psico.querying

(c) 2011 Thomas Holder, MPI for Developmental Biology (c) 2011 Tsjerk Wassenaar (gyradius code)

License: BSD-2-Clause

Functions

centerofmass([selection, state, quiet, _self])	Calculates the center of mass.
csp(sele1[, sele2, quiet, var, _self])	Charge Symmetry Parameter between two selections.
extinction_coefficient([selection, state, ...])	Extinction coefficient at 280 nm.
get_alignment_coords(name[, active_only, ...])	API only function.
get_color(selection[, which, mode, _self])	API only.
get_ensemble_coords(selection, *[, _self])	API only.
get_object_name(selection[, strict, _self])	Returns the object name for given selection.
get_object_state(name, *[, _self])	Returns the effective object state.
get_raw_distances([names, state, selection, ...])	Get the list of pair items from distance objects.
get_sasa(selection[, state, dot_density, ...])	Get solvent accesible surface area
get_sasa_ball(selection[, state, quiet, _self])	Get solvent accesible surface area using BALL.NumericalSAS
get_segis([selection, quiet, _self])	Get the set of segment identifiers.
get_selection_state(selection, *[, _self])	Returns the effective object state for all objects in given selection.
gyradius([selection, state, quiet, _self])	Radius of gyration
isoelectric_point([selection, ph, quiet, _self])	Compute isoelectric point and charge at given pH.
iterate_state_to_list(state, selection, ...)	API-only function to capture "iterate_state" results in a list.
iterate_to_list(selection, expression, *[, ...])	API-only function to capture "iterate" results in a list.
iterate_to_sele(selection, expression, *[, ...])	API-only function to get a selection expression for "iterate" results which evaluate to True.
shortest_distance(selection1, selection2[, ...])	Finds the shortest pairwise distance between two selections.

psico.querying.centerofmass(selection='(all)', state=-1, quiet=1, *, _self=...) → List[float]

Calculates the center of mass. Considers atom mass and occupancy.

Notice: Atoms with occupancy 0 are ignored. This differs from PyMOL’s cmd.centerofmass which treats occupancy 0 as 1.

Arguments

selection = string: atom selection {default: all}

state = integer: object state, -1 for current state, 0 for all states {default: -1}

Example

from psico.querying import * x = centerofmass(‘chain A’) r = gyradius(‘chain A’) cmd.pseudoatom(‘com’, pos=x, vdw=r)

See Also

gyradius

psico.querying.csp(sele1: str, sele2: str = '', quiet=1, var='formal_charge', _self=...) → float

Charge Symmetry Parameter between two selections. Can be used to compute FvCSP according to Sharma 2014.

If only sele1 is given, it must contain excatly two chains.

psico.querying.extinction_coefficient(selection='all', state=-1, *, quiet=1, _self=...) → Tuple[int, float]

Extinction coefficient at 280 nm.

psico.querying.get_alignment_coords(name: str, active_only=0, state=-1, quiet=0, *, _self=...)

API only function. Returns a dictionary with items

(object name, Nx3 coords list)

N is the number of alignment columns without gaps.

Example

import numpy from psico.multistuff import * from psico.querying import *

extra_fit(‘name CA’, cycles=0, object=’aln’) x = get_alignment_coords(‘aln’) m = numpy.array(x.values())

psico.querying.get_color(selection, which=0, mode=0, *, _self=...) → int | str | Tuple[float, float, float]

API only. Returns the color of the first/middle/… guide atom in selection.

Arguments

which = 0: color of first atom which = 1: color of middle atom which = 2: most frequent color

mode = 0: color index or color string mode = 1: color tuple mode = 2: color string in hash-hex format (for HTML, matplotlib, …)

psico.querying.get_ensemble_coords(selection: str, *, _self=...) → np.ndarray[tuple[int, int, Literal[3]], np.dtype[np.float32]]

API only. Returns the (nstates, natoms, 3) coordinate matrix. Considers the object rotation matrix.

psico.querying.get_object_name(selection: str, strict=0, *, _self=...) → str

Returns the object name for given selection.

Arguments

selection = string: atom selection strict = 0: allow multiple objects in selection but only return the first strict = 1: raise exception if selection spans multiple objects

psico.querying.get_object_state(name: str, *, _self=...) → int

Returns the effective object state.

psico.querying.get_raw_distances(names: str = '', state=1, selection='all', quiet=1, *, _self=...)

Get the list of pair items from distance objects. Each list item is a tuple of (index1, index2, distance).

Based on a script from Takanori Nakane, posted on pymol-users mailing list. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10143.html

Arguments

names = string: names of distance objects (no wildcards!) {default: all measurement objects}

state = integer: object state {default: 1}

selection = string: atom selection {default: all}

See Also

select_distances, cmd.find_pairs, cmd.get_raw_alignment

psico.querying.get_sasa(selection: str, state=-1, dot_density=5, quiet=1, *, _self=...) → float

Get solvent accesible surface area

See Also

get_area pymol.util.get_sasa (considered broken!)

psico.querying.get_sasa_ball(selection: str, state=-1, quiet=1, *, _self=...) → float

Get solvent accesible surface area using BALL.NumericalSAS

http://www.ball-project.org/

psico.querying.get_segis(selection='all', *, quiet=1, _self=...) → set[str]

Get the set of segment identifiers.

psico.querying.get_selection_state(selection: str, *, _self=...) → int

Returns the effective object state for all objects in given selection. Raises exception if objects are in different states.

psico.querying.gyradius(selection='(all)', state=-1, quiet=1, *, _self=...) → float

Radius of gyration

Based on: http://pymolwiki.org/index.php/Radius_of_gyration

See Also

centerofmass

psico.querying.isoelectric_point(selection: str = 'polymer', *, ph: float = 7, quiet: int = 1, _self=...) → float

Compute isoelectric point and charge at given pH.

psico.querying.iterate_state_to_list(state: int, selection: str, expression: str, *, space: dict | None = None, _self=...) → list

API-only function to capture “iterate_state” results in a list.

psico.querying.iterate_to_list(selection: str, expression: str, *, space: dict | None = None, _self=...) → list

API-only function to capture “iterate” results in a list.

psico.querying.iterate_to_sele(selection: str, expression: str, *, space: dict | None = None, _self=...) → str

API-only function to get a selection expression for “iterate” results which evaluate to True.

psico.querying.shortest_distance(selection1: str, selection2: str, state1: int = -1, state2: int = -1, name: str = 'shortest', *, quiet: int = 1, _self=...)

Finds the shortest pairwise distance between two selections.

Arguments

selection1 = string: first atom selection

selection2 = string: second atom selection

state1 = state of selection1 {default: current state}

state2 = state of selection2 {default: current state}

name = string: name of the object to create {default: shortest}

quiet = 0 or 1: print results to the terminal {default: 1}

Example

fetch 2xwu shortest_distance chain A, chain B