PyMOL Wiki - User contributions [en]

Apropos

2006-07-20T11:23:35Z

Zac:

'''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:
run apropos.py

3. see example bellow on how to use it

'''USAGE'''
apropos [keyword or regexp]

'''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.groups()[0]
matches_with_help.append( (cc, desc ) )

if len(matches_without_help) > 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)

if len(matches_with_help) > 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)

cmd.extend('apropos',apropos)

</source>

''Author: Ezequiel (Zac) Panepucci''

[[Category:Script_Library|Apropos]]

Apropos

2006-07-20T10:07:59Z

Zac:

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''
<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

<source lang="python">
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.groups()[0]
matches_with_help.append( (cc, desc ) )

if len(matches_without_help) > 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)

if len(matches_with_help) > 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)

cmd.extend('apropos',apropos)

</source>

''Author: Ezequiel (Zac) Panepucci''

[[Category:Script_Library|Apropos]]

Apropos

2006-07-20T10:06:57Z

Zac:

Apropos

2006-07-20T10:03:39Z

Zac: new entry in library

Category:Script Library

2006-07-20T10:02:11Z

Zac:

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

[[Category:Scripting|Script Library]]

Category:Script Library

2005-11-14T09:29:50Z

Zac: removed broken link

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

[[Category:Scripting|Script Library]]

Category:Script Library

2005-06-17T15:22:29Z

Zac:

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[disconnect]] -- unbond a single atom from its neighbors. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

[[Category:Scripting|Script Library]]

Category:Script Library

2005-05-26T08:02:59Z

Zac:

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[disconnect]] -- unbond a single atom from its neighbors. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

[[Category:Scripting|Script Library]]

Selection Algebra

2005-05-23T15:27:47Z

Zac: /* Selection Operator/Modifier Table */

==Selection Algebra==
===Intro===
Selections can be made more precise or inclusive by combining them with logical operators, including the boolean '''and''', '''or''', and '''not'''. The boolean '''and''' selects only those items that have both (or all) of the named properties, and the boolean '''or''' selects items that have either (or any) of them. Venn diagrams show that '''and ''' selects the areas of overlap, while '''or''' selects both areas.

http://pymol.sourceforge.net/newman/user/S0220venn.jpg

===Selection Operator/Modifier Table===
Selection operators and modifiers are listed below. The dummy variables ''s1'' and ''s2'' stand for selection-expressions such as "chain a" or "hydro."

<TABLE BORDER="1">
<TR><TH ALIGN="CENTER" WIDTH="100">Operator</TH><TH>Short form</TH>
<TH>Effect</TH>
</TR>
<TR><TD ALIGN="CENTER">nots1</TD>
<TD ALIGN="CENTER">!s1</TD>
<TD>Selects atoms that are not included in s1
<pre>PyMOL> select sidechains, ! bb</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 and s2</TD>
<TD ALIGN="CENTER"> s1 & s2</TD>
<TD>Selects atoms included in both s1 and s2
<pre>PyMOL> select far_bb, bb &farfrm_ten</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 or s2</TD>
<TD ALIGN="CENTER"> s1 | s2</TD><TD>Selects atoms included in either s1 or s2
<pre>PyMOL> select all_prot, bb | sidechain</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 in s2</TD>
<TD ALIGN="CENTER"> s1 in s2</TD><TD>Selects atoms in s1 whose
identifiers name, resi, resn, chain and segi all match atoms in s2
<pre>PyMOL> select same_atms, pept in prot</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 like s2</TD><TD ALIGN="CENTER"> s1 l. s2</TD><TD>Selects atoms in s1 whose identifiers name and resi match atoms in s2
<pre>PyMOL> select similar_atms, pept like prot</pre>

</TD></TR>
<TR><TD ALIGN="CENTER"> s1 gap X</TD>
<TD ALIGN="CENTER"> s1 gap X</TD><TD>Selects all atoms whose van der Waals radii are separated from the van der Waals radii of s1 by a minimum of X Angstroms.
<pre>PyMOL> select farfrm_ten, resi 10 gap 5</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 around X</TD>
<TD ALIGN="CENTER"> s1 a. X</TD><TD>Selects atoms with centers within X Angstroms of the center of any atom in s1
<pre>PyMOL> select near_ten, resi 10 around 5</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> s1 expand X
</TD><TD ALIGN="CENTER"> s1 e. X</TD><TD>Expands s1 by all atoms within X Angstroms of the center of any atom in s1
<pre>PyMOL> select near_ten_x, near10 expand 3</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">  s1 within X of s2 </TD>
<TD ALIGN="CENTER"> s1 w. X of s2 </TD><TD>Selects atoms in s1 that are within X Angstroms of the s2
<pre>PyMOL> select bbnearten, bb w. 4 of resi 10</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">byres s1</TD>
<TD ALIGN="CENTER">br. s1</TD><TD>Expands selection to complete residues
<pre>PyMOL> select complete_res, br. bbnear10</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">byobject s1</TD>
<TD ALIGN="CENTER">bo. s1</TD><TD>Expands selection to complete objects>
<pre>PyMOL> select near_obj, bo. near_res</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">neighbor s1</TD>
<TD ALIGN="CENTER">nbr. s1</TD><TD>Selects atoms directly bonded to s1
<pre>PyMOL> select vicinos, neighbor resi 10</pre>
</TD></TR>
</TABLE>

===Examples===
Logical selections can be combined. For example, you might select atoms that are part of chain a, but not residue number 125:

<pre>
PyMOL> select chain a and (not resi 125) # selects atoms that are part of
# chain a, but not
# residue number 125.

PyMOL> select (name cb or name cg1 or name cg2) and chain A # These two
# selections are
PyMOL> select name cb+cg1+cg2 and chain A # equivalent.
# select c-beta's,
# c-gamma-1's and
# c-gamma-2's
# that are
# in chain A.
</pre>

Like the results of groups of arithmetic operations, the results of groups of logical operations depend on which operation is performed first. They have an order of precedence. To ensure that the operations are performed in the order you have in mind, use parentheses:

<pre> byres ((chain a or (chain b and (not resi 125))) around 5) </pre>

PyMOL will expand its logical selection out from the innermost parentheses.

[[Category:Selector Quick Reference]]

[[Category:Making Selections]]

Grepset

2005-04-23T14:42:43Z

Zac:

Use this little script to explore PyMOL's myriad settings.

Usefull for newbies and those with not so good memory skills...

To use:

# put the script in a file called '''grepset.py'''
# from within PyMOL execute '''run grepset.py'''
# try it out, see examples below.

Example 1: '''grepset light'''
<pre>
cartoon_highlight_color default
dot_lighting on
light [ -0.40000, -0.40000, -1.00000 ]
mesh_lighting off
two_sided_lighting off
5 settings matched
</pre>

Example 2: '''grepset trans'''
<pre>
cartoon_transparency 0.00000
ray_transparency_contrast 1.00000
ray_transparency_shadows 1
ray_transparency_spec_cut 0.90000
ray_transparency_specular 0.40000
sphere_transparency 0.00000
stick_transparency 0.00000
transparency 0.00000
transparency_mode 2
transparency_picking_mode 2
10 settings matched
</pre>

Example 3: '''grepset ^trans'''
<pre>
transparency 0.00000
transparency_mode 2
transparency_picking_mode 2
3 settings matched
</pre>

== The Script itself: grepset.py ==
<source lang="python">
from pymol import cmd
import pymol.setting

def grepset(regexp=''):
'''
DESCRIPTION
"grepset" greps through the list of settings using a python
regular expression as defined in the 're' module.
It returns a list of settings/values matching the regexp.
No regexp returns every setting.

USAGE
grepset [regexp]

EXAMPLE
grepset line
grepset ray

SEE ALSO
Python re module
'''

from re import compile

count=0
regexp=compile(regexp)
for a in pymol.setting.get_index_list():
setting=pymol.setting._get_name(a)
if regexp.search(setting):
count = count + 1
print '%-30s %s' % (setting, cmd.get_setting_text(a,'',-1))

print '%d settings matched' % count
cmd.extend('grepset',grepset)

</source>

''Author: Ezequiel (Zac) Panepucci''

[[Category:Scripting_Script_Library|grepset]]

Grepset

2005-04-18T15:14:01Z

Zac:

Grepset

2005-04-18T15:11:48Z

Zac:

Grepset

2005-04-18T15:05:18Z

Zac:

Use this little script to explore PyMOL's myriad settings.

Usefull for newbies and those with not so good memory skills...

Example 1: '''grepset light'''
<pre>
cartoon_highlight_color default
dot_lighting on
light [ -0.40000, -0.40000, -1.00000 ]
mesh_lighting off
two_sided_lighting off
5 settings matched
</pre>

Example 2: '''grepset trans'''
<pre>
cartoon_transparency 0.00000
ray_transparency_contrast 1.00000
ray_transparency_shadows 1
ray_transparency_spec_cut 0.90000
ray_transparency_specular 0.40000
sphere_transparency 0.00000
stick_transparency 0.00000
transparency 0.00000
transparency_mode 2
transparency_picking_mode 2
10 settings matched
</pre>

Example 3: '''grepset ^trans'''
<pre>
transparency 0.00000
transparency_mode 2
transparency_picking_mode 2
3 settings matched
</pre>

<source lang="python">
from pymol import cmd
import pymol.setting

def grepset(regexp=''):
'''
DESCRIPTION
"grepset" greps through the list of settings using a python
regular expression as defined in the 're' module.
It returns a list of settings/values matching the regexp.
No regexp returns every setting.

USAGE
grepset [regexp]

EXAMPLE
grepset line
grepset ray

SEE ALSO
Python re module
'''

from re import compile

count=0
regexp=compile(regexp)
for a in pymol.setting.get_index_list():
setting=pymol.setting._get_name(a)
if regexp.search(setting):
count = count + 1
print '%-30s %s' % (setting, cmd.get_setting_text(a,'',-1))

print '%d settings matched' % count
cmd.extend('grepset',grepset)

</source>

XFree86 Configuration

2005-02-17T09:59:15Z

Zac:

== Iiyama HM204DT + Nvidia Quadro FX 1100 on Fedora Core 2 (updated as of 2005-02-17) ==

<code>
Section "Module"
Load "dbe"
Load "extmod"
Load "fbdevhw"
Load "glx"
Load "record"
Load "freetype"
Load "type1"
#Load "dri" # THIS MUST BE COMMENTED OUT
EndSection

Section "Monitor"
Identifier "hm204dt"
VendorName "Iiyama"
ModelName "HM204DT"
HorizSync 30 - 142
VertRefresh 50 - 200
Option "dpms"

# 1400x1100 @ 120.00 Hz (GTF) hsync: 141.48 kHz; pclk: 275.04 MHz
Modeline "1400x1100_120" 275.04 1400 1520 1672 1944 1100 1101 1104 1179 -HSync +Vsync
EndSection

Section "Device"
Identifier "quadrofx"
Driver "nvidia"
VendorName "PNY"
BoardName "NVIDIA Quadro FX 1100"
Option "AllowDFPStereo" "true"
Option "Stereo" "3"
EndSection

Section "Screen"
Identifier "Screen0"
Device "quadrofx"
Monitor "hm204dt"
DefaultDepth 24
SubSection "Display"
Viewport 0 0
Depth 24
Modes "1400x1100_120" "1280x1024"
EndSubSection
EndSection
</code>