Psico
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| 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A "outdated" note in the table means that the code in psico is newer (somehow enhanced) than on the corresponding wiki page.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| aaindex2b | AAindex (outdated) |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| alphatoall | AlphaToAll (outdated) |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| angle_between_helices | AngleBetweenHelices (outdated) |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| biomolecule | BiologicalUnit/Quat (outdated) |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| gyradius | radius of gyration (outdated) |
| helix_orientation | AngleBetweenHelices (outdated) |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 |