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Moloc: Molecular Modelling on UNIX Workstations: 13 Pharmacophor Building [php]
Pharmacophor Building [php]
This is the basic facility to build and modify
pharmacophors. These are built up of single agons (features)
which are represented by a point in space with several
properties, first of all a radius characterizing the
extension. They are displayed as wire-frame spheres of the
corresponding radius. The agon type is evident from the
color of the sphere. There are directed agons (H-bond donors
and acceptors). Their directionality is shown by a spot of
different color on the sphere. The extension of the spot
characterizes the angular range over which the directional
property is taken to be active.
n: open new pharmacophor entry
Here a new entry will be generated. This new entry con
sists of a hydrophobic agon (LR) placed at the center of
the visibility volume.
a: add and delete agons
Pick an agon of the entry you want to modify. This leads
to a new menu that affects the picked pharmacophor. In
contrast to atoms molecules the agons are not bonded.
Thus one has to specify which entry should get the added
agons.
t: change agon types
A new menu is entered in which the agon type can be
selected.
r: change agon radius
Specify the agon to be changed by picking it. The radius
is then changed by moving the mouse, keeping shift- and
middle mouse keys pressed. If the left mouse key is
pressed instead of the middle one, the width of the
directionality property is changed instead of the
radius. This is of course only true for directed agons.
When pressing both mouse keys simultaneously, the
actual value radius and second radius (specifying the
width) are printed.
p: change agon position and orientation
The picked agon is moved as in the corresponding option
in the forge menu (shift- and middle mouse keys). Ori
ented agons can be reoriented analogously (shift- and
left mouse keys).
b: add / modify bonds (constraints)
Pick (left mouse button) the two agons to be related by
a distance constraint. An erroneous first pick can be
undone by picking again with the middle button. To
delete a constraint, pick it with the middle mouse but
ton.
g: get pharmacophor out of a Catalyst .filtlog file
h: get pharmacophor from a .hdt file
s: store pharmacophor as .hdt file (hypothesis)
Pharmacophors are also useful in database searches
(Biocad calls them hypotheses). Thus, at present the
file format is such that the files can be directly used
to generate the hypothesis corresponding to the pharma
cophor. However, if a agon carries several properties
simultaneously, a unique selection has to be made for a
correct operation of the hypotheses-generating program.
Nevertheless, multiproperty agons are again recognized
by Moloc upon file reading. The format of the files,
which carry the extension '.hdt\q, is specific to the
hypoedit program of Biocad (being a UNIX shell script
with path specifications). A more general format (file
extension .php) is written and read in the '.'-tool.
13.1 Add and Delete Agons
This menu provides various modes of adding agons to
pharmacophors.
d: add agon in center of display volume or delete agons
A new agon is inserted by picking anywhere with the left
mouse button. The new agon appears in the center of the
visibility volume. If an other agon too close no inser
tion is made and a corresponding message is issued.
Picking with the middle button removes the picked agon.
a: add agon on top of a atom of a picked atom
s: add agon in the centroid of a set of atoms
e: excluded volume agon for set
An excluded volume agon is added on top of each atom of
a specified set
m: move agons
To move an agon, different from the freshly inserted
one, this option can be used. It works exactly as the
corresponding option in the forge menu. As long as its
letter is highlighted, the insert option is silenced.
t: change type of agon to be inserted
A selection box appears from which the property of the
agon to be inserted is selected. Several of the listed
properties can be selected. However, some combinations
are excluded, and the user has to ensure that the final
choice taken by the program in the case of a conflict
corresponds to his intentions. The type chosen shows up
in the menu header.
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