def make_pdbs_png(png,
pdbs,
bgcolor="white",
center_res=None,
top_res=None,
highlight_res=None,
is_sticks=True,
is_putty=False,
width=480,
height=480):
if 'transparent' in bgcolor:
script = 'set opaque_background, off\n'
else:
script = make_bgcolor_script(bgcolor)
temp_fnames = []
if center_res and top_res:
transform = get_pdb_transform(pdbs[0], center_res, top_res)
for i in range(len(pdbs)):
soup = pdbatoms.Soup(pdbs[i])
soup.transform(transform)
new_pdb = util.fname_variant(pdbs[i])
soup.write_pdb(new_pdb)
temp_fnames.append(new_pdb)
pdbs[i] = new_pdb
del soup
script += make_load_pdbs_script(pdbs)
script += make_separate_chain_colors_script(pdbs)
if is_putty:
script += make_putty_script(get_scale_max(max_bfactor, upper_bfactor))
else:
script += cartoon_script
if not is_sticks:
script += "hide stick\n"
else:
script += "show stick\n"
script += make_ligands_as_sticks_script(pdbs)
if highlight_res:
script += make_highlight_res_script(highlight_res)
script += hide_backbone_sticks_script
# script += "clip far, 5\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def make_pdbs_png(
png, pdbs, bgcolor="white", center_res=None, top_res=None,
highlight_res=None, is_sticks=True, is_putty=False,
width=480, height=480):
if 'transparent' in bgcolor:
script = 'set opaque_background, off\n'
else:
script = make_bgcolor_script(bgcolor)
temp_fnames = []
if center_res and top_res:
transform = get_pdb_transform(pdbs[0], center_res, top_res)
for i in range(len(pdbs)):
soup = pdbatoms.Soup(pdbs[i])
soup.transform(transform)
new_pdb = util.fname_variant(pdbs[i])
soup.write_pdb(new_pdb)
temp_fnames.append(new_pdb)
pdbs[i] = new_pdb
del soup
script += make_load_pdbs_script(pdbs)
script += make_separate_chain_colors_script(pdbs)
if is_putty:
script += make_putty_script(get_scale_max(
max_bfactor, upper_bfactor))
else:
script += cartoon_script
if not is_sticks:
script += "hide stick\n"
else:
script += "show stick\n"
script += make_ligands_as_sticks_script(pdbs)
if highlight_res:
script += make_highlight_res_script(highlight_res)
script += hide_backbone_sticks_script
# script += "clip far, 5\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def rescale_positive_negative_bfactors_pdb(
pdb, lower_bfactor, upper_bfactor):
"""
Returns max_bfactor after rescale
"""
soup = pdbatoms.Soup(pdb)
bfactors = [a.bfactor for a in soup.atoms()]
if upper_bfactor is None:
upper_bfactor = max(bfactors)
# cut-off max_values
if upper_bfactor:
for j in range(len(bfactors)):
if bfactors[j] > upper_bfactor:
bfactors[j] = upper_bfactor
if bfactors[j] < -upper_bfactor:
bfactors[j] = -upper_bfactor
# will delete later within pymol script
add_fake_water_atom(soup, 'XXX', upper_bfactor)
add_fake_water_atom(soup, 'XXX', -upper_bfactor)
# cut-off below min_val to zero
if lower_bfactor:
for j in range(len(bfactors)):
if -lower_bfactor < bfactors[j] < lower_bfactor:
bfactors[j] = 0.0
for a, bfactor in zip(soup.atoms(), bfactors):
a.bfactor = bfactor
new_pdb = util.fname_variant(pdb)
soup.write_pdb(new_pdb)
return new_pdb, max(bfactors)
def transform_pdbs_to_residues_of_first_pdb(pdbs, center_res, top_res):
transform = get_pdb_transform(pdbs[0], center_res, top_res)
new_pdbs = []
for pdb in pdbs:
new_pdb = util.fname_variant(pdb)
soup = pdbatoms.Soup(pdb)
soup.transform(transform)
soup.write_pdb(new_pdb)
new_pdbs.append(new_pdb)
return new_pdbs
def transform_pdbs_to_residues_of_first_pdb(pdbs, center_res, top_res):
transform = get_pdb_transform(pdbs[0], center_res, top_res)
new_pdbs = []
for pdb in pdbs:
new_pdb = util.fname_variant(pdb)
soup = pdbatoms.Soup(pdb)
soup.transform(transform)
soup.write_pdb(new_pdb)
new_pdbs.append(new_pdb)
return new_pdbs
def pdb_to_bfactor_png(bfactor_pdb,
png,
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):
"""
Generates a bfactor-colored .png using the standard white-to-red
color scheme with a useful set of options. highlight_res,
center_res & top_res follow the 'A:10' style of residue naming.
"""
pdb, max_bfactor = rescale_positive_bfactors_pdb(bfactor_pdb,
lower_bfactor,
upper_bfactor)
temp_fnames = [pdb]
if center_res or top_res:
pdb = get_pdb_transform(pdb, center_res, top_res)
temp_fnames.append(pdb)
script = ""
script += bfactor_script(pdb, lower_bfactor, upper_bfactor, max_bfactor,
is_putty)
if highlight_res is not None:
pymol_res_id = get_pymol_id_from_res_tag(highlight_res)
script += make_highlight_res_script(pymol_res_id)
script += hide_backbone_sticks_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def get_best_alignment(pdb1, pdb2, segments1, segments2, atom_types): """Returns rmsd and filename of transformed pdb2.""" polymer1 = polymer.Polymer(pdb1) atoms1 = get_superposable_atoms(polymer1, segments1, atom_types) polymer2 = polymer.Polymer(pdb2) atoms2 = get_superposable_atoms(polymer2, segments2, atom_types) center1 = molecule.get_center(atoms1) polymer1.transform(vector3d.Translation(-center1)) polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2))) polymer2.transform(calculate_superposition_matrix(atoms1, atoms2)) rmsd = sum_rmsd(atoms1, atoms2) temp_pdb2 = util.fname_variant(pdb2) polymer2.transform(vector3d.Translation(center1)) polymer2.write_pdb(temp_pdb2) return rmsd, temp_pdb2
def get_best_alignment(pdb1, pdb2, segments1, segments2, atom_types):
"""Returns rmsd and filename of transformed pdb2."""
polymer1 = polymer.Polymer(pdb1)
atoms1 = get_superposable_atoms(polymer1, segments1, atom_types)
polymer2 = polymer.Polymer(pdb2)
atoms2 = get_superposable_atoms(polymer2, segments2, atom_types)
center1 = molecule.get_center(atoms1) # centruje pierwsza
polymer1.transform(vector3d.Translation(-center1))
polymer2.transform(vector3d.Translation(-molecule.get_center(atoms2)))
polymer2.transform(calculate_superposition_matrix(atoms1, atoms2))
rmsd = sum_rmsd(atoms1, atoms2)
temp_pdb2 = util.fname_variant(pdb2)
polymer2.transform(vector3d.Translation(center1))
polymer2.write_pdb(temp_pdb2)
return rmsd, temp_pdb2
def rescale_positive_bfactors_pdb(pdb, lower_bfactor, upper_bfactor):
"""
Returns max_bfactor after rescale (needed for worm
calculation)
"""
soup = pdbatoms.Soup(pdb)
bfactors = [a.bfactor for a in soup.atoms()]
# cut-off max_values
if upper_bfactor:
bfactors = [upper_bfactor if b > upper_bfactor else b
for b in bfactors]
# will delete later within pymol script
add_fake_water_atom(soup, 'XXX', upper_bfactor)
# cut-off below min_val to zero
if lower_bfactor:
for j in range(len(bfactors)):
bfactors = [0 if b < lower_bfactor else b for b in bfactors]
for a, bfactor in zip(soup.atoms(), bfactors):
a.bfactor = bfactor
new_pdb = util.fname_variant(pdb)
soup.write_pdb(new_pdb)
return new_pdb, max(bfactors)
def pdb_to_bfactor_png(
bfactor_pdb, png, 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):
"""
Generates a bfactor-colored .png using the standard white-to-red
color scheme with a useful set of options. highlight_res,
center_res & top_res follow the 'A:10' style of residue naming.
"""
pdb, max_bfactor = rescale_positive_bfactors_pdb(
bfactor_pdb, lower_bfactor, upper_bfactor)
temp_fnames = [pdb]
if center_res or top_res:
pdb = get_pdb_transform(pdb, center_res, top_res)
temp_fnames.append(pdb)
script = ""
script += bfactor_script(
pdb, lower_bfactor, upper_bfactor,
max_bfactor, is_putty)
if highlight_res is not None:
pymol_res_id = get_pymol_id_from_res_tag(highlight_res)
script += make_highlight_res_script(pymol_res_id)
script += hide_backbone_sticks_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def strip_solvent_pdb(pdb): new_pdb = util.fname_variant(pdb) txt = pdbtext.strip_solvent(open(pdb).read()) open(new_pdb, 'w').write(txt) return new_pdb
def strip_solvent_pdb(pdb):
new_pdb = util.fname_variant(pdb)
txt = pdbtext.strip_solvent(open(pdb).read())
open(new_pdb, 'w').write(txt)
return new_pdb