Topcrd2crd: Difference between revisions

Latest revision as of 22:32, 3 March 2020

Navigation: Documentation / Commands / topcrd2crd

topcrd2crd: version 2.231.418d045(2020-03-01 18:49) [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 (ASCII)
bcrd - amber restart file (NetCDF)
pdb - PDB file
pqr - PDB file with atomic radii and charges
xyz - xyz file
xyzr - xyz file with atomic radii
com - gaussian input file
orca - orca input file
pc - point charges 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 otherwise all atoms are used. Mutually exclusive with 'maskfile' option.

-f, --maskfile MASKFILE

only atoms selected according to the mask will be converted otherwise all atoms are used. 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.

--chrgmask MASK

only atoms selected according to MASK will be included as point charges. Mutually exclusive with 'chrgmaskfile' option.

--chrgmaskfile MASKFILE

only atoms selected according to the mask will be included as point charges. 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 'chrgmask' 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

@@ Line 2: / Line 2: @@
 Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]]
 ----
-<div style="text-align: center">topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
+<div style="text-align: center">topcrd2crd: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]</div>'''Name'''
 <span style="margin-left: 15px;">topcrd2crd</span>
@@ Line 31: / Line 31: @@
 |<span style="color: blue;">-i, --input FORMAT</span><br/><div style="margin-left: 30px;">specify input format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>  - amber restart file<br /><span></span>   <span style="color: green;">xyz</span>  - xyz file</div><span style="color:purple; margin-left: 30px;">(Default: crd)</span>
 |- style="vertical-align: top;"
-|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>        - amber restart file<br /><span></span>   <span style="color: green;">pdb</span>        - PDB file<br /><span></span>   <span style="color: green;">pqr</span>        - PDB file with atomic radii and charges<br /><span></span>   <span style="color: green;">xyz</span>        - xyz file<br /><span></span>   <span style="color: green;">xyzr</span>       - xyz file with atomic radii<br /><span></span>   <span style="color: green;">com</span>        - gaussian input file<br /><span></span>   <span style="color: green;">rbox</span>       - rbox format for qhull<br /><span></span>   <span style="color: green;">traj</span>       - amber trajectory file<br /><span></span>   <span style="color: green;">adf</span>        - plain ADF input<br /><span></span>   <span style="color: green;">adffrag</span>    - plain ADF input with one fragment<br /><span></span>   <span style="color: green;">adf3drism</span>  - plain ADF input for 3D-RISM</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
+|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>        - amber restart file (ASCII)<br /><span></span>   <span style="color: green;">bcrd</span>       - amber restart file (NetCDF)<br /><span></span>   <span style="color: green;">pdb</span>        - PDB file<br /><span></span>   <span style="color: green;">pqr</span>        - PDB file with atomic radii and charges<br /><span></span>   <span style="color: green;">xyz</span>        - xyz file<br /><span></span>   <span style="color: green;">xyzr</span>       - xyz file with atomic radii<br /><span></span>   <span style="color: green;">com</span>        - gaussian input file<br /><span></span>   <span style="color: green;">orca</span>       - orca input file<br /><span></span>   <span style="color: green;">pc</span>         - point charges file<br /><span></span>   <span style="color: green;">rbox</span>       - rbox format for qhull<br /><span></span>   <span style="color: green;">traj</span>       - amber trajectory file<br /><span></span>   <span style="color: green;">adf</span>        - plain ADF input<br /><span></span>   <span style="color: green;">adffrag</span>    - plain ADF input with one fragment<br /><span></span>   <span style="color: green;">adf3drism</span>  - plain ADF input for 3D-RISM</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.</div>
+|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted otherwise all atoms are used. Mutually exclusive with 'maskfile' option.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">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.</div>
+|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">only atoms selected according to the mask will be converted otherwise all atoms are used. 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.</div>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-t, --mangle FORMAT</span><br/><div style="margin-left: 30px;">specify atom names mangling scheme:<br /><span></span>   <span style="color: green;">none</span>   - no translation (1234)<br /><span></span>   <span style="color: green;">pdb</span>    - pdb scheme (4123), keep amber names<br /><span></span>   <span style="color: green;">charmm</span> - charmm name scheme (1234), mangle parm99 names</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
+|<span style="color: blue;">--chrgmask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be included as point charges. Mutually exclusive with 'chrgmaskfile' option.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--rscale</span><br/><div style="margin-left: 30px;">scale factor for atomic radii (r_new = r * scale + offset)</div>
+|<span style="color: blue;">--chrgmaskfile MASKFILE</span><br/><div style="margin-left: 30px;">only atoms selected according to the mask will be included as point charges. 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 'chrgmask' option.</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--roffset</span><br/><div style="margin-left: 30px;">offset for atomic radii (r_new = r * scale + offset)</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-r, --reindex</span><br/><div style="margin-left: 30px;">reindex atom and residue numbers counting from 1</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--copybox</span><br/><div style="margin-left: 30px;">copy box information to output file</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--novelocities</span><br/><div style="margin-left: 30px;">do not transfer velocities</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--nochains</span><br/><div style="margin-left: 30px;">do not print chain IDs into pdb files</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:topcrd2crd}}
-Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]]
-----
-<div style="text-align: center">topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">topcrd2crd</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">topcrd2crd</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">PARM</span> <span style="color: purple;">CRD</span> <span style="color: purple;">OUT</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Converts AMBER topology and coordinates to coordinates in other format.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">CRD</span><br/><div style="margin-left: 30px;">input coordinates file name or - for standard input</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output coordinates file name or - for standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-i, --input FORMAT</span><br/><div style="margin-left: 30px;">specify input format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>  - amber restart file<br /><span></span>   <span style="color: green;">xyz</span>  - xyz file</div><span style="color:purple; margin-left: 30px;">(Default: crd)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>        - amber restart file<br /><span></span>   <span style="color: green;">pdb</span>        - PDB file<br /><span></span>   <span style="color: green;">pqr</span>        - PDB file with atomic radii and charges<br /><span></span>   <span style="color: green;">xyz</span>        - xyz file<br /><span></span>   <span style="color: green;">xyzr</span>       - xyz file with atomic radii<br /><span></span>   <span style="color: green;">com</span>        - gaussian input file<br /><span></span>   <span style="color: green;">rbox</span>       - rbox format for qhull<br /><span></span>   <span style="color: green;">traj</span>       - amber trajectory file<br /><span></span>   <span style="color: green;">adf</span>        - plain ADF input<br /><span></span>   <span style="color: green;">adffrag</span>    - plain ADF input with one fragment<br /><span></span>   <span style="color: green;">adf3drism</span>  - plain ADF input for 3D-RISM</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">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.</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-t, --mangle FORMAT</span><br/><div style="margin-left: 30px;">specify atom names mangling scheme:<br /><span></span>   <span style="color: green;">none</span>   - no translation (1234)<br /><span></span>   <span style="color: green;">pdb</span>    - pdb scheme (4123), keep amber names<br /><span></span>   <span style="color: green;">charmm</span> - charmm name scheme (1234), mangle parm99 names</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--rscale</span><br/><div style="margin-left: 30px;">scale factor for atomic radii (r_new = r * scale + offset)</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--roffset</span><br/><div style="margin-left: 30px;">offset for atomic radii (r_new = r * scale + offset)</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-r, --reindex</span><br/><div style="margin-left: 30px;">reindex atom and residue numbers counting from 1</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--copybox</span><br/><div style="margin-left: 30px;">copy box information to output file</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--novelocities</span><br/><div style="margin-left: 30px;">do not transfer velocities</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--nochains</span><br/><div style="margin-left: 30px;">do not print chain IDs into pdb files</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:topcut}}
-Navigation: [[Documentation]] / [[Commands]] / [[topcut]]
-----
-<div style="text-align: center">topcut: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">topcut</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">topcut</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">OLD</span> <span style="color: purple;">MASK</span> <span style="color: purple;">NEW</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">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.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">OLD</span><br/><div style="margin-left: 30px;">old topology name. If - is provided then topology is read from standard input stream.</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">MASK</span><br/><div style="margin-left: 30px;">mask specification</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">NEW</span><br/><div style="margin-left: 30px;">new topology name. If - is provided then topology is written to standard output stream.</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-c, --coords CRD</span><br/><div style="margin-left: 30px;">optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-f, --maskfile</span><br/><div style="margin-left: 30px;">read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--copybox</span><br/><div style="margin-left: 30px;">copy old box information to new topology</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--ignoreerrors</span><br/><div style="margin-left: 30px;">ignore open valences in newly created topology</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--ver6</span><br/><div style="margin-left: 30px;">save new topology in version AMBER 6</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:blur}}
-Navigation: [[Documentation]] / [[Commands]] / [[blur]]
-----
-<div style="text-align: center">blur: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">blur</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">blur</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">treshold</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Blur 3D-density map in X-Plore format by data filtering in reciprocal Fourier space.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input data file or - for data taken from standard input</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">treshold</span><br/><div style="margin-left: 30px;">filter treshold value</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output result file or - for result printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-f, --filter STRING</span><br/><div style="margin-left: 30px;">filter type: either low-pass or gauss is implemeted</div><span style="color:purple; margin-left: 30px;">(Default: low-pass)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:cats}}
-Navigation: [[Documentation]] / [[Commands]] / [[cats]]
-----
-<div style="text-align: center">cats: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">cats</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">cats</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">[SCRIPT] [ARG1 [ARG2] ...]</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">CATs QScript interpretter.</p>
-Arguments:<br /><span></span>   SCRIPT                    file to be interpreted<br />
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-i, --interactive</span><br/><div style="margin-left: 30px;">run in interactive mode</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:d2u}}
-Navigation: [[Documentation]] / [[Commands]] / [[d2u]]
-----
-<div style="text-align: center">d2u: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">d2u</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">d2u</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">FILE1 [FILE2 ...]</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">d2u converts given file(s) from DOS (\r\n) to UNIX (\n) end line character style.</p>
-Arguments:<br /><span></span>   FILE1                      file to be converted or - for conversion from standard input to standard output<br />
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:gauss-aw-gen}}
-Navigation: [[Documentation]] / [[Commands]] / [[gauss-aw-gen]]
-----
-<div style="text-align: center">gauss-aw-gen: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">gauss-aw-gen</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">gauss-aw-gen</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">N</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Numerically determines abscissas and weights used in Gaussian quadrature.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">N</span><br/><div style="margin-left: 30px;">number of points used in Gaussian quadrature</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output result file or - for results printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-l, --start REAL</span><br/><div style="margin-left: 30px;">left boundary of integration interval</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-r, --stop REAL</span><br/><div style="margin-left: 30px;">right boundary of integration interval</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-p, --polynom NAME</span><br/><div style="margin-left: 30px;">name of orthogonal polynom: legendre</div><span style="color:purple; margin-left: 30px;">(Default: legendre)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-o, --output NAME</span><br/><div style="margin-left: 30px;">output format: abscissas, weights, or both</div><span style="color:purple; margin-left: 30px;">(Default: both)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">do not print header to output</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--reverse</span><br/><div style="margin-left: 30px;">print results in reverse order</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--af FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of abscissas values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--wf FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of weights error values</div><span style="color:purple; margin-left: 30px;">(Default: %15.6e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:gauss-integrate}}
-Navigation: [[Documentation]] / [[Commands]] / [[gauss-integrate]]
-----
-<div style="text-align: center">gauss-integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">gauss-integrate</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">gauss-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">N</span> <span style="color: purple;">input</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Numerically integrate data using Gaussian quadrature.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">N</span><br/><div style="margin-left: 30px;">number of points used in Gaussian quadrature</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input data file or - for data taken from standard input</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output result file or - for results printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-l, --start REAL</span><br/><div style="margin-left: 30px;">left boundary of integration interval</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-r, --stop REAL</span><br/><div style="margin-left: 30px;">right boundary of integration interval</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--offset REAL</span><br/><div style="margin-left: 30px;">specify integration constant</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-p, --polynom NAME</span><br/><div style="margin-left: 30px;">name of orthogonal polynom: legendre</div><span style="color:purple; margin-left: 30px;">(Default: legendre)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--progress</span><br/><div style="margin-left: 30px;">show integration progress</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">do not print header to output</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--nosigma</span><br/><div style="margin-left: 30px;">standard deviation of derivative is not present in input data</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed x values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fy FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed derivative values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed sigma values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fi FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of integrated values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of integrated error values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:histogram}}
-Navigation: [[Documentation]] / [[Commands]] / [[histogram]]
-----
-<div style="text-align: center">histogram: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">histogram</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">histogram</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Perform histogram analysis.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input data file or - for data taken from standard input</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output result file or - for result printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-s, --skip LINES</span><br/><div style="margin-left: 30px;">number of lines skipped from the beginning of input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-a, --anal LINES</span><br/><div style="margin-left: 30px;">number of LINES from input file to be analyzed</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-p, --pad LINES</span><br/><div style="margin-left: 30px;">number of padding LINES between used records from input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-c, --column NUM</span><br/><div style="margin-left: 30px;">NUM is the index of column to be analyzed</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-l, --start REAL</span><br/><div style="margin-left: 30px;">REAL is the left value of the histogram interval</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-r, --stop REAL</span><br/><div style="margin-left: 30px;">REAL is the right value of the histogram interval</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--nbins NUM</span><br/><div style="margin-left: 30px;">NUM is the number of histogram bins</div><span style="color:purple; margin-left: 30px;">(Default: 40)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-n, --normalize</span><br/><div style="margin-left: 30px;">normalize histogram</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of X values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fn FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of N(X) values</div><span style="color:purple; margin-left: 30px;">(Default: %15d)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fr FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of r(X) values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">do not print header to output</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:integrate}}
-Navigation: [[Documentation]] / [[Commands]] / [[integrate]]
-----
-<div style="text-align: center">integrate: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">integrate</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Integrate numerically given data by Simpson method. Program reads three numbers from input file (x coordinate, derivative, and standard deviation of derivative). As output program prints copy of input data plus integrated values and its standard error.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input data file or - for data taken from standard input</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output result file or - for result printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--offset REAL</span><br/><div style="margin-left: 30px;">specify integration constant</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-s, --skip LINES</span><br/><div style="margin-left: 30px;">number of lines skipped from the beginning of input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-a, --anal LINES</span><br/><div style="margin-left: 30px;">number of LINES from input file to be analyzed</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-p, --pad LINES</span><br/><div style="margin-left: 30px;">number of padding LINES between used records from input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--nosigma</span><br/><div style="margin-left: 30px;">standard deviation of derivative is not present in input data</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">do not print header to output</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed x values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fy FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed derivative values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed sigma values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fi FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of integrated values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of integrated error values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:pdb2fasta}}
-Navigation: [[Documentation]] / [[Commands]] / [[pdb2fasta]]
-----
-<div style="text-align: center">pdb2fasta: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">pdb2fasta</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">pdb2fasta</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Extracts FASTA sequences of all chains from PDB file.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input pdb file or - for data taken from standard input</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">output file with FASTA sequences or - for result printed to standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:propsum}}
-Navigation: [[Documentation]] / [[Commands]] / [[propsum]]
-----
-<div style="text-align: center">propsum: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">propsum</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">propsum</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Calculate total sum of value X, its average , root-mean-square deviation of X, and standard deviation of .</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">input data file or - for data taken from standard input</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-s, --skip LINES</span><br/><div style="margin-left: 30px;">number of lines skipped from the beginning of input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-a, --anal LINES</span><br/><div style="margin-left: 30px;">number of LINES from input file to be analyzed</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-p, --pad LINES</span><br/><div style="margin-left: 30px;">number of padding LINES between used records from input file</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-c, --column NUM</span><br/><div style="margin-left: 30px;">NUM is the index of column to be analyzed</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--intermediates</span><br/><div style="margin-left: 30px;">print running intermediates</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">do not print header for running intermediates</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fn FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of the number of X values</div><span style="color:purple; margin-left: 30px;">(Default: %15d)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of echoed X values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fsum FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of sum(X) values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fave FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of ave(X) values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--frmsd FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of RMSD(X) values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--fsigma FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of sigma() values</div><span style="color:purple; margin-left: 30px;">(Default: %14.6e)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-client}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-client]]
-----
-<div style="text-align: center">vs-client: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">vs-client</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">vs-client</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">svs://server[:port]/command</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Client of the server/client virtual screening infrastructure.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">svs://server[:port]/command</span><br/><div style="margin-left: 30px;">Specifies fully qualified administration request. Trasport protocol svs:// has to be always specified, which is followed by the server specification (DNS name or IP address of the server and optionally by the server port). This is followed by the command, which can be one of the following:<br /><span></span>   register   = register client on server side<br /><span></span>   unregister = unregister client on server side (unregister?id=client_id)<br /><span></span>   get        = get unprocessed structure from database (get?id=client_id,structure=file.ext[,type=xyz])<br /><span></span>   write      = write data to database and set structure as processed (write?id=client_id,molid=molecule_id[,structure=file.ext,type=log])<br /><span></span>   load       = load structure from database (load?id=client_id,molid=molecule_id[,structure=file.ext,type=xyz])<br /><span></span>   save       = save structure to database (save?id=client_id,molid=molecule_id[,structure=file.ext,type=log])<br /><span></span>   installpkg = install client package to current directory<br /><span></span>   appname    = get client application name<br /><span></span>   info       = prints information about registered clients<br /><span></span>   shutdown   = stops server execution<br /><span></span>   errors     = prints errors from the server stack<br /></div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">name of file containing server description (name, port, and password) (mutually exclusive with 'password' option)</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">name of file containing server magic word, if not specified then password is read interactively</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-project-add-structures}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-project-add-structures]]
-----
-<div style="text-align: center">svs-project-add-structures: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">svs-project-add-structures</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">svs-project-add-structures</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">structuredb</span> <span style="color: purple;">projectdb</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Initialize the project database by records from the structure database.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">structuredb</span><br/><div style="margin-left: 30px;">pathname to the structure database</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">projectdb</span><br/><div style="margin-left: 30px;">filename with the project database</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-i, --input FORMAT</span><br/><div style="margin-left: 30px;">input molecule format</div><span style="color:purple; margin-left: 30px;">(Default: xyz)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-p, --progress</span><br/><div style="margin-left: 30px;">print progress</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-u, --usehiearchy</span><br/><div style="margin-left: 30px;">use hiearchy</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-project-alter}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-project-alter]]
-----
-<div style="text-align: center">svs-project-alter: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">svs-project-alter</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">svs-project-alter</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">projectdb</span> <span style="color: purple;">command</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Alter a project setup.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">projectdb</span><br/><div style="margin-left: 30px;">filename with the project database</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">command</span><br/><div style="margin-left: 30px;">Supported commands:<br /><span></span>   softreset   = set processing items into unprocessed state<br /><span></span>   hardreset   = set all items into unprocessed state<br /><span></span>   finalizeall = set all items into processed state<br /><span></span>   addindx     = add primary index to the ID column<br /><span></span>   removeindx  = remove primary index from the ID solumn<br /><span></span>   rebuildindx = removeindx + addindx<br /><span></span>   deleteall   = delete all records from project database<br /></div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-project-create}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-project-create]]
-----
-<div style="text-align: center">svs-project-create: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">svs-project-create</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">svs-project-create</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">projectdb</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Create a new virtual screening project.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">projectdb</span><br/><div style="margin-left: 30px;">filename with the project database</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-project-info}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-project-info]]
-----
-<div style="text-align: center">svs-project-info: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">svs-project-info</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">svs-project-info</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">projectdb</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Print information about the project.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">projectdb</span><br/><div style="margin-left: 30px;">filename with the project database</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-project-sql}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-project-sql]]
-----
-<div style="text-align: center">svs-project-sql: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">svs-project-sql</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">svs-project-sql</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">[projectdb ...]</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">SQL command line interface to virtual screening projects.</p>
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-server}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-server]]
-----
-<div style="text-align: center">vs-server: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">vs-server</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">vs-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Server of the server/client virtual screening infrastructure.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">name of control file or - for data from the standard input</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:svs-split-mol}}
-Navigation: [[Documentation]] / [[Commands]] / [[svs-split-mol]]
-----
-<div style="text-align: center">mol-split: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">mol-split</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">mol-split</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">structuredb</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Split a multiple structure file into individual structures. The input file can be processed either by openbalel (--format <span style="font-style: italic;">auto</span> or user specified input format) or by a special parser (--lineentries) in the case of <span style="font-style: italic;">ssmi</span> (stream SMILE file). The format <span style="font-style: italic;">ssmi</span> contains two entries on every line. The first entry is an ID of molecule and the second entry is SMILE representation of a molecule.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">name of input file or - for input from the standard input stream</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">structuredb</span><br/><div style="margin-left: 30px;">pathname to the structure database</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-f, --informat FORMAT</span><br/><div style="margin-left: 30px;">input molecule format</div><span style="color:purple; margin-left: 30px;">(Default: auto)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-o, --outformat FORMAT</span><br/><div style="margin-left: 30px;">output molecule format</div><span style="color:purple; margin-left: 30px;">(Default: xyz)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-a, --unisID NAME</span><br/><div style="margin-left: 30px;">UNIS type (four characters) with autoindexing or 'title' for UNIS ID extracted from molecule title</div><span style="color:purple; margin-left: 30px;">(Default: UNIS)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-l, --lineentries</span><br/><div style="margin-left: 30px;">read as line entries</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-c, --createhiearchy</span><br/><div style="margin-left: 30px;">create directory hiearchy</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-d, --printduplicit</span><br/><div style="margin-left: 30px;">print IDs of duplicit molecules</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:top2delphi}}
-Navigation: [[Documentation]] / [[Commands]] / [[top2delphi]]
-----
-<div style="text-align: center">top2delphi: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">top2delphi</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">top2delphi</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">TOPOLOGY</span> <span style="color: purple;">RADII</span> <span style="color: purple;">CHARGES</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Extract radii and charges information in DELPHI format from AMBER topology.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">TOPOLOGY</span><br/><div style="margin-left: 30px;">topology name. If - is provided then topology is read from standard input stream.</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">RADII</span><br/><div style="margin-left: 30px;">radii file name</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">CHARGES</span><br/><div style="margin-left: 30px;">charges file name</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:top2params}}
-Navigation: [[Documentation]] / [[Commands]] / [[top2params]]
-----
-<div style="text-align: center">top2params: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">top2params</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">top2params</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">TOPOLOGY</span> <span style="color: purple;">PARAMS</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Extract force field information from given topology.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">TOPOLOGY</span><br/><div style="margin-left: 30px;">topology name. If - is provided then topology is read from standard input stream.</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">PARAMS</span><br/><div style="margin-left: 30px;">parameter file name. If - is provided then parameters are written to standard output stream.</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:topcharges}}
-Navigation: [[Documentation]] / [[Commands]] / [[topcharges]]
-----
-<div style="text-align: center">topcharges: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">topcharges</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">topcharges</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">TOP</span> <span style="color: purple;">OUT</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Manipulate with topology charges.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">TOP</span><br/><div style="margin-left: 30px;">topology name. If - is provided then topology is read from standard input stream.</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output file name. If - is provided then output is written to standard output stream.</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">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.</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--getcharges</span><br/><div style="margin-left: 30px;">get topology charges</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--setcharges FILE</span><br/><div style="margin-left: 30px;">set charges from FILE</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
-|}
-{{DISPLAYTITLE:topcrd2crd}}
-Navigation: [[Documentation]] / [[Commands]] / [[topcrd2crd]]
-----
-<div style="text-align: center">topcrd2crd: version 2.203.4878adb(2018-07-03 23:15) [CATs - Conversion And Analysis Tools]</div>'''Name'''
-<span style="margin-left: 15px;">topcrd2crd</span>
-'''Synopsis'''
-<span style="color: maroon; margin-left: 15px;">topcrd2crd</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">PARM</span> <span style="color: purple;">CRD</span> <span style="color: purple;">OUT</span>
-'''Description'''
-<p style="text-indent: 1em; text-align: justify;">Converts AMBER topology and coordinates to coordinates in other format.</p>
-'''Arguments'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name</div>
-|- style="vertical-align: top;"
-| <span style="color: purple;">CRD</span><br/><div style="margin-left: 30px;">input coordinates file name or - for standard input</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">OUT</span><br/><div style="margin-left: 30px;">output coordinates file name or - for standard output</div>
-|}
-'''Options'''
-{| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-i, --input FORMAT</span><br/><div style="margin-left: 30px;">specify input format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>  - amber restart file<br /><span></span>   <span style="color: green;">xyz</span>  - xyz file</div><span style="color:purple; margin-left: 30px;">(Default: crd)</span>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format for coordinates:<br /><span></span>   <span style="color: green;">crd</span>        - amber restart file<br /><span></span>   <span style="color: green;">pdb</span>        - PDB file<br /><span></span>   <span style="color: green;">pqr</span>        - PDB file with atomic radii and charges<br /><span></span>   <span style="color: green;">xyz</span>        - xyz file<br /><span></span>   <span style="color: green;">xyzr</span>       - xyz file with atomic radii<br /><span></span>   <span style="color: green;">com</span>        - gaussian input file<br /><span></span>   <span style="color: green;">rbox</span>       - rbox format for qhull<br /><span></span>   <span style="color: green;">traj</span>       - amber trajectory file<br /><span></span>   <span style="color: green;">adf</span>        - plain ADF input<br /><span></span>   <span style="color: green;">adffrag</span>    - plain ADF input with one fragment<br /><span></span>   <span style="color: green;">adf3drism</span>  - plain ADF input for 3D-RISM</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-m, --mask MASK</span><br/><div style="margin-left: 30px;">only atoms selected according to MASK will be converted. Mutually exclusive with 'maskfile' option.</div>
-|- style="vertical-align: top;"
-|<span style="color: blue;">-f, --maskfile MASKFILE</span><br/><div style="margin-left: 30px;">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.</div>
 |- style="vertical-align: top; background-color: #e6e6e6;"
 |<span style="color: blue;">-t, --mangle FORMAT</span><br/><div style="margin-left: 30px;">specify atom names mangling scheme:<br /><span></span>   <span style="color: green;">none</span>   - no translation (1234)<br /><span></span>   <span style="color: green;">pdb</span>    - pdb scheme (4123), keep amber names<br /><span></span>   <span style="color: green;">charmm</span> - charmm name scheme (1234), mangle parm99 names</div><span style="color:purple; margin-left: 30px;">(Default: pdb)</span>

Topcrd2crd: Difference between revisions

Latest revision as of 22:32, 3 March 2020

Navigation menu

Search