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2016-1 Schrodinger Python API
Package schrodinger :: Package application :: Package combiglide :: Module combenumdock
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Module combenumdock

Creates the Combiglide Interactive Enumeration and Dock panel.

This panel has several modes - the default mode is the Combiglide version. The panel can also be opened without any docking widgets for those uses that don't require docking.

The panel emits a job_submitted(jobid) signal when an enumeration job is submitted, allowing other panels to react and track the job if necessary.

Typical usage would be:

   panel = combenumdock.SimpleEnumDockPanel(enum_only=True,
                                            untangle=False,
                                            create_qapp=False,
                                            jobname=jobname,
                                            quiet_launch=True,
                                            close_on_launch=True)
   panel.mainWindow.show()
   panel.job_submitted.connect(self.followEnumerationJob)

To simply show a new instance of the panel without maintaining a pointer to it, use:

   combenumdock.show_panel(key='myapp panel')

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  _fakeEvent
  CgHydrogenFragmentAnnotator
  collectionViewerModel
  editableViewerTable
  glidePrecisionDialog
  SimpleEnumDockPanel
This is the main class for the panel, to show the panel simply create an instance of this class.
  _StructView
  _zoomViewItem
  _StructViewItem
  ConnectionStorage
This class is used to store the data of the current connection table.
  simpleEnumDockDelegate
  createFragmentDelegate
Functions [hide private]
 
QC(obj1, signal, obj2)
A helper function for QObject.connect
 
setup_qapp()
str
get_unique_title(beginning, structs)
Adds FRAGMENT_INCREMENT_TAGx (x=integer) to the beginning string in order to create a title that is unique in the set of titles in structs.
set
uniquify_titles(structs)
Modify any duplicate and blank titles in structs so that all titles are unique.
 
resolve_links(path)
Return the target of a symbolic link, can handle symlinks to symlinks Uses 'linkresolver.exe' on Windows to resolve shortcuts ('.lnk')
 
get_maestro_groupname()
 
get_sidebar_dict(dir_kws)
This function is used to get a dictionary to be used with filedialog.py
 
show_panel(enum_only=False, default_collection=None, create_qapp=True, untangle=True, key='Combiglide')
Create the panel if necessary and show it
Variables [hide private]
  maestro = False
hash(x)
  STEREO = 6
  BLACK_COLOR_MAP = {5: 4278190080, 7: 4278190080, 8: 4278190080...
  APPDATA_DIR = '/home/buildbot/.schrodinger'
  SCHROD_TMP = '/home/buildbot/.schrodinger/tmp'
  PERSONAL_FRAGS_DIR = '/home/buildbot/.schrodinger/cg/interacti...
  PERSONAL_PALS_DIR = '/home/buildbot/.schrodinger/cg/interactiv...
  MMSHARE_DATA_DIR = '/nfs/builds/objects/NB/2016-1/Linux-x86_64...
  SCHROD_FRAGS_DIR = '/nfs/builds/objects/NB/2016-1/Linux-x86_64...
  SCHROD_PALS_DIR = '/nfs/builds/objects/NB/2016-1/Linux-x86_64/...
  LINK_TO_URL = {'my_frags': '/home/buildbot/.schrodinger/cg/int...
  LINK_TO_TXT = {'my_frags': 'My Collections', 'my_pals': 'My Pa...
  NULL_LINKER = '\n{ \n s_m_m2io_version\n :::\n 1.1.0 \n} \n...
  FRAGFILE_STR = '\nFragment-rules ::=\n{\n name "#ATTACHNAME#...
  DELETE_SELECTED_MENU_ITEM = 'Delete selected structures'
  RETAIN_ONLY_SELECTED_MENU_ITEM = 'Retain only selected structu...
  EXPORT_SELECTED_MENU_ITEM = 'Export selected structures to pro...
  DELETE_STRUCTURE_MENU_ITEM = 'Delete this structure'
  RETAIN_ONLY_STRUCTURE_MENU_ITEM = 'Retain only this structure'
  SHOW_IN_WORKSPACE_MENU_ITEM = 'Show this structure in workspace'
  EXPORT_STRUCTURE_MENU_ITEM = 'Export this structure to project...
  CHANGE_TITLE_MENU_ITEM = 'Rename structure'
  GENERIC_FRAGMENT_TITLE = 'frag'
  FRAGMENT_INCREMENT_TAG = '-ied'
  panels = {}
  __package__ = 'schrodinger.application.combiglide'
  ldir = '/home/buildbot/.schrodinger/tmp'
Function Details [hide private]

get_unique_title(beginning, structs)

 

Adds FRAGMENT_INCREMENT_TAGx (x=integer) to the beginning string in order to create a title that is unique in the set of titles in structs.

This method strips off any 'FRAGMENT_INCREMENT_TAGx' (where x=integer) ending off of the beginning string before adding the new suffix in order to avoid names like frag-ied1-ied1.

Parameters:
  • beginning (str) - The string that will begin the title and have an integer appended to it to be unique
  • structs (list) - A list of Structure objects to use to check if a title is unique
Returns: str
A title unlike any currently found in the list of structures

uniquify_titles(structs)

 

Modify any duplicate and blank titles in structs so that all titles are unique. Note that this directly modifies the structures in the list.

Parameters:
  • structs (list) - A list of Structure objects to use to check if a title is unique
Returns: set
set of modified structure titles

show_panel(enum_only=False, default_collection=None, create_qapp=True, untangle=True, key='Combiglide')

 

Create the panel if necessary and show it

Parameters:
  • enum_only (bool) - If True, hide all GUI items relating to Docking and rename the panel, if False show panel in default mode.
  • default_collection (str) - The path to the default collection file
  • create_qapp (bool) - True if a QApplication should be created if the panel is being run outside of Maestro, False if not
  • untangle (bool) - True if the combgen untangle option should be used when enumerating structures, False if not
  • key (hashable) - Panel instances are stored in a dictionary. If a panel with this key already exists, that panel will simply be re-shown. If a panel with this key does not exist, a new panel will be created, stored in the dictionary under this key, and shown. Default is 'Combiglide', which is the panel with all default options.

Variables Details [hide private]

BLACK_COLOR_MAP

Value:
{5: 4278190080,
 7: 4278190080,
 8: 4278190080,
 9: 4278190080,
 13: 4278190080,
 14: 4278190080,
 15: 4278190080,
 16: 4278190080,
...

PERSONAL_FRAGS_DIR

Value:
'/home/buildbot/.schrodinger/cg/interactive_fragments'

PERSONAL_PALS_DIR

Value:
'/home/buildbot/.schrodinger/cg/interactive_palettes'

MMSHARE_DATA_DIR

Value:
'/nfs/builds/objects/NB/2016-1/Linux-x86_64/build-144/mmshare-v3.3/dat\
a'

SCHROD_FRAGS_DIR

Value:
'/nfs/builds/objects/NB/2016-1/Linux-x86_64/build-144/mmshare-v3.3/dat\
a/cg/interactive_fragments/'

SCHROD_PALS_DIR

Value:
'/nfs/builds/objects/NB/2016-1/Linux-x86_64/build-144/mmshare-v3.3/dat\
a/cg/interactive_palettes/'

LINK_TO_URL

Value:
{'my_frags': '/home/buildbot/.schrodinger/cg/interactive_fragments',
 'my_pals': '/home/buildbot/.schrodinger/cg/interactive_palettes',
 'schrod_frags': '/nfs/builds/objects/NB/2016-1/Linux-x86_64/build-144\
/mmshare-v3.3/data/cg/interactive_fragments/',
 'schrod_pals': '/nfs/builds/objects/NB/2016-1/Linux-x86_64/build-144/\
mmshare-v3.3/data/cg/interactive_palettes/'}

LINK_TO_TXT

Value:
{'my_frags': 'My Collections',
 'my_pals': 'My Palettes',
 'schrod_frags': 'Schrodinger Collections',
 'schrod_pals': 'Schrodinger Palettes'}

NULL_LINKER

Value:
'''
{ 
  s_m_m2io_version
  :::
  1.1.0 
} 

f_m_ct { 
...

FRAGFILE_STR

Value:
'''
Fragment-rules ::=
{
   name "#ATTACHNAME#",
   grow-directions {
      {
         name "forward",
                res-num-treatment increment,
...

RETAIN_ONLY_SELECTED_MENU_ITEM

Value:
'Retain only selected structures'

EXPORT_SELECTED_MENU_ITEM

Value:
'Export selected structures to project table'

EXPORT_STRUCTURE_MENU_ITEM

Value:
'Export this structure to project table'

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2016-1 Schrodinger Python API
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