Gauss-integrate: Difference between revisions

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Navigation: Documentation / Commands / topcrd2crd


topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topcrd2crd

Synopsis

topcrd2crd [OPTIONS] [--] PARM CRD OUT

Description

Converts AMBER topology and coordinates to coordinates in other format.

Arguments

PARM
topology file name
CRD
input coordinates file name or - for standard input
OUT
output coordinates file name or - for standard output

Options

-i, --input FORMAT
specify input format for coordinates:
crd - amber restart file
xyz - xyz file
(Default: crd)
-o, --output FORMAT
specify output format for coordinates:
crd - amber restart file
pdb - PDB file
pqr - PDB file with atomic radii and charges
xyz - xyz file
xyzr - xyz file with atomic radii
com - gaussian input file
rbox - rbox format for qhull
traj - amber trajectory file
adf - plain ADF input
adffrag - plain ADF input with one fragment
adf3drism - plain ADF input for 3D-RISM
(Default: pdb)
-m, --mask MASK
only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
-f, --maskfile MASKFILE
only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
-t, --mangle FORMAT
specify atom names mangling scheme:
none - no translation (1234)
pdb - pdb scheme (4123), keep amber names
charmm - charmm name scheme (1234), mangle parm99 names
(Default: pdb)
--rscale
scale factor for atomic radii (r_new = r * scale + offset)
--roffset
offset for atomic radii (r_new = r * scale + offset)
-r, --reindex
reindex atom and residue numbers counting from 1
--copybox
copy box information to output file
--novelocities
do not transfer velocities
--nochains
do not print chain IDs into pdb files
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / topcrd2crd


topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topcrd2crd

Synopsis

topcrd2crd [OPTIONS] [--] PARM CRD OUT

Description

Converts AMBER topology and coordinates to coordinates in other format.

Arguments

PARM
topology file name
CRD
input coordinates file name or - for standard input
OUT
output coordinates file name or - for standard output

Options

-i, --input FORMAT
specify input format for coordinates:
crd - amber restart file
xyz - xyz file
(Default: crd)
-o, --output FORMAT
specify output format for coordinates:
crd - amber restart file
pdb - PDB file
pqr - PDB file with atomic radii and charges
xyz - xyz file
xyzr - xyz file with atomic radii
com - gaussian input file
rbox - rbox format for qhull
traj - amber trajectory file
adf - plain ADF input
adffrag - plain ADF input with one fragment
adf3drism - plain ADF input for 3D-RISM
(Default: pdb)
-m, --mask MASK
only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.
-f, --maskfile MASKFILE
only atoms selected according to the mask will be converted. The mask specification is read from the first line of the file of name MASKFILE. This option is suitable for the specification of very long masks. Mutually exclusive with 'mask' option.
-t, --mangle FORMAT
specify atom names mangling scheme:
none - no translation (1234)
pdb - pdb scheme (4123), keep amber names
charmm - charmm name scheme (1234), mangle parm99 names
(Default: pdb)
--rscale
scale factor for atomic radii (r_new = r * scale + offset)
--roffset
offset for atomic radii (r_new = r * scale + offset)
-r, --reindex
reindex atom and residue numbers counting from 1
--copybox
copy box information to output file
--novelocities
do not transfer velocities
--nochains
do not print chain IDs into pdb files
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / topcut


topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

topcut

Synopsis

topcut [OPTIONS] [--] OLD MASK NEW

Description

Cut AMBER topology and saves it as new one. Artifical topologies with open valences could be save too but use them only for visualisation purposes not for energy evaluation.

Arguments

OLD
old topology name. If - is provided then topology is read from standard input stream.
MASK
mask specification
NEW
new topology name. If - is provided then topology is written to standard output stream.

Options

-c, --coords CRD
optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)
-f, --maskfile
read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.
--copybox
copy old box information to new topology
--ignoreerrors
ignore open valences in newly created topology
--ver6
save new topology in version AMBER 6
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / blur


blur: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

blur

Synopsis

blur [OPTIONS] [--] input treshold output

Description

Blur 3D-density map in X-Plore format by data filtering in reciprocal Fourier space.

Arguments

input
input data file or - for data taken from standard input
treshold
filter treshold value
output
output result file or - for result printed to standard output

Options

-f, --filter STRING
filter type: either low-pass or gauss is implemeted
(Default: low-pass)
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / cats


cats: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

cats

Synopsis

cats [OPTIONS] [--] [SCRIPT] [ARG1 [ARG2] ...]

Description

CATs QScript interpretter.

Arguments:
SCRIPT file to be interpreted

Options

-i, --interactive
run in interactive mode
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / d2u


d2u: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

d2u

Synopsis

d2u [OPTIONS] [--] FILE1 [FILE2 ...]

Description

d2u converts given file(s) from DOS (\r\n) to UNIX (\n) end line character style.

Arguments:
FILE1 file to be converted or - for conversion from standard input to standard output

Options

--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / gauss-aw-gen


gauss-aw-gen: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

gauss-aw-gen

Synopsis

gauss-aw-gen [OPTIONS] [--] N output

Description

Numerically determines abscissas and weights used in Gaussian quadrature.

Arguments

N
number of points used in Gaussian quadrature
output
output result file or - for results printed to standard output

Options

-l, --start REAL
left boundary of integration interval
(Default: 0)
-r, --stop REAL
right boundary of integration interval
(Default: 1)
-p, --polynom NAME
name of orthogonal polynom: legendre
(Default: legendre)
-o, --output NAME
output format: abscissas, weights, or both
(Default: both)
--noheader
do not print header to output
--reverse
print results in reverse order
--af FORMAT
output FORMAT of abscissas values
(Default: %15.7e)
--wf FORMAT
output FORMAT of weights error values
(Default: %15.6e)
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit


Navigation: Documentation / Commands / gauss-integrate


gauss-integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]

Name

gauss-integrate

Synopsis

gauss-integrate [OPTIONS] [--] N input output

Description

Numerically integrate data using Gaussian quadrature.

Arguments

N
number of points used in Gaussian quadrature
input
input data file or - for data taken from standard input
output
output result file or - for results printed to standard output

Options

-l, --start REAL
left boundary of integration interval
(Default: 0)
-r, --stop REAL
right boundary of integration interval
(Default: 1)
--offset REAL
specify integration constant
(Default: 0)
-p, --polynom NAME
name of orthogonal polynom: legendre
(Default: legendre)
--progress
show integration progress
--noheader
do not print header to output
--nosigma
standard deviation of derivative is not present in input data
--fx FORMAT
output FORMAT of echoed x values
(Default: %15.7e)
--fy FORMAT
output FORMAT of echoed derivative values
(Default: %15.7e)
--fs FORMAT
output FORMAT of echoed sigma values
(Default: %14.6e)
--fi FORMAT
output FORMAT of integrated values
(Default: %15.7e)
--fe FORMAT
output FORMAT of integrated error values
(Default: %14.6e)
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit