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[[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 [[:Category:Script Library|Script Library]], but it contains also many new stuff.
 
[[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 [[:Category:Script Library|Script Library]], but it contains also many new stuff.
 +
 +
== Installation ==
 +
 +
Using PyMOL 2.0 from the [https://anaconda.org/schrodinger/ schrodinger anaconda channel]:
 +
 +
conda install -c schrodinger pymol
 +
conda install -c schrodinger pymol-psico
 +
 +
Alternatively, copy the '''psico''' folder to your PYTHONPATH or use the '''setup.py''' based installation.
  
 
== Usage ==
 
== Usage ==
Line 22: Line 31:
 
import psico.helping
 
import psico.helping
 
psico.helping.write_html_ref('psico-commands.html')
 
psico.helping.write_html_ref('psico-commands.html')
 +
</syntaxhighlight>
 +
 +
== Initialization ==
 +
 +
By importing '''psico.fullinit''', the PyMOL core commands [[save]] and [[fetch]] become overloaded. In addition, all psico commands will be added to the '''pymol.cmd''' namespace. The save command will have enhanced PDB output, namely saving of secondary structure and crystal information, if available. The fetch command will also fetch 5-letter codes (code + chain) as well as CATH and SCOP identifiers (SCOP requires setting up a MySQL database). To skip the overloading, initialize psico like this:
 +
 +
<syntaxhighlight lang="python">
 +
import psico
 +
psico.init(save=0, fetch=0, pymolapi=0)
 
</syntaxhighlight>
 
</syntaxhighlight>
  
Line 31: Line 49:
  
 
{| class=wikitable
 
{| class=wikitable
−
! Command || Already in PyMOLWiki...
+
! Command || Already in PyMOLWiki... || Added to PyMOL
 +
|-
 +
| add_missing_atoms ||
 
|-
 
|-
 
| aaindex2b || [[AAindex]] (outdated)
 
| aaindex2b || [[AAindex]] (outdated)
Line 39: Line 59:
 
| alphatoall || [[AlphaToAll]] (outdated)
 
| alphatoall || [[AlphaToAll]] (outdated)
 
|-
 
|-
−
| angle_between_domains ||  
+
| [[angle_between_domains]] ||  
 
|-
 
|-
 
| angle_between_helices || [[AngleBetweenHelices]] (outdated)
 
| angle_between_helices || [[AngleBetweenHelices]] (outdated)
 
|-
 
|-
−
| api_info ||  
+
| apbs_surface ||
 +
|-
 +
| api_info || || 1.7.2 (as [[api]])
 
|-
 
|-
 
| apropos || [[apropos]]
 
| apropos || [[apropos]]
 +
|-
 +
| atmtypenumbers ||
 
|-
 
|-
 
| biomolecule || [[BiologicalUnit/Quat]] (outdated)
 
| biomolecule || [[BiologicalUnit/Quat]] (outdated)
Line 55: Line 79:
 
| cbs ||  
 
| cbs ||  
 
|-
 
|-
−
| centerofmass || similar: [[center_of_mass]]
+
| centerofmass || similar: [[center_of_mass]] || [[centerofmass|1.7.2]]
 +
|-
 +
| closest_keyframe ||
 
|-
 
|-
 
| collapse_resi || similar: [[CollapseSel]]
 
| collapse_resi || similar: [[CollapseSel]]
 
|-
 
|-
 
| consurfdb ||  
 
| consurfdb ||  
 +
|-
 +
| corina ||
 
|-
 
|-
 
| delaunay || similar: [[PyDet]] plugin
 
| delaunay || similar: [[PyDet]] plugin
Line 65: Line 93:
 
| diff ||  
 
| diff ||  
 
|-
 
|-
−
| dssp || similar: [[dssp stride]] plugin
+
| dss_promotif ||
 +
|-
 +
| [[dssp]] || similar: [[dssp stride]] plugin
 
|-
 
|-
 
| dyndom ||  
 
| dyndom ||  
 
|-
 
|-
−
| extra_fit || [[extra_fit]]
+
| extra_fit || [[extra_fit]] || 1.7.2
 
|-
 
|-
 
| fasta || see also: [[Aa_codes]]
 
| fasta || see also: [[Aa_codes]]
Line 78: Line 108:
 
|-
 
|-
 
| gdt_ts ||  
 
| gdt_ts ||  
 +
|-
 +
| get_keyframes ||
 
|-
 
|-
 
| get_raw_distances || [[get_raw_distances]]
 
| get_raw_distances || [[get_raw_distances]]
Line 95: Line 127:
 
| hydropathy2b ||  
 
| hydropathy2b ||  
 
|-
 
|-
−
| intra_theseus ||  
+
| intra_promix ||
 +
|-
 +
| [[theseus|intra_theseus]] ||
 +
|-
 +
| [[intra_xfit]] ||  
 
|-
 
|-
 
| iterate_plot ||  
 
| iterate_plot ||  
 
|-
 
|-
−
| join_states ||  
+
| join_states || || [[join_states|1.7.2]]
 
|-
 
|-
 
| load_3d ||  
 
| load_3d ||  
 
|-
 
|-
−
| load_aln ||  
+
| [[load_aln]] ||  
 
|-
 
|-
 
| load_consurf ||  
 
| load_consurf ||  
 
|-
 
|-
 
| load_gro ||  
 
| load_gro ||  
 +
|-
 +
| load_msms_surface ||
 +
|-
 +
| load_mtz_cctbx ||
 
|-
 
|-
 
| load_traj_crd ||  
 
| load_traj_crd ||  
 
|-
 
|-
−
| loadall ||  
+
| loadall || || [[loadall|1.7.2]]
 
|-
 
|-
 
| local_rms ||  
 
| local_rms ||  
 
|-
 
|-
 
| loop_orientation || [[AngleBetweenHelices]]
 
| loop_orientation || [[AngleBetweenHelices]]
 +
|-
 +
| map_new_apbs ||
 +
|-
 +
| matrix_to_ttt ||
 +
|-
 +
| [[mcsalign]] ||
 
|-
 
|-
 
| morpheasy ||  
 
| morpheasy ||  
 
|-
 
|-
−
| mse2met ||  
+
| morpheasy_linear ||
 +
|-
 +
| mse2met || || [[mse2met|1.6.0]]
 +
|-
 +
| [[msms_surface]] ||  
 
|-
 
|-
 
| mutate ||  
 
| mutate ||  
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|-
 
|-
 
| normalmodes_pdbmat ||  
 
| normalmodes_pdbmat ||  
 +
|-
 +
| normalmodes_prody ||
 
|-
 
|-
 
| paper_png ||  
 
| paper_png ||  
Line 136: Line 188:
 
|-
 
|-
 
| pca_plot ||  
 
| pca_plot ||  
 +
|-
 +
| pdb2pqr ||
 +
|-
 +
| peptide_rebuild ||
 +
|-
 +
| peptide_rebuild_modeller ||
 
|-
 
|-
 
| pir ||  
 
| pir ||  
Line 142: Line 200:
 
|-
 
|-
 
| polyala ||  
 
| polyala ||  
 +
|-
 +
| promix ||
 +
|-
 +
| prosmart ||
 +
|-
 +
| ramp_levels ||
 
|-
 
|-
 
| remove_alt || similar: [[removealt]]
 
| remove_alt || similar: [[removealt]]
Line 159: Line 223:
 
| save_settings || [[save_settings]]
 
| save_settings || [[save_settings]]
 
|-
 
|-
−
| save_traj || [[save2traj]] (outdated)
+
| [[save_traj]] || [[save2traj]] (outdated)
 +
|-
 +
| save_xyzr ||
 +
|-
 +
| sculpt_relax ||
 
|-
 
|-
 
| select_distances || [[get_raw_distances]]
 
| select_distances || [[get_raw_distances]]
Line 179: Line 247:
 
| spectrum_states || [[spectrum_states]]
 
| spectrum_states || [[spectrum_states]]
 
|-
 
|-
−
| spectrumany || [[spectrumany]]
+
| spectrumany || [[spectrumany]] || 1.6.0 (as [[spectrum]])
 
|-
 
|-
−
| split_chains || [[split_chains]]
+
| split_chains || [[split_chains]] || 1.6.0
 +
|-
 +
| split_molecules || similar: [[split_object]]
 +
|-
 +
| [[sst]] ||
 
|-
 
|-
 
| stride || similar: [[dssp stride]] plugin
 
| stride || similar: [[dssp stride]] plugin
Line 193: Line 265:
 
| symexpcell || [[supercell]]
 
| symexpcell || [[supercell]]
 
|-
 
|-
−
| theseus ||  
+
| [[theseus]] ||  
 
|-
 
|-
 
| tmalign || [[TMalign]]
 
| tmalign || [[TMalign]]
 +
|-
 +
| update_identifiers ||
 +
|-
 +
| [[xfit]] ||
 
|}
 
|}
  
 
[[Category:Script Library]]
 
[[Category:Script Library]]

Latest revision as of 03:58, 4 March 2019

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.

Installation

Using PyMOL 2.0 from the schrodinger anaconda channel: 

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico

Alternatively, copy the psico folder to your PYTHONPATH or use the setup.py based installation.

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')

Initialization

By importing psico.fullinit, the PyMOL core commands save and fetch become overloaded. In addition, all psico commands will be added to the pymol.cmd namespace. The save command will have enhanced PDB output, namely saving of secondary structure and crystal information, if available. The fetch command will also fetch 5-letter codes (code + chain) as well as CATH and SCOP identifiers (SCOP requires setting up a MySQL database). To skip the overloading, initialize psico like this: 

import psico
psico.init(save=0, fetch=0, pymolapi=0)

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... Added to PyMOL
add_missing_atoms
aaindex2b AAindex (outdated)
alignwithanymethod TMalign
alphatoall AlphaToAll (outdated)
angle_between_domains
angle_between_helices AngleBetweenHelices (outdated)
apbs_surface
api_info 1.7.2 (as api)
apropos apropos
atmtypenumbers
biomolecule BiologicalUnit/Quat (outdated)
cafit_orientation AngleBetweenHelices
cbm similar: Color Objects
cbs
centerofmass similar: center_of_mass 1.7.2
closest_keyframe
collapse_resi similar: CollapseSel
consurfdb
corina
delaunay similar: PyDet plugin
diff
dss_promotif
dssp similar: dssp stride plugin
dyndom
extra_fit extra_fit 1.7.2
fasta see also: Aa_codes
fetch
frames2states
gdt_ts
get_keyframes
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_promix
intra_theseus
intra_xfit
iterate_plot
join_states 1.7.2
load_3d
load_aln
load_consurf
load_gro
load_msms_surface
load_mtz_cctbx
load_traj_crd
loadall 1.7.2
local_rms
loop_orientation AngleBetweenHelices
map_new_apbs
matrix_to_ttt
mcsalign
morpheasy
morpheasy_linear
mse2met 1.6.0
msms_surface
mutate
mutate_all
nice
normalmodes_mmtk
normalmodes_pdbmat
normalmodes_prody
paper_png
paper_settings
pca_plot
pdb2pqr
peptide_rebuild
peptide_rebuild_modeller
pir
plane_orientation
polyala
promix
prosmart
ramp_levels
remove_alt similar: removealt
rms_plot
rmsf2b
save
save_colored_fasta
save_movie_mpeg1
save_pdb
save_settings save_settings
save_traj save2traj (outdated)
save_xyzr
sculpt_relax
select_distances get_raw_distances
select_pepseq
select_sspick
set_phipsi
set_sequence
sidechaincenters
snp_ncbi
snp_uniprot
spectrum_states spectrum_states
spectrumany spectrumany 1.6.0 (as spectrum)
split_chains split_chains 1.6.0
split_molecules similar: split_object
sst
stride similar: dssp stride plugin
stub2ala
supercell supercell
symdiff
symexpcell supercell
theseus
tmalign TMalign
update_identifiers
xfit
Retrieved from "http://wiki.pymol.org/index.php?title=Psico&oldid=14551"