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psico.helping.write_html_ref('psico-commands.html')
 
psico.helping.write_html_ref('psico-commands.html')
 
</syntaxhighlight>
 
</syntaxhighlight>
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== Command List ==
 +
 +
This list might change. If you install psico, it's recommended to generate a reference document as described above to see which commands are actually available.
 +
 +
A "outdated" note in the table means that the code in psico is newer (somehow enhanced) than on the corresponding wiki page.
 +
 +
{| class=wikitable
 +
! Command || Already in PyMOLWiki...
 +
|-
 +
| aaindex2b || [[AAindex]] (outdated)
 +
|-
 +
| alignwithanymethod || [[TMalign]]
 +
|-
 +
| alphatoall || [[AlphaToAll]] (outdated)
 +
|-
 +
| angle_between_domains ||
 +
|-
 +
| angle_between_helices || [[AngleBetweenHelices]] (outdated)
 +
|-
 +
| api_info ||
 +
|-
 +
| apropos || [[apropos]]
 +
|-
 +
| biomolecule || [[BiologicalUnit/Quat]] (outdated)
 +
|-
 +
| cafit_orientation || [[AngleBetweenHelices]]
 +
|-
 +
| cbm || similar: [[Color Objects]]
 +
|-
 +
| cbs ||
 +
|-
 +
| centerofmass || similar: [[center_of_mass]]
 +
|-
 +
| collapse_resi || similar: [[CollapseSel]]
 +
|-
 +
| consurfdb ||
 +
|-
 +
| delaunay || similar: [[PyDet]] plugin
 +
|-
 +
| diff ||
 +
|-
 +
| dssp || similar: [[dssp stride]] plugin
 +
|-
 +
| dyndom ||
 +
|-
 +
| extra_fit || [[extra_fit]]
 +
|-
 +
| fasta || see also: [[Aa_codes]]
 +
|-
 +
| fetch ||
 +
|-
 +
| frames2states ||
 +
|-
 +
| gdt_ts ||
 +
|-
 +
| get_raw_distances || [[get_raw_distances]]
 +
|-
 +
| get_sasa ||
 +
|-
 +
| get_sasa_ball ||
 +
|-
 +
| get_sasa_mmtk ||
 +
|-
 +
| grepset || [[grepset]]
 +
|-
 +
| gyradius || [[radius of gyration]] (outdated)
 +
|-
 +
| helix_orientation || [[AngleBetweenHelices]] (outdated)
 +
|-
 +
| hydropathy2b ||
 +
|-
 +
| intra_theseus ||
 +
|-
 +
| iterate_plot ||
 +
|-
 +
| join_states ||
 +
|-
 +
| load_3d ||
 +
|-
 +
| load_aln ||
 +
|-
 +
| load_consurf ||
 +
|-
 +
| load_gro ||
 +
|-
 +
| load_traj_crd ||
 +
|-
 +
| loadall ||
 +
|-
 +
| local_rms ||
 +
|-
 +
| loop_orientation || [[AngleBetweenHelices]]
 +
|-
 +
| morpheasy ||
 +
|-
 +
| mse2met ||
 +
|-
 +
| mutate ||
 +
|-
 +
| mutate_all ||
 +
|-
 +
| nice ||
 +
|-
 +
| normalmodes_mmtk ||
 +
|-
 +
| normalmodes_pdbmat ||
 +
|-
 +
| paper_png ||
 +
|-
 +
| paper_settings ||
 +
|-
 +
| pca_plot ||
 +
|-
 +
| pir ||
 +
|-
 +
| plane_orientation ||
 +
|-
 +
| polyala ||
 +
|-
 +
| remove_alt || similar: [[removealt]]
 +
|-
 +
| rms_plot ||
 +
|-
 +
| rmsf2b ||
 +
|-
 +
| save ||
 +
|-
 +
| save_colored_fasta ||
 +
|-
 +
| save_movie_mpeg1 ||
 +
|-
 +
| save_pdb ||
 +
|-
 +
| save_settings || [[save_settings]]
 +
|-
 +
| save_traj || [[save2traj]] (outdated)
 +
|-
 +
| select_distances || [[get_raw_distances]]
 +
|-
 +
| select_pepseq ||
 +
|-
 +
| select_sspick ||
 +
|-
 +
| set_phipsi ||
 +
|-
 +
| set_sequence ||
 +
|-
 +
| sidechaincenters ||
 +
|-
 +
| snp_ncbi ||
 +
|-
 +
| snp_uniprot ||
 +
|-
 +
| spectrum_states || [[spectrum_states]]
 +
|-
 +
| spectrumany || [[spectrumany]]
 +
|-
 +
| split_chains || [[split_chains]]
 +
|-
 +
| stride || similar: [[dssp stride]] plugin
 +
|-
 +
| stub2ala ||
 +
|-
 +
| supercell || [[supercell]]
 +
|-
 +
| symdiff ||
 +
|-
 +
| symexpcell || [[supercell]]
 +
|-
 +
| theseus ||
 +
|-
 +
| tmalign || [[TMalign]]
 +
|}
 +
 +
[[Category:Script Library]]

Revision as of 09:07, 20 March 2012

Type Python Module
Download https://github.com/speleo3/pymol-psico
Author(s) Thomas Holder and Steffen Schmidt
License BSD-2-Clause

psico is a python module which extends PyMOL with many commands. It was developed as an in-house script collection, but grew to a quite comprehensive PyMOL extension. Some of the provided commands are already in the PyMOLWiki Script Library, but it contains also many new stuff.

Usage

To import all commands with one line: 

import psico.fullinit

A reference document with all commands can be generated with: 

import psico.fullinit
import psico.helping
psico.helping.write_html_ref('psico-commands.html')

Command List

This list might change. If you install psico, it's recommended to generate a reference document as described above to see which commands are actually available.

A "outdated" note in the table means that the code in psico is newer (somehow enhanced) than on the corresponding wiki page.

Command Already in PyMOLWiki...
aaindex2b AAindex (outdated)
alignwithanymethod TMalign
alphatoall AlphaToAll (outdated)
angle_between_domains
angle_between_helices AngleBetweenHelices (outdated)
api_info
apropos apropos
biomolecule BiologicalUnit/Quat (outdated)
cafit_orientation AngleBetweenHelices
cbm similar: Color Objects
cbs
centerofmass similar: center_of_mass
collapse_resi similar: CollapseSel
consurfdb
delaunay similar: PyDet plugin
diff
dssp similar: dssp stride plugin
dyndom
extra_fit extra_fit
fasta see also: Aa_codes
fetch
frames2states
gdt_ts
get_raw_distances get_raw_distances
get_sasa
get_sasa_ball
get_sasa_mmtk
grepset grepset
gyradius radius of gyration (outdated)
helix_orientation AngleBetweenHelices (outdated)
hydropathy2b
intra_theseus
iterate_plot
join_states
load_3d
load_aln
load_consurf
load_gro
load_traj_crd
loadall
local_rms
loop_orientation AngleBetweenHelices
morpheasy
mse2met
mutate
mutate_all
nice
normalmodes_mmtk
normalmodes_pdbmat
paper_png
paper_settings
pca_plot
pir
plane_orientation
polyala
remove_alt similar: removealt
rms_plot
rmsf2b
save
save_colored_fasta
save_movie_mpeg1
save_pdb
save_settings save_settings
save_traj save2traj (outdated)
select_distances get_raw_distances
select_pepseq
select_sspick
set_phipsi
set_sequence
sidechaincenters
snp_ncbi
snp_uniprot
spectrum_states spectrum_states
spectrumany spectrumany
split_chains split_chains
stride similar: dssp stride plugin
stub2ala
supercell supercell
symdiff
symexpcell supercell
theseus
tmalign TMalign
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