def reparametrize(diheds, selection, start_conf, start_xvg, end_conf, end_xvg,
top):
Nswarms = len(diheds[0])
rsel = res_selection.res_select('%s' % start_conf, '%s' % selection)
# calculate average drift in collective variables space
sys.stderr.write('Residue selection: %s' % rsel)
newpts = []
for interp in range(len(diheds)):
avg = []
for r in rsel:
driftList = []
for i in range(len(diheds[interp])):
vec = []
xvg = open(diheds[interp][i], 'r')
for line in xvg:
if re.search(r'\-%d\n' % r, line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
vec += [phi_val, psi_val]
driftList.append(vec)
# driftList has phi,psi values for residue in every swarm
driftdat = open('dihedrals%d.dat' % interp, 'w')
for pt in driftList:
driftdat.write('%f %f\n' % (pt[0], pt[1]))
avg += [scale((1 / float(Nswarms)), reduce(mapadd, driftList))]
newpts += avg
# extract initial and target dihedral values
initpt = []
for r in rsel:
xvg = open(start_xvg, 'r')
for line in xvg:
if re.search(r'\-%d\n' % r, line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
initpt += [phi_val, psi_val]
targetpt = []
for r in rsel:
xvg = open(end_xvg, 'r')
for line in xvg:
if re.search(r'\-%d\n' % r, line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
targetpt += [phi_val, psi_val]
# something with 1 indexing makes this padding necessary.
paddingpt = [0] * len(initpt)
newpts.insert(0, initpt)
newpts.append(targetpt)
newpts.append(paddingpt)
sys.stderr.write('The new list of points is: %s\n' % newpts)
for pt in newpts:
sys.stderr.write('%s %s\n' % (pt[0], pt[1]))
adjusted = rep_pts(newpts)
# TODO implement a dist_treshold=1.0
iters = [adjusted]
for i in range(100):
iters.append(rep_pts(iters[i]))
adjusted = iters[-1]
# delete the padding point
adjusted = adjusted[:-1]
sys.stderr.write('The adjusted points are:\n')
for pt in adjusted:
sys.stderr.write('%s %s\n' % (pt[0], pt[1]))
# calculate reparam distance
# TODO measure the distance between the reparametrized points and the input points
# write the topology for the next iteration
# treat the reparam values as a stack
# temporary additional restraints for alanine dipeptide
theta_val = [
1.6, 1.48, 1.36, 1.24, 1.12, 1.0, 0.8799999999999999,
0.7599999999999999, 0.6399999999999999, 0.5199999999999998,
0.3999999999999999, 0.2799999999999998, 0.1599999999999997,
0.039999999999999813, -0.0800000000000003, -0.20000000000000018,
-0.3200000000000003, -0.4400000000000004, -0.5600000000000005, -0.8
]
zeta_val = [
-4.3, -3.8, -3.3, -2.8, -2.3, -1.7999999999999998, -1.2999999999999998,
-0.7999999999999998, -0.2999999999999998, 0.20000000000000018,
0.7000000000000002, 1.2000000000000002, 1.7000000000000002, 2.2, 2.7,
3.2, 3.7, 4.2, 4.7, 5.7
]
top = open(top, 'r').read().split('#include dihedral_restraints')
for k in range(1, len(adjusted) - 1):
newtop = open('%d.top' % k, 'w')
newtop.write('%s' % top[0])
sys.stderr.write("Writing restraints for interpolant index %i\n" % k)
newtop.write("[ dihedral_restraints ]\n")
newtop.write(
"; ai aj ak al type label phi dphi kfac power\n")
stack = adjusted[k]
protein = res_selection.protein('%s' % start_conf)
for r in rsel:
# there may be multiple residues matching the resnr, e.g., dimers
phi = [
a for a in protein
if (a.resnr == int(r) and (a.atomname == 'CA' or a.atomname ==
'N' or a.atomname == 'C')) or
(a.resnr == int(r) - 1 and a.atomname == 'C')
]
psi = [
a for a in protein
if (a.resnr == int(r) and (a.atomname == 'N' or a.atomname ==
'CA' or a.atomname == 'C')) or
(a.resnr == int(r) + 1 and a.atomname == 'N')
]
# get phi and psi values from the reparametrization vector
numres = len(phi) / 4
for i in range(numres):
phi_val = stack[i]
psi_val = stack[i + 1]
# write phi, psi angles
# TODO EXPLICIT DIHEDRALS FOR ALANINE DIPEPTIDE
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n" %
(5, 7, 9, 15, 1, 1, phi_val, 0, 1, 2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n" %
(7, 9, 15, 17, 1, 1, psi_val, 0, 1, 2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n" %
(1, 5, 7, 9, 1, 1, theta_val[k], 0, 1, 2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n" %
(9, 15, 17, 19, 1, 1, zeta_val[k], 0, 1, 2))
#newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(phi[i*4].atomnr,phi[i*4+1].atomnr,
# phi[i*4+2].atomnr,phi[i*4+3].atomnr,1,1,phi_val,0,1,2))
#newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(psi[i*4].atomnr,psi[i*4+1].atomnr,
# psi[i*4+2].atomnr,psi[i*4+3].atomnr,1,1,psi_val,0,1,2))
# delete the already added values from the stack
stack = stack[numres * 2 - 1:]
newtop.write('%s' % top[1])
def reparametrize(diheds, selection, start_conf, start_xvg, end_conf, end_xvg, top):
Nswarms = len(diheds[0])
rsel = res_selection.res_select('%s'%start_conf,'%s'%selection)
# calculate average drift in collective variables space
sys.stderr.write('Residue selection: %s' %rsel)
newpts = []
for interp in range(len(diheds)):
avg = []
for r in rsel:
driftList = []
for i in range(len(diheds[interp])):
vec=[]
xvg = open(diheds[interp][i],'r')
for line in xvg:
if re.search(r'\-%d\n'%r,line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
vec+=[phi_val,psi_val]
driftList.append(vec)
# driftList has phi,psi values for residue in every swarm
driftdat=open('dihedrals%d.dat'%interp,'w')
for pt in driftList:
driftdat.write('%f %f\n'%(pt[0],pt[1]))
avg+=[scale((1/float(Nswarms)),reduce(mapadd,driftList))]
newpts+=avg
# extract initial and target dihedral values
initpt = []
for r in rsel:
xvg = open(start_xvg,'r')
for line in xvg:
if re.search(r'\-%d\n'%r,line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
initpt+=[phi_val,psi_val]
targetpt = []
for r in rsel:
xvg = open(end_xvg,'r')
for line in xvg:
if re.search(r'\-%d\n'%r,line):
phi_val = float(line.split()[0])
psi_val = float(line.split()[1])
targetpt+=[phi_val,psi_val]
# something with 1 indexing makes this padding necessary.
paddingpt=[0]*len(initpt)
newpts.insert(0,initpt)
newpts.append(targetpt)
newpts.append(paddingpt)
sys.stderr.write('The new list of points is: %s\n' %newpts)
for pt in newpts:
sys.stderr.write('%s %s\n'%(pt[0],pt[1]))
adjusted=rep_pts(newpts)
# TODO implement a dist_treshold=1.0
iters=[adjusted]
for i in range(100):
iters.append(rep_pts(iters[i]))
adjusted=iters[-1]
# delete the padding point
adjusted=adjusted[:-1]
sys.stderr.write('The adjusted points are:\n')
for pt in adjusted:
sys.stderr.write('%s %s\n'%(pt[0],pt[1]))
# calculate reparam distance
# TODO measure the distance between the reparametrized points and the input points
# write the topology for the next iteration
# treat the reparam values as a stack
# temporary additional restraints for alanine dipeptide
theta_val=[1.6, 1.48, 1.36, 1.24, 1.12, 1.0, 0.8799999999999999, 0.7599999999999999, 0.6399999999999999, 0.5199999999999998, 0.3999999999999999, 0.2799999999999998, 0.1599999999999997, 0.039999999999999813, -0.0800000000000003, -0.20000000000000018, -0.3200000000000003, -0.4400000000000004, -0.5600000000000005, -0.8]
zeta_val=[-4.3, -3.8, -3.3, -2.8, -2.3, -1.7999999999999998, -1.2999999999999998, -0.7999999999999998, -0.2999999999999998, 0.20000000000000018, 0.7000000000000002, 1.2000000000000002, 1.7000000000000002, 2.2, 2.7, 3.2, 3.7, 4.2, 4.7, 5.7]
top=open(top,'r').read().split('#include dihedral_restraints')
for k in range(1,len(adjusted)-1):
newtop=open('%d.top'%k,'w')
newtop.write('%s'%top[0])
sys.stderr.write("Writing restraints for interpolant index %i\n" %k)
newtop.write("[ dihedral_restraints ]\n")
newtop.write("; ai aj ak al type label phi dphi kfac power\n")
stack=adjusted[k]
protein = res_selection.protein('%s'%start_conf)
for r in rsel:
# there may be multiple residues matching the resnr, e.g., dimers
phi = [a for a in protein if (a.resnr == int(r) and
(a.atomname == 'CA' or a.atomname == 'N' or a.atomname == 'C')) or
(a.resnr == int(r)-1 and a.atomname == 'C')]
psi = [a for a in protein if (a.resnr == int(r) and
(a.atomname == 'N' or a.atomname == 'CA' or a.atomname == 'C')) or
(a.resnr == int(r)+1 and a.atomname == 'N')]
# get phi and psi values from the reparametrization vector
numres = len(phi)/4
for i in range(numres):
phi_val=stack[i]
psi_val=stack[i+1]
# write phi, psi angles
# TODO EXPLICIT DIHEDRALS FOR ALANINE DIPEPTIDE
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(5,7,9,15,1,1,phi_val,0,1,2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(7,9,15,17,1,1,psi_val,0,1,2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(1,5,7,9,1,1,theta_val[k],0,1,2))
newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(9,15,17,19,1,1,zeta_val[k],0,1,2))
#newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(phi[i*4].atomnr,phi[i*4+1].atomnr,
# phi[i*4+2].atomnr,phi[i*4+3].atomnr,1,1,phi_val,0,1,2))
#newtop.write("%5d%5d%5d%5d%5d%5d%8.4f%5d%5d%5d\n"%(psi[i*4].atomnr,psi[i*4+1].atomnr,
# psi[i*4+2].atomnr,psi[i*4+3].atomnr,1,1,psi_val,0,1,2))
# delete the already added values from the stack
stack = stack[numres*2-1:]
newtop.write('%s'%top[1])
import argparse
import res_selection
parser = argparse.ArgumentParser()
parser.add_argument('-i',required=True, help='The initial .gro file')
parser.add_argument('-n',required=True, help='The number of interpolation steps')
parser.add_argument('-x',required=True, help='The desired index file (.ndx)')
parser.add_argument('-p',required=True, help='A topology file for the restraints, must contain the line "#include dihedral_restraints" where the restraints are to be written')
args = vars(parser.parse_args())
conf=args['i']
ndx=args['x']
n=int(args['n'])
top = open(args['p'],'r').read()
selection = res_selection.res_select(conf,ndx)
protein = res_selection.protein(conf)
top=top.split('#include dihedral_restraints')
print selection
theta_val=[1.6, 1.48, 1.36, 1.24, 1.12, 1.0, 0.8799999999999999, 0.7599999999999999, 0.6399999999999999, 0.5199999999999998, 0.3999999999999999, 0.2799999999999998, 0.1599999999999997, 0.039999999999999813, -0.0800000000000003, -0.20000000000000018, -0.3200000000000003, -0.4400000000000004, -0.5600000000000005, -0.8]
zeta_val=[-4.3, -3.8, -3.3, -2.8, -2.3, -1.7999999999999998, -1.2999999999999998, -0.7999999999999998, -0.2999999999999998, 0.20000000000000018, 0.7000000000000002, 1.2000000000000002, 1.7000000000000002, 2.2, 2.7, 3.2, 3.7, 4.2, 4.7, 5.7]
for k in range(1,n):
newtop=open('%s.top'%k,'w')
# write the initial part of the topology file
newtop.write('%s'%top[0])
xvg = open('%s.xvg'%k,'r').readlines()
#print "Writing restraints for interpolant number %i" %k
newtop.write("[ dihedral_restraints ]\n")