Creating

flat.creating

Module for creating new molecular objects.

flat.creating.aromatic_centers(selection='all', object='aromatic_centers', name='PS1', *, _self=cmd)
DESCRIPTION

Creates an object with pseudo-atoms representing aromatic centers for each residue in selection.

USAGE

aromatic_centers [selection [, object [, name ]]]

ARGUMENTS
selectionstr, optional

Atom selection.

objectstr, default = ‘aromatic_centers’

Name of object to create.

namestr, default = ‘PS1’

Atom name of created pseudo-atoms.

RETURNS
: chempy.model

Returns molecular model for aromatic centers.

flat.creating.com(selection='all', name='COM', *, _self=cmd)
DESCRIPTION

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

USAGE

com [ selection [, name ]]

ARGUMENTS
selectionstr, optional

Atom selection.

namestr, default = ‘COM’

Name of object to create.

flat.creating.fragment(name, object=None, origin=1, zoom=0, quiet=1, *, _self=cmd)
DESCRIPTION

Retrieves a 3D structure from the fragment library, which is currently pretty meager.

This overload internal fragment function.

USAGE

fragment name [, object [, origin [, zoom ]]]

ARGUMENTS
namestr

Name of library fragment

objectstr, default = None

Name of object to create. Default is fragment name.

originbool, default = True

Center fragment at the current position.

zoombool, default = False

Zoom view to fit fragment

RETURNS
: chempy.model

Chempy model of loaded fragment.

flat.creating.sidechain_centers(selection='all', object='sidechain_centers', method='bahar1996', name='PS1', *, _self=cmd)
DESCRIPTION

Creates an object with sidechain representing pseudoatoms for each residue in selection.

Two methods are available:

  1. Sidechain interaction centers as defined by Bahar and Jernigan 1996 http://www.ncbi.nlm.nih.gov/pubmed/9080182

  2. Sidechain centroids, the pseudoatom is the centroid of all atoms except hydrogens and backbone atoms (N, C and O).

With method bahar1996, if a residue has all relevant side-chain center atoms missing (for example a MET without SD), it will be missing in the created pseudo-atom object.

With method centroid, if you want to exclude C-alpha atoms from side-shains.

USAGE

sidechain_centers [ selection [, object [, method, [ name ]]]]

ARGUMENTS
selectionstr, optional

Atom selection.

objectstr, default = ‘sidechain_centers’

Name of object to create.

methodstr, default = ‘bahar1996’

Method for calculating residue centroid.

namestr, default = ‘PS1’

Atom name of created pseudo-atoms.

SOURCE

From PSICO (c) 2010-2012 Thomas Holder