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(Description of top-level structure)
 
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WARNING: This API is undocumented API, intended for internal use. Use it only when it is necessary.
 
WARNING: This API is undocumented API, intended for internal use. Use it only when it is necessary.
  
−
= Usage =
+
== Usage ==
 
<source lang="python">
 
<source lang="python">
−
# get the session as a dictionary
+
dict cmd.get_session(names='', partial=0)
−
print cmd.get_session()
 
 
</source>
 
</source>
  
−
= Return value =
+
== Return value ==
  
 
The returned dictionary has following key-value pairs.
 
The returned dictionary has following key-value pairs.
 +
Some entries are missing if using ''partial=1''.
  
−
:main: An array encoding window size. For example, [640, 480]
+
* '''main''': An array encoding window size. For example, [640, 480]
 +
* '''color_ext''':
 +
* '''settings''': An array of PyMOL's global settings. They are dumped by SettingAsPyList in layer1/Setting.c. Further details will not be discussed because scripts can access these values from [[get|cmd.get]] API.
 +
* '''colors''': If you have defined color names by [[Set Color]], they are described here. Default color names (red, blue, etc...) will not appear. This dict can also be obtained by [[Get Color Indices|cmd.get_color_indices()]]. To get RGB definition of a color, get its pallet ID by cmd.get_color_index and convert it to RGB tuple by cmd.get_color_tuple.
 +
* '''view''': Same as [[Get View|cmd.get_view()]]
 +
* '''version''': Version number of PyMOL
 +
* '''view_dict''':
 +
* '''names''': This is the most complex but interesting part. Produced by ExecutiveGetNamedEntries, this array describes internal C-objects of the current session. Each element is an array of seven elements.
  
−
:color_ext:
 
  
−
:settings: An array of PyMOL's global settings. They are dumped by SettingAsPyList in layer1/Setting.c. Further details will not be discussed because scripts can access these values from [[get|cmd.get]] API.
+
(documentation in progress... Please feel free to expand)
 +
 
 +
== Examples ==
 +
 
 +
=== Object array ===
 +
 
 +
<syntaxhighlight lang="python">
 +
x = cmd.get_session('myobj', 1)['names'][0]
 +
x = [
 +
    str name ('myobj'),
 +
    int 0=object/1=selection,
 +
    int enabled,
 +
    list representations,
 +
    int object_type,
 +
    list object_data,
 +
    str group_name,
 +
]
 +
</syntaxhighlight>
  
−
:colors: If you have defined color names by [[Set Color]], they are described here. Default color names (red, blue, etc...) will not appear. This dict can also be obtained by [[Get Color Indices|cmd.get_color_indices()]]. To get RGB definition of a color, get its pallet ID by cmd.get_color_index and convert it to RGB tuple by cmd.get_color_tuple.
+
=== Internals of a map object ===
  
−
:view: Same as [[Get View|cmd.get_view()]]
+
The map data as a numpy array:
  
−
:version: Version number of PyMOL
+
<syntaxhighlight lang="python">
 +
import numpy
 +
from pymol import cmd
  
−
:view_dict:
+
cmd.map_new('mymap', 'gaussian', 0.5)
  
−
:names: This is the most complex but interesting part. Produced by ExecutiveGetNamedEntries, this array describes internal C-objects of the current session. Each element is an array of five elements.
+
mymap = cmd.get_session('mymap', 1)['names'][0]
 +
field_data = mymap[5][2][0][14][2]
  
 +
values = numpy.reshape(field_data[6], field_data[4])
 +
</syntaxhighlight>
  
−
(documentation in progress... Please feel free to expand)
+
The dumped map datastructure:
 +
 
 +
<syntaxhighlight lang="python">
 +
mymap[5][2][0] = [
 +
    int Active,
 +
    list Symmetry (like cmd.get_symmetry),
 +
    list Origin,
 +
    list Range (ExtentMax - ExtentMin),
 +
    list Dim (?),
 +
    list Grid (grid spacing),
 +
    list Corner,
 +
    list ExtentMin,
 +
    list ExtentMax,
 +
    int MapSource (?, 4),
 +
    list Div (?, Dim - 1),
 +
    list Min (?),
 +
    list Max (?, ncells),
 +
    list FDim (?, (ncells + 1) + [3]),
 +
    [
 +
        list field->dimensions (FDim[:3]),
 +
        int field->save_points (?, 1),
 +
        [# field->data
 +
            int type (?, 0),
 +
            int n_dim,
 +
            int base_size (?, 4),
 +
            int size (?, len * 4),
 +
            list dim,
 +
            list stride,
 +
            list data,
 +
        ],
 +
        [# field->points
 +
            ...
 +
        ] 
 +
    ],
 +
    [None],
 +
]
 +
</syntaxhighlight>
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 01:46, 28 March 2014

Returns a dictionary representation the currently loaded PyMOL session.The session file (.pse) is a compressed version of its output.

By using this API, user scripts can access many interesting properties which are otherwise inaccessible. Examples include Pymol2glmol and get_raw_distances scripts.

WARNING: This API is undocumented API, intended for internal use. Use it only when it is necessary.

Usage

dict cmd.get_session(names='', partial=0)

Return value

The returned dictionary has following key-value pairs. Some entries are missing if using partial=1.

  • main: An array encoding window size. For example, [640, 480]
  • color_ext:
  • settings: An array of PyMOL's global settings. They are dumped by SettingAsPyList in layer1/Setting.c. Further details will not be discussed because scripts can access these values from cmd.get API.
  • colors: If you have defined color names by Set Color, they are described here. Default color names (red, blue, etc...) will not appear. This dict can also be obtained by cmd.get_color_indices(). To get RGB definition of a color, get its pallet ID by cmd.get_color_index and convert it to RGB tuple by cmd.get_color_tuple.
  • view: Same as cmd.get_view()
  • version: Version number of PyMOL
  • view_dict:
  • names: This is the most complex but interesting part. Produced by ExecutiveGetNamedEntries, this array describes internal C-objects of the current session. Each element is an array of seven elements.


(documentation in progress... Please feel free to expand)

Examples

Object array

x = cmd.get_session('myobj', 1)['names'][0]
x = [
    str name ('myobj'),
    int 0=object/1=selection,
    int enabled,
    list representations,
    int object_type,
    list object_data,
    str group_name,
]

Internals of a map object

The map data as a numpy array: 

import numpy
from pymol import cmd

cmd.map_new('mymap', 'gaussian', 0.5)

mymap = cmd.get_session('mymap', 1)['names'][0]
field_data = mymap[5][2][0][14][2]

values = numpy.reshape(field_data[6], field_data[4])

The dumped map datastructure: 

mymap[5][2][0] = [
    int Active,
    list Symmetry (like cmd.get_symmetry),
    list Origin,
    list Range (ExtentMax - ExtentMin),
    list Dim (?),
    list Grid (grid spacing),
    list Corner,
    list ExtentMin,
    list ExtentMax,
    int MapSource (?, 4),
    list Div (?, Dim - 1),
    list Min (?),
    list Max (?, ncells),
    list FDim (?, (ncells + 1) + [3]),
    [
        list field->dimensions (FDim[:3]),
        int field->save_points (?, 1),
        [# field->data
            int type (?, 0),
            int n_dim,
            int base_size (?, 4),
            int size (?, len * 4),
            list dim,
            list stride,
            list data,
        ],
        [# field->points
            ...
        ]   
    ],
    [None],
]
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