def doit(self, atom1, atom2, angle, mov_atoms, returnVal=0):
mol = atom1.top
if mov_atoms is None:
mov_atoms = mol.subTree(atom1, atom2, mol.allAtoms)
assert len(mov_atoms)
mov_coords = Numeric.array(mov_atoms.coords)
lenCoords = len(mov_coords)
x = Numeric.array(atom1.coords)
y = Numeric.array(atom2.coords)
rot = (angle * 3.14159 / 180.) % (2 * Numeric.pi)
matrix = rotax(x, y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords, 1)
mov_coords = Numeric.concatenate((mov_coords, _ones), 1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:, :3].astype('f')
for i in range(lenCoords):
at = mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
event = EditAtomsEvent('coords', mov_atoms)
self.vf.dispatchEvent(event)
#have to return nc for setTorsionGC
if returnVal:
return nc
def doit(self, mobAtoms):
"""
mobAtoms: AtomSet that is being frozen.
Assuming the AtomSet are from same molecule
"""
# fixme: need checking for mat (matrix) and mobAtoms
geomContainer = mobAtoms[0].top.geomContainer
mGeom = geomContainer.masterGeom
mat = mGeom.rotation
mat = Numeric.reshape(mat, (4, 4))
# update coords
mobAtoms = mobAtoms.findType(Atom)
coords = mobAtoms.coords
hCoords = Numeric.concatenate((coords,Numeric.ones((len(coords),1),\
'd')), 1)
tCoords = Numeric.dot(hCoords, mat)[:, :3]
tCoords = tCoords.tolist()
mobAtoms.updateCoords(tCoords, 0) # overwritten the original coords
# reset the rotation matrix of masterGeom
identity = Numeric.identity(4, 'f').ravel()
mGeom.SetRotation(Numeric.identity(4, 'f').ravel())
event = EditAtomsEvent('coords', mobAtoms)
self.vf.dispatchEvent(event)
mGeom.viewer.Redraw()
return
def __call__(self, opt):
#opt is the optimizer object either cg, md etc...
#opt.atmsel give acces to the current data model
#opt.current_e give acces to the current energy
#print "action"
indices, model = opt.atmsel.get_atom_indices()
self.updatePmvCoord(self.idConf, model)
event = EditAtomsEvent('coords', self.pmvModel.allAtoms)
self.mv.dispatchEvent(event)
#should we update other geom? at least one chain to test
if self.epmv is not None:
self.epmv.updateDataGeom(self.pmvModel)
#self.epmv.helper.updatePoly(self.pmvModel.name+":"+self.pmvModel.chains[0].name+"_cloud",
# vertices=self.pmvModel.chains[0].residues.atoms.coords)
#try tu update viewer ?
if self.redraw:
#print "redraw",self.mv.hasGui
if self.mv.hasGui:
#print "update"
#self.mv.GUI.VIEWER.update()
self.mv.GUI.VIEWER.OneRedraw()
self.mv.GUI.VIEWER.update()
#self.GUI.ROOT.after(5, self.mv.GUI.VIEWER.OneRedraw)
if self.epmv is not None:
self.epmv.helper.update()
if self.store:
#add a conformation for modeller
self.pmvModel.allAtoms.addConformation(
self.pmvModel.allAtoms.coords[:])
self.idConf = len(self.pmvModel.allAtoms[0]._coords) - 1
def doit(self, atom1, atom2):
#Have to find the bond first
theBond = None
for b in atom1.bonds:
at2 = b.atom1
if at2 == atom1:
at2 = b.atom2
if at2 == atom2:
#remove this bond
theBond = b
atom2.bonds.remove(theBond)
#this may not be possible
atom1.bonds.remove(theBond)
atom1.parent.hasBonds = 0
if atom2.parent != atom1.parent:
atom2.parent.hasBonds = 0
if atom1.parent.parent:
atom1.parent.parent.hasBonds = 0
if atom2.parent.parent:
atom2.parent.parent.hasBonds = 0
break
if not theBond:
from warnings import warn
warn('bond not found %s-%s' % (atom1, atom2))
return 'ERROR'
else:
event = EditAtomsEvent('coords', AtomSet([atom1, atom2]))
self.vf.dispatchEvent(event)
def updateMindy(self):
from ARViewer import util
import numpy.oldnumeric as Numeric
imdheader = self.imd_recv_header(self.sock)
vmd_length = imdheader.length
imdtype = imdheader.imdtype
if imdtype == IMD_FCOORDS:
print "recv fcoords ", vmd_length
test = self.imd_recv_fcoords(vmd_length, self.imd_coords)
print self.imd_coords[0]
b = 0
n1 = 0
for i, m in enumerate(self.mol):
n1 += len(m.allAtoms.coords)
try:
#should apply the inverse matrix? to get back to the origin before going on the marker..
if hasattr(self.vf, 'art'):
M = matrix(m.pat.mat_transfo.reshape(4, 4))
vt = util.ApplyMatrix(
Numeric.array(self.imd_coords[b:n1]),
numpy.array(M.I))
print "update coords but back in CS"
print vt[0]
m.allAtoms.updateCoords(vt, self.slot[i])
print m.allAtoms.coords[0]
else:
m.allAtoms.updateCoords(self.imd_coords[b:n1],
self.slot[i])
except:
print "coord update failed"
b = n1
#print m.allAtoms._coords[0]
#print "ipdate coords events"
from Pmv.moleculeViewer import EditAtomsEvent
for i, m in enumerate(self.mol):
event = EditAtomsEvent('coords', m.allAtoms)
try:
self.vf.dispatchEvent(event)
except:
print "event failed"
#here we should update from AR....which is apply the marker transformation
#one marker per mol...should have some mol.mat_transfo attributes
#get the maker position transfo
coords = []
for m in self.mol:
if hasattr(self.vf, 'art'):
M = m.pat.mat_transfo
vt = []
vt = util.ApplyMatrix(Numeric.array(m.allAtoms.coords), M)
else:
vt = m.allAtoms.coords[:]
coords.extend(vt)
self.imd_send_fcoords(self.N, coords)
def repeat_transTors(self, event=None):
deltaAngle = self.extslider.get()
if self.torsionType.get() != '1':
self.transformCoords(deltaAngle)
#this is here in order to create a log message
nc = self.vf.setRelativeTorsion(self.atomList[1],
self.atomList[2],
deltaAngle,
self.mov_atoms,
returnVal=1)
event = EditAtomsEvent('coords', self.mov_atoms)
self.vf.dispatchEvent(event)
def pmv_show(pose, self):
from Pmv.moleculeViewer import EditAtomsEvent
global pmv_state
import time
#if not with_pmv: return
model = self.getMolFromName("test")
model.allAtoms.setConformation(1)
coord = {}
print pose.n_residue(), len(model.chains.residues)
for resi in range(1, pose.n_residue() + 1):
res = pose.residue(resi)
resn = pose.pdb_info().number(resi)
#print resi,res.natoms(),len(model.chains.residues[resi-1].atoms)
k = 0
for atomi in range(1, res.natoms() + 1):
name = res.atom_name(atomi).strip()
if name != 'NV':
a = model.chains.residues[resi - 1].atoms[k]
pmv_name = a.name
k = k + 1
if name != pmv_name:
if name[1:] != pmv_name[:-1]:
print name, pmv_name
else:
coord[(resn, pmv_name)] = res.atom(atomi).xyz()
cood = res.atom(atomi).xyz()
a._coords[1] = [cood.x, cood.y, cood.z]
else:
coord[(resn, name)] = res.atom(atomi).xyz()
cood = res.atom(atomi).xyz()
a._coords[1] = [cood.x, cood.y, cood.z] #return coord
event = EditAtomsEvent('coords', model.allAtoms)
self.dispatchEvent(event)
#modEvent = ModificationEvent('edit','coords', mol.allAtoms)
#mol.geomContainer.updateGeoms(modEvent)
#PMV
#self.GUI.VIEWER.Redraw()
#time.sleep(.1)
#Blender
epmv.insertKeys(model.geomContainer.geoms['cpk'], 1)
epmv.getCurrentScene().update()
Draw.Redraw()
Draw.Redraw(1)
Blender.Redraw()
def mindyGet(self):
from ARViewer import util
import numpy.oldnumeric as Numeric
imdheader = self.imd_recv_header(self.sock)
vmd_length = imdheader.length
imdtype = imdheader.imdtype
if imdtype == IMD_FCOORDS:
#print "recv fcoords ",vmd_length
test = self.imd_recv_fcoords(vmd_length, self.imd_coords)
#print self.imd_coords[0]
b = 0
n1 = 0
for i, m in enumerate(self.mol):
n1 += len(m.allAtoms.coords)
try:
#should apply the inverse matrix? to get back to the origin
#before going on the marker..
#but problem of scaleFactor
if hasattr(self.vf, 'art'):
M = matrix(m.pat.mat_transfo.reshape(4, 4))
vt = util.ApplyMatrix(Numeric.array(
self.imd_coords[b:n1]),
Numeric.array(M.I),
transpose=False)
#print "update coords but back in CS"
#print vt[0]
if True in numpy.isnan(vt[0]):
vt = map(lambda x: x[0], m.allAtoms._coords)
m.allAtoms.updateCoords(vt, self.slot[i])
#print m.allAtoms.coords[0]
else:
m.allAtoms.updateCoords(self.imd_coords[b:n1],
self.slot[i])
except:
print "coord update failed"
b = n1
from Pmv.moleculeViewer import EditAtomsEvent
for i, m in enumerate(self.mol):
event = EditAtomsEvent('coords', m.allAtoms)
try:
self.vf.dispatchEvent(event)
except:
print "event failed"
def applyState(self, ind):
"""None<-applyState(ind)"""
mol = self.mol
# -1 is key for go back to original
if int(ind)==-1:
mol.allAtoms.setConformation(0)
conf = None
else:
#in this case want to get new coords
#coords = self.traj.coords["frame%d"%ind]
coords = self.traj.coords[ind]
coordsarr = (Numeric.array(coords)*10).astype("f")
allAtoms = self.mol.allAtoms
allAtoms.updateCoords(coordsarr[:], self.coordSlot)
if not self.vf.hasGui: return
event = EditAtomsEvent('coords', mol.allAtoms)
self.vf.dispatchEvent(event)
#modEvent = ModificationEvent('edit','coords', mol.allAtoms)
#mol.geomContainer.updateGeoms(modEvent)
self.vf.GUI.VIEWER.Redraw()
def applyState(self, ind):
"""None<-applyState(ind)"""
mol = self.mol
viewer = None # self.vf.GUI.VIEWER
if self.vf.hasGui:
viewer = self.vf.GUI.VIEWER
cache_list = False
# check if we can cache the display list for this frame
if self.dpyLists.has_key(ind):
if self.dpyLists[ind] is not None:
cache_list = True
viewer.currentCamera.dpyList = self.dpyLists[ind]
#viewer.dpyList = self.dpyLists[ind]
if self.vf.hasGui:
viewer.OneRedraw()
#viewer.Redraw()
else:
self.dpyLists.pop(ind)
if not cache_list:
if int(ind)==-1: # -1 is key for go back to original
mol.allAtoms.setConformation(0)
else:
#in this case we want to get new coords
coords = self.traj.coords[ind]
coordsarr = (Numeric.array(coords)*10).astype("f")
allAtoms = self.mol.allAtoms
allAtoms.updateCoords(coordsarr[:], self.coordSlot)
#if not self.vf.hasGui: return
if self.vf.hasGui:
self.vf.GUI.VIEWER.singleDpyList = True
event = EditAtomsEvent('coords', mol.allAtoms)
self.vf.dispatchEvent(event)
if self.vf.hasGui:
viewer.OneRedraw()
#viewer.Redraw()
self.dpyLists[ind] = viewer.currentCamera.dpyList #viewer.dpyList
viewer.currentCamera.dpyList = None
#viewer.dpyList = None
self.vf.GUI.VIEWER.singleDpyList = False
def transformCoords(self, deltaAngle):
""" deltaAngle is NOW not final angle wanted but relative"""
#mov_coords is the array of the coords of the atoms to be moved,
#x2 and x3 are atoms which define the axis of the transformation
#by deltaAngle. NB: effect is that mov_atoms.coords
#are transformed...
if not hasattr(self, 'mov_atoms'): return
if not len(self.mov_atoms): return
x1, x2, x3, x4 = self.atomList
nc = self.vf.setRelativeTorsion.doit(x2,
x3,
deltaAngle,
self.mov_atoms,
returnVal=1)
mol = x2.top
#mov_atoms = mol.subTree(x2, x3, mol.allAtoms)
for i in range(len(nc)):
at = self.mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
event = EditAtomsEvent('coords', self.mov_atoms)
self.vf.dispatchEvent(event)
self.update()
def doit(self, atom1, atom2, **kw):
origin = kw['origin']
bondOrder = kw['bondOrder']
bond = Bond(atom1, atom2, origin=origin, bondOrder=bondOrder)
event = EditAtomsEvent('coords', AtomSet([atom1, atom2]))
self.vf.dispatchEvent(event)