D2u: Difference between revisions

Latest revision as of 22:32, 3 March 2020

Navigation: Documentation / Commands / d2u

d2u: version 2.231.418d045(2020-03-01 18:49) [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

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

@@ Line 1: / Line 1: @@
-{{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: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'''
+<div style="text-align: center">d2u: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]</div>'''Name'''
 <span style="margin-left: 15px;">d2u</span>
@@ Line 253: / Line 14: @@
 <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 />
+'''Arguments'''
+<div style="margin-left: 2em;">Arguments:<br /><span></span>   FILE1                      file to be converted or - for conversion from standard input to standard output</div>
 '''Options'''

D2u: Difference between revisions

Latest revision as of 22:32, 3 March 2020

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