PyMOL Wiki - User contributions [en]

Grepsel

2005-11-28T08:05:42Z

Gawells: A bit cleaner, fixed problems with non-greedy metacharacters

<source lang="python">
#Create named selections using regular expressions for the protein sequence

import pymol
import re

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' ,
'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}

#made this before the sequence view option, probably another way to do it now

def seqoneint(model):
pymol.stored.seq = []
cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
seq = ""
for x in pymol.stored.seq:
if aa.has_key(x):
res = aa[x]
seq = seq+res
else:
seq = seq + '-'
return seq

def grepsel(model="(all)",stretch="",prefix="",combined="0",single="1"):
'''
DESCRIPTION

Create selections matching motifs, using python regular expression syntax.
Motif is automatically converted to uppercase. Motif selections are labelled
as "prefix_motif_###", where ### is the index for the first residue of the
match. Prefix defaults to selection name. combined = 1 creates one selection
for all occurences. single = 1 creates one selection for each occurance
(the default).

USAGE

grepsel selection, motif, [prefix, [combined, [single ]]]

EXAMPLES

Create selections for all motifs matching "ESS" (selection_ESS_###,...):
grepsel selection, ess

Create selections for the PxGY motif with prefix m (m_P.CY_###,...):
grepsel selection, p.gy, m
'''

if selection == "(all)":
selection = "all"
if prefix == "":
prefix=selection

stretch = stretch.upper()
seq = seqoneint(selection)
pymol.stored.resi = []
pymol.stored.chain = []
cmd.iterate("%s and name ca"%selection,"stored.resi.append(resi);stored.chain.append(chain)")
motif = re.compile(stretch)
occurrences = motif.finditer(seq)
stretchmod = stretch.replace("+","\+")
stretchmod = stretchmod.replace("?","\?")

print stretchmod
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch), "none")

for find in occurrences:

mb = pymol.stored.resi[find.start()]
me = pymol.stored.resi[find.end()-1]

ch = pymol.stored.chain[find.start()]
cmd.select("%s_%s_%s%s"%(prefix,stretch,me,ch), "chain %s and (i; %s-%s)"%(ch,int(mb),int(me)))
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch),"\"%s_%s\" | (%s and chain %s and (i; %s-%s))"%(prefix,stretchmod,selection,ch,int(mb),int(me)))

cmd.select("none")
cmd.delete("sel*")

cmd.extend("grepsel",grepsel)
</source>

[[Category:Script_Library|Grep selections]]

Grepsel

2005-11-28T08:01:39Z

Gawells:

<source lang="python">
#Create named selections using regular expressions for the protein sequence

import pymol
import re

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' ,
'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}

#made this before the sequence view option, probably another way to do it now

def seqoneint(model):
pymol.stored.seq = []
cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
seq = ""
for x in pymol.stored.seq:
if aa.has_key(x):
res = aa[x]
seq = seq+res
else:
seq = seq + '-'
return seq

def grepsel(model="(all)",stretch="",prefix="",combined="0",single="1"):
'''
DESCRIPTION
Create selections matching motifs, using python regular expression syntax.
Motif is automatically converted to uppercase. Motif selections are labelled
as "prefix_motif_###", where ### is the index for the first residue of the
match. Prefix defaults to selection name. combined = 1 creates one selection
for all occurences. single = 1 creates one selection for each occurance
(the default).

USAGE

grepsel selection, expression, [prefix, [combined, [single ]]]

EXAMPLES

Make selections for all motifs matching "ESS" (model_ESS_###,...):
grepsel model, ess

Make selections for the PxGY motif with prefix m (m_P.CY_###,...):
grepsel model, p.gy, m

'''

if selection == "(all)":
selection = "all"
if prefix == "":
prefix=selection

stretch = stretch.upper()
seq = seqoneint(selection)
pymol.stored.resi = []
pymol.stored.chain = []
cmd.iterate("%s and name ca"%selection,"stored.resi.append(resi);stored.chain.append(chain)")
motif = re.compile(stretch)
occurrences = motif.finditer(seq)
stretchmod = stretch.replace("+","\+")
stretchmod = stretchmod.replace("?","\?")

print stretchmod
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch), "none")

for find in occurrences:

mb = pymol.stored.resi[find.start()]
me = pymol.stored.resi[find.end()-1]

ch = pymol.stored.chain[find.start()]
cmd.select("%s_%s_%s%s"%(prefix,stretch,me,ch), "chain %s and (i; %s-%s)"%(ch,int(mb),int(me)))
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch),"\"%s_%s\" | (%s and chain %s and (i; %s-%s))"%(prefix,stretchmod,selection,ch,int(mb),int(me)))

cmd.select("none")
cmd.delete("sel*")

cmd.extend("grepsel",grepsel)
</source>

[[Category:Script_Library|Grep selections]]

Grepsel

2005-09-10T10:24:37Z

Gawells: fixed selection from "chainless" models

<source lang="python">
#Create named selections using regular expressions for the protein sequence

import pymol
import re

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' ,
'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}

#made this before the sequence view option, probably another way to do it now

def seqoneint(model):
pymol.stored.seq = []
cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
seq = ""
for x in pymol.stored.seq:
if aa.has_key(x):
res = aa[x]
seq = seq+res
else:
seq = seq + '-'
return seq

def grepsel(model="(all)",stretch="",prefix="",combined="0",single="1"):
'''
DESCRIPTION

Make selections matching regular expressions. Selections are labelled
as "prefix_expression_###", where ### is the index for the first residue
of the match. Prefix defaults to model name. combined = 1 creates one
selection for all occurences. single = 1 creates one selection for each
occurance (the default).

USAGE

grepsel selection, expression, [prefix, [combined, [single ]]]

EXAMPLES

Make selections for all motifs matching "ESS" (model_ESS_###,...):
grepsel model, ess

Make selections for the PxGY motif with prefix m (m_P.CY_###,...):
grepsel model, p.gy, m

'''

if model == "(all)":
model = "all"
if prefix == "":
prefix=model

stretch = stretch.upper()
seq = seqoneint(model)
pymol.stored.resi = []
pymol.stored.chain = []
cmd.iterate("%s and name ca"%model,"stored.resi.append(resi);stored.chain.append(chain)")
motif = re.compile(stretch)
occurrences = motif.finditer(seq)
if combined == "1":
cmd.do("select %s_%s, none"%(prefix,stretch))

for match in occurrences:
fx = match.start()
pos = 0
for fy in range(int(fx),int(fx)+len(stretch)):
ch = pymol.stored.chain[fy]
ri = pymol.stored.resi[fy]
if pos == 0:
pos = ri
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "none")
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "%s_%s_%s%s | ///%s/%s/"%(prefix,stretch,pos,ch,ch,ri))
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch), "%s_%s | ////%s/"%(prefix,stretch,ri))
cmd.select("none")
cmd.delete("sel*")

cmd.extend("grepsel",grepsel)
</source>

[[Category:Script_Library|Grep selections]]

Category:Script Library

2005-07-20T16:15:14Z

Gawells:

* [[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)

* [[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]]

Grepsel

2005-07-20T16:11:33Z

Gawells:

<source lang="python">
#Create named selections using regular expressions for the protein sequence

import pymol
import re

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' ,
'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}

#made this before the sequence view option, probably another way to do it now

def seqoneint(model):
pymol.stored.seq = []
cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
seq = ""
for x in pymol.stored.seq:
if aa.has_key(x):
res = aa[x]
seq = seq+res
else:
seq = seq + '-'
return seq

def grepsel(model="(all)",stretch="",prefix="",combined="0",single="1"):
'''
DESCRIPTION

Make selections matching regular expressions. Selections are labelled
as "prefix_expression_###", where ### is the index for the first residue
of the match. Prefix defaults to model name. combined = 1 creates one
selection for all occurences. single = 1 creates one selection for each
occurance (the default).

USAGE

grepsel selection, expression, [prefix, [combined, [single ]]]

EXAMPLES

Make selections for all motifs matching "ESS" (model_ESS_###,...):
grepsel model, ess

Make selections for the PxGY motif with prefix m (m_P.CY_###,...):
grepsel model, p.gy, m

'''

if model == "(all)":
model = "all"
if prefix == "":
prefix=model

stretch = stretch.upper()
seq = seqoneint(model)
pymol.stored.resi = []
pymol.stored.chain = []
cmd.iterate("%s and name ca"%model,"stored.resi.append(resi);stored.chain.append(chain)")
motif = re.compile(stretch)
occurrences = motif.finditer(seq)
if combined == "1":
cmd.do("select %s_%s, none"%(prefix,stretch))

for match in occurrences:
fx = match.start()
pos = 0
for fy in range(int(fx),int(fx)+len(stretch)):
ch = pymol.stored.chain[fy]
ri = pymol.stored.resi[fy]
if pos == 0:
pos = ri
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "none")
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "%s_%s_%s%s | %s/%s/"%(prefix,stretch,pos,ch,ch,ri))
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch), "%s_%s | %s//"%(prefix,stretch,ri))
cmd.select("none")
cmd.delete("sel*")

cmd.extend("grepsel",grepsel)
</source>

[[Category:Script_Library|Grep selections]]

Grepsel

2005-07-20T16:09:54Z

Gawells:

<source lang="python">
#Create named selections using regular expressions for the protein sequence

import pymol
import re

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' ,
'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}

#made this before the sequence view option, probably another way to do it now

def seqoneint(model):
pymol.stored.seq = []
cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
seq = ""
for x in pymol.stored.seq:
if aa.has_key(x):
res = aa[x]
seq = seq+res
else:
seq = seq + '-'
return seq

def grepsel(model="(all)",stretch="",prefix="",combined="0",single="1"):
'''
DESCRIPTION

Make selections matching regular expressions. Selections are labelled
as "prefix_expression_###", where ### is the index for the first residue
of the match. Prefix defaults to model name. combined = 1 creates one
selection for all occurences. single = 1 creates one selection for each
occurance (the default).

USAGE

grepsel selection, expression, [prefix, [combined, [single ]]]

EXAMPLES

Make selections for all motifs matching "ESS" (model_ESS_###,...):
grepsel model, ess

Make selections for the PxGY motif with prefix m (m_P.CY_###,...):
grepsel model, p.gy, m

'''

if model == "(all)":
model = "all"
if prefix == "":
prefix=model

stretch = stretch.upper()
seq = seqoneint(model)
pymol.stored.resi = []
pymol.stored.chain = []
cmd.iterate("%s and name ca"%model,"stored.resi.append(resi);stored.chain.append(chain)")
motif = re.compile(stretch)
occurrences = motif.finditer(seq)
if combined == "1":
cmd.do("select %s_%s, none"%(prefix,stretch))

for match in occurrences:
fx = match.start()
pos = 0
for fy in range(int(fx),int(fx)+len(stretch)):
ch = pymol.stored.chain[fy]
ri = pymol.stored.resi[fy]
if pos == 0:
pos = ri
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "none")
if single == "1":
cmd.select("%s_%s_%s%s"%(prefix,stretch,pos,ch), "%s_%s_%s%s | %s/%s/"%(prefix,stretch,pos,ch,ch,ri))
if combined == "1":
cmd.select("%s_%s"%(prefix,stretch), "%s_%s | %s//"%(prefix,stretch,ri))
cmd.select("none")
cmd.delete("sel*")

cmd.extend("grepsel",grepsel)
</source>

[[Category:Script_Library|grep selections]]