Flexibase Format - Revision history

Frodo at 17:59, 21 October 2012

2012-10-21T17:59:45Z

← Older revision		Revision as of 17:59, 21 October 2012
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	</pre></code>		</pre></code>

	~~[[Category:Articles needing style editing]]~~
	[[Category:Formats]]		[[Category:Formats]]

Therese: 16 revisions

2012-10-08T20:24:12Z

16 revisions

← Older revision	Revision as of 20:24, 8 October 2012
(No difference)

Rgc: making documentation match reality

2012-02-28T18:06:29Z

making documentation match reality

← Older revision		Revision as of 18:06, 28 February 2012
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	Family header: Line #9 is designed for future use. The word Family is followed by a chemical family number. This is hard coded to 1 (first number)~~, but will be changed in the future to group molecules into families~~. The second number is the number of molecules in this family (matches the number of occurrences of line #10), the third is the number of branches that get attached to each molecule. The last number is the number of branches in the family. Line #10 has the first 50 characters of the molecule name and the last letter and number of the identification code (e.g., MFCD ~~à D~~, SPEC ~~à C~~). After a space there can be up to 10 branches listed (10i2). The rigid fragment is considered branch one so the example molecule has branches two and three. By listed which branches make up which molecules, I can later rebuild each molecule and recombine side chains. Any branch in the first position can be combined with any branch in the second position, etc.		Family header: Line #9 is designed for future use. The word Family is followed by a chemical family number. This is hard coded to 1 (first number). The second number is the number of molecules in this family (matches the number of occurrences of line #10), the third is the number of branches that get attached to each molecule. The last number is the number of branches in the family. Line #10 has the first 50 characters of the molecule name and the last letter and number of the identification code (e.g., MFCD, SPEC, ZINC). After a space there can be up to 10 branches listed (10i2). The rigid fragment is considered branch one so the example molecule has branches two and three. By listed which branches make up which molecules, I can later rebuild each molecule and recombine side chains. Any branch in the first position can be combined with any branch in the second position, etc.

Rgc at 19:26, 19 January 2012

2012-01-19T19:26:12Z

← Older revision		Revision as of 19:26, 19 January 2012
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	Here are some additional notes on the color table, note that the atom names are sybyl atom names http://tripos.com/mol2/atom_types.html :		Here are some additional notes on the color table, note that the atom names are sybyl atom names http://tripos.com/mol2/atom_types.html :

	rules are last match counts. so even though all Ns are positive, the later		rules are last match counts. so even though all Ns are positive, the later
	rule N.ar matches acceptor so N.ar is an acceptor		rule N.ar matches acceptor so N.ar is an acceptor
	first rules are beginning of sybyl atom text -> type		first rules are beginning of sybyl atom text -> type
	later rules are Atom NotBondedTo Atom -> type like		later rules are Atom NotBondedTo Atom -> type like
	O. -1 N.2 -> negative		O. -1 N.2 -> negative
	other rules are Atom BondsAwayFrom Atom -> type like		other rules are Atom BondsAwayFrom Atom -> type like
	C.2 1 N. -> positive or		C.2 1 N. -> positive or
	0.2 2 N.3 -> amide_o		0.2 2 N.3 -> amide_o
	again rules are read in order and the last matching rule is the one used		again rules are read in order and the last matching rule is the one used

Rgc: adding more info on colors

2012-01-19T19:25:49Z

adding more info on colors

← Older revision		Revision as of 19:25, 19 January 2012
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	color_table This keyword marks the beginning of the color table. The color table follows the syntax rules for the mol2db (dock 3.5) color table. The end of the color table is marked by the keyword default_color and the value neutral		color_table This keyword marks the beginning of the color table. The color table follows the syntax rules for the mol2db (dock 3.5) color table. The end of the color table is marked by the keyword default_color and the value neutral

			Here are some additional notes on the color table, note that the atom names are sybyl atom names http://tripos.com/mol2/atom_types.html :

			rules are last match counts. so even though all Ns are positive, the later
			rule N.ar matches acceptor so N.ar is an acceptor
			first rules are beginning of sybyl atom text -> type
			later rules are Atom NotBondedTo Atom -> type like
			O. -1 N.2 -> negative
			other rules are Atom BondsAwayFrom Atom -> type like
			C.2 1 N. -> positive or
			0.2 2 N.3 -> amide_o
			again rules are read in order and the last matching rule is the one used


	4. Hierarchy database format		4. Hierarchy database format

Rgc: adding a note about id numbers, which magdalena "discovered"

2011-04-01T20:36:27Z

adding a note about id numbers, which magdalena "discovered"

← Older revision		Revision as of 20:36, 1 April 2011
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	2. Solvation file		2. Solvation file

	This file contains abbreviated output from AMSOL. Each molecule record begins with a line containing the identification number followed by the total number of atoms and the formal charge. The next numbers are the total polar solvation energy, the total solvent accessible surface, total apolar solvation energy and total solvation energy. After this header, there is a line of data for each atom. The first number is the partial atomic charge, followed by the polar solvation energy, the solvent accessible surface area, apolor solvation energy and finally the total solvation energy of the atom.		This file contains abbreviated output from AMSOL. Each molecule record begins with a line containing the identification number followed by the total number of atoms and the formal charge. An important note is that the identification number here must match the identification number in the mol2 file! The next numbers are the total polar solvation energy, the total solvent accessible surface, total apolar solvation energy and total solvation energy. After this header, there is a line of data for each atom. The first number is the partial atomic charge, followed by the polar solvation energy, the solvent accessible surface area, apolor solvation energy and finally the total solvation energy of the atom.

Rgc: correcting documentation since partial charges are actually multiplied by 10000 not 1000.

2010-03-03T18:56:47Z

correcting documentation since partial charges are actually multiplied by 10000 not 1000.

← Older revision		Revision as of 18:56, 3 March 2010
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	* Hierarchy level: The rigid fragment is 9. All groups attached to the rigid fragment are numbered in the 10's; groups attached to those are numbered in the 20's. The tens (and if need be the hundreds place) denotes distance from the rigid fragment. The ones place differentiates independent groups within the branch. Branches from the rigid fragment can be numbered either, 19, 18, etc., or all 19. Originally the each needed to be different, but as the code evolved this was no longer required.		* Hierarchy level: The rigid fragment is 9. All groups attached to the rigid fragment are numbered in the 10's; groups attached to those are numbered in the 20's. The tens (and if need be the hundreds place) denotes distance from the rigid fragment. The ones place differentiates independent groups within the branch. Branches from the rigid fragment can be numbered either, 19, 18, etc., or all 19. Originally the each needed to be different, but as the code evolved this was no longer required.
	* Atom information: This block of information (line #12-23, #37, and #45-52) contains information we consider to be the same for all conformations. It also describes all of the parts (number of atoms each group) required to complete the branch. After the hierarchy information, the van der Waals type as described in the Dock 3.5 manual is listed. Next the partial atomic charge multiplied by ~~1000~~. This is historical; the multiplication should probably be removed at some point. At the end of the charge is a column that is set to zero. This value is the flag (see dock 2.5). Currently the hierarchy generator and dock do not use flagging. Next is the color, corresponding to the color table at the top of the database file. The last two columns are the polar and apolar partial atomic desolvation values.		* Atom information: This block of information (line #12-23, #37, and #45-52) contains information we consider to be the same for all conformations. It also describes all of the parts (number of atoms each group) required to complete the branch. After the hierarchy information, the van der Waals type as described in the Dock 3.5 manual is listed. Next the partial atomic charge multiplied by 10000. This is historical; the multiplication should probably be removed at some point. At the end of the charge is a column that is set to zero. This value is the flag (see dock 2.5). Currently the hierarchy generator and dock do not use flagging. Next is the color, corresponding to the color table at the top of the database file. The last two columns are the polar and apolar partial atomic desolvation values.
	* Atom coordinates: The first number is the hierarchy level followed by the xyz coordinates for the atom (multiplied by 1000). Line #38-42 list six different sets of coordinates for the hydrogen described in line #37. Line #53-55 are the one set of coordinates for the two carbons and hydrogen in group 18. For each position of group 18 (line #53-55, #69-71, #85-87, and #101-103) there are three positions for group 29 (Cl and 2 H) and two positions for group 28, the carboxylic acid. Since groups 29 and 28 can move independently, they have different group numbers. For each of the four positions for group 18 there are six downstream combinations of 29 and 28. This leads to the reported 24 positions for the branch. Any of these positions can be combined with any of the six torsions of the hydrogen leading to 144 conformations for the molecule. Note that the information about how many different sets of coordinates is not encoded anywhere, you have to count the lines, when there is one atom and then 6 different sets of coordinates (like lines #38-42) you know there are 6 conformations for that atom. When there are 3 atoms and 9 lines of coordinates (like lines #56-64), you know there are 3 conformations for that set of atoms. Note also that no information about the tree is explicitly encoded, if you are reading from group 49 for instance and then read a line of group 29 you have to move back up the tree of conformations to that level. The output order of the tree of conformations is 'infix'.		* Atom coordinates: The first number is the hierarchy level followed by the xyz coordinates for the atom (multiplied by 1000). Line #38-42 list six different sets of coordinates for the hydrogen described in line #37. Line #53-55 are the one set of coordinates for the two carbons and hydrogen in group 18. For each position of group 18 (line #53-55, #69-71, #85-87, and #101-103) there are three positions for group 29 (Cl and 2 H) and two positions for group 28, the carboxylic acid. Since groups 29 and 28 can move independently, they have different group numbers. For each of the four positions for group 18 there are six downstream combinations of 29 and 28. This leads to the reported 24 positions for the branch. Any of these positions can be combined with any of the six torsions of the hydrogen leading to 144 conformations for the molecule. Note that the information about how many different sets of coordinates is not encoded anywhere, you have to count the lines, when there is one atom and then 6 different sets of coordinates (like lines #38-42) you know there are 6 conformations for that atom. When there are 3 atoms and 9 lines of coordinates (like lines #56-64), you know there are 3 conformations for that set of atoms. Note also that no information about the tree is explicitly encoded, if you are reading from group 49 for instance and then read a line of group 29 you have to move back up the tree of conformations to that level. The output order of the tree of conformations is 'infix'.

Rgc: adding note about the column spacing being wrong

2010-01-20T19:33:24Z

adding note about the column spacing being wrong

← Older revision		Revision as of 19:33, 20 January 2010
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	The recursion routine used in generating the hierarchy has problems with macrocyles that are not the rigid fragment. Nothing is written to the database file.		The recursion routine used in generating the hierarchy has problems with macrocyles that are not the rigid fragment. Nothing is written to the database file.


			Here is the example file for the molecule shown above. The line numbers are shown at left, the column spacing is not accurate due to formatting changes.
	<code><pre>		<code><pre>
	# 1 DOCK 5.1 ligand_atoms		# 1 DOCK 5.1 ligand_atoms

Rgc at 19:23, 20 January 2010

2010-01-20T19:23:11Z

← Older revision		Revision as of 19:23, 20 January 2010
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	[[Category:Articles needing style editing]]		[[Category:Articles needing style editing]]
	[{Category:Formats]]		[[Category:Formats]]

Rgc: fixing carriage returns

2010-01-20T19:20:56Z

fixing carriage returns

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