Frodo at 00:48, 11 March 2014

2014-03-11T00:48:46Z

← Older revision		Revision as of 00:48, 11 March 2014
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	{{Template:Coleman}}		{{Template:Coleman}}
	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
	[[Category:~~File formats~~]]		[[Category:Formats]]
	[[Category:Internal]]		[[Category:Internal]]

Frodo at 03:47, 23 February 2014

2014-02-23T03:47:50Z

← Older revision		Revision as of 03:47, 23 February 2014
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			mol2db format describes files created by the [[mol2db2]] program for input into the [[DOCK 3.7]] molecular docking program.

			mol2db2 format was designed by Ryan Coleman as part of his postdoctoral research in the [[Shoichet Lab]].

			It was first introduced with [[DOCK 3.7]] and is not compatible with previous versions of the DOCK series such as [[DOCK 3.6]]


			= File format description =

	<pre>		<pre>
	Mol2db2 Format 2		Mol2db2 Format 2
Line 147:		Line 156:
	!E does not get a format line		!E does not get a format line
	</pre>		</pre>


	{{Template:CC-BY-SA-30}}		{{Template:CC-BY-SA-30}}
	{{Template:Coleman}}		{{Template:Coleman}}
	[[Category:DOCK 3.7]]		[[Category:DOCK 3.7]]
			[[Category:File formats]]
			[[Category:Internal]]

Frodo: Created page with "

 Mol2db2 Format 2 File Format  T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."

2014-02-13T21:27:55Z

Created page with "<pre> Mol2db2 Format 2 File Format T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."

New page

<pre>
Mol2db2 Format 2
File Format

T type information (implicitly assumed)
M molecule (4 lines req'd, after that they are optional, 24 lines max)
A atoms
B bond
X xyz
R rigid xyz for matching (can actually be any xyzs)
C conformation
S sets
D clusters
E end of molecule
T ## namexxxx (implicitly assumed to be the standard 7)
M zincname protname #atoms #bonds #xyz #confs #sets #rigid #Mlines #clusters
M charge polar_solv apolar_solv total_solv surface_area
M smiles
M longname
[M arbitrary information preserved for writing out]
A stuff about each atom, 1 per line
B stuff about each bond, 1 per line
X coordnum atomnum confnum x y z
R rigidnum color x y z
C confnum coordstart coordend
S setnum #lines #confs_total broken hydrogens omega_energy
S setnum linenum #confs confs [until full column]
D clusternum setstart setend matchstart matchend #additionalmatching
D matchnum color x y z
E
With the above descriptions, here is a description of the columns that are used. Format statements for python/fortran will also appear at some point. If speed/size becomes an issue this might get replaced with a binary file format.
notes: 17 children groups/group per line in current scheme. 9 children confs/group per line. 9 children confs/conf per line. 8 confs/set per line. groups/confs with no children are written out.
on the atom line, dt is dock type and co is color.
1 2 3 4 5 6 7
01234567890123456789012345678901234567890123456789012345678901234567890123456789
T ## typename
M ZINCCODEXXXXXXXX PROTCODEX ATO BON XYZXXX CONFSX SETSXX RIGIDX MLINES NUMCLU
M +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
M SMILESXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
M LONGNAMEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
[M ARBITRARY_INFORMATION_PRESERVEDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX]
A NUM NAME TYPEX DT CO +CHA.RGEX +POLAR.SOL +APOLA.SOL +TOTAL.SOL SURFA.REA
B NUM ATO ATO TY
X COORDNUMX ATO CONFNU +XCO.ORDX +YCO.ORDX +ZCO.ORDX
R NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
C CONFNO COORDSTAR COORDENDX
S SETIDX #LINES #CO C H +ENERGY.XXX
S SETIDX LINENO # CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS CCONFS
D CLUSID STASET ENDSET MST MEN ADD
D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
E
the type lines following are assumed by dock unless overriden:
T 1 positive
T 2 negative
T 3 acceptor
T 4 donor
T 5 ester_o
T 6 amide_o
T 7 neutral
the following are the format statements for python for each line
T %2d %8s\n
M %16s %9s %3d %3d %6d %6d %6d %6d &6d %6d\n
M %+9.4f %+10.3f %+10.3f %+10.3f %9.3f\n
M %77s\n
M %77s\n
M %77s\n
A %3d %-4s %-5s %2d %2d %+9.4f %+10.3f %+10.3f %+10.3f %9.3f\n
B %3d %3d %3d %-2s\n
X %9d %3d %6d %+9.4f %+9.4f %+9.4f\n
R %3d %2d %+9.4f %+9.4f %+9.4f\n
C %6d %9d %9d\n
S %6d %6d %3d %1d %1d %+11.3f\n
S %6d %6d %1d %6d %6d %6d %6d %6d %6d %6d %6d\n
D %6d %6d %6d %3d %3d %3d\n
D %3d %2d %+9.4f %+9.4f %+9.4f\n
E\n
The following are the fortran77 format statements
!T ## namexxxx (implicitly assumed to be the standard 7)
1000 format(2x,i2,1x,a8)
!M zincname protname #atoms #bonds #xyz #groups #confs #sets #rigid #mlines #clusters
2000 format(2x,a16,1x,a9,1x,i3,1x,i3,1x,i6,1x,i6,1x,i6,x,i6,x,i6,x,i6,x,i6)
!M charge polar_solv apolar_solv total_solv surface_area
2100 format(2x,f9.4,1x,f10.3,1x,f10.3,1x,f10.3,1x,f9.3)
!M smiles or longname
2200 format(2x,a77)
!A stuff about each atom, 1 per line
3000 format(2x,i3,1x,a4,1x,a5,1x,i2,1x,i2,1x,f9.4,1x,f10.3,1x,
& f10.3,1x,f10.3,1x,f9.3)
!B stuff about each bond, 1 per line
4000 format(2x,i3,1x,i3,1x,i3,1x,a2)
!X atomnum confnum x y z
5000 format(2x,i9,1x,i3,1x,i6,x,f9.4,1x,f9.4,1x,f9.4)
!R rigidnum color x y z
6000 format(2x,i3,x,i2,x,f9.4,1x,f9.4,1x,f9.4)
!C confnum #startcoord #endcoord
7000 format(2x,i6,1x,i9,1x,i9)
!S setnum #lines #confs_total broken hydrogens omega_energy
8000 format(2x,i6,1x,i6,1x,i3,1x,i1,1x,i1,1x,f11.3)
!S setnum linenum #confs confs [until full column]
8100 format(2x,i6,1x,i6,1x,i1,1x,i6,1x,i6,1x,i6,1x,i6,
& 1x,i6,1x,i6,1x,i6,1x,i6)
!D CLUSID STARTSETX ENDSETXXX ADD MST MEN
9000 format(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)
!D NUM CO +XCO.ORDX +YCO.ORDX +ZCO.ORDX
!re-use 6000
!E
!E does not get a format line
The following are Fortran95 format statements:
!T ## namexxxx (implicitly assumed to be the standard 7)
character (len=*), parameter :: DB2NAME = '(2x,i2,x,a8)' !1000
!M zincname protname #atoms #bonds #xyz #confs #sets #rigid #maxmlines #clusters
character (len=*), parameter :: DB2M1 =
& '(2x,a16,x,a9,x,i3,x,i3,x,i6,x,i6,x,i6,x,i6,x,i6,x,i6)' !2000
!M charge polar_solv apolar_solv total_solv surface_area
character (len=*), parameter :: DB2M2 =
& '(2x,f9.4,x,f10.3,x,f10.3,x,f10.3,x,f9.3)' !2100
!M smiles/longname/arbitrary
character (len=*), parameter :: DB2M3 = '(2x,a78)' !2200
!A stuff about each atom, 1 per line
character (len=*), parameter :: DB2ATOM =
& '(2x,i3,x,a4,x,a5,x,i2,x,i2,x,f9.4,x,f10.3,x,
& f10.3,x,f10.3,x,f9.3)' !3000
!B stuff about each bond, 1 per line
character (len=*), parameter :: DB2BOND =
& '(2x,i3,x,i3,x,i3,x,a2)' !4000
!X coordnumx atomnum confnum x y z
character (len=*), parameter :: DB2COORD =
& '(2x,i9,x,i3,x,i6,x,f9.4,x,f9.4,x,f9.4)' !5000
!R rigidnum color x y z
character (len=*), parameter :: DB2RIGID =
& '(2x,i6,x,i2,x,f9.4,x,f9.4,x,f9.4)' !6000
!C confnum coordstart coordend
character (len=*), parameter :: DB2CONF = '(2x,i6,x,i9,x,i9)' !7000
!S setnum #lines #confs_total broken hydrogens omega_energy
character (len=*), parameter :: DB2SET1 =
& '(2x,i6,x,i6,x,i3,x,i1,x,i1,x,f11.3)' !8000
!S setnum linenum #confs confs [until full column]
character (len=*), parameter :: DB2SET2 =
& '(2x,i6,x,i6,x,i1,x,i6,x,i6,x,i6,x,i6,
& 1x,i6,x,i6,x,i6,x,i6)' !8100
!D CLUSID STASET ENDSET ADD(ittional matching spheres count) MST(art) MEN(d)
character (len=*), parameter :: DB2CLUSTER =
& '(2x,i6,x,i6,x,i6,x,i3,x,i3,x,i3)' !9000
!D NUM CO x y z
!reuse DB2RIGID
!E
!E does not get a format line
</pre>

{{Template:CC-BY-SA-30}}
{{Template:Coleman}}
[[Category:DOCK 3.7]]

Mol2db2 format - Revision history

Frodo at 00:48, 11 March 2014

Frodo at 03:47, 23 February 2014

Frodo: Created page with "
Mol2db2 Format 2 File Format T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."