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Updates 2008

Updates 2008

DateMenu-OptionDescription of Change
081207lib/b/l This new switch allows to display label 'L', or data 'D' (if available) of the current entry.
081004lib/e/y/l A leave-one-out test has been implemented in the regression analysis utility.
081003lib/e/y For libraries, the entries of which have data associated with them, regression analyses on these data can be performed. Examination can be made by a graph or by browsing (see lib/b/a). This new module is mainly used for method development within Moloc, but it may be of general interest.
081003lib/b/a This new option allows to select entries of a library to be browsed, by picking agons of a positions entry (see lib/e/v).
081003lib/e/v For libraries, the entries of which have data associated with them, a positions entry can be generated, the agons of which are associated with the entries of the library. The coordinates of these entries are associated with the values of specified data fields. Such data entries are also automatically produced in certain places in Moloc. In the browse utility (lib/b) entries can be selected by picking an agon of such a positions entry.
080929.../g/o A new input parameter 'name-tag' can be defined. I causes the program to take molecule-names from the corresponding tags in a .sd file.
080914lib/f The element count option of the filter utility did not work for some time now. This has been mended. BUG
080822MAB The table for bond radii has been updated. This affects mainly some of the less common element.
080508Mngsd A new option, -C, has been introduced to handle files propery which contain several conformations per structure.
080501cnf/c/p Mcnf In a conformation analysis, to avoid that the program gets stack during enumeration of symmetries for highly symmetric structures. A limit for the number of enumerating permutations can be set. When this limit is reached, enumeration of symmetries is abandoned.
080501cnf/f In addition to filtering it is now possible to write just a table with the values of the quantities for which filtering can be performed. Averages and rmsd's are also given.
080425cnf/f Mfltr A new filtering option, -M, has been introduced to allow to extract structures on which the MAB force field cannot be considered very reliable.
080424.../g/o When reading files, kations can now be freed of any bond specified in the file. The corresponding input parameter is called 'kation-bnd'. This feature is the default in Mol3d and can be removed by setting the flag '-k'.
080423Mngsd When writing a table (option -s or -t) missing data are now indicated by a character '~' instead of '-'.
080422Mol3d Option -h has been extended. It now also allows to have the result file with added hydrogens.
080405Movo Option -l has been extended to allow specification of several library-list files.
080323Dyn/o Movo A memory leak has been removed, which caused a crash after building of a few hundred structures. BUG
080323Dyn/o/l lib/m/l A new option, 'p', has been introduced in the fragment library menu. It allows to modify building parameters of fragment libraries.
080323Dyn/o/l lib/m/l A new option, 'i', has been introduced in the fragment library menu. It allows to build (modify) a fragment library interactively.
080214Dyn/o/l lib/m/l A new option, 's', has been introduced in the fragment library menu. It allows to display the fragments simultaneously with the possibility to spread them appart for overview purposes.
080214dTp/s/l This new option allows to select substituents from a user-defined fragment library.
080205.../k/f This new option allows to play a full movie, consisting of several scenes.
080130lib/l/o The flag, z, has been changed such that the default (z=0) leads to evaluation of test molecules of any size, while z=1 skips molecules with more agons (pharmacophoric units) then the maximum in the training set.
080130lib/l/o A new parameter, d, has been introduced which determines the minimum number of components (dimension) the individual models must have.
080129dTp/a,b For entries in half-bond coloring, newly intoduced bonds are now also correspondingly displayed.
080129.../+/c When copying an entry, the copy is now presented in the color of the original. In addition a color selector is presented which allows to change the color.
080127lib/c Mdck Variation of initial orientation can now be specified also for the case of a single atom as positioning center.
080127.../:/k The recovery mechanism has been extended to allow for a save history. If a negative value is specified for the save-time a sequence of recovery files is kept which are distinguished by a sequence number in their file name.
080119lib/l/c The output of check runs for minimal indicator models now also gives the Matthiews coefficient.
080119Mdls The path of model files listed in the .mdl files was not correctly parsed in all cases. This has been corrected. BUG
080119Mdls The help text to this program has been extended to facilitate installation of models.
080118lib/e/d Reading data from a .sd file was limited to a maximum of 256 data occuring in the file. This limit has been removed.
080101lib/b/v Now, when choosing this option with the SHIFT key pressed, a spreading mode is entered: all members of the library are displayed and can be spread appart, and rotated simultaneously.