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MGLTools 1.5.4 Release Notes

by Ruth Huey last modified 2011-05-18 10:07

PMV Release Notes. Release 1.5.4 (May 2009)

Colors:

  •     Carbon atoms are now shown in dark gray and hydrogen atoms in white.
  •     The color by molecule and chain has a new “carbon-only” option which applies this scheme to carbon atoms only.
  •     Users can now edit color palletes used for color by Molecules, Chains and Residues in addition to color by Atom that has been introduced in the previous version. Also, the changes made in these color palletes are saved as a user preference.

Adding a new custom color in the color chooser saves that color and can be used for subsequent runs.

New PMV commands:

    A new command under File->Read->"Multiple Molecules" allows reading molecules from a specified directory and lets user load molecules using patterns such as wildcards.

Added a new feature in ViewerFramework that allow users to saves the geometry of the GUI and whether the camera is docked or not. This feature can be enabled or disabled using "Saves GUI perspective on Exit" option in Preferences.

New splash screen images by Stefano Forli.

Molecule Viewer now centres the scene for very new molecule read, that allows users to see loaded molecules that were not visible previously because they were outside of the viewing area.

Redesigned the GUI for modifying default user preferences. The new GUI shows preferences grouped in separate pages that makes them easier to find.

AutoLigand GUI converts the flood fill into MolKit molecule which makes it possible, for instance, to compute molecular surfaces.

When loading new commands using File->"Browse Commands" the GUI shows a conformation dialogue with an information about how to access newly loaded commands using menu buttons.

Bug Fixes:

  •     ALT-TAB problem for PMV/ADT and Vision.
  •     #970 - Deleting an atom set does not update the displayed lines.
  •     #987 - Long molecule names cover up buttons in dashboard.
  •     #1031 - Secondary structure data does not get written to the pdb file.

=============================================================================
                AutoDockTools Release Notes
                   Release 1.5.4 (May 2009)
=============================================================================

----------------------------
autotorsCommands.py
----------------------------
CHANGE:
    -replaced 'AD4.1' with 'AD4.2' in Graphical User Interface
    -removed obsolete commands:
        ADanalyze_showHistogram
        ADtors_changePlanarCarbonsToA
        ADtors_changeAromaticCarbonsToC
    -renamed adt_automergeNPHS 'Automerge NPHS'
    -added check for availability of isocontour library for
        showGridIsocontours commands in updateCmds.

----------------------------
autoanalyzeCommands.py
----------------------------
CHANGE:
    -removed obsolete commands:
        ReadAutoDockClusteringStates
        ADanalyze_writeStates
        ADanalyze_epdbMolecule
        ADanalyze_showHistogram
        ADanalyze_readStates
        ADanalyze_showStatesHISTOGRAM
        ADanalyze_showResultsOutput
        ADanalyze_getChart
        ADanalyze_writeClustering
        ADanalyze_showPopulation
    -removed obsolete warningMsg about ligand not being in input conformation
    -replaced 'adt_playerGUI' with 'Player GUI'
    -added **kw to doit signature to support 'ask' on reading a directory
    of dlg files
    -updated doc-strings replacing 'mv.docked' by 'self.docked'
    because 'mv' has been arbitrarily removed  and is no longer valid
    -replaced  'mv.docked.warnings' with 'self.docked.warnings' to keep up
    with shifting ground in pmv
    -moved preferences into a pickled file. See the new mgltutil.preferences
    for details.
BUG-FIX:
    -replaced checking whether the version of the docking was equal to 4.0
    with checking whether it was equal to or GREATER THAN 4.0

----------------------------
AutoDockBondClassifier.py
----------------------------
BUG-FIX:
    -changed so that detectAll is not on by default in cycle detection. This
    change is in response to a problem encountered by a user whose ligand
    was comprised of two aromatic carbon rings bonded to a cyclohexane. In
    that case, the bond between the cyclohexane and the first benzene should
    be rotatable (and was in v 1.4.6). So now the detectAll option is NOT
    the default

----------------------------
autodpfCommands.py
----------------------------

NEW-FEATURE:
    -'Set AutoDock4[2] Options' widgets now include support for setting
    whether to include a parameter file, rmsatoms, epdb and for previous
    AD4.0 support for setting unbound energy or compute_unbound_extended
    -added SetAutoDock41Parameters command
CHANGE:
    -support for to setting sw default for ad3 dpfs
    -replaced 4.1 with 4.2 in gui
    -removed widgets for setting rmsatoms + epdb
    -removed label+entry for filename for epdb calculation from
    SetAutoDock4Parameters and SetAutoDock41Parameters
    -removed obsolete usage of 'torsdofcoeff' which is now specified
    in the autodock parameter library
    -increased support for restoring default values for epdb, parameter_file,
    rmsatoms,custom_parameter_file, rmsref, seeds et al after customization
BUG-FIX:
    -fixed bug where flexres types were sometimes not included

----------------------------
autoflexCommands.py
----------------------------
NEW-FEATURE:
    -changed format of BEGIN_RES/END_RES: to list res.type, res.number and
    chain.id

----------------------------
autogpfCommands.py
----------------------------
CHANGE:
    -replaced "Choose FlexResMolecule..." with "Choose FlexRes..."
    -replaced "Open Flexible Residues..." with "Open FlexRes..."
    -replaced 'adt_automergeNPHS' with 'Automerge NPHS'
    -replaced 'adt_editHISprotonation' with 'HIS Protonation'
    -moved preferences into a pickled file. See the new mgltutil.preferences for details.

----------------------------
AutoLigandCommand.py
----------------------------
NEW-FEATURE:
    added try/except for pickle

----------------------------
AutoLigand.py
----------------------------
NEW-FEATURE:
    -Web page describing the code and how it works:
        http://www.scripps.edu/~rharris
    -New PP (pseudo-pod) version.
Changes:
    -Improvements were made to the final fill volume optimization of the code.

----------------------------
autotorsCommands.py
----------------------------
CHANGE:
    -removed loading obsolete commands:
        ADtors_changePlanarCarbonsToA
        ADtors_changeAromaticCarbonsToC
        ADanalyze_showHistogram
    -replaced 'AD4.1' with 'AD4.2' in the GUI
    -replaced 'adt_automergeNPHS' with 'Automerge NPHS'
    -moved preferences into a pickled file. See the new mgltutil.preferences for details.
    -added if condition for showGridIsocontours in updateCmds.

----------------------------
cluster.py
----------------------------
NEW-FEATURE:
    -added 'flexres' sort option
    -added 'intermolecular' sort option
    -added method _get_distance_flexres
BUG_FIX:
    -a change to use the correct subset of coords for the rmsd calculation

----------------------------
cmdlib.py
----------------------------
CHANGE:
    -removed obsolete commands:
        ADtors_changePlanarCarbonsToA
        ADtors_changeAromaticCarbonsToC
        ADtors_readStates
        ADanalyze_showHistogram
        ADanalyze_showStatesHISTOGRAM
        ADanalyze_showResultsOutput
        ADanalyze_getChart
        ADanalyze_writeClustering

----------------------------
Conformation.py
----------------------------
NEW-FEATURE:
    -added support for showing dlgfilename for each conformation
CHANGE:
    -now initialize current_pop_ind to 0 (instead of None)
    -added appending conformations to all_populations list
    -if there is only 1 entry in all_populations, set current_pop_ind to 0
    -added 'filename' parameter to parameters for 'add' method in order to
    support conformation know its dlg filename

----------------------------
ConfPlayer.py
----------------------------
NEW-FEATURE:
    - support for showing dlgfilename for each conformation in 'info' panel
CHANGE:
    -updates to default file type extension from pdbq to pdbqt
    -improved support for playing populations
    - moved AddAtomsEvent, DeleteAtomsEvent and EditAtomsEvent from
    ViewerFramework.VF to Pmv.moleculerViewer

----------------------------
DlgParser.py
----------------------------
NEW-FEATURE:
    -added version attribute
CHANGE:
    -added support for version larger than 3
    -added check line for garbage from DPF; updated parsing of population information
BUG-FIX:
    -change to search for ' Run' instead of 'Run' to fix problem arising from a
    dpf filename which included 'Run'

----------------------------
DockingParameters.py
----------------------------
NEW-FEATURE:
    -changes to make psw default for autodock4 and later versions
    -added 'psw_trans_scale', 'psw_rot_scale' and 'psw_tors_scale' keywords
        to modulate local search
    -new keywords unbound_energy, unbound_model, autodock_parameter_version keywords
        support for writing these new keywords and inserted them in appropriate keyword lists
    -added set_version method
    -added quaternion0 keyword
----------------------------
CHANGE:
    -replaced use of quat0 with axisangle0
    -removed torsdofcoeff which is now in the autodock parameter library
    -changed setting torsdof4 from ligand.ndihe to ligand.TORSDOF
    -added check in _parse() for keyword epdb for argument before using it.
    New autodock epdb usage takes no arguments unlike previously.

----------------------------
Docking.py
----------------------------
NEW-FEATURE:
    -added 'filename' parameter  to call to self.ch.add in order to support
        conformation know its dlg filename

----------------------------
GridParameters.py
----------------------------
NEW-FEATURE:
    -in set_grid_parameters(): added special treatment for setting parameter
        'ligand_types': now newvalue is to be a comma-separated list
    -added support for turning-off option 'size_box_to_include_ligand'

----------------------------
__init__.py
----------------------------
CHANGE:
    -updated setADTmode parameter from AD4.1 to AD4.2
    -input flag -n now means '--noSplash'
----------------------------
BUG-FIX:
    -solved ipython issues for adt

----------------------------
MoleculePreparation.py
----------------------------
NEW-FEATURE:
    -Additions so that prepare_ligand script can return a status based on
        a check that all the atoms in the ligand are written to the file.
        The result of the check is used to set ligand attributes 'returnCode'
        and 'returnMsg' appropriately for reporting to the user
    -augmented format of BEGIN_RES/END_RES: now includes chain.id after
        res.type and res.number
----------------------------
CHANGE:
    -added '#Deprecated 2009' comment to obsolete AD4FlexibleDockingPreparation class
    -print a warning and add charges if all the atoms in the molecule have a zero-charge;
----------------------------
BUG-FIX:
    -removed disallowing torsions of bonds between cycles. This was added as an
        attempt to set bonds in large-fused-rings non-rotatable. However, a
        side-effect of that addition was disallowing torsions between cycles not part
        of a large-fused-ring. Consequently, this is a stepback (~v1.4.6). (So the
        detectAll option for cycles is NOT the default.)

----------------------------
XMLParser.py
----------------------------
NEW-FEATURE:
    -added quaternion0 as field save in xml parser
    -added "xml" xml filename "dlg" dlg filename in parser dictionary for xml field.
CHANGES:
    -replaced quat0 by axisangle0


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