Index

A

AAindex (class in psico.aaindex) aaindex2b() (in module psico.aaindex) aakeys (psico.aaindex.Record attribute) add_missing_atoms() (in module psico.modelling) aggrescan1d() (in module psico.aggrescanning) aggrescan1d_scores() (in module psico.aggrescanning) aggrescan3d() (in module psico.aggrescanning) align() (psico.fitting.MatchMaker method)

alignwithanymethod() (in module psico.fitting) alphatoall() (in module psico.editing) angle_between_domains() (in module psico.orientation) angle_between_helices() (in module psico.orientation) apbs_surface() (in module psico.electrostatics) api_info() (in module psico.helping) apropos() (in module psico.helping) area_plot() (in module psico.plotting) atmtypenumbers() (in module psico.msms)

B

biomolecule() (in module psico.xtal)

C

cafit_orientation() (in module psico.orientation) cap_termini() (in module psico.modelling) cath_parse_domall() (in module psico.importing) cbm() (in module psico.viewing) cbs() (in module psico.viewing) cell_axes() (in module psico.xtal) cellbasis() (in module psico.xtal) centerofmass() (in module psico.querying) check() (psico.fitting.MatchMaker method) clean_ob() (in module psico.minimizing)

close() (psico.exporting.CRDOutfile method) closest_keyframe() (in module psico.moving) collapse_resi() (in module psico.selecting) columns (psico.exporting.CRDOutfile attribute) (psico.exporting.RSTOutfile attribute) confgen_rdkit() (in module psico.creating) consurfdb() (in module psico.conservation) contact_map_plot() (in module psico.plotting) corina() (in module psico.creating) CRDOutfile (class in psico.exporting) csp() (in module psico.querying)

D

DCDOutfile (class in psico.exporting) delaunay() (in module psico.geometry) diff() (in module psico.selecting) dss_promotif() (in module psico.editing)

dssp() (in module psico.editing) dump_mviews() (in module psico.moving) dyndom() (in module psico.fitting) dyndom_parse_info() (in module psico.fitting)

E

extend() (psico.aaindex.MatrixRecord method) (psico.aaindex.Record method)

extinction_coefficient() (in module psico.querying) extra_fit() (in module psico.fitting)

F

fasta() (in module psico.fasta) fetch() (in module psico.importing) fetch_cath() (in module psico.importing) fetch_chain() (in module psico.importing) fetch_scop() (in module psico.importing)

fiber() (in module psico.creating) fmt (psico.exporting.CRDOutfile attribute) (psico.exporting.RSTOutfile attribute) frames2states() (in module psico.moving) from_alignment() (psico.fitting.MatchMaker method) func() (in module psico.orientation)

G

gdt_ts() (in module psico.fitting) get() (psico.aaindex.MatrixRecord method) (psico.aaindex.Record method) get_alignment_coords() (in module psico.querying) get_closest_keyframe() (in module psico.moving) get_color() (in module psico.querying) get_color_family() (in module psico.viewing) get_ensemble_coords() (in module psico.querying) get_fixed_indices() (in module psico.minimizing) get_grostr() (in module psico.exporting) get_keyframes() (in module psico.moving) get_mdo_commands() (in module psico.moving) get_model_color() (in module psico.plotting) get_object_name() (in module psico.querying)

get_object_state() (in module psico.querying) get_pdb_seqres() (in module psico.exporting) get_pdb_sss() (in module psico.exporting) get_raw_distances() (in module psico.querying) get_rmsd_func() (in module psico.fitting) get_sasa() (in module psico.querying) get_sasa_ball() (in module psico.querying) get_segis() (in module psico.querying) get_selection_state() (in module psico.querying) get_seq() (in module psico.modelling) goodsell_lighting() (in module psico.viewing) grep() (psico.aaindex.AAindex method) grepset() (in module psico.helping) grid_labels() (in module psico.viewing) gyradius() (in module psico.querying)

H

helix_orientation() (in module psico.orientation)

hydropathy2b() (in module psico.aaindex) hydropathy2b_exposed() (in module psico.aaindex)

I

intra_boxfit() (in module psico.fitting) intra_center() (in module psico.fitting) intra_promix() (in module psico.fitting) intra_theseus() (in module psico.fitting) intra_xfit() (in module psico.fitting)

isoelectric_point() (in module psico.querying) iterate_plot() (in module psico.plotting) iterate_state_to_list() (in module psico.querying) iterate_to_list() (in module psico.querying) iterate_to_sele() (in module psico.querying)

J

join_states() (in module psico.creating)

L

load() (psico.xtal.PutCenterCallback method) load_3d() (in module psico.importing) load_aln() (in module psico.importing) load_consurf() (in module psico.conservation) load_coords() (in module psico.importing) load_gro() (in module psico.importing) load_msms_surface() (in module psico.msms) load_mtz() (in module psico.importing) load_mtz_cctbx() (in module psico.load_mtz_cctbx)

load_or_update() (in module psico.minimizing) load_smi() (in module psico.importing) load_traj_crd() (in module psico.importing) load_traj_dcd() (in module psico.importing) loadall() (in module psico.importing) loadall_traj() (in module psico.importing) local_mirror_pdb() (in module psico.importing) local_rms() (in module psico.fitting) loop_orientation() (in module psico.orientation)

M

map_new_apbs() (in module psico.electrostatics) MatchMaker (class in psico.fitting) matrix_to_ttt() (in module psico.moving) MatrixRecord (class in psico.aaindex) mean() (in module psico.aggrescanning) median() (psico.aaindex.MatrixRecord method) (psico.aaindex.Record method) minimize_ob() (in module psico.minimizing) minimize_rdkit() (in module psico.minimizing) module psico.aaindex psico.aggrescanning psico.conservation psico.creating psico.editing psico.electrostatics psico.exporting psico.fasta psico.fitting psico.geometry psico.helping psico.importing psico.load_mtz_cctbx psico.minimizing psico.modelling psico.moving psico.msms psico.nma psico.orientation psico.plotting psico.querying psico.selecting psico.setting psico.viewing psico.wizards psico.xtal

mse2met() (in module psico.editing) msms_surface() (in module psico.msms) mtz2ccp4maps() (in module psico.load_mtz_cctbx) mutate() (in module psico.modelling) mutate_all() (in module psico.modelling)

N

names_sc() (in module psico.wizards) next_keyframe() (in module psico.moving)

nice() (in module psico.viewing) normalmodes_pdbmat() (in module psico.nma) normalmodes_prody() (in module psico.nma)

P

paper_png() (in module psico.exporting) paper_settings() (in module psico.setting) parse() (psico.aaindex.AAindex method) parse_eigenfacs() (in module psico.nma) pca_plot() (in module psico.plotting) pdb2pqr() (in module psico.creating) pdbremarks() (in module psico.xtal) peptide_rebuild() (in module psico.modelling) peptide_rebuild_modeller() (in module psico.modelling) pir() (in module psico.fasta) plane_orientation() (in module psico.orientation) polyala() (in module psico.editing) prepwizard() (in module psico.creating) prev_keyframe() (in module psico.moving) prev_v (psico.xtal.PutCenterCallback attribute) promix() (in module psico.fitting) prosmart() (in module psico.fitting) psico.aaindex module psico.aggrescanning module psico.conservation module psico.creating module psico.editing module psico.electrostatics module psico.exporting module psico.fasta module psico.fitting module

psico.geometry module psico.helping module psico.importing module psico.load_mtz_cctbx module psico.minimizing module psico.modelling module psico.moving module psico.msms module psico.nma module psico.orientation module psico.plotting module psico.querying module psico.selecting module psico.setting module psico.viewing module psico.wizards module psico.xtal module PutCenterCallback (class in psico.xtal)

Q

qdelaunay() (in module psico.geometry)

R

ramp_levels() (in module psico.creating) randomize_coords_if_collapsed() (in module psico.minimizing) Record (class in psico.aaindex) remove_alt() (in module psico.editing)

remove_alt_keep_first() (in module psico.editing) rms_plot() (in module psico.plotting) rmsf2b() (in module psico.editing) RSTOutfile (class in psico.exporting)

S

save() (in module psico.exporting) save_colored_fasta() (in module psico.fasta) save_lightdock_restraints() (in module psico.exporting) save_mdtraj() (in module psico.exporting) save_movie_mpeg1() (in module psico.moving) save_pdb() (in module psico.exporting) save_pdb_without_ter() (in module psico.exporting) save_settings() (in module psico.setting) save_traj() (in module psico.exporting) save_xyzr() (in module psico.msms) scene_preserve (class in psico.viewing) sculpt_homolog() (in module psico.modelling) sculpt_relax() (in module psico.modelling) search() (psico.aaindex.AAindex method) select_distances() (in module psico.selecting) select_nucseq() (in module psico.selecting) select_pepseq() (in module psico.selecting) select_range() (in module psico.selecting) select_sspick() (in module psico.selecting)

select_temporary (class in psico.selecting) set_phipsi() (in module psico.editing) set_raw_alignment() (in module psico.importing) set_sequence() (in module psico.editing) set_temporary (class in psico.setting) shortest_distance() (in module psico.querying) show_ptm() (in module psico.viewing) sidechaincenters() (in module psico.creating) spectrum_states() (in module psico.viewing) spectrumany() (in module psico.viewing) split() (in module psico.editing) split_chains() (in module psico.editing) split_molecules() (in module psico.editing) split_segis() (in module psico.editing) sst() (in module psico.editing) stride() (in module psico.editing) stub2ala() (in module psico.editing) supercell() (in module psico.xtal) symdiff() (in module psico.selecting) symexpcell() (in module psico.xtal)

T

theseus() (in module psico.fitting)

tmalign() (in module psico.fitting) trapezoidal_integration() (in module psico.aggrescanning)

U

unittouu() (in module psico.exporting) update_align() (in module psico.modelling)

update_identifiers() (in module psico.editing) usalign() (in module psico.fitting)

V

validate_apbs_exe() (in module psico.electrostatics) visualize_orientation() (in module psico.orientation)

volume_esp() (in module psico.electrostatics) volume_fofc() (in module psico.electrostatics)

W

wait_for() (in module psico.selecting) write_html_ref() (in module psico.helping) write_txt_ref() (in module psico.helping)

writeCoordSet() (psico.exporting.CRDOutfile method) (psico.exporting.DCDOutfile method) writeFortran() (psico.exporting.DCDOutfile method)

X

xfit() (in module psico.fitting)