Psico: Difference between revisions
Jump to navigation
Jump to search
(update command list) |
(update commands list) |
||
| Line 41: | Line 41: | ||
{| class=wikitable | {| class=wikitable | ||
! Command || Already in PyMOLWiki... | ! Command || Already in PyMOLWiki... | ||
|- | |||
| add_missing_atoms || | |||
|- | |- | ||
| aaindex2b || [[AAindex]] (outdated) | | aaindex2b || [[AAindex]] (outdated) | ||
| Line 57: | Line 59: | ||
|- | |- | ||
| apropos || [[apropos]] | | apropos || [[apropos]] | ||
|- | |||
| atmtypenumbers || | |||
|- | |- | ||
| biomolecule || [[BiologicalUnit/Quat]] (outdated) | | biomolecule || [[BiologicalUnit/Quat]] (outdated) | ||
| Line 67: | Line 71: | ||
|- | |- | ||
| centerofmass || similar: [[center_of_mass]] | | centerofmass || similar: [[center_of_mass]] | ||
|- | |||
| closest_keyframe || | |||
|- | |- | ||
| collapse_resi || similar: [[CollapseSel]] | | collapse_resi || similar: [[CollapseSel]] | ||
|- | |- | ||
| consurfdb || | | consurfdb || | ||
|- | |||
| corina || | |||
|- | |- | ||
| delaunay || similar: [[PyDet]] plugin | | delaunay || similar: [[PyDet]] plugin | ||
|- | |- | ||
| diff || | | diff || | ||
|- | |||
| dss_promotif || | |||
|- | |- | ||
| dssp || similar: [[dssp stride]] plugin | | dssp || similar: [[dssp stride]] plugin | ||
| Line 89: | Line 99: | ||
|- | |- | ||
| gdt_ts || | | gdt_ts || | ||
|- | |||
| get_keyframes || | |||
|- | |- | ||
| get_raw_distances || [[get_raw_distances]] | | get_raw_distances || [[get_raw_distances]] | ||
| Line 105: | Line 117: | ||
|- | |- | ||
| hydropathy2b || | | hydropathy2b || | ||
|- | |||
| intra_promix || | |||
|- | |- | ||
| intra_theseus || | | intra_theseus || | ||
|- | |||
| intra_xfit || | |||
|- | |- | ||
| iterate_plot || | | iterate_plot || | ||
| Line 120: | Line 136: | ||
| load_gro || | | load_gro || | ||
|- | |- | ||
| | | load_msms_surface || | ||
|- | |||
| load_mtz_cctbx || | |||
|- | |- | ||
| load_traj_crd || | | load_traj_crd || | ||
| Line 131: | Line 149: | ||
|- | |- | ||
| map_new_apbs || | | map_new_apbs || | ||
|- | |||
| matrix_to_ttt || | |||
|- | |||
| mcsalign || | |||
|- | |- | ||
| morpheasy || | | morpheasy || | ||
| Line 137: | Line 159: | ||
|- | |- | ||
| mse2met || | | mse2met || | ||
|- | |||
| msms_surface || | |||
|- | |- | ||
| mutate || | | mutate || | ||
| Line 147: | Line 171: | ||
|- | |- | ||
| normalmodes_pdbmat || | | normalmodes_pdbmat || | ||
|- | |||
| normalmodes_prody || | |||
|- | |- | ||
| paper_png || | | paper_png || | ||
| Line 155: | Line 181: | ||
|- | |- | ||
| pdb2pqr || | | pdb2pqr || | ||
|- | |||
| peptide_rebuild || | |||
|- | |||
| peptide_rebuild_modeller || | |||
|- | |- | ||
| pir || | | pir || | ||
| Line 161: | Line 191: | ||
|- | |- | ||
| polyala || | | polyala || | ||
|- | |||
| promix || | |||
|- | |||
| prosmart || | |||
|- | |- | ||
| ramp_levels || | | ramp_levels || | ||
| Line 181: | Line 215: | ||
|- | |- | ||
| save_traj || [[save2traj]] (outdated) | | save_traj || [[save2traj]] (outdated) | ||
|- | |||
| save_xyzr || | |||
|- | |- | ||
| sculpt_relax || | | sculpt_relax || | ||
| Line 207: | Line 243: | ||
|- | |- | ||
| split_molecules || similar: [[split_object]] | | split_molecules || similar: [[split_object]] | ||
|- | |||
| sst || | |||
|- | |- | ||
| stride || similar: [[dssp stride]] plugin | | stride || similar: [[dssp stride]] plugin | ||
| Line 223: | Line 261: | ||
|- | |- | ||
| update_identifiers || | | update_identifiers || | ||
|- | |||
| xfit || | |||
|} | |} | ||
[[Category:Script Library]] | [[Category:Script Library]] | ||
Revision as of 15:10, 3 August 2016
| 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')
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... |
|---|---|
| add_missing_atoms | |
| aaindex2b | AAindex (outdated) |
| alignwithanymethod | TMalign |
| alphatoall | AlphaToAll (outdated) |
| angle_between_domains | |
| angle_between_helices | AngleBetweenHelices (outdated) |
| apbs_surface | |
| api_info | |
| apropos | apropos |
| atmtypenumbers | |
| biomolecule | BiologicalUnit/Quat (outdated) |
| cafit_orientation | AngleBetweenHelices |
| cbm | similar: Color Objects |
| cbs | |
| centerofmass | similar: center_of_mass |
| 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 |
| 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 | |
| load_3d | |
| load_aln | |
| load_consurf | |
| load_gro | |
| load_msms_surface | |
| load_mtz_cctbx | |
| load_traj_crd | |
| loadall | |
| local_rms | |
| loop_orientation | AngleBetweenHelices |
| map_new_apbs | |
| matrix_to_ttt | |
| mcsalign | |
| morpheasy | |
| morpheasy_linear | |
| mse2met | |
| 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 |
| split_chains | split_chains |
| split_molecules | similar: split_object |
| sst | |
| stride | similar: dssp stride plugin |
| stub2ala | |
| supercell | supercell |
| symdiff | |
| symexpcell | supercell |
| theseus | |
| tmalign | TMalign |
| update_identifiers | |
| xfit |