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	First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation.		First off- the naming is super confusing. Confs don't describe conformations(rotomers), rather they describe a subset of a conformation.
	Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.		Sets are collections of confs, and confs are collections of atom xyz positions. Each set describes a conformation(rotomer) of the molecule.
	A single conf may be a part of one or more sets, thus confs can be used to define exactly where sets overlap		A single conf may be a part of one or more sets, thus confs can be used to define exactly where sets overlap.
	It is common to see confs comprised of a single atom- this may describe a situation where two rotomers happen to overlap at a particular atom.		It is common to see confs comprised of a single atom- this may describe a situation where two rotomers happen to overlap at a particular atom.
	A conf may also be a part of just one set- this describes a situation where none of the atoms in the conf overlap with other sets, and is quite common		A conf may also be a part of just one set- this describes a situation where none of the atoms in the conf overlap with other sets, and is quite common.

	== The nittier grittier ==		== The nittier grittier ==