psico.selecting

License: BSD-2-Clause

Functions

`collapse_resi`([selection, quiet, _self])	Returns a compact selection macro for the given selection on residue number (resi) level.
`diff`(sele1, sele2[, byres, name, operator, ...])	Difference between two molecules
`select_distances`([names, name, state, ...])	Turns a distance object into a named atom selection.
`select_nucseq`(pattern[, selection, name, ...])	Find a nucleic acid sequence pattern in given atom selection.
`select_pepseq`(pattern[, selection, name, ...])	Find a amino acid sequence pattern (regular expression) in given atom selection.
`select_range`([name, selection, merge, _self])	Select all atoms between the first and last atom in the current (or given) selection.
`select_sspick`(selection[, name, caonly, ...])	Extend selection by connected secondary structure elements.
`symdiff`(sele1, sele2[, byres, name, ...])	Symmetric difference between two molecules
`wait_for`(name[, state, quiet, _self])	Wait for "name" to be available as selectable object.

Classes

select_temporary(sele[, prefix, _self])

Context manager for creating a temporary named selection.

psico.selecting.collapse_resi(selection='(sele)', quiet=1, *, _self=...)[source]

Returns a compact selection macro for the given selection on residue number (resi) level.

Arguments

selection = string: atom selection {default: (sele)}

psico.selecting.diff(sele1, sele2, byres=1, name=None, operator='in', quiet=0, *, _self=...)[source]: Difference between two molecules

Arguments

sele1 = string: atom selection

sele2 = string: atom selection

byres = 0/1: report residues, not atoms (does not affect selection) {default: 1}

operator = in/like/align: operator to match atoms {default: in}

See Also

symdiff

psico.selecting.select_distances(names='', name='sele', state=1, selection='all', cutoff=-1, quiet=1, *, _self=...)[source]: Turns a distance object into a named atom selection.

Arguments

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

name = a unique name for the selection {default: sele}

state = int: object state (-1: current, 0: all states) {default: 1}

See Also

get_raw_distances

psico.selecting.select_nucseq(pattern, selection='all', name='sele', state=1, quiet=1, *, _self=...)[source]: Find a nucleic acid sequence pattern in given atom selection.

psico.selecting.select_pepseq(pattern, selection='all', name='sele', state=1, quiet=1, cutoff=4.0, one_letter=None, *, _self=...)[source]: Find a amino acid sequence pattern (regular expression) in given atom selection. Does not span gaps (unless matched by a wildcard).

Usage

select_pepseq pattern [, selection [, name [, state ]]]

Arguments

pattern = string: amino acid sequence in one letter code, can be a regular expression pattern.

selection = string: atom selection of protein (non protein atoms in selection are silently ignored) {default: all})

name = a unique name for the selection {default: sele}

Example

fetch 1a00, async=0 select_pepseq AL[EG]R, chain A+B, sele1 select_pepseq ([LIVAM]{3,}), all, sele2

See Also

There is the pepseq/ps. selection operator. Example: select actsite, protein and ps. ADFG

Similar scripts: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/seq_select.py http://pymolwiki.org/index.php/FindSeq

psico.selecting.select_range(name='', selection='', merge=1, *, _self=...)[source]: Select all atoms between the first and last atom in the current (or given) selection.

Arguments

name = str: Named selection to create {default: current active selection}

selection = str: Selection expression {default: name}

psico.selecting.select_sspick(selection, name=None, caonly=0, quiet=0, *, _self=...)[source]

Extend selection by connected secondary structure elements.

Also available as wizard (type: “wizard sspick”).

select_sspick selection [, name [, caonly [, quiet ]]]

selection = string: selection-expression

name = string: create a named atom selection if not None {default: None}

class psico.selecting.select_temporary(sele, prefix='_sele', *, _self=...)[source]

Context manager for creating a temporary named selection.

>>> with select_temporary(sele_expr) as named_sele:
...     assert named_sele in cmd.get_names()

psico.selecting.symdiff(sele1, sele2, byres=1, name=None, operator='in', quiet=0, *, _self=...)[source]: Symmetric difference between two molecules

See Also

diff

psico.selecting.wait_for(name, state=0, quiet=1, *, _self=...)[source]: Wait for “name” to be available as selectable object.