def loop_orientation(selection,
state=STATE,
visualize=1,
quiet=1,
*,
_self=cmd):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize ]
SEE ALSO
helix_orientation
'''
state, visualize, quiet = int(state), int(visualize), int(quiet)
coords = dict()
_self.iterate_state(state,
'(%s) and name N+C' % (selection),
'coords.setdefault(chain + resi, {})[name] = x,y,z',
space=locals())
vec = cpv.get_null()
center = cpv.get_null()
count = 0
for x in coords.values():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
for coord in x.values():
center = cpv.add(center, coord)
count += 1
if count == 0:
raise CmdException('count == 0')
vec = cpv.normalize(vec)
center = cpv.scale(center, 1. / count)
_common_orientation(selection,
center,
vec,
visualize,
2.0 * len(coords),
quiet,
_self=_self)
return center, vec
def _vec_sum(vec_list):
# this is the same as
# return numpy.array(vec_list).sum(0).tolist()
vec = cpv.get_null()
for x in vec_list:
vec = cpv.add(vec, x)
return vec
def loop_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize]
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name N+C' % (selection),
'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
vec = cpv.get_null()
count = 0
for x in stored.x.itervalues():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
count += 1
if count == 0:
print 'warning: count == 0'
raise CmdException
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def loop_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize]
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
stored.x = dict()
cmd.iterate_state(
STATE, '(%s) and name N+C' % (selection),
'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
vec = cpv.get_null()
count = 0
for x in stored.x.itervalues():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
count += 1
if count == 0:
print 'warning: count == 0'
raise CmdException
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def _vec_sum(vec_list):
# this is the same as
# return numpy.array(vec_list).sum(0).tolist()
vec = cpv.get_null()
for x in vec_list:
vec = cpv.add(vec, x)
return vec
def loop_orientation(selection, state=STATE, visualize=1, quiet=1):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize ]
SEE ALSO
helix_orientation
'''
state, visualize, quiet = int(state), int(visualize), int(quiet)
coords = dict()
cmd.iterate_state(state, '(%s) and name N+C' % (selection),
'coords.setdefault(chain + resi, {})[name] = x,y,z', space=locals())
vec = cpv.get_null()
center = cpv.get_null()
count = 0
for x in coords.itervalues():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
for coord in x.itervalues():
center = cpv.add(center, coord)
count += 1
if count == 0:
print 'warning: count == 0'
raise CmdException
vec = cpv.normalize(vec)
center = cpv.scale(center, 1./count)
_common_orientation(selection, center, vec, visualize, 2.0*len(coords), quiet)
return center, vec
def centerofmass(selection='(all)',
state=CURRENT_STATE,
quiet=1,
*,
_self=cmd):
'''
DESCRIPTION
Calculates the center of mass. Considers atom mass and occupancy.
ARGUMENTS
selection = string: atom selection {default: all}
state = integer: object state, -1 for current state, 0 for all states
{default: -1}
NOTES
If occupancy is 0.0 for an atom, set it to 1.0 for the calculation
(assume it was loaded from a file without occupancy information).
SEE ALSO
get_extent
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 0:
state = _self.get_selection_state(selection)
if state == 0:
states = list(range(1, _self.count_states(selection) + 1))
else:
states = [state]
com = cpv.get_null()
totmass = 0.0
for state in states:
model = _self.get_model(selection, state)
for a in model.atom:
m = a.get_mass() * (a.q or 1.0)
com = cpv.add(com, cpv.scale(a.coord, m))
totmass += m
if not totmass:
raise pymol.CmdException('mass is zero')
com = cpv.scale(com, 1. / totmass)
if not quiet:
print(' Center of Mass: [%8.3f,%8.3f,%8.3f]' % tuple(com))
return com
def centerofmass(selection='(all)', state=-1, quiet=1, _self=cmd):
'''
DESCRIPTION
Calculates the center of mass. Considers atom mass and occupancy.
ARGUMENTS
selection = string: atom selection {default: all}
state = integer: object state, -1 for current state, 0 for all states
{default: -1}
NOTES
If occupancy is 0.0 for an atom, set it to 1.0 for the calculation
(assume it was loaded from a file without occupancy information).
SEE ALSO
get_extent
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 0:
states = [get_selection_state(selection)]
elif state == 0:
states = range(1, _self.count_states(selection)+1)
else:
states = [state]
com = cpv.get_null()
totmass = 0.0
for state in states:
model = _self.get_model(selection, state)
for a in model.atom:
m = a.get_mass() * (a.q or 1.0)
com = cpv.add(com, cpv.scale(a.coord, m))
totmass += m
if not totmass:
raise pymol.CmdException('mass is zero')
com = cpv.scale(com, 1./totmass)
if not quiet:
print ' Center of Mass: [%8.3f,%8.3f,%8.3f]' % tuple(com)
return com
def centerofmass(selection='(all)', state=-1, quiet=1, *, _self=cmd):
'''
DESCRIPTION
Calculates the center of mass. Considers atom mass and occupancy.
ARGUMENTS
selection = string: atom selection {default: all}
state = integer: object state, -1 for current state, 0 for all states
{default: -1}
EXAMPLE
from psico.querying import *
x = centerofmass('chain A')
r = gyradius('chain A')
cmd.pseudoatom('com', pos=x, vdw=r)
SEE ALSO
gyradius
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 0:
states = [_self.get_state()]
elif state == 0:
states = list(range(1, _self.count_states(selection) + 1))
else:
states = [state]
com = cpv.get_null()
totmass = 0.0
for state in states:
model = _self.get_model(selection, state)
for a in model.atom:
if a.q == 0.0:
continue
m = a.get_mass() * a.q
com = cpv.add(com, cpv.scale(a.coord, m))
totmass += m
com = cpv.scale(com, 1. / totmass)
if not quiet:
print(' Center of Mass: [%8.3f,%8.3f,%8.3f]' % tuple(com))
return com
def centerofmass(selection='(all)', state=-1, quiet=1):
'''
DESCRIPTION
Calculates the center of mass. Considers atom mass and occupancy.
ARGUMENTS
selection = string: atom selection {default: all}
state = integer: object state, -1 for current state, 0 for all states
{default: -1}
EXAMPLE
from psico.querying import *
x = centerofmass('chain A')
r = gyradius('chain A')
cmd.pseudoatom('com', pos=x, vdw=r)
SEE ALSO
gyradius
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 0:
states = [cmd.get_state()]
elif state == 0:
states = list(range(1, cmd.count_states(selection)+1))
else:
states = [state]
com = cpv.get_null()
totmass = 0.0
for state in states:
model = cmd.get_model(selection, state)
for a in model.atom:
if a.q == 0.0:
continue
m = a.get_mass() * a.q
com = cpv.add(com, cpv.scale(a.coord, m))
totmass += m
com = cpv.scale(com, 1./totmass)
if not quiet:
print(' Center of Mass: [%8.3f,%8.3f,%8.3f]' % tuple(com))
return com
def centroid(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
centroid = cpv.get_null()
for a in model.atom:
centroid = cpv.add(centroid, a.coord)
centroid = cpv.scale(centroid, 1. / nAtom)
if not int(quiet):
print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
if int(move):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
space={'centroid': centroid, 'sub': cpv.sub})
return centroid
def COM(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
COM = cpv.get_null()
for a in model.atom:
COM = cpv.add(COM, a.coord)
COM = cpv.scale(COM, 1./nAtom)
if not int(quiet):
print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
if int(center):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
space={'COM': COM, 'sub': cpv.sub})
return COM
def COM(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
COM = cpv.get_null()
for a in model.atom:
COM = cpv.add(COM, a.coord)
COM = cpv.scale(COM, 1. / nAtom)
if not int(quiet):
print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
if int(center):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
space={'COM': COM, 'sub': cpv.sub})
return COM
def find_center_of_mass(selection='(all)', state=-1):
"""
Find center of mass of the selection and return the value
USAGE
find_center_of_mass selection
find_center_of_mass selection, state=state
ARGUMENTS
selection a selection-expression
state a state index if positive int, 0 to all, or -1 to current
"""
state = utils.int_to_state(state)
model = cmd.get_model(selection, state=state)
com = cpv.get_null()
# iterate all atoms and add vectors of center of mass of each atoms
for atom in model.atom:
com = cpv.add(com, atom.coord)
com = cpv.scale(com, 1.0 / len(model.atom))
return com
def find_center_of_mass(selection='(all)', state=-1):
"""
Find center of mass of the selection and return the value
USAGE
find_center_of_mass selection
find_center_of_mass selection, state=state
ARGUMENTS
selection a selection-expression
state a state index if positive int, 0 to all, or -1 to current
"""
state = utils.int_to_state(state)
model = cmd.get_model(selection, state=state)
com = cpv.get_null()
# iterate all atoms and add vectors of center of mass of each atoms
for atom in model.atom:
com = cpv.add(com, atom.coord)
com = cpv.scale(com, 1.0 / len(model.atom))
return com
def centroid(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
centroid = cpv.get_null()
for a in model.atom:
centroid = cpv.add(centroid, a.coord)
centroid = cpv.scale(centroid, 1. / nAtom)
if not int(quiet):
print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
if int(center):
cmd.alter_state(1,
selection,
"(x,y,z)=sub((x,y,z), centroid)",
space={
'centroid': centroid,
'sub': cpv.sub
})
return centroid
def sidechaincenters(object='scc', selection='all', method='bahar1996', name='PS1', *, _self=cmd):
'''
DESCRIPTION
Creates an object with sidechain representing pseudoatoms for each residue
in selection.
Two methods are available:
(1) Sidechain interaction centers as defined by Bahar and Jernigan 1996
http://www.ncbi.nlm.nih.gov/pubmed/9080182
(2) Sidechain centroids, the pseudoatom is the centroid of all atoms except
hydrogens and backbone atoms (N, C and O).
NOTE
With method "bahar1996", if a residue has all relevant sidechain center
atoms missing (for example a MET without SD), it will be missing in the
created pseudoatom object.
With method "centroid", if you want to exclude C-alpha atoms from
sidechains, modify the selection like in this example:
sidechaincenters newobject, all and (not name CA or resn GLY), method=2
USAGE
sidechaincenters object [, selection [, method ]]
ARGUMENTS
object = string: name of object to create
selection = string: atoms to consider {default: (all)}
method = string: bahar1996 or centroid {default: bahar1996}
name = string: atom name of pseudoatoms {default: PS1}
SEE ALSO
pseudoatom
'''
from chempy import Atom, cpv, models
atmap = dict()
if method in ['bahar1996', '1', 1]:
modelAll = _self.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 in ['centroid', '2', 2]:
modelAll = _self.get_model('(%s) and polymer 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:
raise CmdException('unknown method: {}'.format(method))
model = models.Indexed()
for centeratoms in atmap.values():
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 [
'segi',
'chain',
'resi_number',
'resi',
'resn',
'hetatm',
'ss',
'b',
]:
setattr(atom, key, getattr(at, key))
model.add_atom(atom)
model.update_index()
if object in _self.get_object_list():
_self.delete(object)
_self.load_model(model, object)
return model
def sidechaincenters(object='scc', selection='all', method='bahar1996', name='PS1'):
'''
DESCRIPTION
Creates an object with sidechain representing pseudoatoms for each residue
in selection.
Two methods are available:
(1) Sidechain interaction centers as defined by Bahar and Jernigan 1996
http://www.ncbi.nlm.nih.gov/pubmed/9080182
(2) Sidechain centroids, the pseudoatom is the centroid of all atoms except
hydrogens and backbone atoms (N, C and O).
NOTE
With method "bahar1996", if a residue has all relevant sidechain center
atoms missing (for example a MET without SD), it will be missing in the
created pseudoatom object.
With method "centroid", if you want to exclude C-alpha atoms from
sidechains, modify the selection like in this example:
sidechaincenters newobject, all and (not name CA or resn GLY), method=2
USAGE
sidechaincenters object [, selection [, method ]]
ARGUMENTS
object = string: name of object to create
selection = string: atoms to consider {default: (all)}
method = string: bahar1996 or centroid {default: bahar1996}
name = string: atom name of pseudoatoms {default: PS1}
SEE ALSO
pseudoatom
'''
from chempy import Atom, cpv, models
atmap = dict()
if method in ['bahar1996', '1', 1]:
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 in ['centroid', '2', 2]:
modelAll = cmd.get_model('(%s) and polymer 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)
raise CmdException
model = models.Indexed()
for centeratoms in atmap.values():
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
