def superpose(self,reference_coords,fit_coords,return_pdbs=False):
"""Superpose the fit_coords on the reference_coords"""
import quatfit
self.refcenter,self.fitcenter,self.rotation=quatfit.qfit(len(reference_coords),reference_coords,fit_coords)
self.newcoords = quatfit.qtransform(len(reference_coords), fit_coords, self.refcenter, self.fitcenter, self.rotation)
#
# Calc rmsd
#
rmsd=0.0
self.rmsd_map=[]
for i in range(len(self.newcoords)):
disp = self.newcoords[i] - reference_coords[i]
self.rmsd_map.append(length(disp))
dist_squared = dot(disp,disp)
rmsd = rmsd + dist_squared
rmsd=rmsd/float(len(self.newcoords))
import math
rmsd=math.sqrt(rmsd)
#
# If asked then return pdblines for the org and aligned atoms (as CA atoms)
#
if return_pdbs:
pdblines=[]
for coords in [reference_coords,self.newcoords]:
theselines=[]
count=1
for coord in coords:
line='ATOM %5i %4s %3s %1s%4i %8.3f%8.3f%8.3f %5s %5s\n' %(count,' CA ','ALA','A',count,float(coord[0]),float(coord[1]),float(coord[2]),'1.0','10.0')
count=count+1
theselines.append(line)
pdblines.append(theselines)
return rmsd,pdblines
return rmsd
def build_hydrogen(self,residue,buildH,coords):
"""Build a hydrogen in the structure when given coordinates, the Hname and the residue"""
fit_coords=[]
findatoms=sorted(coords.keys())
findatoms.remove(buildH)
ref_coords=[]
for atom in findatoms:
fit_coords.append(coords[atom])
#
# Now find the corresponding atom in the structure
#
struct_res=residue
if atom[-2:]=='-1':
try:
struct_res=self.PI.PreviousResidue(residue)
atom=atom[:-2]
except ResidueNotFoundError:
print 'prev not found'
return None
ref_coords.append(self.PI.GetPosition('%s:%s' %(struct_res,atom)))
#
# Get rotation and translation for bb -> bb
#
import quatfit
refcenter,fitcenter,rotation=quatfit.qfit(len(ref_coords),ref_coords,fit_coords)
#
# Get the atoms that should be transformed
#
trans_coords=[coords[buildH],coords[buildH]]
#
# Apply rotation and translation to trans_coords
#
newcoords = quatfit.qtransform(len(trans_coords), trans_coords, refcenter, fitcenter, rotation)
#
# Add the atom
#
struct_atom=self.PI.atoms['%s:CA' %residue]
resnumber=struct_atom['RESNUM']
restype=struct_atom['RESNAME']
chainid=struct_atom['CHAINID']
atomnumber=struct_atom['NUMBER']
uniqueid='%s:%s:%s' %(chainid,resnumber,buildH)
count=0
if not self.PI.atoms.has_key(uniqueid):
self.PI.add_atom(uniqueid,atomnumber=atomnumber,
atomname=buildH,chainid=chainid,residuename=restype,
residuenumber=resnumber,
xcoord=newcoords[count][0],ycoord=newcoords[count][1],zcoord=newcoords[count][2],update=None)
#
# Fix atom numbers
#
self.PI.renumber_atoms()
return
def superpose(self,reference_coords,fit_coords):
"""Superpose the fit_coords on the reference_coords"""
import quatfit
self.refcenter,self.fitcenter,self.rotation=quatfit.qfit(len(reference_coords),reference_coords,fit_coords)
self.newcoords = quatfit.qtransform(len(reference_coords), fit_coords, self.refcenter, self.fitcenter, self.rotation)
#
# Calc rmsd
#
rmsd=0.0
for i in range(len(self.newcoords)):
disp = self.newcoords[i] - reference_coords[i]
#disp=length(disp)*length(disp)
dist_squared = dot(disp,disp)
rmsd = rmsd + dist_squared
rmsd=rmsd/float(len(self.newcoords))
import math
rmsd=math.sqrt(rmsd)
return rmsd
def superpose(self, reference_coords, fit_coords):
"""Superpose the fit_coords on the reference_coords"""
import quatfit
self.refcenter, self.fitcenter, self.rotation = quatfit.qfit(
len(reference_coords), reference_coords, fit_coords)
self.newcoords = quatfit.qtransform(len(reference_coords), fit_coords,
self.refcenter, self.fitcenter,
self.rotation)
#
# Calc rmsd
#
rmsd = 0.0
for i in range(len(self.newcoords)):
disp = self.newcoords[i] - reference_coords[i]
#disp=length(disp)*length(disp)
dist_squared = dot(disp, disp)
rmsd = rmsd + dist_squared
rmsd = rmsd / float(len(self.newcoords))
import math
rmsd = math.sqrt(rmsd)
return rmsd
def superpose(self, reference_coords, fit_coords, return_pdbs=False):
"""Superpose the fit_coords on the reference_coords"""
import quatfit
self.refcenter, self.fitcenter, self.rotation = quatfit.qfit(
len(reference_coords), reference_coords, fit_coords)
self.newcoords = quatfit.qtransform(len(reference_coords), fit_coords,
self.refcenter, self.fitcenter,
self.rotation)
#
# Calc rmsd
#
rmsd = 0.0
self.rmsd_map = []
for i in range(len(self.newcoords)):
disp = self.newcoords[i] - reference_coords[i]
self.rmsd_map.append(length(disp))
dist_squared = dot(disp, disp)
rmsd = rmsd + dist_squared
rmsd = rmsd / float(len(self.newcoords))
import math
rmsd = math.sqrt(rmsd)
#
# If asked then return pdblines for the org and aligned atoms (as CA atoms)
#
if return_pdbs:
pdblines = []
for coords in [reference_coords, self.newcoords]:
theselines = []
count = 1
for coord in coords:
line = 'ATOM %5i %4s %3s %1s%4i %8.3f%8.3f%8.3f %5s %5s\n' % (
count, ' CA ', 'ALA', 'A', count, float(coord[0]),
float(coord[1]), float(coord[2]), '1.0', '10.0')
count = count + 1
theselines.append(line)
pdblines.append(theselines)
return rmsd, pdblines
return rmsd
def mutate(self, residue, newtype, orgtype=None):
"""Mutate the residue to the new type
Normal substitutions: A:0035,GLN,GLU
Deletions: A:0035,delete,GLU"""
#
# Reset score
#
score = None
#
# Store the operations
#
if not getattr(self, 'mutate_operations', None):
self.mutate_operations = []
this_operation = []
local_operation = []
#
# Get phi and psi for this residue
#
#import phipsi
#phi,psi,omega=phipsi.GetPhiPsi(self.PI,residue)
newtype = newtype.upper()
aas = self.rots.keys()
aas.sort()
if not self.aadefs.has_key(newtype):
raise Exception, "invalid aa type"
#
if not self.PI.residues.has_key(residue):
res = self.PI.residues.keys()
res.sort()
raise Exception, "Invalid residue number: %s\nKnown residues are:\n%s" % (
residue, str(res))
#
# Special cases
#
oldtype = self.PI.resname(residue)
#
# If orgtype was specified then check that there's agreement with the pdb file
#
if orgtype:
if orgtype != oldtype:
raise Exception(
'Incorrect original residue type: %s %s. You said: %s' %
(residue, oldtype, orgtype))
#
#
#
if newtype == 'ALA' and (oldtype != 'GLY' and oldtype != 'PRO'):
this_operation = self.fast_mutatetoALA(residue)
score = 0.0
elif newtype == 'GLY':
this_operation = self.fast_mutatetoGLY(residue)
score = 0.0
elif oldtype == 'ASP' and newtype == 'ASN':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = 'ASN'
if self.PI.atname(atom) == 'OD2':
self.PI.atoms[atom]['ATNAME'] = 'ND2'
this_operation.append(['add', atom, self.PI.atoms[atom]])
score = 0.0
elif oldtype == 'ASN' and newtype == 'ASP':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = 'ASP'
if self.PI.atname(atom) == 'ND2':
self.PI.atoms[atom]['ATNAME'] = 'OD2'
this_operation.append(['add', atom, self.PI.atoms[atom]])
score = 0.0
elif oldtype == 'GLU' and newtype == 'GLN':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = 'GLN'
if self.PI.atname(atom) == 'OE2':
self.PI.atoms[atom]['ATNAME'] = 'NE2'
this_operation.append(['add', atom, self.PI.atoms[atom]])
score = 0.0
elif oldtype == 'GLN' and newtype == 'GLU':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = 'GLU'
if self.PI.atname(atom) == 'NE2':
self.PI.atoms[atom]['ATNAME'] = 'OE2'
this_operation.append(['add', atom, self.PI.atoms[atom]])
score = 0.0
elif oldtype == 'TYR' and newtype == 'PHE':
#
# Delete OH
#
for atom in self.PI.residues[residue]:
if self.PI.atname(atom) == 'OH':
this_operation.append(
['delete', atom, self.PI.atoms[atom]])
score = 0.0
else:
#
# Use generic code
#
#
# Get the standard conformation
#
std_conf = self.aadefs[newtype]
#
# See which kind of mutation we do
# 1. Just put standard conformation
# 2. Standard conf + rotamer search
# 3. Use wt rotamer (if possible, otherwise use best rotamer)
# All can be used with and without debumping.
#
#
# Get the torsion angles for this residue
#
org_torsangles = []
number_of_chis = self.get_nonH_torsions(residue)
#print 'Number of chi values for %s is %d' %(residue,number_of_chis)
for chinum in range(1, number_of_chis + 1):
org_torsangles.append(self.get_chi(residue, chinum))
#
# Get the backbone atoms from the structure
#
bb_struct = []
ref_coords = []
for atom in self.PI.residues[residue]:
if (self.PI.is_backbone(atom) or
self.PI.is_CB(atom)) and not self.PI.is_hydrogen(atom):
bb_struct.append(atom)
ref_coords.append(self.PI.GetPosition(atom))
#
# Get the corresponding atoms from the template
#
bb_template = []
fit_coords = []
for s_atom in bb_struct:
s_atname = self.PI.atname(s_atom)
for atom in std_conf['atoms']:
if atom[0] == s_atname:
bb_template.append(atom[0])
fit_coords.append(atom[1])
break
#
# Get rotation and translation for bb -> bb
#
import quatfit
refcenter, fitcenter, rotation = quatfit.qfit(
len(ref_coords), ref_coords, fit_coords)
#
# Get the atoms that should be transformed
#
trans_atoms = []
trans_coords = []
for atom in std_conf['atoms']:
if not atom in bb_template and atom[0] != 'O':
trans_atoms.append(atom[0])
trans_coords.append(atom[1])
#
# Apply rotation and translation to trans_coords
#
newcoords = quatfit.qtransform(len(trans_coords), trans_coords,
refcenter, fitcenter, rotation)
#
# Delete the old side chain atoms and rename the ones that stay
#
for atom in self.PI.residues[residue]:
if atom.split(':')[-1] in ['OXT', 'O2', "O''"]:
# Rename the OXT
local_operation.append(
['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = newtype
local_operation.append(['add', atom, self.PI.atoms[atom]])
elif not atom in bb_struct:
this_operation.append(
['delete', atom, self.PI.atoms[atom]])
self.PI.remove_atom(atom)
else:
local_operation.append(
['delete', atom, self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME'] = newtype
local_operation.append(['add', atom, self.PI.atoms[atom]])
#
# Copy coordinates to Protool array
#
struct_atom = self.PI.atoms[bb_struct[0]]
resnumber = struct_atom['RESNUM']
chainid = struct_atom['CHAINID']
atomnumber = struct_atom['NUMBER']
count = 0
for atom in trans_atoms:
if atom[0] != 'H':
uniqueid = '%s:%s:%s' % (chainid, resnumber, atom)
if not self.PI.atoms.has_key(uniqueid):
self.PI.add_atom(uniqueid,
atomnumber=atomnumber,
atomname=atom,
chainid=chainid,
residuename=newtype,
residuenumber=resnumber,
xcoord=newcoords[count][0],
ycoord=newcoords[count][1],
zcoord=newcoords[count][2])
this_operation.append(
['add', uniqueid, self.PI.atoms[uniqueid]])
count = count + 1
#
# Fix atom numbers
#
self.PI.renumber_atoms()
#
# Set the chiangles just as the parent residue
#
new_number_of_chis = self.get_nonH_torsions(residue)
count = 1
for chi in org_torsangles:
if count > new_number_of_chis:
break
self.set_chi(residue, count, chi)
count = count + 1
#
# Score this rotamer, if bump is zero then keep it
#
score = self.get_bump_value(residue)
if (score is None or score > 0.0) and newtype != 'ALA':
#
# Do rotamer search
#
score = self.get_best_rotamer(residue)
if score is None:
return None
# ----------------------------------------------------
#
# Keep track of the operations
#
updated_op = []
for op, uniqueid, atom in this_operation:
if op == 'delete':
updated_op.append([op, uniqueid, {}])
else:
added_atom = self.PI.atoms[uniqueid].copy()
not_needed = ['CHAINID', 'tag', 'BOUND_TO', 'RESNUM']
for delete in not_needed:
if added_atom.has_key(delete):
del added_atom[delete]
updated_op.append([op, uniqueid, self.PI.atoms[uniqueid]])
self.mutate_operations = self.mutate_operations + updated_op
#
# Score is bump score
#
return score
return center_ref,center_fit,vect_ref,vect_fit
#
# Validate the superpos function every time this module is imported
#
import copy
rv=array([[1,1,1],[0,-1,1],[1,-2,1],[1,-3,1],[-1,-3,2]])
fv=array([[1,1,0],[-1,2,0],[-2,1,0],[-3,1,0],[-3,3,1]])
import quatfit
refcenter,fitcenter,rotation=quatfit.qfit(len(rv),rv,fv)
newcoords = quatfit.qtransform(len(rv), fv, refcenter, fitcenter, rotation)
#
# Calc rmsd
#
rmsd=0.0
for i in range(len(newcoords)):
disp = newcoords[i] - rv[i]
dist = dot(disp,disp)
rmsd = rmsd + dist
if rmsd>0.0000001:
print 'Superpositioning test failed!!! in geometry.py'
print 'RMSD',rmsd
print newcoords
import sys
sys.exit(1)
else:
return center_ref, center_fit, vect_ref, vect_fit
#
# Validate the superpos function every time this module is imported
#
import copy
rv = array([[1, 1, 1], [0, -1, 1], [1, -2, 1], [1, -3, 1], [-1, -3, 2]])
fv = array([[1, 1, 0], [-1, 2, 0], [-2, 1, 0], [-3, 1, 0], [-3, 3, 1]])
import quatfit
refcenter, fitcenter, rotation = quatfit.qfit(len(rv), rv, fv)
newcoords = quatfit.qtransform(len(rv), fv, refcenter, fitcenter, rotation)
#
# Calc rmsd
#
rmsd = 0.0
for i in range(len(newcoords)):
disp = newcoords[i] - rv[i]
dist = dot(disp, disp)
rmsd = rmsd + dist
if rmsd > 0.0000001:
print 'Superpositioning test failed!!! in geometry.py'
print 'RMSD', rmsd
print newcoords
import sys
sys.exit(1)
else:
def mutate(self,residue,newtype,orgtype=None):
"""Mutate the residue to the new type
Normal substitutions: A:0035,GLN,GLU
Deletions: A:0035,delete,GLU"""
#
# Reset score
#
score=None
#
# Store the operations
#
if not getattr(self,'mutate_operations',None):
self.mutate_operations=[]
this_operation=[]
local_operation=[]
#
# Get phi and psi for this residue
#
#import phipsi
#phi,psi,omega=phipsi.GetPhiPsi(self.PI,residue)
newtype=newtype.upper()
aas=self.rots.keys()
aas.sort()
if not self.aadefs.has_key(newtype):
raise Exception,"invalid aa type"
#
if not self.PI.residues.has_key(residue):
res=self.PI.residues.keys()
res.sort()
raise Exception,"Invalid residue number: %s\nKnown residues are:\n%s" %(residue,str(res))
#
# Special cases
#
oldtype=self.PI.resname(residue)
#
# If orgtype was specified then check that there's agreement with the pdb file
#
if orgtype:
if orgtype!=oldtype:
raise Exception('Incorrect original residue type: %s %s. You said: %s' %(residue,oldtype,orgtype))
#
#
#
if newtype=='ALA' and (oldtype!='GLY' and oldtype!='PRO'):
this_operation=self.fast_mutatetoALA(residue)
score=0.0
elif newtype=='GLY':
this_operation=self.fast_mutatetoGLY(residue)
score=0.0
elif oldtype=='ASP' and newtype=='ASN':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']='ASN'
if self.PI.atname(atom)=='OD2':
self.PI.atoms[atom]['ATNAME']='ND2'
this_operation.append(['add',atom,self.PI.atoms[atom]])
score=0.0
elif oldtype=='ASN' and newtype=='ASP':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']='ASP'
if self.PI.atname(atom)=='ND2':
self.PI.atoms[atom]['ATNAME']='OD2'
this_operation.append(['add',atom,self.PI.atoms[atom]])
score=0.0
elif oldtype=='GLU' and newtype=='GLN':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']='GLN'
if self.PI.atname(atom)=='OE2':
self.PI.atoms[atom]['ATNAME']='NE2'
this_operation.append(['add',atom,self.PI.atoms[atom]])
score=0.0
elif oldtype=='GLN' and newtype=='GLU':
#
# Just rename
#
for atom in self.PI.residues[residue]:
this_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']='GLU'
if self.PI.atname(atom)=='NE2':
self.PI.atoms[atom]['ATNAME']='OE2'
this_operation.append(['add',atom,self.PI.atoms[atom]])
score=0.0
elif oldtype=='TYR' and newtype=='PHE':
#
# Delete OH
#
for atom in self.PI.residues[residue]:
if self.PI.atname(atom)=='OH':
this_operation.append(['delete',atom,self.PI.atoms[atom]])
score=0.0
else:
#
# Use generic code
#
#
# Get the standard conformation
#
std_conf=self.aadefs[newtype]
#
# See which kind of mutation we do
# 1. Just put standard conformation
# 2. Standard conf + rotamer search
# 3. Use wt rotamer (if possible, otherwise use best rotamer)
# All can be used with and without debumping.
#
#
# Get the torsion angles for this residue
#
org_torsangles=[]
number_of_chis=self.get_nonH_torsions(residue)
#print 'Number of chi values for %s is %d' %(residue,number_of_chis)
for chinum in range(1,number_of_chis+1):
org_torsangles.append(self.get_chi(residue,chinum))
#
# Get the backbone atoms from the structure
#
bb_struct=[]
ref_coords=[]
for atom in self.PI.residues[residue]:
if (self.PI.is_backbone(atom) or self.PI.is_CB(atom)) and not self.PI.is_hydrogen(atom):
bb_struct.append(atom)
ref_coords.append(self.PI.GetPosition(atom))
#
# Get the corresponding atoms from the template
#
bb_template=[]
fit_coords=[]
for s_atom in bb_struct:
s_atname=self.PI.atname(s_atom)
for atom in std_conf['atoms']:
if atom[0]==s_atname:
bb_template.append(atom[0])
fit_coords.append(atom[1])
break
#
# Get rotation and translation for bb -> bb
#
import quatfit
refcenter,fitcenter,rotation=quatfit.qfit(len(ref_coords),ref_coords,fit_coords)
#
# Get the atoms that should be transformed
#
trans_atoms=[]
trans_coords=[]
for atom in std_conf['atoms']:
if not atom in bb_template and atom[0]!='O':
trans_atoms.append(atom[0])
trans_coords.append(atom[1])
#
# Apply rotation and translation to trans_coords
#
newcoords = quatfit.qtransform(len(trans_coords), trans_coords, refcenter, fitcenter, rotation)
#
# Delete the old side chain atoms and rename the ones that stay
#
for atom in self.PI.residues[residue]:
if atom.split(':')[-1] in ['OXT','O2',"O''"]:
# Rename the OXT
local_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']=newtype
local_operation.append(['add',atom,self.PI.atoms[atom]])
elif not atom in bb_struct:
this_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.remove_atom(atom)
else:
local_operation.append(['delete',atom,self.PI.atoms[atom]])
self.PI.atoms[atom]['RESNAME']=newtype
local_operation.append(['add',atom,self.PI.atoms[atom]])
#
# Copy coordinates to Protool array
#
struct_atom=self.PI.atoms[bb_struct[0]]
resnumber=struct_atom['RESNUM']
chainid=struct_atom['CHAINID']
atomnumber=struct_atom['NUMBER']
count=0
for atom in trans_atoms:
if atom[0]!='H':
uniqueid='%s:%s:%s' %(chainid,resnumber,atom)
if not self.PI.atoms.has_key(uniqueid):
self.PI.add_atom(uniqueid,atomnumber=atomnumber,
atomname=atom,chainid=chainid,residuename=newtype,
residuenumber=resnumber,
xcoord=newcoords[count][0],ycoord=newcoords[count][1],zcoord=newcoords[count][2])
this_operation.append(['add',uniqueid,self.PI.atoms[uniqueid]])
count=count+1
#
# Fix atom numbers
#
self.PI.renumber_atoms()
#
# Set the chiangles just as the parent residue
#
new_number_of_chis=self.get_nonH_torsions(residue)
count=1
for chi in org_torsangles:
if count>new_number_of_chis:
break
self.set_chi(residue,count,chi)
count=count+1
#
# Score this rotamer, if bump is zero then keep it
#
score=self.get_bump_value(residue)
if (score is None or score>0.0) and newtype!='ALA':
#
# Do rotamer search
#
score=self.get_best_rotamer(residue)
if score is None:
return None
# ----------------------------------------------------
#
# Keep track of the operations
#
updated_op=[]
for op,uniqueid,atom in this_operation:
if op=='delete':
updated_op.append([op,uniqueid,{}])
else:
added_atom=self.PI.atoms[uniqueid].copy()
not_needed=['CHAINID','tag','BOUND_TO','RESNUM']
for delete in not_needed:
if added_atom.has_key(delete):
del added_atom[delete]
updated_op.append([op,uniqueid,self.PI.atoms[uniqueid]])
self.mutate_operations=self.mutate_operations+updated_op
#
# Score is bump score
#
return score