Moloc
Updates
Recent | 2014 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997   Moloc
Home
Updates 2005

Updates 2005

DateMenu-OptionDescription of Change
051207opt/e/r,s The display of attractive (negative) van der Waals energies has been extended. Now, by default pairs of a polar atom in close distance to a apolar one are shown. The previous negative-vdW-energy display is only geneated for a small value of the relative-distance parameter to be set in option 's'.
051207.../g/i Reading of .cif files has been made independent of the presence of CR characters (which occur under Windows).
051116lib/l Mtprmp An additional option to calculate topological similarity models has been introduced. It calculates linear regression with a constant. This is now the default.
051102Mngsd With the new option '-r' the .sd file can now be provided at standard input (e.g. by piping from a precursor program). In this case the results appear on standard output (and may be piped into a file). This option does not make sense in all cases. The previous (shortlived) option, '-r', has been renamed to '-F'.
051012Mngsd A new option '-F' allows to remove those structures of an .sd file, the names of which appear in a list file.
051012Mngsd A new option '-d' allows to add data from a table to the structures of an .sd file.
051005Dyn/t/a,s,S Trajectory evaluation has been extended for atom sets. It now allows evaluation of energy terms among atoms included in the set. This option 'a' has been renamed to 's', and the previous option 's' (secondary structure content) to 'S'.
051004Dyn/t/w Trajectory evaluation has been extended to also include angles of atom triples.
051004lib/c Conservation of cis-trans isomery in docked structures did not work properly. This has been mended. BUG
050922lib/a mch/a The atomic-data generating routine has been moved from the match menu 'mch' to the library menu 'lib'.
050921lib/e/d,n Input entry-data can now also be logarithmized.
050916Srf/d/f Writing surface data files (.sfd) can now also be invoked through this menu item.
050914Srf/d/c The procedure for the specification of parameters which govern the calculation of electrostatic fields at the surface has been modified and extended.
050914Srf/c This option has been extended to (optionally) write surface data files (.sfd).
050823Srf/r Lee-Richard surfaces were unaffected by changes in radius parameters. This has been mended. BUG
050816mch/c/y This new option allows to scale a hierarchical tree just in one dimension, such that the branches keep constant lengths while distance between leaves changes.
050816Tutorial The web page 'Linear Regression Models', located in Moloc's expert corner has been updated and now also describes the handling of minimal models.
050815Mtprmp The linear-model batch program, Mtprmp, has been augmented to also handle minimal models.
050815lib/l/c This new option provides a validation procedure for minimal models.
050815lib/l The menu for linear models has been augmented by a new model type, minimal models. Model generation is straightforward and adaption to test compounds is automatic.
050712MAB The angular terms of the force field have been modified for the case of atoms with a coordination higher then four.
050712pca/t/n This new option allows to change amino acid type and sequence number of a C-alpha structure.
050629.../: In this menu the actual size of the graphics window is given in the header.
050616Mdck The new switch -E allows to also specify electron density maps as target. The program decides on the format of the map file from its extension, which must have the appropriate default value.
050616lib/c Docking with electron density maps as target has been improved.
050615Mfebd Option -x has been augmented to have a column with score values written. With option -m set, receptor structures are now only written if part of the receptor is specified as non-fixed (i.e. f<=500 or the set u0 does not contain all receptor atoms).
050614lib/m Pharmacophore targeting has been introduced into the template matching utility. If a pharmacophore target entry is specified, the score also includes similarity of the templates to that entry in addition to the geometrical score.
050610lib/m A collision check has been introduced into the template matching utility. Matches are eliminated for which any template heavy atom approaches any heavy atom of a specified environment entry closer then a given distance.
050610lib The library menu has been reorganized.
050610.../s/n Writing .sd files has been improved with respect to bond type assignment. The earlier version sometimes led to resonance structures that were not always properly recognized by other programs. A bug concerning charged structures, introduced in this process, has now been removed.
050601.../g/i Single-entry wise storage on .cif files has been introduced. To use the option, select 'i' with the SHIFT key pressed.
050530lib/e/p Pruning of libraries (removing of duplicates) has been taken over from lib/l/p and has been refined.
050530lib/e/d Reading of structures with data from a .sd file has been taken over from lib/l/d and has been refined.
050530lib lib/e The library menu has been reorganized. Elementary library functions have been deferred to a submenu 'e'.
050527lib/c Mdck The initial-match option in the docking procedure has been complemented for the case that only one or two positions are specified. For these cases a orientational variation has been added.
050527lib/c Mdck Docking did not adhere to stereochemical conformation constraints. This has been complemented.
050525lib/j The library enumeration option has been extended to allow for a set of templates with non-specified attachment atoms.
050525lib/d/z This new option allows to write a file of substituents occurring on a specific attachment point within the set of considered structures.
050513lib/d mch/s This menu has been extended by an option, 'u', to transfer atomic user sets from template atoms of an example structure to other structures. Furthermore, two options were renamed: 'm' -> 'e' and 'd' -> 'm'.
050512lib/f Mfltr The atomic charge options have been extended. An additional parameter, 'm', allows to switch between formal atomic charges (now the default) and pharmacophoric relevant charge accumulations.
050429match Procedures in the match menu have been unified.
050429mch/m/m,b In certain instances optimization failed. This has been mended. BUG
050427Mtprmp The default extension of the result file has been changed to .txt. This allows easy opening in Excel or Calc.
050425Mdck A flag, -M, has been introduced to allow handling of .mab files. In these files user-defined sets are stored, such that option -c-1 can be used, which performes an initial match of user-specified atoms onto the positions of a positions-entry (see lib/c for help).
050425lib/j This new option allows to attach several substituent sets onto corresponding attachment atoms of a central template (combinatorial enumeration).
050418lib/c Initial positioning of structures to be docked has been augmented by the option to match atoms, specified in user sets, onto corresponding positions of a positions-entry. The recently added menu for multiple set assignment (lib/z) provides a convenient tool to specify the sets interactively.
050414lib/z This new menu allows to specify several user sets simultaneously on single structures.
050414pca/u When updating an entry from a full structure, alternate location coordinates of the original can, optionally, be carried over.
050414.../+/c Copies of an entry now also receive alternate location coordinates of the original.
050413frg/n mch/r When moving entire entries by means of one of these options, alternate location coordinates are now also transformed.
050413Mndrws A new option '-e' has been added to cause the program to also calculate efficiencies (values normalized by the number of heavy atoms).
050324cnF/d/f This new option allows to take geometrical specifications from a .Gntr file.
050310lib/k Mndrws Counting of degrees of freedom (DOF) has been modified to include OH and NH2 groups in accord with literature. In addition, structures carrying explicit hydrogens are now properly treated.
050310Expert Corner A new tutorial on 'Linear Regression Models' has been written.
050310Mtprmp This batch program has been completely restructured to comply with the new feature of partitioned linear models.
050310dTp/v Topological pharmacophore models can also be evaluated directly from here.
050310lib/l This new menu allows to generate and evaluate linear regression models on the basis of topological pharmacophore similarity.
050310Dyn/g/r Writing of REFMAC geometry files has been updated to improve recognition of planar groups.
050309.../:/m A new display parameter, ringsize, has been introduced. It allows to vary the ring (cage) size of atoms marked in the set menu. The default value of zero yields the previous markers.
050308.../g/p Alternate conformations of heterogens were not read. This has been mended.
050216.../s Names of files to be written are checked for illegal characters.
050204.../g/i Reading .cif files has been extended to also include anisotropic R-factors.
050203.../g/s Reading SHELLX files has been updated to account for new formatting of SFAC records.