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Moloc: Molecular Modelling on UNIX Workstations: 14 Match Utility [mch]

Match Utility [mch]

Various methods of matching structures on top of each other are assembled in this utility. Also provided are tools to handle the transformations that result from these matches, as well as the possibility to move molecules with previously generated transformations.

Handling Transformations

Various manipulations with transformations can be performed, in particular reading from or writing to a file. The result of this option is the last generated or chosen transformation, unless it is left by quitting.

Pair-wise Matching

Pairs of topologically non-identical molecules can be matched on top of each other after corresponding atom pairs to match each other have been specified. For Calf structures sequences-wise specification is possible. Corresponding pairs are linked by a dotted distance line.

The following items only show up if the two structures are proteins or Calf structures.

Matching Structures of Identical Topology [mmch]

Any number of structures of identical topology can be compared here. Either only tests are performed (options t, r, q) or matching operations are included (options m, d, p). Since this is a multi-match facility, no transformation is returned.

The following items are for proteins only.

Substructure Matching

First the (connected) substructure to be superimposed has to be defined. This can be done by specifying its SMILES string or by defining it as a set in any of the structures. Then a search for this fragment in all structures must be initiated (option s). Finally, the user has to specify the entries that he wants to participate in the match. Only then the actual match can be performed. This is also a multi-match facility and no transformation is returned.

Pharmacophor Matching [mchp]

Two arbitrary structures can be superimposed. The criteria of optimal superposition can be chosen to be one of the following three possibilities or an arbitrary mix of them: Overlap of occupied volume (O), overlap of H-bond donor- and acceptor properties (including directionality) (H), and overlap of atomic charges (C), which have to be defined in advance. The mix (P) is termed pharmacophor (P) and its ratios are susceptible to the users choice (see option w).

Diversity Analysis [dvrs]

For a set of structures a analysis of pharmacophoric diversity can be performed. To that end a couple of preliminary preparations are necessary. Depending on the mode of pharmacophoric comparison (positional, fixed point, or one of the two cases of axial) more or less of the menu points need to be addressed before the actual calculation can be done.

Cluster Analysis [clan]

Analysis of a binary cluster tree can be done here. When the tree data are associated with structures simultaneous visualization is possible. If no other option is highlighted, the tree can be moved by pressing the shift key and operating the mouse (see forge menu). Similarly, picking a bond of a branch causes the entire branch to be highlighted. If entries are attributed to the tree data the ones belonging to the picked branch are displayed in addition to the tree. The shown entries are matched onto the center entry of the branch. If the branch has many elements and the matching requires much computing, this option may take some time before the entries are displayed. Matching can be omitted with the M<->m toggle option.

View Branch

The entries of a branch, or of a selection can be examined. Picking an entry with the left hand (middle) mouse button adds it to (removes it from) the selection. Selected entries show up in half-bond representation, others in their natural color. While the mouse changes the view as usual, keeping the 'shift\q button pressed causes the single entries to rotate about their fixed atom (if defined) or about their individual centroid. By this token the whole set can conveniently be examined, especially so, if the entries have been spread apart beforehand. Leaving the menu with x removes the spreading, while q keeps the current spread.

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