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Updates 2001

Updates 2001

DateMenu-OptionDescription of Change
011207.../e/b A ribbon-type display of DNA/RDA structures has been introduced.
011119MAB In the force field, the assignment of hybridization states of conjugated heteroatoms has been corrected for potential sp1-cases.
011116mch/q When matching structures by means of topological pharmacophores the assignment of constraints to atom pairs has been augmented by distance dependent weighting to improve the resulting overlap.
011116.../:/h
mch/d/a/v/l
A new switch has been introduced to display entry-data, if available, instead of entry labels.
011115mch/m/t Automatic assignments of match-pairs can be made, based on distance criteria.
011114mch/m When matching two structures, the moved structure can also be moved by hand (Shift key and mouse movement).
011114xnr/f In some cases generation of the full structure from crystal symmetry remained incomplete. This has been amended. BUG
011112Msrfvl A new flag '-c' has been added which expects the name of a file (.smi) containing SMILES codes. During execution the program counts the occurrence of the substructures defined by these SMILES codes, and adds count-columns headed 'sub#'.
011105srf/d/p This new utility allows to remove problematic surface points to facilitate tessellation.
011105srf/d/b/l With this new option all but the largest fragments of a surface can be deleted.
011105set/b A new utility with which one can generate a subset of a given set of atoms that have a minimal degree of burriedness with respect to a specified set of entries.
011102.../e/b The ribbon representation of C-alpha structures has been modified to indicate the run direction of the protein thread.
011102geo/s Absolute chirality (R/S) of atoms can be determined.
011031dTp/m SMILES representations that close rings with a double (or triple) bond can now be handled.
011030dyn/y Adding explicit hydrogens has been refined to include all hydrogens of a polar atoms that participates in at least one H-bond.
011029mch/p The menu of the pharmacophore match has been reorganized. Apart from reshuffling the options, a new feature 'S' has been introduced which allows to match a whole set of entries, one by one, onto a target.
011026mch/q,d
php/w
Generation of topological pharmacophores has been extended to allow for specification of atoms that are ignored with respect to their pharmacophoric properties.
011026mch/q,d
php/w
Entry coloring with respect to topological pharmacophore features has been modified, making use of hafbond coloring. This leads to better recognition clusters and orphan atoms.
011022mch/p The H-bonding term in the pharmacophore matching utility has been modified such as to take MAB hydrogen-bonding strengths of the polar atoms instead of a constant value.
011011xnr/w/v To the evaluation of self-avoiding walks on a lattice, several geometrical quantities have been added. In addition a display of surface lattice points is produced which shows the average coverage of the points by the walks.
011008.../g 'Locating files' has been modified such that file paths containing blanks are now recognized.
011006opt(MAB) The hydrogen-bonding interactions have been augmented by a term that acts among pairs of pure donors or pure acceptors. The term has the form of the Coulomb repulsion using the same finite range potential as the (optional) Coulomb interaction. Like for the hydrogen bonding strengths, the values for the atomic charges stem from the setup phase of the MAB force field.
011006opt(MAB) The dihedral potentials of the force field have been augmented by terms of multiplicity one (displaying a single maximum and minimum upon rotation by 360 degrees). These terms account for Coulomb type interaction of the charges of the end atoms. Values for the atomic charges stem from the setup phase of the MAB force field.
010921.Moloc The color for Hydrogen atoms in ball-and-stick and half-bond representation can now be set separately, instead of being identical to the color of Carbon atoms.
010921xnr/w/v Evaluation now includes calculating radii of gyration of the walks.
010920opt/k This new option allows to modify PI-electron systems by specifying cut-bonds (no conjugation) and by charging bonds (modify the number of electrons in a PI-system).
010824mch/q,o The topological pharmacophore match can be performed with the new option of biflexibility. This type of matching is restricted to two participants, and both are allowed to change conformation in the minimization steps.
010820.../+/c When copying entries, the copy now is put in the ACTIVE state.
010810Mtprsml
Mtprmp
A likeness parameter 'L' has been introduced in the similarity calculation for topological pharmacophores. For the default value (L=1) aliphatic and aromatic portion of hydrophobic agons (pharmacophoric units) are treated equally. For the value L=0 the similarity between a fully aliphatic and a fully aromatic agon vanishes.
010810.../g/k/e Conformational libraries in MAESTRO format can be read (default extension .mal).
010803mch/s/r The list of substituent descriptors has ben augmented by values for polar and hydrophobic surfaces. Furthermore, the first spatial moments with respect to the point of attachment of these two quantities are also calculated.
010731Mol3d
Mndrws
Mtprmp
These three batch programs have a new switch -r that causes them to read the input .sd file from stdin and to produce the modified output .sd file to stdout. Mol3d produces new coordinates, Mndrws adds a data field 'MNDRWS'. Mtprmp requires a label added to -r which characterizes the actual model it calculates predicted values for.
010731Mol3d A new switch -e has been added, which allows to provide an environment structure in .mab format. During minimization this structure is held fixed. By this token a library of docked structures can afterwards be minimized with the MAB force field.
010727Msmab A new switch -c has been added, which causes atomic partial charges to be calculated.
010724Mndrws This new batch program allows to calculate maximal binding free energies of ligands (batch version of lib/k).
010724Mtprmp This new batch program allows to calculate model values for a set of structures on a .sd file from topological pharmacophore models.
010724.../g/o A new input option has been added which allows to keep only the largest connected fragment of a structure (salts).
010719mch/s/g A file with scaffold geometrical data, evaluated for all specified structures, can be written.
010717Msrfvl A new switch (-r) has been introduced to allow to run the program in redirection mode. It then expects an .sd file from stdin and writes a .sd file to stdout which carries the calculated data under the label MSRFVL.
010717DYN/f Trajectories can now be viewed and evaluated for several file types.
010717.../g/a AMBER files can now be read. Letters for file types have been reshuffled: a = AMBER, g = GROMOS, z = CHARMM.
010706??? When using the search mode (with Ctrl-key), an empty search string will start the Navigator with the Moloc home page.
010706mch/m/n When matching C-alfa structures, specification by sequence numbers has been generalized.
010625map/g Maps written in Sybyl format (.acnt) can be read.
010622.../g/e MAESTRO structure files (.mae) for small molecules can be read.
010614xnr/w A utility to generate self avoiding walks on a diamond lattice.
010614.../f/r For the SGI-platform rgb-files of the actual window can directly be written from here.
010528mch/s/r/t The points of attachment of substituents, generated in option 's' are, by default, equiped with an explicit hydrogen. The new option 't' now allows to choose any atom type to mark these points of attachment.
010509pca/c/m A new option has been introduced in the C-alpha builder which allows to generate a new Moloc entry directly by entering a protein sequence in single letter code format.
010507mch/s/r/s Substituents occurring in the model compounds can be copied into separate entries which are also made members of position dependent libraries. The point of attachment of these entries is equiped with an explicit hydrogen for further evaluation. The previous option 's' has been renamed to 'f'!
010427mch/s/c Chirality changes of substructures encountered in entries with respect to the chirality of a target substructure can be monitored.
010427mch/s/i This new option in the substructure matching utility allows to define several substructures of equal atom numbers and connectivity but with different atom types to be searched for.
010425mch/s/r/o Substituent matching now also includes coloring of the substituents with agon-specific colors.
010425mch/s/r/s The agon strengths values of substituents have been augmented by values of the topological agon distance from the substituent root.
010417mch/s/r/s A file of agon strengths of substituents can be written. The sequence of agons is determined by user-specified target substituents onto which the substituents of the actual structure are matched by comparing their rooted topological pharmacophores.
010411mch/s/r/a If substituent characterization is performed in terms of rooted topological pharmacophores matching of substituents onto a target substituent by means of superimposing similar pharmacophore features can be performed.
010403xnr/f For some file formats, containing crystallographic information, structures may be given as incomplete fragments, because full structures can be generated from the fragment by applying crystallographic symmetry operations. This new option performs just this task.
010321mch/d/r/c Hierarchical trees can be colored with respect to color indices attributed to the entries associated with the tree leaves. Color indices can be attributed to entries in option lib/n.
010320map/k Contouring of small maps (up to 10000 points) can now be done interactively, i.e. while changing the contour level the contour is continuously updated.
010320map/g Maps originating from the program GRID, which calculates molecular fields near molecules, can now be read, contoured, and displayed.
010319mch/q When matching using topological pharmacophores the user can have a file written in which the strengths of all agons that match onto a target agon are listed in a column below the corresponding target agon. These strengths allow to identify important features for binding properties.
010319lib/e This new option calculates data for the entries of a library. At present the force-field energy contributions are available.
010316.../g/f Reading .frc files (fractional coordinates) has been modified. In earlier versions non-contiguous atom names lead to erroneous coordinates. BUG
010302Mtprmdl Two new parameters have been introduced:
-s adds statistical data at the end of the list of test substances.
-t[number] causes the program to omit test pharmacophores with more than [number] agons. 't' has been chosen to be consistent with the programs Mtprgn and Mtprsml. The previous parameter 't' has been changed to 'q'!
010219mch/d/d,r,a/!,d,D When calculating diversity descriptors, the user can now set the threshold for the eigenvalues of the diversity matrix that will be considered for generating descriptors.
010219mch/s/r If substituent characterization is performed in terms of rooted topological pharmacophores a diversity analysis can now be performed for each substituent position.
010219.../g If a file containing multiple entries is read, the user can now group these entries into a library by specifying a library name.
010207dyn/h The menu for driving torsional angles has been modified. The map menu can now be directly accessed (option r). Specification of torsion angles (option t) is now possible either by picking a bond or by picking four atoms in a row. Some menue points have changed letters to avoid duplicates.
010201.../g/s SHELLX files are now also read when they contain multiple entries. Such files can be produced by the CSD database software CONQUEST. This is the only file type produced by this software that transfers crystal information correctly and completely into Moloc.
010201mch/s/r
Mtprmdl
In addition to model values of compounds or incremental values for substituents, loading defect values are also calculated and printed to enable to judge the applicability of the model.
010119.../+/c When copying an entry in ball and stick representation, the copy used to display balls for the atoms and simple lines for the bonds. Now the atom representation of the copy is also reset to simple markers or nothing, depending on the marker flag.
010119mch/s/p,r For topological pharmacophor data, if a linear statistical model has been produced, its parameters can be read in and substituents for the various positions can be ranked according to their predicted influence on the model values.
010115mch/s/p,r Substituent data at atoms of a fragment have been augmented by descriptors, derived from a similarity model of rooted topological pharmacophores, taken for all occuring substituents.
010109mch/s/p,r Substituent data at atoms of a fragment, common to a set of entries, can be written to the text port. Currently, SMILES codes are implemented.
010105MAB The H-bond pattern evaluation algorithm has beeen improved to alow for bifurcated bonds of charged atoms (amines). In addition, in some cases H-bonds are now found which were lost previously.
010104opt/e/w/h,H Values of single H-bonds can be evaluated by picking the two partner atoms. The result is detailed into radial and angular components. The previous option 'h' which yieded a list of all H-bonds has been renamed to 'H'.