Creating

flat.creating

Module for creating new molecular objects.

Custom fragments

List of custom fragments added to library:

Code	Name
CSD	CYSTEINESULFINIC ACID
DAH	DOPA
IAS	ASPARTIC ACID
KYN	KYNURENINE
OCS	CYSTEINESULFONIC ACID
OHI
OMT	DIOXYMETHIONINE
PCA	PYROGLUTAMIC ACID
SMC	METHYLCYSTEINE
SME	METHIONINE SULFOXIDE
SNN	SUCCINIMIDE
TPO	PHOSPHOTHREONINE

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