Difference between revisions of "Get raw distances"
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(Infobox psico) |
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|author = [[User:TakanoriNakane|Takanori Nakane]] and [[User:Speleo3|Thomas Holder]] | |author = [[User:TakanoriNakane|Takanori Nakane]] and [[User:Speleo3|Thomas Holder]] | ||
|license = BSD-2-Clause | |license = BSD-2-Clause | ||
| + | }} | ||
| + | |||
| + | {{Infobox psico | ||
| + | |module = psico.querying | ||
}} | }} | ||
[[get_raw_distances]] can dump distance objects, created with [[distance]]. | [[get_raw_distances]] can dump distance objects, created with [[distance]]. | ||
| + | |||
| + | This script also provides the command '''select_distances''', which selects atoms from distance objects. | ||
| + | |||
| + | ''Warning: the atoms are hashed by coordinates; this could cause issues if coordinates are altered after distance objects have been created (see also [[dynamic_measures]] setting).'' | ||
| + | |||
| + | == Usage == | ||
| + | |||
| + | get_raw_distances [ names [, state [, selection ]]] | ||
| + | |||
| + | select_distances [ names [, name [, state [, selection [, cutoff ]]]]] | ||
== Arguments == | == Arguments == | ||
| Line 23: | Line 37: | ||
# dump (model,index) information | # dump (model,index) information | ||
| − | get_raw_distances | + | get_raw_distances iface_hbonds |
| + | </syntaxhighlight> | ||
| + | |||
| + | == Example Atom Selection == | ||
| + | |||
| + | <syntaxhighlight lang="python"> | ||
| + | # select atoms | ||
| + | select_distances iface_hbonds, hbsele | ||
| + | |||
| + | # nice representation | ||
| + | set cartoon_side_chain_helper | ||
| + | set sphere_scale, 0.5 | ||
| + | as cartoon, 2xwu | ||
| + | show sticks, byres hbsele | ||
| + | show spheres, hbsele | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| Line 29: | Line 57: | ||
* [[distance]] | * [[distance]] | ||
| + | * [[dynamic_measures]] | ||
* [[find_pairs]] | * [[find_pairs]] | ||
* [[get_raw_alignment]] | * [[get_raw_alignment]] | ||
[[Category:Script Library]] | [[Category:Script Library]] | ||
| + | [[Category:ObjSel_Scripts]] | ||
| + | [[Category:Pymol-script-repo]] | ||
Latest revision as of 03:48, 31 July 2012
| Type | Python Module |
|---|---|
| Download | get_raw_distances.py |
| Author(s) | Takanori Nakane and Thomas Holder |
| License | BSD-2-Clause |
| This code has been put under version control in the project Pymol-script-repo | |
|
Included in psico | |
| Module | psico.querying |
|---|---|
get_raw_distances can dump distance objects, created with distance.
This script also provides the command select_distances, which selects atoms from distance objects.
Warning: the atoms are hashed by coordinates; this could cause issues if coordinates are altered after distance objects have been created (see also dynamic_measures setting).
Usage
get_raw_distances [ names [, state [, selection ]]]
select_distances [ names [, name [, state [, selection [, cutoff ]]]]]
Arguments
- names = string: names of distance objects (no wildcards!) {default: all measurement objects}
- state = integer: object state {default: 1}
- selection = string: atom selection {default: all}
Example
fetch 2xwu, async=0
# interface polar contacts
distance iface_hbonds, chain A, chain B, mode=2
# dump (model,index) information
get_raw_distances iface_hbonds
Example Atom Selection
# select atoms
select_distances iface_hbonds, hbsele
# nice representation
set cartoon_side_chain_helper
set sphere_scale, 0.5
as cartoon, 2xwu
show sticks, byres hbsele
show spheres, hbsele