def soup_to_bfactor_png(
soup, png, bfactors, lower_bfactor=None, upper_bfactor=None,
highlight_res=None, is_putty=False):
temp_pdb = util.temp_fname('.pdb')
soup.load_residue_bfactors(bfactors)
max_bfactor = rescale_positive_bfactors_pdb(soup, temp_pdb,
lower_bfactor, upper_bfactor)
temp2_pdb = strip_solvent_pdb(temp_pdb)
script = bgcolor_script('white')
script += bfactor_script(
temp2_pdb, lower_bfactor, upper_bfactor, max_bfactor, is_putty)
if highlight_res is not None:
script += highlight_res_script(highlight_res)
script += hide_backbone_sticks_script()
if 'frame_pymol_script' in soup.__dict__:
script += soup.frame_pymol_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
width, height = 480, 480
if 'width' in soup.__dict__:
width = soup.width
if 'height' in soup.__dict__:
height = soup.height
run_pymol_script(script, width, height)
util.clean_fname(temp_pdb, temp2_pdb)
def convert_amber_to_pdb(top, crd, pdb):
"""Converts an amber .crd (or .rst) file to .pdb."""
tmp_pdb = util.temp_fname('.pdb')
os.system("ambpdb -bres -p %s < %s > %s 2> /dev/null" \
% (top, crd, tmp_pdb))
# clean-up the amber format to conform with standard
# pdb format with HETATM fields and chain id's
lines = open(tmp_pdb, 'r').readlines()
i_chain = 0
is_water = False
new_lines = []
for line in lines:
is_water = False
if line.startswith('ATOM'):
is_water = line[17:20] == 'WAT'
if line.startswith('ATOM'): # normal protein chain
if is_water:
new_lines.append("HETATM" + line[6:17] + "HOH" + line[20:])
else: # normal protein chain
chain_id = string.ascii_uppercase[i_chain]
new_lines.append(line[:21] + chain_id + line[22:])
elif line.startswith('TER'):
if not is_water:
new_lines.append(line)
else:
new_lines.append(line)
if not is_water and line.startswith('TER'):
i_chain += 1
open(pdb, 'w').write(''.join(new_lines))
os.remove(tmp_pdb)
def get_molecule(pdb):
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
bare_fname = util.temp_fname('.pdb')
open(bare_fname, 'w').write(txt)
mol = pdbstruct.Molecule(bare_fname)
if os.path.isfile(bare_fname):
os.remove(bare_fname)
return mol
def soup_to_bfactor_png(
soup, png, bfactors, lower_bfactor=None, upper_bfactor=None,
highlight_res=None, is_putty=False, is_sticks=True,
center_res=None, top_res=None, height=480, width=480):
"""
Wrapper around pdb_to_bfactor that loads in external values
for the residue bfactors with a reusable soup object.
"""
pdb = util.temp_fname('.pdb')
temp_fnames = [pdb]
soup.load_residue_bfactors(bfactors)
soup.write_pdb(pdb)
pdb_to_bfactor_png(
pdb, png, lower_bfactor, upper_bfactor,
highlight_res, is_putty, is_sticks,
center_res, top_res, height, width)
util.clean_fname(*temp_fnames)
def soup_to_bfactor_png(soup,
png,
bfactors,
lower_bfactor=None,
upper_bfactor=None,
highlight_res=None,
is_putty=False,
is_sticks=True,
center_res=None,
top_res=None,
height=480,
width=480):
"""
Wrapper around pdb_to_bfactor that loads in external values
for the residue bfactors with a reusable soup object.
"""
pdb = util.temp_fname('.pdb')
temp_fnames = [pdb]
soup.load_residue_bfactors(bfactors)
soup.write_pdb(pdb)
pdb_to_bfactor_png(pdb, png, lower_bfactor, upper_bfactor, highlight_res,
is_putty, is_sticks, center_res, top_res, height, width)
util.clean_fname(*temp_fnames)
def make_namd_from_pdb(pdb, psf, out_pdb):
"""
Creates charmm .pdb and .psf file. Can only make NAMD
generate CHARMM topology files, not OPLS ones - that
requires XPLOR but I don't care. Still, if OPLS
topology files are provided - can still run.
"""
def is_non_water_hetatm(line):
if not line.startswith("HETATM"):
return False
if line[17:20] != 'HOH':
return True
return False
in_pdb = util.temp_fname('.pdb')
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, is_non_water_hetatm)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
txt = pdbtext.strip_hydrogens(txt)
txt = pdbtext.renumber_residues(txt)
f = open(in_pdb, 'w')
f.write(txt)
f.close()
name = psf.replace('.psf', '')
psfgen_in = name + ".psfgen.in"
psfgen_out = name + ".psfgen.out"
replace = { 'pdb': in_pdb,
'out_pdb': out_pdb,
'psf': psf,
'module_dir': module_dir,
'topology': 'parms/charmm22.topology'
}
template = _psfgen_template
soup = Soup(in_pdb)
chains = soup.chains()
water_names = ['WAT', "TIP", "TIP3", "HOH"]
waters = [chain for chain in chains
if chain.n_residue() > 0 and chain.residue(0).type in water_names]
chains = [chain for chain in chains if chain.n_residue() > 0 and chain.residue(0).type not in water_names]
if len(waters) > 0:
template = template.replace("# insert water", _water_psfgen_template)
water_pdb = name + ".waters.pdb"
water_soup = Soup()
for water in waters:
water_soup.insert_chain(water)
water_soup.write_pdb(water_pdb)
replace['water_pdb'] = water_pdb
chains_template = ""
for i, chain in enumerate(chains):
id = 'ch%d' % i
pdb = name + '.' + id + '.pdb'
chain_soup = Soup()
chain_soup.append_chain(chain)
chain_soup.write_pdb(pdb)
chain_replace = { 'chain_id': id, 'chain_pdb': pdb }
chain_template = _chain_psfgen_template
chains_template += util.replace_dict(chain_template, chain_replace)
template = template.replace("# insert protein", chains_template)
template = util.replace_dict(template, replace)
open(psfgen_in, "w").write(template)
os.system("psfgen %s > %s" % (psfgen_in, psfgen_out))
os.remove(in_pdb)
def convert_pdb_to_amber(pdb, top, crd, solvent_buffer=0.0):
"""Convert a .pdb file into amber .top and .crd file."""
script = "# generate %s and %s files from %s\n" % (top, crd, pdb)
script += "\n"
script += "# load in amber force field\n"
script += "source leaprc.ff96\n"
script += "\n"
script += "# use AMBER6 GB radii for igb=1, gbparm=2\n"
script += "set default PBradii amber6\n"
# strip pdb and then load into soup
bare_pdb = util.temp_fname('.pdb')
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('HETATM'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
txt = pdbtext.strip_hydrogens(txt)
txt = pdbtext.renumber_residues(txt)
open(bare_pdb, 'w').write(txt)
soup = pdbstruct.Soup(bare_pdb)
os.remove(bare_pdb)
script += "\n"
residues = [r.type for r in soup.residues()]
if 'PHD' in residues:
script += "\n"
script += "# non-standard amino acid PHD"
script += "source leaprc.gaff\n"
script += "loadAmberPrep %s/parms/phd.prepin\n" % module_dir
script += "loadAmberParams %s/parms/phd.frcmod\n" % module_dir
for chain in soup.chains():
if isinstance(chain, pdbstruct.Protein):
if not chain.is_capped():
chain.charge_c_end()
in_pdb = pdb.replace('.pdb', '.tleap.pdb')
soup.write_pdb(in_pdb)
script += "\n"
script += " # insert protein\n"
script += "pdb = loadpdb %s\n" % in_pdb
script += "check pdb\n"
script += "\n"
script += " # disulfide bonds\n"
n = len(soup.residues())
for i in range(n):
for j in range(i+1, n):
if soup.residue(i).type in 'CYS' and soup.residue(j).type in 'CYS':
p1 = soup.residue(i).atom('SG').pos
p2 = soup.residue(j).atom('SG').pos
if vector3d.pos_distance(p1, p2) < 3.0:
soup.residue(i).type = 'CYX'
for atom in soup.residue(i).atoms():
atom.res_type = 'CYX'
soup.residue(j).type = 'CYX'
for atom in soup.residue(j).atoms():
atom.res_type = 'CYX'
script += "bond pdb.%d.SG pdb.%d.SG\n" % (i+1, j+1)
soup.write_pdb(in_pdb)
if solvent_buffer > 0.0:
script += "\n"
script += " # add explicit waters\n"
script += "solvateBox pdb TIP3PBOX %f iso\n" % solvent_buffer
script += "\n"
script += "\n"
script += " # write files\n"
script += "saveAmberParm pdb %s %s\n" % (top, crd)
script += "\n"
script += "quit\n"
script += "\n"
name = crd.replace('.crd', '')
tleap_in = name + ".tleap.in"
open(tleap_in, "w").write(script)
tleap_out = name + ".tleap.out"
os.system("tleap -f %s > %s" % (tleap_in, tleap_out))
convert_amber_to_pdb(top, crd, name + '.pdb')
os.remove("leap.log")
mol selection {backbone}
mol representation NewCartoon 0.40 20.00 2.50 0
mol addrep top
mol selection {all}
mol representation CPK 0.5 2 8 6
mol addrep top
mol smoothrep top 0 2
mol smoothrep top 1 2
"""
if len(sys.argv) < 2:
print "Usage: vmdtraj.py md"
sys.exit(1)
in_md = sys.argv[1]
parms = {"ext_top": "parm7", "ext_trj": "crd", "top": in_md + ".top", "trj": in_md + ".trj"}
if not has_files(parms["top"], parms["trj"]):
parms = {"ext_top": "gro", "ext_trj": "trr", "top": in_md + ".gro", "trj": in_md + ".trr"}
if not has_files(parms["top"], parms["trj"]):
parms = {"ext_top": "psf", "ext_trj": "dcd", "top": in_md + ".psf", "trj": in_md + ".dcd"}
if not has_files(parms["top"], parms["trj"]):
print "Can't recognize trajectories with basename", in_md
cmd_fname = util.temp_fname(".vmd")
script = util.replace_dict(s, parms)
open(cmd_fname, "w").write(script)
os.system(vmd + " -e " + cmd_fname)
os.remove(cmd_fname)
