Apropos - Revision history

Cchem: 1 revision

2019-03-04T03:58:18Z

1 revision

Speleo3: psico

2019-02-25T10:39:24Z

psico

Pyadmin: 7 revisions

2014-03-28T01:31:03Z

7 revisions

Newacct at 06:59, 23 December 2009

2009-12-23T06:59:13Z

New page

'''DESCRIPTION'''

"apropos" searches through the documentation of all currently defined commands and lists those commands for which the keyword is either contained in the documentation or matches the command name itself.

If an appropriate '''DESCRIPTION''' section is provided in the documentation of the command, the first 80 characters are listed as a summary.

'''INSTALLATION'''

1. copy the script bellow to a folder and name it ''apropos.py''

2. run it from within pymol with the '''run''' command:
<source lang="python">
run apropos.py
</source>

3. see example bellow on how to use it

'''USAGE'''
<source lang="python">
apropos [keyword or regexp]
</source>

'''EXAMPLE'''

''apropos fit''
<pre>
###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.

###The following commands are NOT documented.

vdw_fit

###The following commands are documented. 'help command'

fit : "fit" superimposes the model in the first selection on to the model
intra_fit : "intra_fit" fits all states of an object to an atom selection
rms : "rms" computes a RMS fit between two atom selections, but does not
pair_fit : "pair_fit" fits a set of atom pairs between two models. Each atom
intra_rms_cur : "intra_rms_cur" calculates rms values for all states of an object
commands : >>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<
zoom : "zoom" scales and translates the window and the origin to cover the
intra_rms : "intra_rms" calculates rms fit values for all states of an object
align : "align" performs a sequence alignment followed by a structural
rms_cur : "rms_cur" computes the RMS difference between two atom
fitting : "fitting" allows the superpositioning of object1 onto object2 using
</pre>

'''SEE ALSO'''
grepset(www.pymolwiki.org), Python re module

'''apropos.py'''
<source lang="python">
#
# apropos.py
# Author: Ezequiel Panepucci
# Date: 2006-07-20
#
from pymol import cmd
import re

def apropos(regexp=''):
'''
DESCRIPTION
"apropos" searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.

If an appropriate "DESCRIPTION" section is provided in the documentation
of the command, the first 80 characters are listed as a summary.

USAGE
apropos [keyword or regexp]

EXAMPLE
apropos fit

###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.

###The following commands are NOT documented.

vdw_fit

###The following commands are documented. 'help command'

fit : "fit" superimposes the model in the first selection on to the model
intra_fit : "intra_fit" fits all states of an object to an atom selection
rms : "rms" computes a RMS fit between two atom selections, but does not
pair_fit : "pair_fit" fits a set of atom pairs between two models. Each atom
intra_rms_cur : "intra_rms_cur" calculates rms values for all states of an object
commands : >>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<
zoom : "zoom" scales and translates the window and the origin to cover the
intra_rms : "intra_rms" calculates rms fit values for all states of an object
align : "align" performs a sequence alignment followed by a structural
rms_cur : "rms_cur" computes the RMS difference between two atom
fitting : "fitting" allows the superpositioning of object1 onto object2 using

SEE ALSO
grepset(www.pymolwiki.org), Python re module
'''
cmd.set("text","1",quiet=1)

count=0
docre = re.compile(regexp, re.MULTILINE | re.IGNORECASE)
cmdre = re.compile(regexp, re.IGNORECASE)

matches_with_help = []
matches_without_help = []

maxcclen=0
for cc in cmd.keyword:
if cc == regexp:
print '\n###EXACT MATCH FOR: %s ==> try \'help %s\' at the prompt.' % (cc,cc)

doc = cmd.keyword[cc][0].__doc__

if doc == None:
if re.search(regexp, cc, re.IGNORECASE):
count += 1
matches_without_help.append(cc)
continue

if re.search(regexp, doc, re.MULTILINE | re.IGNORECASE):
count += 1
if len(cc) > maxcclen:
maxcclen = len(cc)

docmatches = re.match(r"""^\s+DESCRIPTION\s+(.{0,80})\S*""", doc, re.IGNORECASE)
if docmatches == None:
desc = '>>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<'
else:
desc = docmatches.group(1)
matches_with_help.append( (cc, desc ) )

if len(matches_without_help) > 0:
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print '%*s' % (maxcclen, cc)

if len(matches_with_help) > 0:
print '\n###The following commands are documented. \'help command\' \n'
for cc,desc in matches_with_help:
print '%*s : %s' % (maxcclen, cc,desc)

cmd.extend('apropos',apropos)

</source>

''Author: Ezequiel (Zac) Panepucci''

[[Category:Script_Library|Apropos]]
[[Category:UI_Scripts]]

Zac at 11:23, 20 July 2006

2006-07-20T11:23:35Z

Zac at 10:07, 20 July 2006

2006-07-20T10:07:59Z

Zac at 10:06, 20 July 2006

2006-07-20T10:06:57Z

Zac: new entry in library

2006-07-20T10:03:39Z

new entry in library

New page

DESCRIPTION
"apropos" searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.

If an appropriate "DESCRIPTION" section is provided in the documentation
of the command, the first 80 characters are listed as a summary.

USAGE
apropos [keyword or regexp]

EXAMPLE
apropos fit

###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.

###The following commands are NOT documented.

vdw_fit

###The following commands are documented. 'help command'

fit : "fit" superimposes the model in the first selection on to the model
intra_fit : "intra_fit" fits all states of an object to an atom selection
rms : "rms" computes a RMS fit between two atom selections, but does not
pair_fit : "pair_fit" fits a set of atom pairs between two models. Each atom
intra_rms_cur : "intra_rms_cur" calculates rms values for all states of an object
commands : >>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<
zoom : "zoom" scales and translates the window and the origin to cover the
intra_rms : "intra_rms" calculates rms fit values for all states of an object
align : "align" performs a sequence alignment followed by a structural
rms_cur : "rms_cur" computes the RMS difference between two atom
fitting : "fitting" allows the superpositioning of object1 onto object2 using

SEE ALSO
grepset(www.pymolwiki.org), Python re module

← Older revision		Revision as of 10:39, 25 February 2019
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		+	{{Infobox psico
		+	\|module = psico.helping
		+	}}
		+
	'''DESCRIPTION'''		'''DESCRIPTION'''

← Older revision	Revision as of 03:58, 4 March 2019
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← Older revision	Revision as of 01:31, 28 March 2014
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@@ Line 1: / Line 1: @@
-DESCRIPTION
+'''DESCRIPTION'''
 "apropos" searches through the documentation of all currently defined commands and lists those commands for which the keyword is either contained in the documentation or matches the command name itself.
@@ Line 5: / Line 5: @@
 If an appropriate '''DESCRIPTION''' section is provided in the documentation of the command, the first 80 characters are listed as a summary.
-USAGE
+'''INSTALLATION'''
          apropos [keyword or regexp]
-EXAMPLE
+'''EXAMPLE'''
 ''apropos fit''
@@ Line 33: / Line 43: @@
 </pre>
-SEE ALSO
+'''SEE ALSO'''
      grepset(www.pymolwiki.org), Python re module
+'''apropos.py'''
 <source lang="python">
 from pymol import cmd
 import re

← Older revision		Revision as of 10:07, 20 July 2006
Line 131:		Line 131:

	</source>		</source>
		+
		+	''Author: Ezequiel (Zac) Panepucci''
		+
		+	[[Category:Script_Library\|Apropos]]