Introduction
Force Field Assembly
Calculate
The
Analyzer module currently defines ten functions
for the analysis of the Reduced Representation DNA
model. This module is in the Yup package at
Yup.Models.rrDNAv1. The import statement is some
variant of:
from
Yup.Models.rrDNAv1.Analyzer import
*.
The
ShowStretching(),
ShowBending(),
ShowTwisting()
and ShowConstraints()
functions report (to the standard output) the
active terms of the Longitudinal Stretching, Roll
and Tilt Rotations, Helical Twisting and a
collection of constraints respectively. All
functions take two arguments: the Model object of a
rrDNAv1 model and optionally a file name in which
case the report will be saved to the file instead
of appearing on the standard output. See the
following for the contents of these reports; the
constraints report contains output from the Bonds
term (see Stretching for format), Angles (see
Bending) and SoftSphereX (see
Constraints):
The WriteArchive() function prints the coordinates of a
chain to the standard output, in ARC3
format.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
WriteArchive
|
3
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
limit
|
AtomMap
|
None
|
|
report
|
string
|
''
(blank string)
|
The
M argument specifies a model which is
assumed to contain exactly one DNA chain if the
limit argument is at its default value of
None. Otherwise, limit should be set to an
AtomMap that encloses exactly one chain. The last
argument has a default value of a blank string,
which results in the output going to the standard
output. This can be diverted to a file by setting
the last argument to a string containing the name
of the file.
The ShowInternal() function prints the internal
coordinates of a chain to the standard
output.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
ShowInternal
|
2
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
report
|
string
|
''
(blank string)
|
The
M argument specifies any model. The last
argument has a default value of a blank string,
which results in the output going to the standard
output. This can be diverted to a file by setting
the last argument to a string containing the name
of the file.
The Writhe() function reports the writhing number for
the specified model or a part of the
model.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
Writhe
|
2
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
limit
|
AtomMap
|
None
|
If
the limit option results in selecting part of a
DNA, the writhing number is calculated for the
discontinuous chain. However, it is assumed that
only one chain is supplied to the
function.
The Link() function reports the linking number for the
specified model or a part of the model.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
Link
|
2
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
limit
|
AtomMap
|
None
|
The
limit option should result in the selection of two
equal-length and closed chains. Otherwise, the
calculation will fail and even if results are
available they will be completely
meaningless.
The
WriteParmTop()
function outputs parmtop and coordinate files for
AMBER.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
WriteParmTop
|
2
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
prefix
|
string
|
'rrDNAv1'
|
The
M argument specifies a rrDNAv1 model. The
prefix argument provides a prefix for the
names of the output files: the coordinate file will
be named 'prefix.inpcrd' while the parmtop
file will be named
'prefix.prmtop'.
The
WritePDB()
function outputs Protein Data Bank files.
|
Function
Name
|
Number
of Arguments
|
Return
Value
|
|
WritePDB
|
2
|
-
|
|
Argument
|
Type
|
Preset
Value
|
|
M
|
Model
|
-
|
|
filename
|
string
|
-
|
The
M argument specifies a rrDNAv1 model. The filename argument specifies a
name for the output file.
Service
Functions
|