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Updates 2000

Updates 2000

DateMenu-OptionDescription of Change
001222NT version The NT version of Moloc now also runs with the graphics board ELSA Gloria II, including stereo option with shutter glasses.
001218.../s/i Storing a cyclic C-alpha structure led to looping of the program. BUG
001129.../v, 'Alt w' Window stereo has been implemented on the NT platform. A 'FireGL 1000 Pro' graphics-board was used (www.diamondmm.com).
001129lib/k The Andrews analysis has been augmented by inclusion of sulfonate groups.
001124Msmab New options '-p' and '-P' have been added to allow to control protonation of the compounds.
001123Msmab A new option '-h' has been introduced to add explicit hydrogens to the structures.
001123dTp/m
Msmab
E and Z isomers in isomeric smiles were not properly recognized in certain cases. This has been mended. BUG
001106php/m This new option allows to generate a 3-d pharmacophore from an all-atom structure.
001103mch/c
mch/d/r
The specification of the type of cluster linkage has been changed from a y/n question to a choice selector.
001103mch/d/d,r,a/m In the rooted pharmacophore match the weight for the root atom has been increased. This yields better supperposition of the roots.
001103www The 'Beginners Corner' has an additional web page 'Diversity Analysis of Pharmacophoric Properties'.
001025.../g/o,n A new option-switch 'sd3d' has been introduced. When reading in .sd (.mol) files with flat structures, a 3-dimensional conformation will be generated if the switch is set.
000929.../l This new option allows to transfer entry display settings from a single entry to a whole library (list) of entries.
000928lib/k A online help facility has been added to selectors. By clicking the legend of a selectable item an extended help text will appear on the text port. Help texts will be added one by one in corresponding places.
000926lib/k Average full binding energies can be calculated after Andrews et.al. J.Med.Chem 27, 1648 (1984).
000831mch/o Options for the topological pharmacophore match have been augmented to allow for full, super, sub, and partial matching for the rigidbody case. Setting all match options is now transferred to this new menu point 'o'.
000726mch/s/o An additional option has been introduced to mach molecules flexible onto the target but keeping the atoms of the specified fragment fixed (after rigidbody match). Now, all options (including multimatch) appear under this single menu point.
000726.../:/h A new switch has been introduced to allow to present entry lists in alphabetic order.
000725mch/s/o,O,w A toggle switch has been introduced to offer the possibility of flexible matching when substructures are matched pairwise onto a target (option 'd'). The old menu point 'o' (for output) has been replaced by 'w' (write file).
000719map/b,e Brick picking has been improved. An inaccuracy in the geometry was eliminated.
000713mch/s/o Data writing has been generalized to output all data per atom that have been generated in mch/a. The user can also edit the table headers.
000713mch/a Instead of calculating just atomic charges, a selection of various atomic properties can be chosen which will be calculated for all atoms of the specified entries.
000704mch/d/a/M When matching structures on the ground of topological pharmacophore similarity, they are colored such as to display their pharmacophoric agons: green for hydrophobs, blue to red for H-binders coresponding to donor- and acceptor strength, respectively.
000509mch/s/o A file can be written with the charge values for all fragment atoms listed for every entry containing the fragment.
000407mch/s/h Hydrogen counts on a substructure fragment can be modified in all entries containing the substructure.
000407srf/d/m Surface normals can be displayed.
000330Mtprgn A new option 'S' has been introduced indicating that the program will receive a .sd file containing all hydrogens explicitly.
000330frg/n A new option 'n' has been introduced to enable moving entire entries after picking them.
000229srf/c,q
Msrfvl
When calculating Lee-Richard surfaces atomic radii were scrambled, which led to inaccuracies in the total surface and in particular for the hydrophobic and hydrophilic contributions. This has been mended. BUG
000215xnr/p/s,c Secondary structure coloring (option s) has been added to the protein display menu. The previous menu item 's' for scale of colors has been changed to 'c'.
000214Mol3d A new switch '-p' allows to orient the structures along priciple axes. The centroids are put into the origin.
000210mch/d/a/!,d,D This switch has newly the additinal value 'D' which will, in addition to calculating a diversity analysis, produces similarity descriptors.
000210Msrfvl A new option, -n name-key, has been introduced which allows to specify a key used in the .sd-file to indicate the identifier of the molecule. This identifier will then appear in the output table of Msrfvl (see Legend).
000210.../:/f
.../:/m
All font sizes are now handled here. The corresponding option in the foto menu has been removed.
000110mch/d/a/c
mch/d/a/z
The tree can be colored according to entry-specific data. Such data can be read in option lib/n. The previous option 'c' has been renamed to 'z'!
000110lib/n If the entry names are the identifier column of a table, data columns can also be read by moloc as entry specific data.
000110mch/d/c Automatic backward-forward assignment of entries to cluster leaves has been implemented.