import fpdb
pdb = fpdb.fPDB('waterDimer.pdb')
residues = pdb.topology.residues
minDist = 10e8
keeper = None
for i, resi in enumerate(residues):
for resj in residues[:i]:
for atomi in resi.atoms:
for atomj in resj.atoms:
d_2 = fpdb.dist_2(atomi, atomj)
if d_2 < minDist:
minDist = d_2
keeper = (resi, atomi, resj, atomj)
resi, atomi, resj, atomj = keeper
print(("\nmin distance atom pair are atom %s%d:%s%d and %s%d:%s%d\n" % (
resi.name,
resi.index,
atomi.name,
atomi.index,
resj.name,
resj.index,
atomj.name,
atomj.index,
)))
#!/usr/bin/env python
import sys,os
import fpdb
after = 'shift_in_box.pdb'
init = 'tleap_out.pdb'
lig = 'lig.pdb'
pdb1 = fpdb.fPDB(init)
pdb2 = fpdb.fPDB(after)
coord1 = pdb1.topology.residues[0].atoms[0].posi
coord2 = pdb2.topology.residues[0].atoms[0].posi
print coord1
print coord2
dx = coord2[0] - coord1[0]
dy = coord2[1] - coord1[1]
dz = coord2[2] - coord1[2]
with open('lig_shift.pdb','w') as ofp:
for line in open(lig):
if len(line) >= 6 and line[:6] in ("ATOM ","HETATM"):
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
nx = x + dx
ny = y + dy
nz = z + dz
newline = "%s%8.3f%8.3f%8.3f%s"%(line[:30],nx,ny,nz,line[54:])
else:
def prepare_md(dirpath, output=sys.stdout):
dirpath = "%s/%s" % ("/home/fuqy/work/SPA_database/www/submit_jobs",
dirpath)
assert os.path.isdir(dirpath)
assert os.path.isfile("%s/rec.pdb" % dirpath)
assert os.path.isfile("%s/lig.pdb" % dirpath)
os.chdir(dirpath)
if True:
## receptor
# assert(1==0)
# load receptor
rec = fpdb.fPDB("%s/rec.pdb" % dirpath)
# fix his name
if os.path.isfile("%s/his.list" % dirpath):
# if his.list exist
# load his.list
histype = dict()
for line in open("%s/his.list" % dirpath):
histype[int(line.split()[0])] = line.split()[1]
for resi in rec.topology.residues:
if resi.index in list(histype.keys()):
resi.name = histype[resi.index]
else:
# else
for resi in rec.topology.residues:
if resi.name in ("HIS", "HID", "HIP", "HIE"):
#use HID by default
resi.name = "HID"
for resi in rec.topology.residues:
if resi.name in ("CYS", "CYZ"):
#use HID by default
resi.name = "CYX"
print(">>>>> OUTPUT of fSPA.prepare_md(): ")
rec.write_pdb("ftmp.pdb")
cgi_system("addter.py ftmp.pdb ftmp_ter.pdb", output)
#cgi_system("addter.py ftmp.pdb ftmp_ter.pdb").read()
with open("leap.in", 'w') as ofp:
ofp.write("""
source leaprc.ff14SB
rec = loadpdb ftmp_ter.pdb
savepdb rec tleap_out.pdb
quit
""")
cgi_system("tleap -f leap.in", output)
cgi_system("sed -i s/CYX/CYS/g tleap_out.pdb", output)
cgi_system("atomtypeconvert.py a2g tleap_out.pdb tleap_out_trans.pdb",
output)
# cgi_system("gmx pdb2gmx -f tleap_out_trans.pdb -o rec.gro -merge all -water tip3p -ff amber99sb",output)
# add box
# cgi_system("gmx editconf -f rec.gro -o box.gro -d 1.0",output)
## ligand
if False:
# fix atom coordinate, nothing to do
# compute shift
line_o = open('rec.gro').readlines()[2]
line_f = open('box.gro').readlines()[2]
xo = float(line_o[20:28]) * 10
yo = float(line_o[28:36]) * 10
zo = float(line_o[36:44]) * 10
xf = float(line_f[20:28]) * 10
yf = float(line_f[28:36]) * 10
zf = float(line_f[36:44]) * 10
xs, ys, zs = xf - xo, yf - yo, zf - zo
# adjust ligand coordinate
with open("lig_shift.pdb", 'w') as ofp:
for line in open("lig.pdb"):
if len(line) >= 6 and line[:6] in ("ATOM ", "HETATM"):
x = float(line[30:38]) + xs
y = float(line[38:46]) + ys
z = float(line[46:54]) + zs
ofp.write("%s%8.3f%8.3f%8.3f%s" %
(line[:30], x, y, z, line[54:]))
else:
ofp.write(line)
## cp mdp files
# cgi_system("cp -r %s/mdp ./"%fpdb.__path__[0][:-4],output)
## minimize receptor
# cgi_system("gmx grompp -f mdp/em.mdp -o em.tpr -c box.gro -p topol.top -maxwarn 10",output)
# cgi_system("gmx mdrun -deffnm em",output)
## add solvent
# cgi_system("gmx solvate -cp em.gro -cs spc216 -o sys.gro -p topol.top",output)
## minimize solvent
# cgi_system("gmx grompp -f mdp/em.mdp -o em_sys.tpr -c sys.gro -p topol.top -r box.gro -maxwarn 10",output)
#cgi_system("gmx mdrun -deffnm em_sys",output)
## check rmsd
## if too large of some atoms, warning
## generate sge files
## return to cgi, wait for submit
return 0
#!/usr/bin/python
import fpdb
import sys, os
traj = 'prod/traj.pdb'
os.system("shift_lig.py")
frame = next(fpdb.next_frame(traj))
with open("prod/a1.pdb", 'w') as ofp:
for line in frame:
ofp.write(line)
with open("prod/rec.pdb", 'w') as ofp:
for resi in fpdb.fPDB(frame).topology.get_protein_residues():
resi.write_pdb(ofp)
n = 0
with open("runspa.bash", 'w') as ofp:
ofp.write("#!/bin/bash\n")
ofp.write("source ~/.bashrc\n")
while True:
if os.path.isdir("spa_%d" % n):
os.system("cp prod/a1.pdb spa_%d" % n)
os.system("cp prod/rec.pdb spa_%d" % n)
os.system("cp lig_shift.pdb spa_%d/a1_lig.pdb" % n)
os.system("cp %s/para/SPA.amoeba.para spa_%d/SPA.para" %
(os.environ['SPAHOME'], n))
ofp.write("cd spa_%d\n" % n)
ofp.write("%s/bin/SPA_main SPA.para\n" % os.environ['SPAHOME'])
## pbsa
if True:
origin_lig = '%s.acpype/%s_GMX.pdb'%(ligname,ligname)
origin_rec = 'rec.gro'
box = 'box.gro'
## lig.pdb
origin_line = open(origin_rec).readlines()[2]
box_line = open(box).readlines()[2]
ox = float(origin_line[20:28])
oy = float(origin_line[28:36])
oz = float(origin_line[36:44])
bx = float(box_line[20:28])
by = float(box_line[28:36])
bz = float(box_line[36:44])
lig_o = fpdb.fPDB(origin_lig).topology.residues[0]
for atom in lig_o.atoms:
x,y,z = atom.posi[:3]
x += 10*(bx-ox)
y += 10*(by-oy)
z += 10*(bz-oz)
atom.posi = (x,y,z)
lig_o.write_pdb(open('lig.pdb','w'))
## restr_rec.itp
with open("pbsa.restr.itp",'w') as ofp:
ofp.write("[ position_restraints ]\n")
ofp.write("; atom type fx fy fz \n")
pdb = fpdb.fPDB("com.pdb")
for resi in pdb.topology.residues:
#!/usr/bin/python
import sys,os
import fpdb
ligfile = sys.argv[1]
flexfile = sys.argv[2]
recfile = sys.argv[3]
outfile = sys.argv[4]
# load residues
flex_resi = dict()
for resi in fpdb.fPDB(flexfile).topology.residues:
flex_resi[resi.index] = resi
rec_resi = fpdb.fPDB(recfile).topology.residues
lig_resi = fpdb.fPDB(ligfile).topology.residues[0]
# forge flex resides, add "N", "HN", "C", "O"
for template_resi in rec_resi:
index = template_resi.index
if flex_resi.has_key(index):
target_resi = flex_resi[index]
for atom in template_resi.atoms:
if target_resi.atoms_d.has_key(atom.name):
atom.posi = target_resi.atoms_d[atom.name].posi
# output residues
ofp = open(outfile,'w')
for resi in rec_resi:
resi.write_pdb(ofp)
default=(0, 0, 0))
parser.add_argument('-box',
nargs=3,
help='Box size',
type=float,
default=(0, 0, 0))
args = parser.parse_args()
infile = args.i
outfile = args.o
box = args.box
center = args.center
print ">>>>> Centering traj.."
n = 0
center_coord = None
pdb = fpdb.fPDB(infile)
if center == (0, 0, 0):
center_coord = pdb.find_protein_center()
else:
center_coord = center
print "----- Center Coordination :", center_coord
n = 0
ofp = open(outfile, 'w')
pdb = fpdb.fPDB(infile)
pdb.center(center_posi=center_coord, box=box)
pdb.write_pdb(ofp)
print "----- All done."
#!/usr/bin/python
import sys, os
import fpdb
import gmx_top
nonbonded = 'amber99sb.ffnonbonded.itp'
rtp = 'amber99sb.aminoacids.rtp'
waterfile = 'tip3p.itp'
gmxtop = gmx_top.gmxtop(nonbonded, rtp, waterfile)
pdb = fpdb.fPDB(sys.argv[1])
r1 = fpdb.topology.residues[0]
r2 = fpdb.topology.residues[1]
atom1 = r1.atoms['CA']
vs = cs = 0
for atom2 in r2.atoms:
v, c = fpdb.potential_atom_atom(atom1, atom2)
vs += v
cs += c
vdw, chg = fpdb.potential_resi(r1, r2)
vdw, chg = fpdb.potential_atom_atom(atom1, atom2)
print(">>>>> vDW:", vdw)
print(">>>>> Charge:", chg)
import fpdb
infile = sys.argv[1]
a1_file = 'a1.pdb'
lig_file = 'a1_lig.pdb'
rec_file = 'rec.pdb'
para_source = '/home/fuqiuyu/work/nmr_druggability/md/finished/1dhm/spa/SPA.para'
para_file = 'SPA.para'
print ">>>>> preparing SPA input files"
for model in fpdb.next_frame(infile):
pdb = fpdb.fPDB(model)
pdb.write_pdb(a1_file)
print "----- sys pdb done."
ofp_rec = open(rec_file, 'w')
for residue in pdb.topology.residues:
if residue.name in fpdb.standard_protein_residues:
residue.write_pdb(ofp_rec)
print "----- rec pdb done."
ofp_lig = open(lig_file, 'w')
for line in open(rec_file):
if len(line) >= 6 and line[:6] in ('ATOM ', 'HETATM'):
if line[12:16].strip() not in ('C', 'O', 'N', 'CA'):
if line[13] != 'H':
ofp_lig.write(line)
import fpdb
import sys, os
dir1 = 'part1'
dir2 = 'part2'
dirs = sys.argv[1:-1]
outfile = sys.argv[-1]
graphics = list()
for DIR in dirs:
graphics.append('%s/%s' % (DIR, 'graphic.pdb'))
pdbs = list()
for graphic in graphics:
pdbs.append(fpdb.fPDB(graphic))
waters = list()
for pdb in pdbs:
waters.append(pdb.topology.get_water_residues())
all_waters = list()
for tmp in waters:
all_waters.extend(tmp)
cutoff = 1.0
nr_waters = list()
for test_water in all_waters:
dist = 9999
neighbor_water = None
for water in nr_waters: