Sidechaincenters - Revision history

Bell: 9 revisions

2014-03-28T03:53:33Z

9 revisions

Tlinnet at 20:17, 13 December 2011

2011-12-13T20:17:39Z

Speleo3: figure added

2011-02-22T19:12:13Z

figure added

New page

[[File:SidechaincentersExample.png|400px|thumb|right|sidechain centers]]

Pseudo single-atom representation of sidechains. Usefull for [[AAindex|pair potential calculation]] for example.

= Example =

<source lang="python">
fetch 2x19
sidechaincenters scc, 2x19
</source>

= The Script =

<source lang="python">
'''
(c) 2010 Thomas Holder
'''

from pymol import cmd
from chempy import Atom, cpv, models

sidechaincenteratoms = {
'GLY': ('CA',),
'ALA': ('CB',),
'VAL': ('CG1', 'CG2'),
'ILE': ('CD1',),
'LEU': ('CD1', 'CD2'),
'SER': ('OG',),
'THR': ('OG1', 'CG2'),
'ASP': ('OD1', 'OD2'),
'ASN': ('OD1', 'ND2'),
'GLU': ('OE1', 'OE2'),
'GLN': ('OE1', 'NE2'),
'LYS': ('NZ',),
'ARG': ('NE', 'NH1', 'NH2'),
'CYS': ('SG',),
'MET': ('SD',),
'MSE': ('SE',),
'PHE': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'),
'TYR': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OH'),
'TRP': ('CG', 'CD1', 'CD2', 'NE1', 'CE2', 'CE3', 'CZ2', 'CZ3'),
'HIS': ('CG', 'ND1', 'CD2', 'CE1', 'NE2'),
'PRO': ('CB', 'CG', 'CD'),
}

def sidechaincenters(object='scc', selection='all', name='PS1', method='bahar1996'):
'''
DESCRIPTION

Creates an object with sidechain representing pseudoatoms for each residue
in selection.

Sidechain interaction centers as defined by Bahar and Jernigan 1996
http://www.ncbi.nlm.nih.gov/pubmed/9080182

USAGE

sidechaincenters object [, selection]

ARGUMENTS

object = string: name of object to create

selection = string: atoms to consider {default: (all)}

name = string: atom name of pseudoatoms {default: PS1}

SEE ALSO

sidechaincentroids, pseudoatom
'''
atmap = dict()
if method == 'bahar1996':
modelAll = cmd.get_model('(%s) and resn %s' % (selection, '+'.join(sidechaincenteratoms)))
for at in modelAll.atom:
if at.name in sidechaincenteratoms[at.resn]:
atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
elif method == 'centroid':
modelAll = cmd.get_model('(%s) and not (hydro or name C+N+O)' % selection)
for at in modelAll.atom:
atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
else:
print 'Error: unknown method:', method
return

model = models.Indexed()
for centeratoms in atmap.itervalues():
center = cpv.get_null()
for at in centeratoms:
center = cpv.add(center, at.coord)
center = cpv.scale(center, 1./len(centeratoms))
atom = Atom()
atom.coord = center
atom.index = model.nAtom + 1
atom.name = name
for key in ['resn','chain','resi','resi_number','hetatm','ss','segi']:
atom.__dict__[key] = at.__dict__[key]
model.add_atom(atom)
model.update_index()
if object in cmd.get_object_list():
cmd.delete(object)
cmd.load_model(model, object)
return model

def sidechaincentroids(object='scc', selection='all', name='PS1'):
'''
DESCRIPTION

Sidechain centroids. Works like "sidechaincenters", but the
pseudoatom is the centroid of all atoms except hydrogens and backbone atoms
(N, C and O).

NOTE

If you want to exclude C-alpha atoms from sidechains, modify the selection
like in this example:

sidechaincentroids newobject, all and (not name CA or resn GLY)

SEE ALSO

sidechaincenters
'''
return sidechaincenters(object, selection, name, method='centroid')

cmd.extend('sidechaincenters', sidechaincenters)
cmd.extend('sidechaincentroids', sidechaincentroids)

cmd.auto_arg[1].update({
'sidechaincenters' : [ cmd.selection_sc , 'selection' , '' ],
'sidechaincentroids' : [ cmd.selection_sc , 'selection' , '' ],
})

# vi: ts=4:sw=4:smarttab:expandtab
</source>

[[Category:Plugins]]
[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]

Speleo3: example fix

2010-11-25T17:49:04Z

example fix

Speleo3: categories

2010-11-25T17:37:37Z

Speleo3: auto_arg update

2010-11-25T17:28:13Z

auto_arg update

Speleo3: drop "pseudo_" prefix

2010-11-25T17:22:45Z

drop "pseudo_" prefix

Speleo3 at 15:36, 25 November 2010

2010-11-25T15:36:03Z

Speleo3: created

2010-11-25T15:35:19Z

created

New page

Pseudo single-atom representation of sidechains. Usefull for [[AAindex|pair potential calculation]] for example.

= Example =

<source lang="python">
fetch 2x19
pseudo_sidechaincenters scc, 2x19
</source>

= The Script =

<source lang="python">
'''
(c) 2010 Thomas Holder
'''

from pymol import cmd
from chempy import Atom, cpv, models

sidechaincenteratoms = {
'GLY': ('CA',),
'ALA': ('CB',),
'VAL': ('CG1', 'CG2'),
'ILE': ('CD1',),
'LEU': ('CD1', 'CD2'),
'SER': ('OG',),
'THR': ('OG1', 'CG2'),
'ASP': ('OD1', 'OD2'),
'ASN': ('OD1', 'ND2'),
'GLU': ('OE1', 'OE2'),
'GLN': ('OE1', 'NE2'),
'LYS': ('NZ',),
'ARG': ('NE', 'NH1', 'NH2'),
'CYS': ('SG',),
'MET': ('SD',),
'MSE': ('SE',),
'PHE': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'),
'TYR': ('CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OH'),
'TRP': ('CG', 'CD1', 'CD2', 'NE1', 'CE2', 'CE3', 'CZ2', 'CZ3'),
'HIS': ('CG', 'ND1', 'CD2', 'CE1', 'NE2'),
'PRO': ('CB', 'CG', 'CD'),
}

def pseudo_sidechaincenters(object='scc', selection='all', name='PS1', method='bahar1996'):
'''
DESCRIPTION

Creates an object with sidechain representing pseudoatoms for each residue
in selection.

Sidechain interaction centers as defined by Bahar and Jernigan 1996
http://www.ncbi.nlm.nih.gov/pubmed/9080182

USAGE

pseudo_sidechaincenters object [, selection]

ARGUMENTS

object = string: name of object to create

selection = string: atoms to consider {default: (all)}

name = string: atom name of pseudoatoms {default: PS1}

SEE ALSO

pseudo_sidechaincentroids, pseudoatom
'''
atmap = dict()
if method == 'bahar1996':
modelAll = cmd.get_model('(%s) and resn %s' % (selection, '+'.join(sidechaincenteratoms)))
for at in modelAll.atom:
if at.name in sidechaincenteratoms[at.resn]:
atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
elif method == 'centroid':
modelAll = cmd.get_model('(%s) and not (hydro or name C+N+O)' % selection)
for at in modelAll.atom:
atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
else:
print 'Error: unknown method'
return

model = models.Indexed()
for centeratoms in atmap.itervalues():
center = cpv.get_null()
for at in centeratoms:
center = cpv.add(center, at.coord)
center = cpv.scale(center, 1./len(centeratoms))
atom = Atom()
atom.coord = center
atom.index = model.nAtom + 1
atom.name = name
for key in ['resn','chain','resi','resi_number','hetatm','ss','segi']:
atom.__dict__[key] = at.__dict__[key]
model.add_atom(atom)
model.update_index()
if object in cmd.get_object_list():
cmd.delete(object)
cmd.load_model(model, object)
return model

def pseudo_sidechaincentroids(object='scc', selection='all', name='PS1'):
'''
DESCRIPTION

Sidechain centroids. Works like "pseudo_sidechaincenters", but the
pseudoatom is the centroid of all atoms except hydrogens and backbone atoms
(N, C and O).

NOTE

If you want to exclude C-alpha atoms from sidechains, modify the selection
like in this example:

pseudo_sidechaincentroids newobject, all and (not name CA or resn GLY)

SEE ALSO

pseudo_sidechaincenters
'''
return pseudo_sidechaincenters(object, selection, name, method='centroids')

cmd.extend('pseudo_sidechaincenters', pseudo_sidechaincenters)
cmd.extend('pseudo_sidechaincentroids', pseudo_sidechaincentroids)

# vi: ts=4:sw=4:smarttab:expandtab
</script>

← Older revision		Revision as of 15:36, 25 November 2010
Line 126:		Line 126:

	# vi: ts=4:sw=4:smarttab:expandtab		# vi: ts=4:sw=4:smarttab:expandtab
−	</~~script~~>	+	</source>

← Older revision	Revision as of 03:53, 28 March 2014
(No difference)

@@ Line 135: / Line 135: @@
 </source>
 [[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]

@@ Line 5: / Line 5: @@
 <source lang="python">
 fetch 2x19
-pseudo_sidechaincenters scc, 2x19
+sidechaincenters scc, 2x19
 </source>

← Older revision		Revision as of 17:37, 25 November 2010
Line 132:		Line 132:
	# vi: ts=4:sw=4:smarttab:expandtab		# vi: ts=4:sw=4:smarttab:expandtab
	</source>		</source>
		+
		+	[[Category:Plugins]]
		+	[[Category:Structural_Biology_Scripts]]

@@ Line 124: / Line 124: @@
 cmd.extend('sidechaincenters', sidechaincenters)
 cmd.extend('sidechaincentroids', sidechaincentroids)
 # vi: ts=4:sw=4:smarttab:expandtab
 </source>

@@ Line 42: / Line 42: @@
+}
-def pseudo_sidechaincenters(object='scc', selection='all', name='PS1', method='bahar1996'):
+def sidechaincenters(object='scc', selection='all', name='PS1', method='bahar1996'):
      '''
 DESCRIPTION
@@ Line 54: / Line 54: @@
 USAGE
-     pseudo_sidechaincenters object [, selection]
+     sidechaincenters object [, selection]
 ARGUMENTS
@@ Line 66: / Line 66: @@
 SEE ALSO
-     pseudo_sidechaincentroids, pseudoatom
+     sidechaincentroids, pseudoatom
      '''
      atmap = dict()
@@ Line 79: / Line 79: @@
              atmap.setdefault((at.segi, at.chain, at.resn, at.resi), []).append(at)
      else:
-         print 'Error: unknown method'
+         print 'Error: unknown method:', method
          return
@@ Line 101: / Line 101: @@
      return model
-def pseudo_sidechaincentroids(object='scc', selection='all', name='PS1'):
+def sidechaincentroids(object='scc', selection='all', name='PS1'):
      '''
 DESCRIPTION
-     Sidechain centroids. Works like "pseudo_sidechaincenters", but the
+     Sidechain centroids. Works like "sidechaincenters", but the
      pseudoatom is the centroid of all atoms except hydrogens and backbone atoms
      (N, C and O).
@@ Line 114: / Line 114: @@
      like in this example:
-     pseudo_sidechaincentroids newobject, all and (not name CA or resn GLY)
+     sidechaincentroids newobject, all and (not name CA or resn GLY)
 SEE ALSO
-     pseudo_sidechaincenters
+     sidechaincenters
      '''
-     return pseudo_sidechaincenters(object, selection, name, method='centroids')
+     return sidechaincenters(object, selection, name, method='centroid')
-cmd.extend('pseudo_sidechaincenters', pseudo_sidechaincenters)
+cmd.extend('sidechaincenters', sidechaincenters)
-cmd.extend('pseudo_sidechaincentroids', pseudo_sidechaincentroids)
+cmd.extend('sidechaincentroids', sidechaincentroids)
 # vi: ts=4:sw=4:smarttab:expandtab
 </source>