@<TRIPOS>U_FEAT
The data records associated with this RTI contain the information necessary to reconstruct UNITY features and constraints defined in the molecule. Each data record following this RTI consists of one line representing either a UNITY feature or a UNITY constraint.
The first three fields in most features' records are class, type, and name. In the description of the features which follow, the shorthand <header> represents these three fields.
Classes:
1
|
Feature
|
2
|
Constraint
|
3
|
Atom
|
4
|
Macro (Donor atom, hydrophobic, etc.)
|
5
|
Spatial constraint
|
Types:
Many features also contain lists of defining properties and features. The format for this is:
<# of properties> <property id # list> <# of features> <feature names or id # list>
Some features may be defined using only properties, and some using only features, but both lists are usually included for ease of parsing. The lists for a feature with no properties and two centroid features looks similar to:
0 2 CENTROID1 CENTROID2
In the description of the features which follow, the shorthand <props and feats> is used to signify these lists.
Centroid
<header> <props and feats>
There are no features, and one property that contains the atoms which define the centroid.
The properties are stored under @<TRIPOS>SET. If the first property is:
ucent$CENT1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
6 11 12 13 14 15 16
then the centroid feature looks like:
1 0 CENT1 1 1 0
This defines a centroid named CENT1 defined on the six atoms 11, 12, 13, 14, 15, and 16.
Plane
<header> <props and feats> rms
There are no features, and one property that contains the atoms which define the plane. The rms value is never used, but is stored as -1.0 for backward compatibility.
A plane feature definition looks like:
1 1 LSPLANE1 1 2 0 -1.000000
where the 2 refers to property 2, which looks like:
ulsp$LSPLANE1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
6 1 2 3 4 5 6
Line
<header> -2 <props and feats> <start point class> <start point index> <end point class> <end point index>
The -2 after the header signifies that this is a line feature for SYBYL 6.4 or later. Earlier versions without the -2 are not documented here.
The point classes are either 1 for feature, or 3 for atom. The atoms are stored in properties. Each point index is an index into the feature list (if the class is 1) or the property list (if the class is 3). So a line feature which is defined from an atom to a centroid feature looks similar to the following (the letters "a-l" refer to the guide below; they do not appear in the .mol2 file):
1 2 LINE1 -2 1 1 1 CENT1 3 0 1 0
a b c d e f g h i j k l
a
|
class (= feature)
|
b
|
type (= line)
|
c
|
name
|
d
|
-2 specifies SYBYL 6.4 version of a line
|
e
|
number of properties
|
f
|
property ID number
|
g
|
number of features
|
h
|
feature name
|
i
|
starting point is an atom
|
j
|
the atom is in property #0 in the property list
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k
|
ending point is a feature
|
l
|
the feature is feature #0 in the feature list
|
The properties are stored under @<TRIPOS>SET. The first property looks like:
uline1$LINE1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
1 5
This specifies a set containing 1 atom, namely atom 5. So the example describes a line from atom 5 to feature CENT1. If the line was from CENT1 to atom 5, the "3 0 1 0" at the end would be "1 0 3 0". If the line was from CENT1 to CENT2, it would look like:
1 2 LINE1 -2 0 2 CENT1 CENT2 1 0 1 1
A line between two atoms would look like:
1 2 LINE1 -2 2 1 2 0 3 0 3 1
Extension Point
The extension point definition has the name at the end, rather than following the class and type.
<class> <type> <property id> <distance> <angle> <dihedral> <1st atom> <2nd atom> <3rd atom> <name>
There is always one property containing the 3 atoms used in the extension point. Since the order of the atoms is important, the atom numbers are also included in the extension point definition itself. So the definition of an extension point looks like:
1 4 7 3.00 90.00 180.00 42 54 49 EXTPT1
which defines an extension point named EXTPT1 on atoms 42, 54, and 49, with a distance of 3 Å, an angle of 90°, and a dihedral angle of 180°. Property number 7 looks like:
uxp$EXTPT1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
3 42 49 54
Normal Point
<header> <distance> <props and feats> <selected point>
There are no features, and one property that contains the atoms which define the normal. The selected point is either 0 or 1, specifying one of the two possible normal points.
A normal point feature named NORMPT1 defined on the atoms in property 4 with distance 1.5 Å looks like:
1 5 NORMPT1 1.500000 1 4 0 1
Distance Constraint
<header> <distance> <tolerance> <props and feats>
A distance constraint has either two properties, two features, or one of each. Each property contains exactly one atom. The features may be point-class features (centroids, extension points, etc.), lines, or planes.
A distance constraint between an atom in property 7 and a centroid feature, with a distance of 5 Å and a tolerance of 0.2 Å is defined:
2 6 DIST1 5.000000 0.200000 1 7 1 CENT1
Angle Constraint
<header> <angle> <tolerance> <class 1> <index 1> <class 2> <index 2> <class 3> <index 3> <props and feats>
The class-index pairs are similar to those used for lines. If the class is 1, the index is for the feature list. If the class is 3, the index is for the property list. An angle constraint of 60° with a tolerance of 5° between atom 5, feature CENT1, and atom 10 is defined:
@<TRIPOS>SET
uang1$ANG1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
1 5
uang2$ANG1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
1 10
@<TRIPOS>U_FEAT
2 7 ANG1 60.00 5.00 3 0 1 0 3 1 2 1 2 1 CENT1
a b c d e f g h i j k l m n o p
a
|
class (= constraint)
|
b
|
type (= angle constraint)
|
c
|
name
|
d
|
angle value
|
e
|
tolerance
|
f
|
first item is an atom
|
g
|
the atom is in property #0 in the property list
|
h
|
second item is a feature
|
i
|
the feature is feature #0 in the feature list
|
j
|
third item is an atom
|
k
|
the atom is in property #1 in the property list
|
l
|
there are two properties
|
m
|
first property ID number (points to uang1$ANG1)
|
n
|
second property ID number (points to uang2$ANG1)
|
o
|
there is one feature
|
p
|
feature name
|
Excluded and Containing Volume Constraints
The single-sphere volume constraints are no longer used, but are still supported for backward compatibility. All volumes are now stored as multi-sphere constraints.
Line/Plane Angle Constraint
<header> <angle> <tolerance> 0 0 0 0 <props and feats>
Older versions of this feature had class-index pairs which are no longer used, so the four 0's are written for backward compatibility. The ordering of the line or plane features does not matter. The number of properties is always 0, and the number of features is always 2. An angle constraint between LINE1 and PLANE1 looks like:
2 11 LPANG1 90.00 10.00 0 0 0 0 0 2 LINE1 PLANE1
Receptor Site
Macro Reference
<header> <macro name> <target coordinate> <props and feats> <center coordinate> <vector 1> <vector 2> <color>
The number of properties is always 0. The number of features is 1 if there is a connection attribute (the feature is the other macro reference that this macro reference is connected to). The center coordinate and the vectors are for internal SYBYL use when adding a spatial constraint to the macro reference.
4 13 ACCEPTOR_ATOM1 ACCEPTOR_ATOM 1.0 2.0 3.0 0 0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
4 13 DONOR_SITE1 DONOR_SITE 4.0 5.0 6.0 0 1
ACCEPTOR_ATOM1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
This describes an acceptor atom at coordinates (1.0, 2.0, 3.0), and a donor site at coordinates (4.0, 5.0, 6.0) which is connected to the acceptor atom.
Spatial Point
<header> <tolerance> <target coordinate> <props and feats> <color>
There is either one feature or one property. The property contains one atom.
A spatial point constraint on a centroid with a tolerance of 0.5 Å and a target coordinate (1.4388, -4.727, 0.8463) is defined:
5 14 SPATIALPT1 0.500000 1.438800 -4.727000 0.846300 \
0 1 CENT1 GREEN
Spatial Torus
<header> <radius> <center coordinate> <tolerance> <normal vector> <props and feats> <color>
There is either one feature or one property. The property contains one atom.
A spatial torus constraint on an atom defined in property 4 with a radius of 1.2 Å, a tolerance of 0.3 Å, a center coordinate (1.4388, -4.727, 0.8463), and a normal vector (-0.988, -0.016, 0.156) looks like:
5 15 TORUS1 1.2000 1.4388 -4.7270 0.8463 0.3000 \
-0.9880 -0.0160 0.1560 1 4 0 YELLOW
Tetrahedral
<header> <central atom id> <distance> <property id>
The property contains 4 atoms, but the central atom is the atom to which the tetrahedral is attached.
utet$TETRA1 STATIC ATOMS UNITY
SYSTEM|DELETE_EMPTY
4 5 9 11 22
then a tetrahedral feature on atoms 5, 9, 11, and 22, with the tetrahedral attached to atom 9 at a distance of 3 Å, looks like:
1 16 TETRA1 9 3.000000 6
4-Point (Torsion) Angle Constraint
This is identical to the Angle Constraint, except that there are four class-index pairs rather than three, and the type is 17 rather than 11.
Partial Match Directive
<header> <min> <max> <color> <props and feats>
There are no properties. The features are those which are included in the partial match.
A partial match directive on 5 features with minimum 3 and maximum 4 looks like:
2 18 PARTIAL1 3 4 RED 0 5 CENT1 CENT2 DONOR1 HYD1
LSPLANE2
Spatial Line
<header> <angle> <tolerance> <starting coordinate> <vector> <props and feats> <color>
There are no properties, and one line feature.
A spatial line constraint with an angle of 0 degrees, a tolerance of 10 Å, a starting coordinate (-0.0035, 1.1756, 1.5260), and a vector (-0.0025, 0.7322, -0.6810) is defined:
5 19 SPATLINE1 0.00 10.00 -0.0035 1.1756 1.5260 \
-0.0025 0.7322 -0.6810 0 1 LINE1 BLUE
Spatial Plane
<header> <angle> <tolerance> <starting coordinate> <vector> <props and feats> <color>
There are no properties and one plane feature.
A spatial plane constraint with a tolerance of 10 Å, a starting coordinate (-0.0035, 1.1756, 1.5260), and a vector (-0.0025, 0.7322, -0.6810) looks like:
5 20 SPATPLANE1 10.00 -0.0035 1.1756 1.5260 -0.0025 \
0.7322 -0.6810 0 1 LSPLANE1 ORANGE
Multi-Sphere Excluded and Containing Volume Constraints
<header> <vdw ratio> <sphere count> \
<radius 1> <coordinate 1> \
<radius 2> <coordinate 2> \
. . .
<radius n> <coordinate n>
An excluded volume constraint with a vdw ratio of 0.9 and 3 spheres is defined:
2 21 EXCVOL1 0.900000 3 \
3.500000 1.000000 2.000000 3.000000 \
2.000000 4.000000 5.000000 6.000000 \
2.800000 7.000000 8.000000 9.000000
A containing volume looks the same, except that the type is 22 instead of 21.
Fragment
Identical in structure to a Centroid, except the type is 23 instead of 0.
Spatial Cap
<header> <point> <center coordinate> <tolerance> <bend angle> <twist angle> <vector 1> <vector 2> <rotatable> <props and feats> <color>
There are no properties and one feature. <rotatable> is 1 if the cap is rotatable, 0 otherwise.
A rotatable spatial cap on a donor atom with a tolerance of 0.5 Å, a bend angle of 70° and a twist angle of 30° looks like:
5 24 SPATIAL_CAP1 4.947179 -3.548140 -11.860902 \
6.604500 -2.884300 -9.575600 0.500000 70.000000 \
30.000000 0.575350 -0.253583 -0.777604 0.575350 \
-0.253583 -0.777604 1 0 1 DONOR1 MAGENTA
Markush
<header> <markush definition>
A feature for a Markush with name NORC and definition N|C is defined:
1 25 U_MARKUSH_NORC N|C
Surface Volume Constraint
<header> <usurf file name> <vdw ratio>
A surface volume constraint which has a vdw ratio of 0.8 and is defined in a file named SURFACE1.usurf looks like:
2 26 SURFACE1 /home/user/SURFACE1.usurf 0.800000
Bond Path Constraint
<header> <min> <max> 0 2 <feature 1> <feature 2>
A bond path constraint of 1 to 10 bonds between two features looks like:
2 27 BP_HYDRO1_ACCEPT_AT1_1 1 10 0 2 HYDRO1 ACCEPT_AT1
