=============================================================================
                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    because 'mv' has been arbitrarily removed  and is no longer valid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

=============================================================================
