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Updates 2007

Updates 2007

DateMenu-OptionDescription of Change
071231lib/m/l/m This new option allows to read in single libraries directly from .mab files.
071229lib/t/g This option did not work any more after option 'lib/m/a' was implemented. This has been mended. BUG
071209M3dsml This new program makes 3d-similarity calculations available in batch mode. The algorithm is identical with that of the interactive option mch/d. However, while this menu is restricted to diversity analysis (calculation of similarity matrices), the batch option includes a database-search mode (two files: 'database' and 'query').
071206lib/l/t The generation of linear models has been extended. The user is asked whether he wants to generate an indicator model. If so, a specified threshold value discriminates between 'active' and 'inactive' compounds. Compounds without a value are assigned 'inactive'. For non-indicator models, compounds without a value are now eliminated automatically.
071206Mol3d Mfltr For entries in the input .sd file without structure data, Mol3d did not produce a correct output. This has been mended. Such entries are now omitted. BUG
071111lib/e/w This new option allows to write a library with entry data onto a .sd-file.
071111lib/e/d This option has been extended (press SHIFT key) to also read tables of SMILES-codes with data.
071110lib/l An error in the evaluation of minimal linear models, which was introduced by mistake in the 02-apr-2007 version has been corrected. BUG
071109lib/m/e Geometrical constraints for template replacement can now be equipped with exit vector types. Thus, fragments to replace the original template are only considered, if their exit vectors match the corresponding ones of the constraint pharmacophore.
071031lib/m/a For the template replacing utility, the necessary geometrical constraints (pharmacophore entry) can now be automatically generated by specifying the set of atoms making up the template to be replaced.
071031Php/n When generating a new pharmacophore entry the menu to add agons is entered automatically. This avoids initializing with an arbitrary starting agon. If the user leaves the menu without having created any agon, the entry is deleted again.
071028lib/m This option has been organized in a separate submenu and can be called in two different ways: in the old-style mode (with the SHIFT key pressed) and in a new mode. In either case specifications are now kept. In the new mode, fragments to be searched have Moloc's fragment-library structure instead of just being a set of Moloc entries with explicit hydrogens attached at exit atoms.
071028Dyn/o This menu for de novo building of structures has been reorganized mainly by separating the library handling options into a submenu 'l'. This submenu is also utilized in the template matching utility 'lib/m/l'.
071026mch/t/p Printing transformation parameters was subject to computational inaccuracies for rotation angles near 0 or 180 degrees. This has been mended.
071021.../g,e Optical color selection from a customizable wheel has been implemented.
071010dTp/h This option can now be chosen with the SHIFT key pressed. Then, H-counts of specified entries are recalculated from scratch using geometrical criteria. This can be of use when heterogens are red from .pdb files in which the 'ATOM' keyword is used instead of 'HETATM', which may lead to incorrect H-counts.
071005Mngsd A new option, -K, has been introduced which allows to remove user-specified data-fields in .sd files.
071005Mcnf The energy data field (MCNF) has been renamed to MAB_ENERGIES for consistency with the programm Msmab. It now also contains term-wise energy values.
070928mch/k The charge-matching utility has been reorganized.
070926Msmab If option '-s' is set, the resulting .sd file contains an additional data field, MAB_ENERGIES, which lists values for the total as well as for term-wise energies.
070926Msmab The option '-r', redirection, has been added to the programm Msmab. The old option '-r' (limit to the number of rotatable bonds) has been renamed to '-b' and been modified to provide the possibility of keeping only structures without any rotatable bond.
070903Dyn/o Movo A first version of the 'de novo' building utility, 'ab ovo', has been completed. I serves to build structures into a cavity or onto a template molecule (lead). Building blocks are templates taken from a set of libraries. Those are derived from decomposing known structures. Movo is the corresponding batch program.
070901Mcnf Mcnf is a program that reads structures from a .sd (.mab, .mol2) file and prododuces conformations by means of randomizing atomic coordinates and subsequent energy minimization. It can be used as a module in piping mode.
070824lib/t/P When pruning a template library, a new option 's' is now available. It serves to remove templates which are substructuers of another, the difference only being in missing extensions.
070819M... Options files for batch jobs now allow for '#'-separated comments at the end of lines defining options.
070712xry/y/s Space group information of entries can be printed.
070706lib/f Mfltr Filtering with respect to the occurence of substructures can now be performed by ignoring atom types (option 't').
070706mch/s lib/d Substructure seach can now be performed by ignoring atom types.
070706mch/s lib/f Substructure seach for bicyclic structures did not work in all cases. This has been mended. BUG
070610Php/V The cage-generation algorithm for the receptor case has been improved.
070602Dyn/o/p Pharmacophore weights can now be set. This allows to emphasize cage and targets with respect to the receptor (in atom representation) during force-field optimization.
070602lib/c/h Mdck An overall pharmacophore weight can now be set. This allows to emphasize targets with respect to the receptor (in atom representation) during force-field optimization.
070602lib/c Running cavity docking has been put into a separate menu. This allows to preserve specifications for later runs.
070525opt/d Dynamics failed in certain situations due to out-of-range values of random forces. This has been corrected. BUG
070511lib/t/e Filtering of template libraries with respect to planarity of extensions has been implemented.
070506lib/f Mfltr Structure filtering has been augmented by an element-count option.
070502Php/c Cage volumes of pharmacophores can be calculated. The calculation automatically added in options 'v' and 'V'.
070402tutorial The 'Display' tutorial in the Beginner's Corner has been augmented by a section on handling views and camera movies.
070330lib/T Tautomer enumeration has been improved. A heuristic energy estimate yield the basis for tautomer ranking in vacuo and in water.
070217.../k/i Camera movies can be stored onto a .cif file for later replay.
070216.../k/d Camera movies can be shown forwards or backwards (Shift d). When atoms are moved during a movie, resetting atom positions requires backward playing.
070216.../k frg/m The movie option of camera positions has been augmented by the possibility to simultaneously move about a set of atoms. For this, views must be taken (Alt v) with the move option 'm' of the forge menu 'frg' activated.
070208.../k .../: A new menu, '.../k', has been created to handle views (camera positions). Options 'v', 'w', and 'r' have been moved from menu '.../:' to this new menu. In addition, new options allow to store (retrieve) multiple views on a single file. Furthermore, a sequence of views can be shown as a movie (with interpolated frames). The frames of a movie may also be stored as a set of bitmap files.