def FindMutantResidue(self):
""" Finds which residue is the alanine mutant in a pair of prmtop files
"""
origres = self.orig_prm.parm_data['RESIDUE_LABEL']
newres = self.new_prm.parm_data['RESIDUE_LABEL']
diffs = 0
mutres = -1
if len(origres) != len(newres):
raise MutateError(('Mutant prmtop (%s) has a different number of ' +
'residues than the original (%s)!') %
(self.new_prm.prm_name, self.orig_prm.prm_name))
for i in range(len(origres)):
if origres[i] != newres[i]:
diffs += 1
if newres[i] != 'GLY':
raise MutantResError('Mutant residue %s is %s but must be GLY!' %
(i+1, newres[i]))
mutres = i + 1
if diffs == 0:
raise MutateError(('Your mutant prmtop (%s) has the same sequence ' +
'as the original!') % (self.new_prm.prm_name,
self.orig_prm.prm_name))
elif diffs > 1:
raise MutateError('Your mutant prmtop (%s) can only have one mutation!'
% self.new_prm.prm_name)
return mutres
def _getnumatms(resname):
""" Returns the number of atoms in a given Amino acid residue """
if resname in 'GLY':
return 7
if resname in ('ALA', 'CYM', 'CYX'):
return 10
if resname in ('CYS', 'SER'):
return 11
if resname in ('ASP'):
return 12
if resname in ('ASN', 'PRO', 'THR'):
return 14
if resname in ('GLU'):
return 15
if resname in ('GLH', 'VAL'):
return 16
if resname in ('GLN', 'HID', 'HIE', 'MET'):
return 17
if resname in ('HIP'):
return 18
if resname in ('ILE', 'LEU'):
return 19
if resname in ('PHE'):
return 20
if resname in ('LYN', 'TYR'):
return 21
if resname in ('LYS'):
return 22
if resname in ('ARG', 'TRP'):
return 24
raise MutateError(('Unrecognized residue! Add %s to _getnumatms(resname) ' +
'in alamdcrd.py and reinstall gmx_MMPBSA' % resname))
def _scaledistance(coords, dist):
""" Scales the distance between 2 3-D cartesian coordinates to the specified
distance
"""
from math import sqrt
if len(coords) != 6:
raise MutateError('_scaledistance requires x,y,z coords for 2 atoms')
coords[3] -= coords[0] # set first 3 coordinates as origin
coords[4] -= coords[1]
coords[5] -= coords[2]
actualdist = sqrt(coords[3]*coords[3] + coords[4]*coords[4] +
coords[5]*coords[5])
scalefactor = dist / actualdist # determine scale factor
coords[3] *= scalefactor # scale original coordinates
coords[4] *= scalefactor
coords[5] *= scalefactor
coords[3] += coords[0] # move back to original place
coords[4] += coords[1]
coords[5] += coords[2]
return coords # return the coordinates
def _mutate(self, resname, coords):
list_one = 'ARG ASH ASN ASP CYM CYS CYX GLH GLN GLU HID HIE HIP ' + \
'LEU LYN LYS MET PHE SER TRP TYR ALA ILE THR VAL'
list_two = 'PRO'
chdist = 1.09
nhdist = 1.01
coords_tosend = [] # Coordinates to send to be scaled
new_coords = [] # Mutated coordinates to return
coords_received = [] # Scaled coordinates received
cterm = False
if _getnumatms(resname) * 3 == len(coords):
startindex = 0
cterm = False
elif (_getnumatms(resname) + 2) * 3 == len(coords):
startindex = 2
cterm = False
elif (_getnumatms(resname) + 1) * 3 == len(coords):
startindex = 0
cterm = True
else:
raise MutateError(('Mismatch in atom # in residue %s. (%d in ' +
'alamdcrd.py and %d passed in)') % (resname,
_getnumatms(resname), len(coords)))
if resname in list_one:
for i in range((4+startindex)*3):
new_coords.append(coords[i])
for i in range(3):
coords_tosend.append(coords[(2+startindex)*3+i])
for i in range(3):
coords_tosend.append(coords[(4+startindex)*3+i])
coords_received = _scaledistance(coords_tosend, chdist)
for i in range(3):
new_coords.append(coords_received[i+3])
elif resname in list_two:
for i in range((1+startindex)*3):
new_coords.append(coords[i])
coords_tosend = coords[startindex*3:startindex*3 + 6]
coords_received = _scaledistance(coords_tosend, nhdist)
for i in range(3):
new_coords.append(coords_received[i+3])
for i in range(6):
new_coords.append(coords[(10+startindex)*3+i])
coords_tosend = []
coords_received = []
for i in range(3):
coords_tosend.append(coords[(10+startindex)*3+i])
for i in range(3):
coords_tosend.append(coords[(7+startindex)*3+i])
coords_received = _scaledistance(coords_tosend, chdist)
for i in range(3):
new_coords.append(coords_received[i+3])
else:
raise MutateError("Residue %s not recognized! Can't mutate." % resname)
if cterm:
for i in range(9):
new_coords.append(coords[len(coords)-9+i])
else:
for i in range(6):
new_coords.append(coords[len(coords)-6+i])
return new_coords
def MutateTraj(self, newname):
""" Mutates a given mdcrd file based on 2 prmtops """
mutres = self.mutres
orig_resname = self.orig_prm.parm_data['RESIDUE_LABEL'][mutres-1]
resstart = self.orig_prm.parm_data['RESIDUE_POINTER'][mutres-1]
try:
nextresstart = self.orig_prm.parm_data['RESIDUE_POINTER'][mutres]
except IndexError:
nextresstart = self.orig_prm.ptr('natom')
number_atoms_mut = self.new_prm.ptr('natom')
if self.orig_prm.ptr('ifbox'):
number_atoms_mut += 1
coordsperline = 10 # number of coordinates in each line
coordsize = 8 # how large coordinates are in characters
counter = 0
coords_done = 0
coords_tomutate = []
temp_holder = []
new_coords = []
# location is 0 before modified coordinates, 1 during modified
# coordinates, and 2 after modified coordinates
location = 0
if orig_resname == 'GLY':
raise MutateError('You are trying to mutate GLY to ALA! ' +
'Not currently supported.')
new_mdcrd = open(newname, 'w')
mdcrd = open(self.traj, 'r')
for line in mdcrd:
counter += 1
# First line is always a comment
if counter == 1:
new_mdcrd.write('%-80s' % (line.strip() +
' and mutated by gmx_MMPBSA for alanine scanning'))
continue
if location == 0 and coords_done <= max(resstart * 3 - 4, 0) and \
coords_done + coordsperline > max(resstart * 3 - 4, 0):
location = 1
words = _getCoords(line, coordsperline, coordsize)
for i in range(coordsperline):
if coords_done <= resstart * 3 - 4:
if coords_done % coordsperline == 0:
new_mdcrd.write('\n')
new_mdcrd.write('%8.3f' % words[i])
coords_done += 1
else:
coords_tomutate.append(words[i])
continue
elif location == 1:
words = _getCoords(line, coordsperline, coordsize)
if coordsperline + len(coords_tomutate) >= \
3 * (nextresstart - resstart):
location = 2
for i in range(coordsperline):
if len(coords_tomutate) < 3 * (nextresstart - resstart):
coords_tomutate.append(words[i])
else:
temp_holder.append(words[i])
new_coords = self._mutate(orig_resname, coords_tomutate)
for i in range(len(new_coords)):
if coords_done % coordsperline == 0:
new_mdcrd.write('\n')
new_mdcrd.write('%8.3f' % new_coords[i])
coords_done += 1
if len(temp_holder) != 0:
for i in range(len(temp_holder)):
if coords_done % coordsperline == 0:
new_mdcrd.write('\n')
new_mdcrd.write('%8.3f' % temp_holder[i])
coords_done += 1
coords_tomutate = []
temp_holder = []
else:
for i in range(coordsperline):
coords_tomutate.append(words[i])
continue
elif location == 2:
words = _getCoords(line, coordsperline, coordsize)
for i in range(len(words)):
if coords_done % coordsperline == 0:
if not self.hasbox or coords_done < number_atoms_mut * 3 - 3:
new_mdcrd.write('\n')
new_mdcrd.write('%8.3f' % words[i])
coords_done += 1
if self.hasbox and coords_done == number_atoms_mut * 3 - 3:
new_mdcrd.write('\n')
if coords_done == number_atoms_mut * 3:
coords_done = 0
location = 0
continue
else:
if coords_done % coordsperline == 0:
new_mdcrd.write('\n')
new_mdcrd.write(line[:len(line)-1])
coords_done = coords_done + coordsperline
continue
new_mdcrd.write('\n')
mdcrd.close()
new_mdcrd.close()