Editing
flat.editing
Module for editing molecular objects.
- flat.editing.align2eigen(selection='all', state=0, *, _self=cmd)
- DESCRIPTION
Align selection with it’s eigen vector.
- USAGE
align2eigen [ selection [, state ]]
- ARGUMENTS
- selectionstr, optional
Atoms selection.
- stateint, default = 0
Which state to consider.
- flat.editing.align2points(selection='all', pk1='(pk1)', pk2='(pk2)', pk3='(pk3)', state=0, *, _self=cmd)
- DESCRIPTION
Align selection with three selected point i.e. angle formed by selections (pk1), (pk2), and (pk3) which can be set using the PkAt mouse action (typically, Ctrl + middle-click).
New vector base is defined as:
y (pk3) | | (pk2) -- x (pk1) / z
- USAGE
align2points [ selection [, pk1, [, pk2 [, pk3, [, state ]]]]]
- ARGUMENTS
- selectionstr, optional
Atoms selection.
- pk1, pk2, pk3str, default = ‘(pk1)’, ‘(pk2)’, ‘(pk2)’
Points that will be used to define new orthonormal base.
- stateint, default = 0
Which state to consider.
- flat.editing.copy_identifiers(target, source, identifiers='segi chain resi', match='align', *, _self=cmd)
- DESCRIPTION
Transfers identifiers e.g. segi, chain, and resi from one selection to another. This works by mapping old to new identifiers and alters also not aligned atoms (works if any other atom from the same residue got aligned).
- USAGE
copy_identifiers target, source [, identifiers [, match ]]
- ARGUMENTS
- targetstr
Target selection.
- sourcestr
Source selection.
- identifiersstr, default = ‘segi chain resi’
Identifiers to copy. Separator is optional.
- matchstr, default = ‘align’
Method how to match atoms.
- SOURCE
From PSICO (c) 2011 Thomas Holder, MPI for Developmental Biology
- flat.editing.remove_alt(selection='all', keep='first', quiet=1, *, _self=cmd)
- DESCRIPTION
Remove alternative location atoms.
- USAGE
remove_alt [ selection [, keep ]]
- ARGUMENTS
- selectionstr
Atom selection.
- keepstr | int, default = ‘first’
AltLoc to keep, or first to keep the first observed AltLoc
- SOURCE
From PSICO (c) 2011 Thomas Holder, MPI for Developmental Biology
- flat.editing.renumber(selection, start=1, *, quiet=0, _self=cmd)
- DESCRIPTION
Renumber sets new residue numbers (resi) for a polymer based on connectivity.
- USAGE
renumber selection [, start ]
- ARGUMENTS
- selectionstr
Atom selection.
- startint, default = 1
Numbering start.
- RETURNS
- : Tuple(int, int)
First and last index in renumbering.
- flat.editing.split(operator, selection='all', name='obj', *, _self=cmd)
- DESCRIPTION
Create a single object for each entity in selection, defined by operator (e.g. bymolecule, bysegment, …). Returns the number of created objects.
- USAGE
split operator [, selection [, name ]]
- ARGUMENTS
- operatorstr
Operator to split selection by (e.g. bymolecule).
- selectionstr, optional
Atoms selection.
- namestr, default = ‘obj’
Name of generated object(s).
- RETURNS
- : int
Number of created objects.
- SOURCE
From PSICO (c) 2011 Thomas Holder, MPI for Developmental Biology
- flat.editing.unwrap(selection='all', mode='chains', *, _self=cmd)
- DESCRIPTION
Move all atoms in an selection so that bonds don’t split over images:
+-----------+ +-----------+ |-3-4 1-2-| --> | 1-2-|-3-4 +-----------+ +-----------+
- USAGE
unwrap [ selection [, mode ]]
- ARGUMENTS
- selectionstr, optional
Atoms selection.
- modestr, default = ‘chains’
The group which will be kept together through the shifting process: residues, chains, segments, or bonds.
- flat.editing.wrap(selection='all', *, _self=cmd)
- DESCRIPTION
Shift the contents of a given selection back into the unit cell:
+-----------+ +-----------+ | 1-2-|-3-4 --> |-3-4 1-2-| +-----------+ +-----------+
- USAGE
wrap [ selection ]
- ARGUMENTS
- selectionstr, optional
Atoms selection.