ListSelection2 - Revision history

Bell: 1 revision

2014-05-26T23:33:26Z

1 revision

PietroGattiLafranconi: download link and license update

2014-05-22T16:59:19Z

download link and license update

Pyadmin: 6 revisions

2014-03-28T01:47:15Z

6 revisions

PietroGattiLafranconi at 15:45, 14 March 2013

2013-03-14T15:45:56Z

PietroGattiLafranconi at 15:44, 14 March 2013

2013-03-14T15:44:06Z

PietroGattiLafranconi at 15:42, 14 March 2013

2013-03-14T15:42:17Z

PietroGattiLafranconi at 10:49, 14 March 2013

2013-03-14T10:49:30Z

PietroGattiLafranconi: small code update

2013-03-14T10:42:14Z

small code update

PietroGattiLafranconi: small script to list the content of pymol selections

2013-03-13T17:39:30Z

small script to list the content of pymol selections

New page

= Overview =
Alternative script to [[List_Selection]] that will:
* list multiple residues once
* include water and hetatoms
* account for different chains/objects
* produce a screen/printed output

= Usage =
<source lang="python">
listselection selection, [output=N/S/P, [HOH=Y/N ]]
</source>

= Code =
<source lang="python">
from pymol import cmd, stored

def listselection (selection, output="N", HOH="Y"):
"""
usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]
"""
printedselection=""
extra=""
counter=0
sel=selection
objs=cmd.get_object_list(sel)

if HOH=="N":
sel=selection+" and not resn HOH"
extra=", without HOH"

for a in range(len(objs)):
m1=cmd.get_model(sel+" and "+objs[a])
for x in range(len(m1.atom)-1):
if m1.atom[x].resi!=m1.atom[x+1].resi:
printedselection+="%s\%s\%s\%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resi, m1.atom[x].resn)
counter+=1

print "Residues in '%s%s': %s" % (selection, extra, counter)
if output=="S": print printedselection
if output=="P":
f=open('listselection_'+selection+'.txt','w')
f.write("Residues in '%s%s': %s\n" % (selection, extra, counter))
f.write(printedselection)
f.close()
print "Results saved in listselection_%s.txt" % selection

cmd.extend('listselection',listselection)
</source>
[[Category:Script_Library|List Selection]]
[[Category:ObjSel_Scripts]]

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = script
-|download  =
+|download  = [http://dx.doi.org/10.6084/m9.figshare.1031599 figshare]
 |author    = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
-|license   = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
+|license   = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
 }}

@@ Line 27: / Line 27: @@
 <source lang="python">
 PyMOL>listselection sele, output=S, HOH=N
-Residues in 'sele, without HOH': 5
+Residues in 'sele, without HOH': 7
-P9H\A\101\ARG
+LBH/A/ARG/86
-P9H\A\102\SER
+LBH/A/ALA/87
-P9H\A\103\GLY
+LBH/A/ASP/88
-P9H\A\104\VAL
+LBH/A/GLN/89
-P9H\A\105\GLU
+LBH/A/LEU/90
 </source>
@@ Line 38: / Line 40: @@
 <source lang="python">
 PyMOL>listselection 1efa and resn LEU, output=S
-Residues in '1EFA and resn LEU': 108
+Residues in '1efa and resn LEU': 108
-efa\A\6\LEU
+efa/A/LEU/6
-efa\A\45\LEU
+efa/A/LEU/45
 [...]
-efa\C\323\LEU
+efa/C/LEU/323
-efa\C\330\LEU
+efa/C/LEU/330
 </source>

@@ Line 76: / Line 76: @@
 		for x in range(len(m1.atom)):
 			if m1.atom[x-1].resi!=m1.atom[x].resi:
-				printedselection+="%s\%s\%s\%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resi, m1.atom[x].resn)
+				printedselection+="%s/%s/%s/%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resn, m1.atom[x].resi)
 				counter+=1

← Older revision	Revision as of 23:33, 26 May 2014
(No difference)

← Older revision	Revision as of 01:47, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
 = Overview =
 Alternative script to [[List_Selection]] that will:
@@ Line 93: / Line 100: @@
 cmd.extend('listselection',listselection)
 </source>
-[[Category:Script_Library|List Selection]]
 [[Category:ObjSel_Scripts]]

@@ Line 56: / Line 56: @@
 	"""
 	usage: listselection selection, [output=N/S/P, [HOH=Y/N ]]
 	"""
 	printedselection=""

@@ Line 5: / Line 5: @@
 * account for different chains/objects
 * produce a screen/printed output
 = Usage =
@@ Line 10: / Line 11: @@
 listselection selection, [output=N/S/P, [HOH=Y/N ]]
 </source>
 = Code =
 <source lang="python">
 from pymol import cmd, stored
@@ Line 28: / Line 66: @@
 		sel=selection+" and not resn HOH"
 		extra=", without HOH"
-−
 	for a in range(len(objs)):
 		m1=cmd.get_model(sel+" and "+objs[a])
-		for x in range(len(m1.atom)-1):
+		for x in range(len(m1.atom)):
-			if m1.atom[x].resi!=m1.atom[x+1].resi:
+			if m1.atom[x-1].resi!=m1.atom[x].resi:
 				printedselection+="%s\%s\%s\%s\n" % (objs[a], m1.atom[x].chain, m1.atom[x].resi, m1.atom[x].resn)
 				counter+=1
-−
 	print "Residues in '%s%s': %s" % (selection, extra, counter)
 	if output=="S": print printedselection