Moloc Updates |
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Date | Menu-Option | Description of Change |
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061229 | .../s/I | Structures can be stored as InChI records. No tautomer analysis is performed. The atom ordering is taken from the actual arrangement. |
061203 | tutorial | A new tutorial about handling .sd files is available in the Beginner's Corner: moloc/www/bgnr/sdf.html |
061112 | lib/T | This new option allows to enumerate tautomers of structures. Ranking with respect to energy is not implemented! |
061109 | .../:/h | The confirmation option for atom deleting (dTp/a) has been extended to a general delete-confirmation in various places. A new switch in '.../:/h' governs, whether delete-conformation is active or not. It's value can be set in the startup file, .Moloc (parameter 'delconfirm'). |
061109 | geo/w/g,p | Geometrical data can now be evaluated with unit- or atomic-mass weighting. Option 'a' has been replaced by 'o' and correspondingly extended. |
061011 | lib/n | This new option allows to find the most similar structures out of a specified (target) set for each structure of a test set. This is e.g. useful for comparing generated (ab ovo) structures (test set) with a set of experimental ones (target). |
061003 | opt/o | The last optimization step can now be undone by choosing the option 'o' with the SHIFT key pressed. |
061003 | dTp/a | When deleting single atoms by picking the user is now asked for a conformation in order to avoid unintentional deletes. |
061001 | dTp/s/b | This new option allows to add fragments via bond condensation. |
060930 | Srf/d/c | Coloring of surfaces according to H-bond type now also distinguishes between saturated (white) and unsaturated (green) non-polar atoms. |
060927 | Srf/s | This new option generates automatically a colored receptor-site surface once the user has specified ligand(s) and the receptor. |
060917 | .../g/I | A first version of reading in InChI files (default extension .ici) has been implemented. |
060916 | lib/b | Multibrowsing has been augmented by an option 'm' which allows for automatic superimposition in case of identical topology. |
060904 | Php/v Srf/p | The parameter set for void generation has been augmented to allow for finer tuning. |
060831 | Php/v Srf/p | The algorithm has been extended to handle more then a single start atom. |
060831 | Php/l | This new option allows to insert copies of the agons of a pharmacophore into a second pharmacophore. |
060804 | Php/v | This new option allows to cast a pharmacophore into a (protein) cavity. It makes use of the new void insertion algorithm of 'Srf/p' and proceeds to decorate the inserted agons with pharmacophoric properties complementary to the cavity. The file writing options have been renamed from 'w' and 'v' to 'f' and 'F'. |
060804 | Srf/p | The void inserting option has been augmented by an alternative which starts from a picked atom and continues to add new voids in the neiborhood of already existing ones. |
060726 | cnf/b/g | Display of geometry data has been enabled for browsing through conformations. |
060707 | Moloc | Command line input of conformation libraries (.mcl) failed. BUG |
060707 | Mdck | A new switch, -L, has been added which causes the program to write a conformation (poses) library (.mcl) for each docked ligand. This facilitates geometrical analysis, by making the conformation tool, cnf, directly available. |
060707 | cnf/c/n cnf/m/i | At these operations a choice is now offered to (mis)use the energy field as identifier for the conformations. |
060622 | tutorial | The tutorial 'Template Matching' in the Expert's Corner has been augmented by a section on the generation of template libraries. |
060612 | lib/e/s | Sorting of entries of a library has been extended to general data fields. |
060608 | lib/t | This new menu allows to generate and modify template libraries. |
060517 | .../s/i | Writing .cif files resulted in certain cases (protein and C-alpha structure) in files which could not be read back unless some editing was performed. This has been mended. BUG |
060510 | lib/l Mtprmp | The evaluation algoritm of minimal linear models has been improved. |
060505 | Mtprmp | The redundant options '-l' and '-t' have been removed. |
060411 | Mdls tutorial | This new executable can be used to address minimal linear models located in a 'mdl' directory (subdirectory of the installation directory 'moloc'). For details see the newly added section in the 'Regression' tutorial of the Expert's Corner and the description provided when starting 'Mdls' without arguments. |
060403 | Mdck lib/c | An additional parameter (b, bond-order threshold) has been introduced. It governs whether a rotatable bond is varied (MAB-Pi-bond-order below threshold) or not. |
060331 | MAB mch/p,d | The angular dependence of H-bond terms in pharmacophore-type description has been modified. This affects mostly the cases with a wide angular range (e.g. carbonyl oxygens) which previously were equiped with a too narrow range. MAB's regular H-bond terms are NOT affected. |
060313 | Msrfvl | Help text has been added. It is printed on typing the command: Msrfvl ?. |
060306 | Moloc | Moloc now accepts the names of view files (extension .vw) as put parameters and sets the corresponding view. Such files can also be specified in input list files (extension .ils). |
060227 | Mngsd | A new option, -k, allows to keep only specified data fields. |
060224 | iMoloc | Running Moloc on Mac OSX has been made independent of the presence non-standard run-time libraries. |
060224 | lib/l Mtprmp | For minimal models a new option allows to take the average between results obtained with and without a constant for the linear regression calculation. This is now the default. |
060224 | Mngsd | Table writing (options 's' and 't') did not work properly in all cases (missing data). This has been mended. BUG |
060223 | lib/b lib/e/b | The functionality of menu item lib/e has been reduced to strict library browsing. Browsing through all available entries has beed deferred to lib/e/b. |
060222 | Srf/e | Definition of a surface restricting sphere worked differently for Connolly and Lee-Richard type surfaces. This has been unified to correspond to previous behaviour in the Connolly case. |
060222 | Srf/r | Setting a radius factor for atoms did not work properly for Connolly-type surfaces. This has been mended. BUG |
060217 | set | Sets are now also displayed in ball and stick representation. |
060217 | Dyn/g/r | In REFMAC .cif files the table header for planes was written more then once in certain cases. This has been mended. BUG |
060209 | lib/d/s mch/s/s | Substructure recognition did not work in all cases. This has been improved. BUG |
060206 | lib/c Mdck | Docking has been extended to allow for simultaneous ligand cavity and superposition target specification. |
060117 | M... | Protonation options, '-p', for batch programs (where applicable) have been modified and extended to better comply with third party software. |
060104 | M... | For batch programs options can be listed in a file. They are applied by adding the argument '+filename'. |
060104 | M... | For some batch programs extended help can be obtained by using '?' as parameter. In the future, this option will be made available for an increasing number of programs. |