def rtrun(cmd, selection, suffix):
f = tempfile.NamedTemporaryFile(delete=False) # True)
output = os.path.dirname(f.name) + os.sep + selection + '.pdb'
output2 = os.path.dirname(f.name) + os.sep + selection + '_mut.pdb'
exe(cmdline)
print(cmdline)
cmd.save(output, selection)
def testPseSupport(self):
cmd.load_callback(callback.Callback(), 'c1')
with testing.mktemp('tmp.pse') as session_filename:
cmd.save(session_filename)
cmd.delete('*')
cmd.load(session_filename)
self.assertTrue('c1' in cmd.get_names())
def save_surface(arg1):
cmd.disable()
cmd.enable(arg1)
cmd.hide("everything", arg1)
cmd.show("surface", arg1)
cmd.save("%s.obj" % arg1, arg1)
cmd.enable()
def main():
parser=argparse.ArgumentParser()
parser.add_argument('-p', action='store', required=True, dest='pdbfile',
help='pathfile is a textfile of name of pdb')
parser.add_argument('-l', action='store', required=True, dest='loop',
help='loop is an int number')
inputs=parser.parse_args()
pdbfile=inputs.pdbfile
loop=int(inputs.loop)
print "loop is %s "% loop
dirname=os.getcwd()+'/interface_analyzer/pdbdata/'+pdbfile
pdbfileselect=pdbfile.split('.')
savefile=os.getcwd()+'/interface_analyzer/pdbdata/'+pdbfileselect[0]+'_antigen.pdb'
print "remove antibody of complex,so can caculate the value of antigen sasa "
pymol.finish_launching()
if loop!=0:
pymol.cmd.reinitialize()
cmd.load(dirname)
cmd.remove('hetatm')
cmd.select('target1',pdbfileselect[0])
cmd.save(dirname,(('target1')))
cmd.delete('target1')
cmd.remove('solvent')
cmd.remove('hydrogens')
cmd.remove('chain L+H')
cmd.select('target',pdbfileselect[0])
cmd.save(savefile,(('target')))
cmd.delete(all)
cmd.sync()
cmd.quit()
print "remove the antibody of complex have done"
def ForceSaveObject(self, file, objname, objtype):
basepath, filename = os.path.split(file)
filebasename, fileextname = os.path.splitext(filename)
self.Set_Object_Variables(objtype)
if self.savepath != basepath:
newfile = os.path.join(self.savepath,filebasename + '.pdb')
if os.path.isfile(newfile):
answer = tkMessageBox.askquestion("Question",
message= "An object with that name already exists in your '" + \
objtype + "' folder. Would you like to overwrite it?",
icon='warning')
if str(answer) == 'no':
return 2
try:
cmd.save(newfile, objname, state=1)
except:
self.DisplayMessage(" ERROR: The file could not be saved in your '" + objtype + "' folder.", 2)
return 1
self.VarPath.set(newfile)
return 0
def testMAEsaveLoadSessions(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
allpropdata = {}
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
allpropdata[obj] = {}
for prop in props:
allpropdata[obj][prop] = cmd.get_property(prop, obj)
with testing.mktemp('.pse') as psefilename:
cmd.save(psefilename)
cmd.load(psefilename)
# this is to fail the test on purpose
# cmd.set_property('i_m_ct_format', 3, '1d_smiles.mol_13')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
# test to make sure there are no extra properties or not enough properties
self.assertEqual(set(props), set(allpropdata[obj].keys()))
# test to make sure all property values are the same
for prop in props:
try:
self.assertTrue(allpropdata[obj][prop] == cmd.get_property(prop, obj))
except:
self.fail('properties are not the same: obj=%s prop=%s' % (obj, prop))
def load_save1():
while 1:
time.sleep(random.random())
cmd.delete("obj1")
cmd.load("dat/pept.pdb","obj1")
time.sleep(random.random())
cmd.save("tmp/T01a.pdb","obj1")
def mutate_atoms(desired_sequence):
# Acquire the lock once you execute this program
lock.acquire()
cmd.reset()
# Check the length of peptide sequence
# If the sequence does not match the MHC structure, the program will terminate.
try:
if len(desired_sequence) != 9:
raise AssertionError
except AssertionError:
sys.exit(
"Please input a peptide sequence with exactly 9 residues (in short abbreviation, no space)!"
)
# Execute the mutation command based on the PyMOL API.
# For each round, we construct a new PyMOL object to avoid the problem of different mutation affecting each other.
cmd.wizard("mutagenesis")
cmd.load("structures/3pwn_clear_original.pdb")
new_sequence = translate_sequence(desired_sequence)
for i in range(len(new_sequence)):
cmd.refresh_wizard()
cmd.get_wizard().set_mode(new_sequence[i])
cmd.get_wizard().do_select("C/%d/" % (i + 1))
cmd.get_wizard().apply()
cmd.save("structures/mutated_intermediate/mutated_pmhc_complex.pdb")
cmd.quit()
# Release the lock when the program ends
lock.release()
def reload_system(self, ln: str, smis: oechem.OEMol, old_pdb: str, is_oe_already: bool = False):
with self.logger("reload_system") as logger:
logger.log("Loading {} with new smiles {}".format(old_pdb, ln))
with tempfile.TemporaryDirectory() as dirpath:
ofs = oechem.oemolostream("{}/newlig.mol2".format(dirpath))
oechem.OEWriteMolecule(ofs, smis)
ofs.close()
cmd.reinitialize()
cmd.load(old_pdb)
cmd.remove("not polymer")
cmd.load("{}/newlig.mol2".format(dirpath), "UNL")
cmd.alter("UNL", "resn='UNL'")
cmd.alter("UNL", "chain='A'")
self.config.pdb_file_name = self.config.tempdir() + "reloaded.pdb"
cmd.save(self.config.pdb_file_name)
cmd.save(self.config.tempdir() + "apo.pdb")
with open(self.config.pdb_file_name, 'r') as f:
self.pdb = app.PDBFile(f)
self.positions, self.topology = self.pdb.getPositions(), self.pdb.getTopology()
if self.config.explicit and self.config.method == 'amber':
self.system, self.topology, self.positions = self.__setup_system_ex_amber(
pdbfile=self.config.pdb_file_name)
elif self.config.explicit:
self.system, self.topology, self.positions = self.__setup_system_ex_mm()
else:
self.system, self.topology, self.positions = self.__setup_system_im( pdbfile=self.config.pdb_file_name)
return self.system
def writePdb(sel, prefix=""):
pdbfn = prefix + sel + ".pdb"
npdbfn = pdbfn.replace(" or ", "")
npdbfn = npdbfn.replace(" and ", "")
npdbfn = npdbfn.translate(None, string.whitespace)
cmd.save(npdbfn, sel)
return npdbfn
def test(self):
cmd.viewport(100, 100)
# make map
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isomesh('mesh', 'map')
# check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'mesh')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
# continue without map
cmd.delete('map')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
def torsion_drive(atom1, atom2, atom3, atom4, interval, selection, path, mol_name,):
"""
This function generates input pdbs of dihedral angles selected of intervals specified with interval
:param atom1: name of atom 1 of dihedral
:param atom2: name of atom 2 of dihedral
:param atom3: name of atom 3 of dihedral
:param atom4: name of atom 4 of dihedral
:param interval: int or float (in degrees) of intervals to generate torsion scan for
:param selection: name of selection for molecule
:param path: path to where pdb files should be saved
:param mole_name: name of molecule to append to filenamen
"""
atom1 = selection + " and name " + atom1
atom2 = selection + " and name " + atom2
atom3 = selection + " and name " + atom3
atom4 = selection + " and name " + atom4
for angle in range(0, 360 + int(interval), int(interval)):
try:
os.makedirs('%s/%i' % (path, angle))
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else:
raise
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle)
filename = '%s/%i/%s_%i.pdb' % (path, angle, mol_name, angle)
cmd.save(filename, selection, 1)
def testMMTFExportEmpty(self):
with testing.mktemp('.mmtf') as filename:
cmd.save(filename)
cmd.load(filename, 'm1')
self.assertEqual(cmd.count_atoms(), 0)
self.assertEqual(cmd.get_names(), ['m1'])
def testMMTF(self):
'''Styled MMTF export/import'''
S = 0b10 # 1 << 1 spheres
D = 0b1000000000 # 1 << 9 dots
B = 2 # blue
R = 4 # red
cmd.fragment('gly')
cmd.color(B)
cmd.color(R, 'elem C')
cmd.show_as('spheres')
cmd.show_as('dots', 'elem C')
with testing.mktemp('.mmtf') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.load(filename)
color_list = []
reps_list = []
cmd.iterate('*', 'color_list.append(color)', space=locals())
cmd.iterate('*', 'reps_list.append(reps)', space=locals())
self.assertEqual(color_list, [B, R, R, B, B, B, B])
self.assertEqual(reps_list, [S, D, D, S, S, S, S])
def testSaveRef(self, format):
# for rms_cur (not all formats save all identifiers)
m = -1
cmd.set('retain_order')
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
cmd.copy('m3', 'm1')
cmd.rotate('y', 90, 'm2')
cmd.align('m3', 'm2')
# with ref=m3
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2', ref='m3')
cmd.load(filename, 'm4')
self.assertAlmostEqual(cmd.rms_cur('m4', 'm1', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m4', 'm2', matchmaker=m), 1.87, delta=1e-2)
# without ref
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2')
cmd.load(filename, 'm5')
self.assertAlmostEqual(cmd.rms_cur('m5', 'm2', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m5', 'm1', matchmaker=m), 1.87, delta=1e-2)
def builderNanodisc(protein, membrane, scaffold, prefixName, runNumber, x=0, y=0, refine=False):
"""
builds a MP-nanodisc systems
scaffold in this case is a double belt of MSP
"""
# Checking time of builder function execution
if protein != None:
print('protein is: ' + protein)
print('scaffold is: ' + scaffold)
print('membrane is: ' + membrane)
empty = False
if protein is None: empty = True
if not empty:
tmp_prot = "tmp_prot" + str(runNumber)
cmd.copy(tmp_prot, protein) # store initial
cmd.translate("[{},{},0]".format(x, y), tmp_prot)
print("State of empty/not-empty: {}".format(empty))
# copies to delete later
tmp_scaffold = "tmp_scaffold" + str(runNumber)
tmp_memb = "tmp_memb" + str(runNumber)
tmp_origin = "origin" + str(runNumber)
cmd.copy(tmp_scaffold, scaffold) # store initial
cmd.copy(tmp_memb, membrane) # store initial
center(tmp_memb)
center(tmp_scaffold)
cmd.pseudoatom(tmp_origin, pos=[0, 0, 0])
cmd.origin(tmp_origin)
#outRadius = findAverDist(tmp_scaffold) #doubles time for each run
outRadius = TMdistCheck(tmp_scaffold, 0.2)
print("Max distance from origin to scaffold in xy plane: {}".format(outRadius))
# remove lipids beyond border encased by MSP
cmd.remove("br. org and {} beyond {} of {}".format(tmp_memb, outRadius, tmp_origin))
# remove lipids clashing with tmp_protein core
if not empty:
avXY = TMdistCheck(tmp_prot, 0.2)
if avXY == -1: return "bad model"
minXY = avXY / 2.0
# remove lipids inside pore
cmd.remove("br. org and {} within {} of {}".format(tmp_memb, minXY, tmp_origin))
print("Mean distance if TM cross-section in xy plane: {}".format(avXY))
if empty:
cmd.remove("br. org and {} within 0.4 of {} and not hydro".format(tmp_memb, tmp_scaffold))
s = "empty_{}_{}".format(membrane, scaffold)
else:
cmd.remove("br. org and {} within 0.3 of pol. and not hydro".format(tmp_memb))
s = "{}_{}_{}".format(protein, membrane, scaffold)
if refine: s += "{}_{}".format(int(x), int(y))
if prefixName:
s = "{}{}".format(prefixName, s)
cmd.create(s, "({},{}, {})".format(protein, tmp_scaffold, tmp_memb))
cmd.save(s + ".pdb", s)
cmd.delete(tmp_memb)
cmd.delete(tmp_scaffold)
cmd.delete(tmp_prot)
cmd.delete(tmp_origin)
return s
def plot(self, outfile):
ctrl_id, case_id, snp_df_sub = self.score_on_var()
df = pd.merge(snp_df_sub, self.snps2aa, on='id')
#pymol.finish_launching()
cmd.reinitialize()
cmd.fetch(self.pdb)
cmd.alter(self.pdb, 'b = 0.5')
cmd.show_as('cartoon', self.pdb)
cmd.color('white', self.pdb)
for i, row in df.iterrows():
resi = row['structure_position']
chain = row['chain']
pheno = row['es']
selec = 'snp%s' % i
selec_atom = 'snp_atom%s' % i
cmd.select(selec,
'name ca and resi %s and chain %s' % (resi, chain))
cmd.create(selec_atom, selec)
cmd.set("sphere_scale", 0.8)
cmd.show('sphere', selec_atom)
cmd.alter(selec_atom, 'b=%s' % pheno)
cmd.spectrum("b",
"blue_white_red",
selec_atom,
maximum=1.0,
minimum=0.0)
cmd.bg_color("white")
cmd.zoom()
cmd.orient()
cmd.save('%s.pse' % outfile)
cmd.png('%s.png' % outfile, width=2400, height=2400, dpi=300, ray=1)
def load_save2():
while 1:
time.sleep(random.random())
cmd.delete("obj2")
cmd.load("dat/water.pdb","obj2")
time.sleep(random.random())
cmd.save("tmp/T01b.pdb","obj2")
def testExportStyle(self):
cmd.fab('ACDEF', 'm1')
cmd.hide()
cmd.show('cartoon', 'resi 1-3')
cmd.show('lines', 'resn CYS')
cmd.show('sticks', 'resn ASP+PHE')
cmd.show('spheres', 'resn GLU')
cmd.set('stick_ball', 1, 'resn PHE')
cmd.set('stick_ball_ratio', 1.5, 'm1')
testlabel = 'Hello "World"'
cmd.label('name SG', repr(testlabel))
with testing.mktemp('.mae') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.load(filename, 'm2')
g_labels = []
cmd.iterate('name SG', 'g_labels.append(label)', space=locals())
cmd.alter('*', 'b = 1 if s.stick_ball else 0')
self._assertCountEqual('rep cartoon & guide', 'resi 1-3 & guide')
self._assertCountEqual('rep lines', 'resn CYS', delta=1)
self._assertCountEqual('rep sticks', 'resn ASP+PHE')
self._assertCountEqual('rep spheres', 'resn GLU')
self._assertCountEqual('b > 0.5', 'resn PHE')
self.assertTrue(cmd.get_setting_float('stick_ball_ratio', 'm2') > 1.1)
self.assertEqual(g_labels[0], testlabel)
def stride(selection="(all)", exe="stride", raw="", state=-1, quiet=1):
"""
DESCRIPTION
Secondary structure assignment with STRIDE.
http://webclu.bio.wzw.tum.de/stride/
SEE ALSO
dss, dssp
"""
from subprocess import Popen, PIPE
import tempfile, os
state, quiet = int(state), int(quiet)
ss_map = {"C": "L", "B": "S", "b": "S", "E": "S", "T": "L", "G": "H", "H": "H"}
tmpfilepdb = tempfile.mktemp(".pdb")
ss_dict = dict()
for model in cmd.get_object_list(selection):
cmd.save(tmpfilepdb, "%s and (%s)" % (model, selection), state)
try:
process = Popen([exe, tmpfilepdb], stdout=PIPE)
except OSError:
print "Error: Cannot execute exe=" + exe
raise CmdException
for line in process.stdout:
if not line.startswith("ASG"):
continue
chain = line[9].strip("-")
resi = line[11:16].strip()
ss = line[24]
ss_dict[model, chain, resi] = ss
os.remove(tmpfilepdb)
_common_ss_alter(selection, ss_dict, ss_map, raw)
def get_group_env(file_name, group, output_name):
pymol.finish_launching()
cmd.delete('all')
cmd.load(file_name)
cmd.load(group)
cmd.select('group_env', 'br. ' + group.split('.')[0] + ' around 4 and poly')
cmd.save(output_name, 'group_env')
def sav_tmp():
from shutil import copyfile
import datetime
try:
TMP_FOLDER + ' '
except:
print(
"Error: Set up TMP_FOLDER in your ~/.pymolrc, e.g. TMP_FOLDER = '/home/magnus/Desktop/PyMOL/'"
)
return
try:
os.mkdir(TMP_FOLDER)
except:
pass
date = datetime.datetime.today().strftime('%Y-%m-%d.%S')
try:
fn = TMP_FOLDER + os.sep + id + '_' + date + '.pse'
except TypeError:
fn = TMP_FOLDER + os.sep + '_' + date + '.pse'
cmd.save(fn)
print('Save...' + fn)
cmd.save(fn.replace('.pse', '.png'))
copyfile(fn, TMP_FOLDER + '/last.pse')
def pymol_mutate(file_name, chain, res_index):
pymol.finish_launching()
cmd.delete('all')
selection = chain + '/' + res_index + '/'
mutant = 'CYS'
cmd.wizard("mutagenesis")
pdb = file_name[:-4]
cmd.load(file_name)
cmd.remove('not (alt ''+A)')
cmd.select('mut', 'resi ' + res_index + ' and chain ' + chain)
if cmd.count_atoms('mut') == 0:
return False
cmd.refresh_wizard()
cmd.get_wizard().set_mode(mutant)
cmd.get_wizard().do_select(selection)
nStates = cmd.count_states("mutation")
for i in range(1, nStates + 1):
cmd.get_wizard().do_select(selection)
cmd.frame(i)
cmd.get_wizard().apply()
cmd.save("rec_" + str(res_index) + "_" + str(i) + ".pdb")
cmd.set_wizard()
cmd.remove(file_name[:-4])
return True
def test(self):
cmd.viewport(100, 100)
# make map
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isomesh('mesh', 'map')
# check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'mesh')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
# continue without map
cmd.delete('map')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
def interface_area(rec_file, lig_file):
cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)
#==============================================================================
# rec_file = sys.argv[1]
# lig_file = sys.argv[2]
#
#==============================================================================
#==============================================================================
#rec_file = '/home/athar/Dimer/dock-std/true/12as/rec.pdb'
#lig_file = '/home/athar/Dimer/dock-std/true/12as/lig.pdb'
#==============================================================================
#complex_file = sys.argv[3]
cmd.load(rec_file) # use the name of your pdb file
rec_area = cmd.get_area('rec')
cmd.load(lig_file)
lig_area = cmd.get_area('lig.2')
cmd.save('complexfile.pdb')
cmd.delete(all)
cmd.load('complexfile.pdb')
total_area = cmd.get_area('complexfile')
area = (abs(rec_area + lig_area - total_area)) * 0.5 # using sasa area
# print area
return area
def crysolRefinementNanodisc(z_min, z_max, z_step, \
protName, membName, scafName, dataName, prefixName):
'''Refine the membrane protein detergent complex against experimental data'''
zs = np.arange(z_min, z_max, z_step)
res = {"angle": -9999, "number-of-scaffolds": -9999, "chi2": 9999}
with tempdir.TemporaryDirectory() as tmpdir:
# copy data file
tmpdir.copy_in(dataName)
best = ""
fitBest = ""
for counter1, z in enumerate(zs):
cmd.refresh()
modelName = builderNanodisc(protName, membName, scafName,
prefixName, z, True)
cmd.save(modelName + ".pdb", modelName)
fit, fitResult = fitcrysol(modelName, dataName, "yes", False)
cmd.wizard(
"message", f"Refinement: {counter1 } out of {len(zs)} steps."
f"Chi2: {fitResult['chi2']}")
# if model fits better - store it
if float(fitResult['chi2']) < float(res['chi2']):
if best != "": cmd.delete(best)
res['chi2'] = fitResult['chi2']
res['vertical-offset'] = z
best = modelName
fitBest = fit
else:
cmd.delete(modelName)
tmpdir.move_out(best + ".pdb")
tmpdir.move_out(fitBest)
print(f"Best model: Vertical Offset : {res['vertical-offset']}")
print(f"Chi^2 : {res['chi2']} Best model name : {best}")
return best, fitBest
def writeKeyViewFile(filename):
global views
global frames
global scenes
global actions
global settings
global models
global fades
keyviewfile = open(filename + ".key", "w")
for i, view in enumerate(views):
keyviewfile.write("VIEW: %4d " % i)
for v in view:
keyviewfile.write(str(v) + " ")
keyviewfile.write("\n")
keyviewfile.write("FRAMES: %d\n" % frames[i])
if i in actions:
keyviewfile.write("ACTIONS: %s\n" % actions[i])
if i in scenes:
keyviewfile.write("SCENES: %s\n" % scenes[i])
if i in models:
keyviewfile.write("MODELS: %s\n" % models[i])
if i in settings:
settingName, selection, startVal, endVal = settings[i]
keyviewfile.write("SETTINGS: %s, %s, %f, %f\n" % (settingName, selection, startVal, endVal))
if i in fades:
startVisSelection, endVisSelection, sticksOnly = fades[i]
keyviewfile.write("FADES: %s, %s, %d\n" % (startVisSelection, endVisSelection, sticksOnly))
keyviewfile.write("\n")
keyviewfile.close()
cmd.save(filename + ".pse")
print "Wrote files ", filename + ".key", filename + ".pse"
def writePdb(sel, prefix = ""):
pdbfn = prefix + sel + ".pdb"
npdbfn = pdbfn.replace(" or ", "");
npdbfn = npdbfn.replace(" and ", "");
npdbfn = npdbfn.translate(None, string.whitespace)
cmd.save(npdbfn, sel)
return npdbfn
def project(model, resi1_str, resi2_str, resi3_str, \
symQ, syms_for_use, syms_for_del, sym_d=3, \
segis_for_save='all', segis_for_del=''):
all_segis = prepare(model, resi1_str, resi2_str, resi3_str, segis_for_save, segis_for_del)
new_model, segi_count = make_segis(model, resi1, resi2, resi3, all_segis)
cmd.alter(new_model, \
'segi = new_segi(segi, sorted(all_segis))', \
space={'new_segi': new_segi, 'all_segis': all_segis, 'sorted': sorted})
if symQ:
cmd.symexp('{}_sym'.format(model), \
'{}_save'.format(model), \
'({}_save)'.format(model), \
sym_d)
for i in range(len(syms_for_use)):
cmd.alter('{}_sym{}'.format(model, syms_for_use[i]), 'segi=segi+"mod{}"'.format(i + 1))
merge(model, ['{}_save'.format(model)] + ['{}_sym{}'.format(model, s) for s in syms_for_use])
else: merge(model, ['{}_save'.format(model)])
for sym in syms_for_del:
cmd.delete('{}_sym{}'.format(model, sym))
cmd.alter('all', 'chain="A"')
cmd.save('{}_calc.cif'.format(model), '{}_calc'.format(model))
print(cmd.rms_cur('{}_calc'.format(model), '{}_sym'.format(model)))
def saveMultiplepng(pnamein, nbstates):
finish_launching()
for state in range(0,nbstates):
print(state, nbstates)
finish_launching()
pfilin = pnamein + "_state" + str(state) + ".pdb"
print (pfilin)
cmd.load(pfilin, "state" + str(state))
cmd.hide("everything", "all")
for state in range(0, nbstates):
cmd.show("surface", selection="state" + str(state))
cmd.set("transparency", value=0.4)
cmd.show("cartoon", selection="state" + str(state))
cmd.spectrum("b", "chocolate_firebrick_red_tv_red_deepsalmon_darksalmon_salmon_lightpink_white",
selection="all", minimum=0, maximum=100)
cmd.select("lig" + str(state), "resn UNK and state" + str(state))
cmd.show("stick", selection="lig" + str(state))
cmd.bg_color("white")
cmd.ray(2000, 2000)
cmd.save(pnamein + "_state" + str(state) + ".png", selection="state" + str(state))
cmd.hide("everything", "all")
cmd.quit()
def get_pdb():
""" """
tmpfn = '/tmp/pymol_get_pdb.pdb'
cmd.save(tmpfn, '(sele)')
s = RNAStructure(tmpfn)
for l in s.lines:
print(l)
def main():
"""Main function.
"""
parser = argparse.ArgumentParser(
description=
"Take a selection of chains from a set of structures and save them as new structures."
)
parser.add_argument('structure',
nargs='+',
help='Any format supported by Pymol.')
parser.add_argument(
'-c',
'--chains',
default='A',
help=
'Chain string containing all the chains to be get, no space between chain IDs. Only single letter chain IDs are supported [default: %(default)s].'
)
parser.add_argument(
'--hetatm',
action='store_true',
default=False,
help="Include hetatm in the output files [default: %(default)s].")
parser.add_argument('-v',
'--version',
action='version',
version='1.0',
help="Show program's version number and exit.")
args = parser.parse_args()
chains = "".join(sorted(set(args.chains)))
cmd.reinitialize() # Just to print Pymol usage as a module waring in here.
for f in args.structure:
try:
cmd.load(f)
except:
sys.stderr.write(
"WARNING: Can not load file {}. Ignoring it.\n".format(f))
continue
if not has_chains(f, chains):
sys.stderr.write(
"WARNING: Structure {} does not have all requested chains: {}. Ignoring it.\n"
.format(f, chains))
continue
if args.hetatm:
cmd.save("{}_{}.pdb".format(rootname(f), chains),
"{} and chain {}".format(rootname(f), "+".join(chains)))
else:
cmd.save(
"{}_{}.pdb".format(rootname(f), chains),
"{} and not hetatm and chain {}".format(
rootname(f), "+".join(chains)))
cmd.delete(rootname(f))
def clarna(selection):
"""Get contacts classification of the selected fragment based on ClaRNA (for each object).
Example::
PyMOL>clarna sele
rna_clarna_run.py -ipdb /var/folders/yc/ssr9692s5fzf7k165grnhpk80000gp/T/tmp1h_bwvtx.pdb -bp+stack
chains: X 15 16
X 15 X 16 bp A A >< 0.9427
.. image:: ../../rna_tools/tools/PyMOL4RNA/doc/clarna.png
"""
f = tempfile.NamedTemporaryFile(delete=False) # True)
output = f.name + '_clarna.pdb'
cmd.save(output, selection)
CLARNA_RUN = 'rna_clarna_run.py'
cmdline = CLARNA_RUN + " -ipdb " + output + ' -bp+stack'
print(cmdline)
out, err = exe(cmdline)
print('\n'.join(
out.split('\n')[1:])) # to remove first line of py3dna /tmp/xxx
if err:
print(err)
cmd.load(output)
f.close()
def scene_photo(rec, xtal, covalentized, photo_name):
pymol.finish_launching()
cmd.delete('all')
for file_name in [rec, xtal, covalentized]:
cmd.load(file_name)
cmd.select('lig', 'org')
if cmd.count_atoms('lig') == 0:
return 0
cmd.set('valence', 0)
cmd.color('cyan', xtal.split('.')[0])
cmd.select('cov', covalentized.split('.')[0])
cmd.select('cysteine', 'br. ' + covalentized.split('.')[0] + ' around 2 and resn CYS')
cmd.select('cys_cov', 'cysteine or cov')
cmd.save('tmp.pdb', 'cys_cov')
cmd.load('tmp.pdb')
cmd.hide('(hydro)')
cmd.delete('cov')
cmd.select('cov', 'tmp and org')
cmd.select('cysteine', 'tmp and resn cys')
cmd.color('white', 'cysteine')
cmd.color('magenta', 'cov')
cmd.color('green', rec.split('.')[0])
cmd.util.cnc('all')
cmd.select('all_mols', 'tmp or ' + xtal.split('.')[0])
cmd.orient('all_mols')
pnghack('./tmp.png')
os.rename('tmp0001.png', photo_name)
os.remove('tmp.pdb')
def ross_load(molecule):
'''
for Jennifer Ross.
'''
# if pic == 0:
cmd.reinitialize()
# cmd.depth_cue(1) # fails
# cmd.set_depth_cue("off") # fails
cmd.set("depth_cue","off")
cmd.bg_color('white')
fasta = molecule + '.fasta'
pdb = molecule + '.pdb'
print molecule
print fasta
print pdb
cmd.load(fasta)
if not os.path.exists(pdb):
cmd.save(pdb)
# cmd.show( string representation="", string selection="" )
cmd.show('spheres','all')
def Btn_ExtractLigand_Clicked(self):
state = cmd.get_state()
# Get the Drop Down List Selection Name
ddlSelection = self.defaultOption.get()
if ddlSelection == '' or self.Validate_ObjectSelection(
ddlSelection, 'Ligand', state):
return
LigandPath = tkFileDialog.asksaveasfilename(
filetypes=[('PDB File', '*.pdb')],
initialdir=self.top.FlexAIDLigandProject_Dir,
title='Save the PDB File',
initialfile=ddlSelection,
defaultextension='.pdb')
if len(LigandPath) > 0:
LigandPath = os.path.normpath(LigandPath)
if General.validate_String(LigandPath, '.pdb', True, False, True):
self.DisplayMessage(
" ERROR: Could not save the file because you entered an invalid name.",
2)
return
if self.top.ValidateSaveProject(LigandPath, 'Ligand'):
self.DisplayMessage(
" ERROR: The file can only be saved at its default location",
2)
return
try:
cmd.save(LigandPath, ddlSelection, state)
LigandName = os.path.basename(os.path.splitext(LigandPath)[0])
cmd.extract(self.ExtractObject, ddlSelection)
cmd.set_name(self.ExtractObject, LigandName)
if ddlSelection != LigandName:
# as if the object was renamed, delete the object
cmd.delete(ddlSelection)
except:
self.DisplayMessage(
" ERROR: An error occured while extracting the ligand object.",
1)
return
self.LigandPath.set(os.path.normpath(LigandPath))
self.LigandName.set(LigandName)
#self.LigandMD5.set(General.hashfile(self.LigandPath.get()))
self.Reset_Ligand()
self.DisplayMessage(
' Successfully extracted the ligand: ' +
self.LigandName.get() + "'", 0)
def ForceSaveObject(self, file, objname, objtype):
basepath, filename = os.path.split(file)
filebasename, fileextname = os.path.splitext(filename)
self.Set_Object_Variables(objtype)
if self.savepath != basepath:
newfile = os.path.join(self.savepath, filebasename + '.pdb')
if os.path.isfile(newfile):
answer = tkMessageBox.askquestion("Question",
message= "An object with that name already exists in your '" + \
objtype + "' folder. Would you like to overwrite it?",
icon='warning')
if str(answer) == 'no':
return 2
try:
cmd.save(newfile, objname, state=1)
except:
self.DisplayMessage(
" ERROR: The file could not be saved in your '" +
objtype + "' folder.", 2)
return 1
self.VarPath.set(newfile)
return 0
def testMAEsaveLoadSessions(self):
cmd.load(self.datafile('1d_smiles.mae'), '1d_smiles', object_props='*')
allpropdata = {}
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
allpropdata[obj] = {}
for prop in props:
allpropdata[obj][prop] = cmd.get_property(prop, obj)
with testing.mktemp('.pse') as psefilename:
cmd.save(psefilename)
cmd.load(psefilename)
# this is to fail the test on purpose
# cmd.set_property('i_m_ct_format', 3, '1d_smiles.mol_13')
objs = cmd.get_object_list()
for obj in objs:
props = cmd.get_property_list(obj)
# test to make sure there are no extra properties or not enough properties
self.assertEqual(set(props), set(allpropdata[obj].keys()))
# test to make sure all property values are the same
for prop in props:
try:
self.assertTrue(allpropdata[obj][prop] == cmd.get_property(prop, obj))
except:
self.fail('properties are not the same: obj=%s prop=%s' % (obj, prop))
def writeKeyViewFile( filename ):
global views
global frames
global scenes
global actions
global settings
global models
global fades
keyviewfile = open( filename + ".key", 'w' )
i=0
for view in views:
keyviewfile.write( "VIEW: %4d " % i )
for v in view:
keyviewfile.write( str(v) + " " )
keyviewfile.write('\n')
keyviewfile.write( "FRAMES: %d\n" % frames[i] )
if actions.has_key( i ):
keyviewfile.write( "ACTIONS: %s\n" % actions[i] )
if scenes.has_key( i ):
keyviewfile.write( "SCENES: %s\n" % scenes[i] )
if models.has_key( i ):
keyviewfile.write( "MODELS: %s\n" % models[i] )
if settings.has_key( i ):
settingName, selection, startVal, endVal = settings[i]
keyviewfile.write( "SETTINGS: %s, %s, %f, %f\n" % (settingName, selection, startVal, endVal))
if fades.has_key( i ):
startVisSelection, endVisSelection, sticksOnly = fades[i]
keyviewfile.write( "FADES: %s, %s, %d\n" % (startVisSelection, endVisSelection, sticksOnly))
i += 1
keyviewfile.write("\n")
keyviewfile.close()
cmd.save( filename + ".pse" )
print "Wrote files " , filename + ".key", filename + ".pse"
def revert(self):
v = cmd.get_view()
cmd.remove(self.rdes.obj+" and not chain A")
m = cmd.get_model(self.rdes.obj)
n = self.oldcrd
if not n:
cmd.create("tmp12345",self.rnat.sel())
cmd.align("tmp12345",self.rdes.sel())
n = cmd.get_model("tmp12345").atom
cmd.delete("tmp12345")
di,ni = 0,0
while m.atom[di].resi != str(self.rdes.resi): di += 1
dj = di
while m.atom[dj].resi == str(self.rdes.resi): dj += 1
if self.oldcrd: self.oldcrd = None
else: self.oldcrd = m.atom[di:dj]
m.atom = m.atom[:di] + n + m.atom[dj:]
for i in range(di,di+len(n)):
m.atom[i].resi = str(self.rdes.resi)
m.atom[i].chain = str(self.rdes.chain)
cmd.load_model(m,self.rdes.obj,1)
cmd.save("tmp.pdb",self.rdes.obj)
cmd.delete(self.rdes.obj)
cmd.load("tmp.pdb",self.rdes.obj,1)
cmd.show('car',self.rdes.obj)
cmd.show('lines')
redopent(self.rdes.obj)
cmd.set_view(v)
print "revert removing "+"".join(self.aas)+" from aas!"
self.aas = [getaa('A',self.rdes.resi,self.manager.d.obj)]
def draw_ENM(structure_filepath, script_filepath, structure_name="CAonly", output_dir='.', view=None):
""" Draws elastic network model of a structure and saves image.
"""
cmd.delete('all')
cmd.load(structure_filepath, "CAonly")
cmd.run(script_filepath)
# Set name
if structure_name == "CAonly":
pass
else:
cmd.set_name("CAonly", structure_name)
# Set view
if view == None:
cmd.orient()
else:
cmd.set_view(view)
cmd.viewport(width=1200, height=1200)
cmd.zoom(complete=1)
png_filepath = os.path.join(output_dir, structure_name) + ".png"
pse_filepath = os.path.join(output_dir, structure_name) + ".pse"
cmd.save(pse_filepath)
cmd.set('ray_opaque_background', 0)
cmd.png(png_filepath, width=1200, height=1200, ray=1)
return (pse_filepath, png_filepath)
def testIsosurface(self):
cmd.viewport(100, 100)
cmd.fragment('gly', 'm1')
cmd.set('gaussian_b_floor', 30)
cmd.set('mesh_width', 5)
cmd.map_new('map')
cmd.delete('m1')
# make mesh
cmd.isosurface('surface', 'map')
cmd.isosurface('surface', 'map', source_state=1, state=-2)
## check mesh presence by color
meshcolor = 'red'
cmd.color(meshcolor, 'surface')
self.ambientOnly()
self.assertImageHasColor(meshcolor)
cmd.frame(2)
self.assertEqual(cmd.get_state(), 2)
self.assertImageHasColor(meshcolor)
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.delete('*')
self.assertImageHasNotColor(meshcolor)
cmd.load(filename)
self.assertImageHasColor(meshcolor)
cmd.frame(2)
self.assertEqual(cmd.get_state(), 2)
self.assertImageHasColor(meshcolor)
def output_PNG(this_PDB_file, OUTPUT_FOLDER_PNG, OUTPUT_FOLDER_SESSION):
# show complex
cmd.hide("all")
cmd.bg_color("white")
cmd.show("cartoon", "this_complex")
# show protein A
cmd.set_color("A_interface_color", [167, 244, 66]) # lightgreen
cmd.set_color("A_C_term_color", [252, 245, 146]) # pale yellow
cmd.color("yellow", "chain A")
cmd.color("A_interface_color", "A_interface")
cmd.alter("A_center_pseudoatom", "vdw=2")
cmd.show("sphere", "A_center_pseudoatom")
cmd.color("green", "A_center_pseudoatom")
cmd.show("sphere", "A_N_term")
cmd.color("yellow", "A_N_term")
cmd.show("sphere", "A_C_term")
cmd.color("A_C_term_color", "A_C_term")
# show protein B
cmd.set_color("B_interface_color", [80, 181, 244]) # medium blue
cmd.set_color("B_C_term_color", [179, 229, 229]) # pale cyan
cmd.color("cyan", "chain B")
cmd.color("B_interface_color", "B_interface")
cmd.alter("B_center_pseudoatom", "vdw=2")
cmd.show("sphere", "B_center_pseudoatom")
cmd.color("blue", "B_center_pseudoatom")
cmd.show("sphere", "B_N_term")
cmd.color("cyan", "B_N_term")
cmd.show("sphere", "B_C_term")
cmd.color("B_C_term_color", "B_C_term")
# nice output
cmd.rebuild()
cmd.zoom("all")
cmd.png("%s/%s.png" % (OUTPUT_FOLDER_PNG, this_PDB_file), quiet=1)
# save session
cmd.save("%s/%s.pse" % (OUTPUT_FOLDER_SESSION, this_PDB_file))
def save_session(self, outfolder, override=None):
"""Saves a PyMOL session file."""
filename = '%s_%s' % (self.protname.upper(), "_".join(
[self.hetid, self.plcomplex.chain, self.plcomplex.position]))
if override is not None:
filename = override
cmd.save("/".join([outfolder, "%s.pse" % filename]))
def intra_theseus(selection, state=1, cov=0, cycles=200,
exe='theseus', preserve=0, quiet=1):
'''
DESCRIPTION
Fits all states of an object to an atom selection with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
selection = string: atoms to fit
state = integer: keep transformation of this state unchanged {default: 1}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
intra_fit, intra_rms_cur
'''
import tempfile, os
state, cov, cycles = int(state), int(cov), int(cycles)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
filename = os.path.join(tempdir, 'mobile.pdb')
cmd.save(filename, selection, 0)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles, filename]
translations = []
rotations = []
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [-t[0]] + R[3:6] + [-t[1]] + R[6:9] + [-t[2], 0,0,0, 1]
for (R, t) in zip(rotations, translations)]
# intra fit states
obj_list = cmd.get_object_list('(' + selection + ')')
for i, m in enumerate(matrices):
for obj in obj_list:
cmd.transform_object(obj, m, i+1, transpose=1)
# fit back to given state
if 0 < state <= len(matrices):
m = list(matrices[state-1])
for i in [3,7,11]:
m[i] *= -1
for obj in obj_list:
cmd.transform_object(obj, m, 0)
if not quiet:
print(' intra_theseus: %d states aligned' % (len(matrices)))
def prepareinput(self, selection='(all)', startpoint='(0,0,0)'):
if self.varremovewater.get():
selection = '(%s) and not resn HOH and not resn H2O and not resn WAT' % (selection)
print selection
outdir = self.pymol_outdir.getvalue()
tmppdb = os.path.join(outdir, "tmp.pdb")
cmd.save(tmppdb, selection)
def testCOLLADA(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.dae') as filename:
cmd.save(filename)
contents = file_get_contents(filename)
self.assertTrue('<COLLADA' in contents)
def testVRML(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.wrl') as filename:
cmd.save(filename)
contents = file_get_contents(filename)
self.assertTrue(contents.startswith('#VRML V2'))
def prosmart(mobile, target, mobile_state=1, target_state=1,
exe='prosmart', transform=1, object=None, quiet=0):
'''
DESCRIPTION
ProSMART wrapper.
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
'''
import subprocess, tempfile, os, shutil, glob
quiet = int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
cmd.save(mobile_filename, mobile, state=mobile_state)
cmd.save(target_filename, target, state=target_state)
exe = cmd.exp_path(exe)
args = [exe, '-p1', mobile_filename, '-p2', target_filename, '-a']
xglob = lambda x: glob.glob(os.path.join(tempdir, 'ProSMART_Output/Output_Files', x))
try:
subprocess.check_call(args, cwd=tempdir)
transfiles = xglob('Superposition/Transformations/*/*.txt')
with open(transfiles[0]) as f:
f = iter(f)
for line in f:
if line.startswith('ROTATION'):
matrix = [list(map(float, next(f).split())) + [0] for _ in range(3)]
elif line.startswith('TRANSLATION'):
matrix.append([-float(v) for v in next(f).split()] + [1])
break
if int(transform):
matrix = [v for m in matrix for v in m]
assert len(matrix) == 4*4
for model in cmd.get_object_list('(' + mobile + ')'):
cmd.transform_object(model, matrix, state=0)
if object:
from .importing import load_aln
alnfiles = xglob('Residue_Alignment_Scores/*/*.txt')
alnfiles = [x for x in alnfiles if not x.endswith('_clusters.txt')]
load_aln(alnfiles[0], object, mobile, target)
except OSError:
print(' Error: Cannot execute "%s", please provide full path to prosmart executable' % (exe))
raise CmdException
finally:
shutil.rmtree(tempdir)
if not quiet:
print(' prosmart: done')
def propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL",makebonds="yes"):
Script_Version="20110823"
### First we have to be sure, we give reasonable arguments
if pkafile!="NIL":
method='file'
assert method in ['upload', 'file'], "'method' has to be either: method=upload or method=file"
### If molecule="all", then try to get the last molecule
##assert molecule not in ['NIL'], "You always have to provide molecule name. Example: molecule=4ins"
if molecule=="NIL":
assert len(cmd.get_names())!=0, "Did you forget to load a molecule? There are no objects in pymol."
molecule=cmd.get_names()[-1]
### To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
if resi != "0": resi_range = ResiRange(resi)
else: resi_range=[]
### Also works for residue names. They are all converted to bigger letters. Example: resn="cys.Tyr"
if resn != "NIL": resn_range = ResnRange(resn)
else: resn_range = resn
### Make chain range, and upper case.
chain = ChainRange(chain)
### Make result directory. We also the absolut path to the new directory.
Newdir = createdirs()
if method=="upload":
### We try to load mechanize. If this fail, one can always get the .pka file manual and the run: method=file
try: from modules import mechanize; importedmechanize='yes'
except ImportError: print("Import error. Is a module missing?"); print(sys.exc_info()); print("Look if missing module is in your python path\n%s")%sys.path;importedmechanize='no'; import modules.mechanize as mechanize
### The name for the new molecule
newmolecule = "%s%s"%(molecule,logtime)
### Create the new molecule from original loaded and for the specified chains. Save it, and disable the old molecule.
cmd.create("%s"%newmolecule, "%s and chain %s"%(molecule,chain))
cmd.save("%s%s.pdb"%(Newdir,newmolecule), "%s"%newmolecule)
cmd.disable("%s"%molecule)
if molecule=="all": cmd.enable("%s"%molecule); cmd.show("cartoon", "%s"%molecule)
### Let the new molecule be shown in cartoon.
cmd.hide("everything", "%s"%newmolecule)
cmd.show("cartoon", "%s"%newmolecule)
### Make the absolut path to the newly created .pdb file.
PDB="%s%s.pdb"%(Newdir,newmolecule);source="upload"; PDBID=""
### Request server, and get the absolut path to the result file.
pkafile = getpropka(PDB,chain,resi,resn,source,PDBID,logtime,server_wait,version,verbose,showresult)
### Open the result file and put in into a handy list.
list_results,ligands_results = importpropkaresult(pkafile)
if method=="file":
assert pkafile not in ['NIL'], "You have to provide path to file. Example: pkafile=./Results_propka/4ins_2011.pka"
assert ".pka" in pkafile, 'The propka result file should end with ".pka" \nExample: pkafile=./Results_propka/4ins_2011.pka \npkafile=%s'%(pkafile)
### The name for the molecule we pass to the writing script of pymol commands
newmolecule = "%s"%molecule
cmd.hide("everything", "%s"%newmolecule)
cmd.show("cartoon", "%s"%newmolecule)
### We open the result file we have got in the manual way and put in into a handy list.
list_results,ligands_results = importpropkaresult(pkafile)
### Then we print the interesting residues to the screen.
printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult, ligands_results)
### Now create the pymol command file. This should label the protein. We get back the absolut path to the file, so we can execute it.
result_pka_pymol_name = writepymolcmd(newmolecule,pkafile,verbose,makebonds)
### Now run our command file. But only if we are running pymol.
if runningpymol=='yes': cmd.do("run %s"%result_pka_pymol_name)
##if runningpymol=='yes': cmd.do("@%s"%result_pka_pymol_name)
return(list_results)
def pdb():
"""Get PDB content of selection.
.. image:: ../../rna_tools/utils/PyMOL4RNA/doc/pdb.png"""
tmpfn = '/tmp/pymol_get_pdb.pdb'
cmd.save(tmpfn, '(sele)')
s = RNAStructure(tmpfn)
for l in s.lines:
print(l)
def dss_promotif(selection="all", exe="", raw="", state=-1, quiet=1):
"""
DESCRIPTION
Secondary structure assignment with PROMOTIF.
http://www.rubic.rdg.ac.uk/~gail/#Software
SEE ALSO
dss, dssp, stride
"""
from subprocess import Popen, PIPE
import tempfile, os, shutil
state, quiet = int(state), int(quiet)
ss_map = {"B": "S", "E": "S", "H": "H", "G": "H"}
exe = cmd.exp_path(exe)
if not exe:
from . import which
motifdir = os.environ.get("motifdir")
exe = which("p_sstruc3", "p_sstruc2", "promotif.scr", path=[motifdir] if motifdir else None)
tmpdir = tempfile.mkdtemp()
tmpfilepdb = os.path.join(tmpdir, "xxxx.pdb")
tmpfilesst = os.path.join(tmpdir, "xxxx.sst")
ss_dict = dict()
try:
for model in cmd.get_object_list("(" + selection + ")"):
cmd.save(tmpfilepdb, "model %s and (%s)" % (model, selection), state)
process = Popen([exe, tmpfilepdb], cwd=tmpdir, stdin=PIPE)
process.communicate(tmpfilepdb + os.linesep)
with open(tmpfilesst) as handle:
for line in handle:
if line.startswith(" num seq.no"):
break
for line in handle:
if not line.strip():
break
chain = line[6].strip("-")
resi = line[7:12].strip()
ss = line[23]
ss_dict[model, chain, resi] = ss
os.remove(tmpfilesst)
except OSError:
print " Error: Cannot execute exe=" + exe
raise CmdException
finally:
shutil.rmtree(tmpdir)
_common_ss_alter(selection, ss_dict, ss_map, raw)
def testSTL(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.stl') as filename:
cmd.save(filename)
contents = file_get_contents(filename, 'rb')
# 80 bytes header
# 4 bytes (uint32) number of triangles
self.assertTrue(len(contents) > 84)
def PyMOL_export_PDB_to_file(obj, data_path, file_out, state = -1): # Export an PDB file from a PyMOL object
tmp = data_path+"/tmp"
if not os.path.exists ( tmp ): os.mkdir ( tmp )
file_path = os.path.join (tmp, file_out)
FILE = file_path
# cmd.save("/home/fernando/Desktop/gordo.pdb", "obj01", -1, "pdb")
cmd.save(FILE, obj, state, "pdb")
return FILE
def theseus(mobile, target, match='align', cov=0, cycles=200,
mobile_state=1, target_state=1, exe='theseus', preserve=0, quiet=1):
'''
DESCRIPTION
Structural superposition of two molecules with maximum likelihood.
THESEUS: Maximum likelihood multiple superpositioning
http://www.theseus3d.org
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
match = string: in, like, align, none or the name of an alignment object
(see "local_rms" help for details) {default: align}
cov = 0/1: 0 is variance weighting, 1 is covariance weighting (slower)
{default: 0}
SEE ALSO
align, super, cealign
'''
import tempfile, os
cov, cycles = int(cov), int(cycles)
mobile_state, target_state = int(mobile_state), int(target_state)
preserve, quiet = int(preserve), int(quiet)
tempdir = tempfile.mkdtemp()
mobile_filename = os.path.join(tempdir, 'mobile.pdb')
target_filename = os.path.join(tempdir, 'target.pdb')
mm = MatchMaker(mobile, target, match)
cmd.save(mobile_filename, mm.mobile, mobile_state)
cmd.save(target_filename, mm.target, target_state)
exe = cmd.exp_path(exe)
args = [exe, '-a0', '-c' if cov else '-v', '-i%d' % cycles,
mobile_filename, target_filename]
translations, rotations = _run_theseus(args, tempdir, preserve, quiet)
matrices = [R[0:3] + [i*t[0]] + R[3:6] + [i*t[1]] + R[6:9] + [i*t[2], 0,0,0, 1]
for (R, t, i) in zip(rotations, translations, [-1,1])]
obj_list = cmd.get_object_list('(' + mobile + ')')
for obj in obj_list:
cmd.transform_object(obj, matrices[0], 0, transpose=1)
cmd.transform_object(obj, matrices[1], 0)
if not quiet:
print(' theseus: done')
def testMol2FormalChargeAssignment(self):
cmd.fragment('lys')
cmd.fragment('lys')
with testing.mktemp('.mol2') as filename:
cmd.save(filename, state=0)
cmd.delete('*')
cmd.load(filename)
self.assertEqual(cmd.get_model('name NZ', state=1).atom[0].formal_charge, 1)
self.assertEqual(cmd.get_model('name NZ', state=2).atom[0].formal_charge, 1)