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lammps/examples/USER/cgdna/util/generate_simple.py
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generate_simple.py
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# Setup tool for oxDNA input in LAMMPS format.
import math,numpy as np,sys,os
# system size
lxmin = -115.0
lxmax = +115.0
lymin = -115.0
lymax = +115.0
lzmin = -115.0
lzmax = +115.0
# rise in z-direction
r0 = 0.7
# definition of single untwisted strand
def single():
strand = inp[1].split(':')
com_start=strand[0].split(',')
posx=float(com_start[0])
posy=float(com_start[1])
posz=float(com_start[2])
risex=0
risey=0
risez=r0
strandstart=len(nucleotide)+1
for letter in strand[1]:
temp=[]
temp.append(nt2num[letter])
temp.append([posx,posy,posz])
vel=[0,0,0,0,0,0]
temp.append(vel)
temp.append(shape)
quat=[1,0,0,0]
temp.append(quat)
posx=posx+risex
posy=posy+risey
posz=posz+risez
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
nucleotide.append(temp)
return
# definition of single twisted strand
def single_helix():
strand = inp[1].split(':')
com_start=strand[0].split(',')
twist=0.6
posx = float(com_start[0])
posy = float(com_start[1])
posz = float(com_start[2])
risex=0
risey=0
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
dcomh=0.76
axisx=dcomh + posx
axisy=posy
strandstart=len(nucleotide)+1
quat=[1,0,0,0]
qrot0=math.cos(0.5*twist)
qrot1=0
qrot2=0
qrot3=math.sin(0.5*twist)
for letter in strand[1]:
temp=[]
temp.append(nt2num[letter])
temp.append([posx,posy,posz])
vel=[0,0,0,0,0,0]
temp.append(vel)
temp.append(shape)
temp.append(quat)
quat0 = quat[0]*qrot0 - quat[1]*qrot1 - quat[2]*qrot2 - quat[3]*qrot3
quat1 = quat[0]*qrot1 + quat[1]*qrot0 + quat[2]*qrot3 - quat[3]*qrot2
quat2 = quat[0]*qrot2 + quat[2]*qrot0 + quat[3]*qrot1 - quat[1]*qrot3
quat3 = quat[0]*qrot3 + quat[3]*qrot0 + quat[1]*qrot2 + quat[2]*qrot1
quat = [quat0,quat1,quat2,quat3]
posx=axisx - dcomh*(quat[0]**2+quat[1]**2-quat[2]**2-quat[3]**2)
posy=axisy - dcomh*(2*(quat[1]*quat[2]+quat[0]*quat[3]))
posz=posz+risez
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
nucleotide.append(temp)
return
# definition of twisted duplex
def duplex():
strand = inp[1].split(':')
com_start=strand[0].split(',')
twist=0.6
compstrand=[]
comptopo=[]
posx1 = float(com_start[0])
posy1 = float(com_start[1])
posz1 = float(com_start[2])
risex=0
risey=0
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
dcomh=0.76
axisx=dcomh + posx1
axisy=posy1
posx2 = axisx + dcomh
posy2 = posy1
posz2 = posz1
strandstart=len(nucleotide)+1
quat1=[1,0,0,0]
quat2=[0,0,-1,0]
qrot0=math.cos(0.5*twist)
qrot1=0
qrot2=0
qrot3=math.sin(0.5*twist)
for letter in strand[1]:
temp1=[]
temp2=[]
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
temp1.append(shape)
temp2.append(shape)
temp1.append(quat1)
temp2.append(quat2)
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[1]),len(nucleotide)+len(strand[1])+1])
nucleotide.append(temp1)
compstrand.append(temp2)
for ib in range(len(compstrand)):
nucleotide.append(compstrand[len(compstrand)-1-ib])
for ib in range(len(comptopo)):
topology.append(comptopo[ib])
return
# definition of array of duplexes
def duplex_array():
strand = inp[1].split(':')
number=strand[0].split(',')
posz1_0 = float(strand[1])
twist=0.6
nx = int(number[0])
ny = int(number[1])
dx = (lxmax-lxmin)/nx
dy = (lymax-lymin)/ny
risex=0
risey=0
risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2)
dcomh=0.76
for ix in range(nx):
axisx=lxmin + dx/2 + ix * dx
for iy in range(ny):
axisy=lymin + dy/2 + iy * dy
compstrand=[]
comptopo=[]
posx1 = axisx - dcomh
posy1 = axisy
posz1 = posz1_0
posx2 = axisx + dcomh
posy2 = posy1
posz2 = posz1
strandstart=len(nucleotide)+1
quat1=[1,0,0,0]
quat2=[0,0,-1,0]
qrot0=math.cos(0.5*twist)
qrot1=0
qrot2=0
qrot3=math.sin(0.5*twist)
for letter in strand[2]:
temp1=[]
temp2=[]
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
temp1.append(shape)
temp2.append(shape)
temp1.append(quat1)
temp2.append(quat2)
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
nucleotide.append(temp1)
compstrand.append(temp2)
for ib in range(len(compstrand)):
nucleotide.append(compstrand[len(compstrand)-1-ib])
for ib in range(len(comptopo)):
topology.append(comptopo[ib])
return
# main part
nt2num = {'A':1, 'C':2, 'G':3, 'T':4}
compnt2num = {'T':1, 'G':2, 'C':3, 'A':4}
shape = [1.1739845031423408,1.1739845031423408,1.1739845031423408]
nucleotide=[]
topology=[]
seqfile = open(sys.argv[1],'r')
# process sequence file line by line
for line in seqfile:
inp = line.split()
if inp[0] == 'single':
single()
if inp[0] == 'single_helix':
single_helix()
if inp[0] == 'duplex':
duplex()
if inp[0] == 'duplex_array':
duplex_array()
# output atom data in LAMMPS format
out = open(sys.argv[2],'w')
out.write('# LAMMPS data file\n')
out.write('%d atoms\n' % len(nucleotide))
out.write('%d ellipsoids\n' % len(nucleotide))
out.write('%d bonds\n' % len(topology))
out.write('\n')
out.write('4 atom types\n')
out.write('1 bond types\n')
out.write('\n')
out.write('# System size\n')
out.write('%f %f xlo xhi\n' % (lxmin,lxmax))
out.write('%f %f ylo yhi\n' % (lymin,lymax))
out.write('%f %f zlo zhi\n' % (lzmin,lzmax))
out.write('\n')
out.write('Masses\n')
out.write('\n')
out.write('1 3.1575\n')
out.write('2 3.1575\n')
out.write('3 3.1575\n')
out.write('4 3.1575\n')
out.write('\n')
out.write('# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
out.write('Atoms\n')
out.write('\n')
for ib in range(len(nucleotide)):
out.write("%d %d %22.16le %22.16le %22.16le 1 1 1\n" % (ib+1,nucleotide[ib][0],nucleotide[ib][1][0],nucleotide[ib][1][1],nucleotide[ib][1][2]))
out.write('\n')
out.write('# Atom-ID, translational, rotational velocity\n')
out.write('Velocities\n')
out.write('\n')
for ib in range(len(nucleotide)):
out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][2][0],nucleotide[ib][2][1],nucleotide[ib][2][2],nucleotide[ib][2][3],nucleotide[ib][2][4],nucleotide[ib][2][5]))
out.write('\n')
out.write('# Atom-ID, shape, quaternion\n')
out.write('Ellipsoids\n')
out.write('\n')
for ib in range(len(nucleotide)):
out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][3][0],nucleotide[ib][3][1],nucleotide[ib][3][2],nucleotide[ib][4][0],nucleotide[ib][4][1],nucleotide[ib][4][2],nucleotide[ib][4][3]))
out.write('\n')
out.write('# Bond topology\n')
out.write('Bonds\n')
out.write('\n')
for ib in range(len(topology)):
out.write("%d %d %d %d\n" % (ib+1,topology[ib][0],topology[ib][1],topology[ib][2]))
out.close()
seqfile.close()
sys.exit(0)
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