gen_ribon.py

#!/usr/bin/python
import sys, math, re
argvs = sys.argv

if (len(argvs) != 4):
    print "Usage $ python %s input_filename output_filename offset_length" % argvs[0]
    quit()
print "Generate ribon bilayer. Stripe length is 2*Lx"

def ReadLineGro(line):
    ret = []
    ret.append(int(line[0:5]))
    ret.append(line[5 :10].strip())
    ret.append(line[10:15].strip())
    ret.append(int(line[15:20]))
    ret.append(float(line[20:28]))
    ret.append(float(line[28:36]))
    ret.append(float(line[36:44]))
    return ret

def RetLipidName(line):
    ret = str(line[0]) + line[1]
    return ret

rf       = open(argvs[1], "r")
rem_d    = float(argvs[3])

rf_lines = rf.readlines()
comment  = rf_lines[0]
alln     = int(rf_lines[1].split()[0])
boxleng  = [float(i) for i in rf_lines[-1].split()]

Lipids = []
Waters = []

cur_lipid = RetLipidName(ReadLineGro(rf_lines[2]))
flag      = ReadLineGro(rf_lines[2])[5] < rem_d
for line in rf_lines[2:len(rf_lines)-1]:
    line_dat = ReadLineGro(line)
    lip_name = RetLipidName(line_dat)
    if(line_dat[2] != 'W'):
        if(lip_name != cur_lipid):
            flag = line_dat[5] < rem_d
            cur_lipid = lip_name
            
        if(flag):
            Waters.append(line_dat)
        else:
            Lipids.append(line_dat)
    else:
        Waters.append(line_dat)

wf       = open(argvs[2], "w")
wf.write(comment)
wf.write(str(alln)+'\n')

cur_lipid  = RetLipidName(Lipids[0])
mol_id     = 1
atom_id    = 1
for lipid in Lipids:
    lip_name = RetLipidName(lipid)
    if(lip_name != cur_lipid):
        cur_lipid = lip_name
        mol_id += 1
    
    wf.write("%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n"%(mol_id, lipid[1], lipid[2], atom_id, lipid[4], lipid[5], lipid[6]))
    atom_id += 1

mol_id += 1
    
for water in Waters:
    wf.write("%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n"%(mol_id, 'W', 'W', atom_id, water[4], water[5], water[6]))
    atom_id += 1
    mol_id  += 1

wf.write("%10.5f%10.5f%10.5f\n"%(boxleng[0], boxleng[1], boxleng[2]))
rf.close()
wf.close()

Generate ribon membrane.

1. Generate plane bilayer membrane by using insane.py
2. python gen_ribon input output dist