Example #1
0
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()
Example #2
0
def mutate_peptide(new_seq):
    '''
    mutate peptide to new_seq starting at second residue in the peptide
    '''

    cmd.copy(new_seq, "peptide_template")

    aa1 = list("ACDEFGHIKLMNPQRSTVWY")
    aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split(
    )
    aa123 = dict(zip(aa1, aa3))

    for ind, aa in enumerate(new_seq, 2):

        cmd.wizard("mutagenesis")
        cmd.do("refresh_wizard")
        print ind
        print aa
        # lets mutate residue 104 to GLN
        cmd.get_wizard().set_mode(aa123[aa])
        cmd.get_wizard().do_select("/{0}//B/{1}".format(new_seq, ind))
        # Select the rotamer
        #cmd.frame(1)

        # Apply the mutation
        cmd.get_wizard().apply()
Example #3
0
def mutate_peptide( new_seq ):
    '''
    mutate peptide to new_seq starting at second residue in the peptide
    '''

    cmd.copy(new_seq, "peptide_template")

    aa1 = list("ACDEFGHIKLMNPQRSTVWY")
    aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split()
    aa123 = dict(zip(aa1,aa3))

    for ind, aa in enumerate(new_seq,2):
	
        cmd.wizard("mutagenesis")
        cmd.do("refresh_wizard")
	print ind
	print aa
        # lets mutate residue 104 to GLN
        cmd.get_wizard().set_mode(aa123[aa])
        cmd.get_wizard().do_select("/{0}//B/{1}".format(new_seq, ind))
        # Select the rotamer
        #cmd.frame(1)

        # Apply the mutation
        cmd.get_wizard().apply()
Example #4
0
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
Example #5
0
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_CanMutateNonCanonicalNucleo(self):
     cmd.load(self.datafile("1k5e.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1k5e/A/A/6")
     cmd.get_wizard().mode = "Adenine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1k5e/A/A").splitlines()[1]
     self.assertEqual(seq, "CGGACAAGAAG")
 def test_CanGetNewDNASequence(self):
     cmd.load(self.datafile("1bna.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1bna/A/A/1")
     cmd.get_wizard().mode = "Adenine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1bna/A/A").splitlines()[1]
     self.assertEqual(seq, "AGCGAATTCGCG")
 def test_CanGetNewRNASequence(self):
     cmd.load(self.datafile("1rna.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1rna/A/A/14")
     cmd.get_wizard().mode = "Guanine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1rna/A/A").splitlines()[1]
     self.assertEqual(seq, "UUAUAUAUAUAUAG")
Example #9
0
 def test_CanGetNewRNASequence(self):
     cmd.load(self.datafile("1rna.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1rna/A/A/14")
     cmd.get_wizard().mode = "Guanine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1rna/A/A").splitlines()[1]
     self.assertEqual(seq, "UUAUAUAUAUAUAG")
Example #10
0
 def test_CanMutateNonCanonicalNucleo(self):
     cmd.load(self.datafile("1k5e.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1k5e/A/A/6")
     cmd.get_wizard().mode = "Adenine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1k5e/A/A").splitlines()[1]
     self.assertEqual(seq, "CGGACAAGAAG")
Example #11
0
 def test_CanGetNewDNASequence(self):
     cmd.load(self.datafile("1bna.cif"))
     cmd.wizard("nucmutagenesis")
     cmd.select("/1bna/A/A/1")
     cmd.get_wizard().mode = "Adenine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     seq = cmd.get_fastastr("/1bna/A/A").splitlines()[1]
     self.assertEqual(seq, "AGCGAATTCGCG")
Example #12
0
def mutate(selection, aa):
    aa = fix_aa(aa)
    cmd.set("retain_order", 0)
    cmd.wizard("mutagenesis")
    cmd.refresh_wizard()
    for single_res in iter_residues(selection):
        mutate_one(single_res, aa)
    cmd.set_wizard()
    cmd.sort()
Example #13
0
def Mutagenesis(kinase1, model, template,peptide_instance):
    """superposition the model and template, remove template and leave peptide behind """

    """replace peptide with instance peptide"""
    list_name = peptide_instance
    with open(input_data_folder+list_name,'r') as f:
        instances = f.readlines()
    instance = [x.strip() for x in instances]
    print "your peptide: ", instance 
    
    for pep in instance:
        cmd.delete('all')
        cmd.fetch(model)  # model_candidate, ex.chk1,chk2...
        cmd.remove("hetatm") #remove the nonstandard residues
        cmd.fetch(template)  #mutagenesis template, ex.2phk
        peptide_template = cmd.get_fastastr( "/"+template+'//B') #get the peptide from the template and generate another one for mutagenesis 
        peptide_template = peptide_template + 'G' #peptide of 2phk is 7 amino acid long, when our input peptide is 8 aa, we need to plus one character
        
        
        for aa in peptide_template[6:].lower(): #creat template_peptide for mutagenesis

            cmd._alt(aa)
        
        
        firstaa = AAcode_1_to_3(peptide_template[6]) #translate template_peptide to 3 letter
        low_firstaa = firstaa[0].lower()

        cmd.alter(low_firstaa, 'chain = "B"') #select this template_peptide        
        cmd.show_as("cartoon")
        cmd.align(model, template) #superpostion of model and template
        cmd.align(low_firstaa,template) #superpostion of template_peptide and template

        remove_part = "("+template+" and not resn ATP"+")" 
        cmd.select("remove_part",remove_part) 

        
        cmd.remove("remove_part") #remove the template except for ATP, there are only model and template_peptide
        cmd.remove("resn hoh") #remove water
        cmd.wizard("mutagenesis")
        peptide_position = 0

        for i in pep:
            #the peptide_position starting point depends the first position of mutagenesis peptide
            #pymol's peptide start from 1, not 0
            mutagenesis_template = '/'+low_firstaa+ '///' + str(peptide_position + 2) # because of 2phk start at 2nd of peptide
            #mutagenesis_template = '/' + template + '//B/' + str(peptide_position + 2)
            cmd.get_wizard().do_select(mutagenesis_template)  # select peptide position of mutation
            replace_aminoacid = AAcode_1_to_3(pep)[peptide_position]
            cmd.get_wizard().set_mode(replace_aminoacid)  # select which residue want to mutate to
            cmd.get_wizard().apply()
            peptide_position += 1
        filename = kinase1 + '_' + model + 'model_' + template + 'muta_' + pep + '.pdb' #build the canonical name
        cmd.save(filename)
        ATPchange(filename) #change ATP naming to the format of ATP.params
    cmd.wizard(None)
    return
Example #14
0
def mutate(protein, resi, mode='ALA', chain='A'):
    cmd.wizard('mutagenesis')
    cmd.do("refresh_wizard")
    cmd.get_wizard().set_mode(mode.upper())
    selection = f'/{protein}//{chain}/{resi}'
    cmd.get_wizard().do_select(selection)
    cmd.frame(str(1))
    cmd.get_wizard().apply()
    cmd.set_wizard('done')
    cmd.refresh()
Example #15
0
def mutate(molecule, chain, resi, target="CYS", mutframe="1"):
    target = target.upper()
    cmd.wizard("mutagenesis")
    cmd.do("refresh_wizard")
    cmd.get_wizard().set_mode("%s" % target)
    selection = "/%s//%s/%s" % (molecule, chain, resi)
    cmd.get_wizard().do_select(selection)
    cmd.frame(str(mutframe))
    cmd.get_wizard().apply()
    # cmd.set_wizard("done")
    cmd.set_wizard()
Example #16
0
def mutate(molecule,chain,resi,target="CYS",mutframe="1"):
	target = target.upper()
	cmd.wizard("mutagenesis")
	cmd.do("refresh_wizard")
	cmd.get_wizard().set_mode("%s"%target)
	selection="/%s//%s/%s"%(molecule,chain,resi)
	cmd.get_wizard().do_select(selection)
	cmd.frame(str(mutframe))
	cmd.get_wizard().apply()
	#cmd.set_wizard("done")
	cmd.set_wizard()
Example #17
0
def mutXYZposition(residues):
    cmd.hide("everything")
    cmd.show("sticks")
    for resi in residues:
        for caa in residues[resi]:
            print(resi, caa)
            filename = "residue" + str(resi) + "to" + caa + ".csv"
            outfile = open(filename, "w")
            row = ("rotamer" + "," + "X" + "," + "Y" + "," + "Z" + "\n")
            cmd.wizard("mutagenesis")
            cmd.do("refresh_wizard")
            cmd.get_wizard().set_mode(caa)
            sel = "/test//A/" + str(resi)
            cmd.get_wizard().do_select(sel)
            fram = cmd.count_states("mutation")
            stored.pos = []
            cmd.iterate_state(0,
                              'mutation',
                              'stored.pos.append((x,y,z))',
                              atomic=0)
            counter = 1
            state = 1
            natom = int(len(stored.pos) / fram)
            for po in stored.pos:
                if counter < natom:
                    row = (str(state) + "," + str(po[0]) + "," + str(po[1]) +
                           "," + str(po[2]) + "\n")
                    outfile.write(row)
                    counter += 1
                elif counter == natom:
                    row = (str(state) + "," + str(po[0]) + "," + str(po[1]) +
                           "," + str(po[2]) + "\n")
                    outfile.write(row)
                    counter = 1
                    state += 1
            outfile.close()
            cmd.frame(fram)
            cmd.get_wizard().apply()
            cmd.set_wizard("done")
            cmd.save("residue" + str(resi) + "to" + caa + "rotamer" +
                     str(fram) + ".pdb")
            for f in range(1, fram):
                fra = fram - f
                cmd.wizard("mutagenesis")
                cmd.do("refresh_wizard")
                cmd.get_wizard().do_select(sel)
                cmd.frame(fra)
                cmd.get_wizard().apply()
                cmd.set_wizard("done")
                cmd.save("residue" + str(resi) + "to" + caa + "rotamer" +
                         str(fra) + ".pdb")
Example #18
0
 def test_CorrectChiDihedral(self):
     cmd.load(self.datafile("1rna.cif"))
     src_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
                                     "/1rna/A/A/14 & name C1'",
                                     "/1rna/A/A/14 & name N9",
                                     "/1rna/A/A/14 & name C4'")
     cmd.wizard("nucmutagenesis")
     cmd.select("/1rna/A/A/14")
     cmd.get_wizard().mode = "Guanine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     des_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
                                     "/1rna/A/A/14 & name C1'",
                                     "/1rna/A/A/14 & name N9",
                                     "/1rna/A/A/14 & name C4'")
     self.assertAlmostEqual(src_dihedral, des_dihedral, delta=2.0)
 def test_CorrectChiDihedral(self):
     cmd.load(self.datafile("1rna.cif"))
     src_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
                                     "/1rna/A/A/14 & name C1'",
                                     "/1rna/A/A/14 & name N9",
                                     "/1rna/A/A/14 & name C4'")
     cmd.wizard("nucmutagenesis")
     cmd.select("/1rna/A/A/14")
     cmd.get_wizard().mode = "Guanine"
     cmd.get_wizard().do_select("sele")
     cmd.get_wizard().apply()
     des_dihedral = cmd.get_dihedral("/1rna/A/A/14 & name O4'",
                                     "/1rna/A/A/14 & name C1'",
                                     "/1rna/A/A/14 & name N9",
                                     "/1rna/A/A/14 & name C4'")
     self.assertAlmostEqual(src_dihedral, des_dihedral, delta = 2.0)
Example #20
0
def mutate_to_cys(pdb, resnum_i):
	selection_i = "resi " + str(resnum_i)
	cmd.wizard("mutagenesis")

	cmd.get_wizard().set_mode("CYS")

	cmd.do("refresh_wizard")

	cmd.get_wizard().do_select(selection_i)
	cmd.get_wizard().do_select(selection_i)

	for frame_i in [1, 2, 3]:
		cmd.frame(frame_i)
		cmd.create("rotamer_" + str(resnum_i) + "_" + str(frame_i), "mutation", frame_i, 1)
		rotamer_i_pymol_prefix = "/" + "rotamer_" + str(resnum_i) + "_" + str(frame_i) + "///" + resnum_i + "/"

	cmd.set_wizard("done")
Example #21
0
def crysolRefinementDetergent(rot_min_ang, rot_max_ang, rot_step_ang,
                              dens_min_ang, dens_max_ang, dens_step_ang,
                              protName, membName, dataName, prefixName, runNumber):
    """Refine the membrane protein detergent complex against experimental data"""
    angs = np.arange(rot_min_ang, rot_max_ang, rot_step_ang)
    dens = np.arange(dens_min_ang, dens_max_ang, dens_step_ang)
    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, ang in enumerate(angs):
            for counter2, densAng in enumerate(dens):
                cmd.refresh()
                modelName = builderDetergent(protName, membName, prefixName, runNumber, ang, densAng, True)
                runNumber += 1
                if modelName == "bad model":
                    print("Bad model parameters: ang: {} densAng: {}".format(ang, densAng))
                    continue
                cmd.save(modelName + ".pdb", modelName)
                fit, fitResult = fitcrysol(modelName, os.path.basename(dataName), "yes", False)
                cmd.wizard("message",
                           "Refinement: {} ".format(1 + counter2 + counter1 * (len(dens))) +
                           " out of {} steps. Chi2: {}".format(len(dens) * len(angs), 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['lipid density'] = densAng
                    res['max-polar-angle'] = ang
                    best = modelName
                    fitBest = fit
                else:
                    cmd.delete(modelName)
        if res['chi2'] < 9999:
            tmpdir.move_out(best + ".pdb")
            tmpdir.move_out(fitBest)
        else:
            return "Bad parameters", "No good fit found!"
    print("Best model: Lipid Density : {} Max Polar Angle = {})".format(res['lipid density'], res['max-polar-angle']))
    print("Chi^2 : {} Best model name : {}".format(res['chi2'], best))
    return best, fitBest, counter1*counter2
Example #22
0
def doubleMut(original, positions, residues):
    cmd.hide("everything")
    cmd.show("sticks")

    posone = positions[0][0]
    chainone = positions[0][1]
    postwo = positions[1][0]
    chaintwo = positions[1][1]

    outfile = open("forheatmap.csv", "w")

    #generate the protein with one mutation
    for a in residues:
        cmd.create(a, original)
        cmd.wizard("mutagenesis")
        cmd.do("refresh_wizard")
        cmd.get_wizard().set_mode(a)
        sel = "/" + a + "//" + str(chainone) + "/" + str(posone)
        cmd.get_wizard().do_select(sel)
        cmd.get_wizard().apply()

    for m in residues:  #for all the mutations generated
        for i in residues:  #for each residue to which will be mutated
            name = m + "2"
            cmd.create(name, m)
            cmd.wizard("mutagenesis")
            cmd.do("refresh_wizard")
            cmd.get_wizard().set_mode(i)
            se = "/" + name + "//" + str(chaintwo) + "/" + str(postwo)
            cmd.get_wizard().do_select(se)
            mut_name = "mutation"
            if cmd.count_states(mut_name) != 1:
                bump_name = "_bump_check"
                cmd.sculpt_activate(bump_name)
                scores = []
                for rotamer in range(1, 1 + cmd.count_states(bump_name)):
                    score = cmd.sculpt_iterate(bump_name, rotamer, 1)
                    scores.append(score)
                scores.sort(reverse=True)
                row = (i + "," + m + "," + str(scores[0]) + "\n")
            else:
                row = (i + "," + m + "," + "?" + "\n")
            outfile.write(row)
    outfile.close()
Example #23
0
def crysolRefinementSalipro(rot_min_ang, rot_max_ang, rot_step_ang, \
                            scaffold_min, scaffold_max, scaffold_step, \
                            protName, membName, scafName,  dataName, \
                            prefixName):
    '''Refine the membrane protein lipids scaffolding proteins
     complex against experimental data'''
    angs = np.arange(rot_min_ang, rot_max_ang, rot_step_ang)
    numScaffoldCopies = np.arange(scaffold_min, scaffold_max, scaffold_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, ang in enumerate(angs):
            for counter2, num in enumerate(numScaffoldCopies):
                cmd.refresh()
                modelName = builderSalipro(protName, scafName, membName,
                                           prefixName, num, ang, True)
                cmd.save(modelName + ".pdb", modelName)
                fit, fitResult = fitcrysol(modelName, dataName, "yes", False)
                cmd.wizard(
                    "message",
                    f"Refinement: {counter2 + counter1 * (len(numScaffoldCopies))} "
                    f"out of {len(numScaffoldCopies) * len(angs)} steps. Chi2: {fitResult['chi2']}"
                )
                if float(fitResult['chi2']) < float(res['chi2']):
                    if best != "": cmd.delete(best)
                    res['chi2'] = fitResult['chi2']
                    res['number-of-scaffolds'] = num
                    res['angle'] = ang
                    best = modelName
                    fitBest = fit
                else:
                    cmd.delete(modelName)
        tmpdir.move_out(best + ".pdb")
        tmpdir.move_out(fitBest)
    cmd.wizard()
    print(
        f"Best model: Number of Scaffolds = {res['number-of-scaffolds']}; Angle = {res['angle']}"
    )
    print(f"Chi^2 : {res['chi2']} Best model name : {best}")
    return best, fitBest
Example #24
0
def pymol_mutate(file_name, chain, res_index, number, mutant):
    pymol.finish_launching()
    cmd.delete(file_name[:-4])
    selection = chain + '/' + res_index + '/'
    cmd.wizard("mutagenesis")
    pdb = file_name[:-4]
    cmd.load(file_name)
    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])
Example #25
0
def crysolRefinementSalipro(rot_min_ang, rot_max_ang, rot_step_ang,
                            scaffold_min, scaffold_max, scaffold_step,
                            protName, membName, scafName, dataName,
                            prefixName, runNumber):
    """Refine the membrane protein lipids scaffolding proteins
     complex against experimental data"""
    angs = np.arange(rot_min_ang, rot_max_ang, rot_step_ang)
    numScaffoldCopies = np.arange(scaffold_min, scaffold_max, scaffold_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, ang in enumerate(angs):
            for counter2, num in enumerate(numScaffoldCopies):
                cmd.refresh()
                modelName = builderSalipro(protName, scafName, membName, prefixName, runNumber, num, ang, True)
                runNumber += 1
                if modelName == "bad model":
                    print("Bad model parameters: ang: {} num: {}".format(ang, num))
                    continue
                cmd.save(modelName + ".pdb", modelName)
                fit, fitResult = fitcrysol(modelName, os.path.basename(dataName), "yes", False)
                cmd.wizard("message",
                           "Refinement: {} ".format(1 + counter2 + counter1 * (len(numScaffoldCopies))) +
                           " out of {} steps. Chi2: {}".format(len(numScaffoldCopies) * len(angs), fitResult['chi2']))
                if float(fitResult['chi2']) < float(res['chi2']):
                    if best != "": cmd.delete(best)
                    res['chi2'] = fitResult['chi2']
                    res['number-of-scaffolds'] = num
                    res['angle'] = ang
                    best = modelName
                    fitBest = fit
                else:
                    cmd.delete(modelName)
        tmpdir.move_out(best + ".pdb")
        tmpdir.move_out(fitBest)
    cmd.wizard()
    print("Best model: Number of Scaffolds = {}; Angle = {}".format(res['number-of-scaffolds'], res['angle']))
    print("Chi^2 : {} Best model name : {}".format(res['chi2'], best))
    return best, fitBest, counter1*counter2
Example #26
0
def crysolRefinementDetergent(rot_min_ang, rot_max_ang, rot_step_ang, \
                              dens_min_ang, dens_max_ang, dens_step_ang, \
                              protName, membName, dataName, prefixName):
    '''Refine the membrane protein detergent complex against experimental data'''
    angs = np.arange(rot_min_ang, rot_max_ang, rot_step_ang)
    dens = np.arange(dens_min_ang, dens_max_ang, dens_step_ang)
    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, ang in enumerate(angs):
            for counter2, densAng in enumerate(dens):
                cmd.refresh()
                modelName = builderDetergent(protName, membName, prefixName,
                                             ang, densAng, True)
                cmd.save(modelName + ".pdb", modelName)
                fit, fitResult = fitcrysol(modelName, dataName, "yes", False)
                cmd.wizard(
                    "message",
                    f"Refinement: {counter2 + counter1 * (len(dens))} out of {len(dens) * len(angs)} 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['lipid density'] = densAng
                    res['max-polar-angle'] = ang
                    best = modelName
                    fitBest = fit
                else:
                    cmd.delete(modelName)
        tmpdir.move_out(best + ".pdb")
        tmpdir.move_out(fitBest)
    print(
        f"Best model: Lipid Density : {res['lipid density']} Max Polar Angle = {res['max-polar-angle']})"
    )
    print(f"Chi^2 : {res['chi2']} Best model name : {best}")
    return best, fitBest
Example #27
0
def pymol_mutate(file_name, chain, res_index, number):
    pymol.finish_launching()
    cmd.delete(file_name[:-4])
    selection = chain + '/' + res_index + '/'
    mutant = 'CYS'
    cmd.wizard("mutagenesis")
    pdb = file_name[:-4]
    cmd.load(file_name)
    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])
Example #28
0
def crysolRefinementNanodisc(x_min, x_max, x_step, y_min, y_max, y_step,
                             protName, membName, scafName, dataName, prefixName, runNumber):
    """Refine the membrane protein detergent complex against experimental data"""
    xs = np.arange(x_min, x_max, x_step)
    ys = np.arange(y_min, y_max, y_step)
    res = {"x-offset": -9999, "y-offset": -9999, "chi2": 9999}
    with tempdir.TemporaryDirectory() as tmpdir:
        # copy data file
        tmpdir.copy_in(dataName)
        best = ""
        fitBest = ""

        for counter1, x in enumerate(xs):
            for counter2, y in enumerate(ys):
                cmd.refresh()
                modelName = builderNanodisc(protName, membName, scafName, prefixName, runNumber, x, y, True)
                runNumber += 1
                if modelName == "bad model":
                    # print("Bad model parameters: " + str(z))
                    continue
                cmd.save(modelName + ".pdb", modelName)
                fit, fitResult = fitcrysol(modelName, os.path.basename(dataName), "yes", False)
                cmd.wizard("message",
                           "Refinement: {} ".format(1 + counter2 + counter1 * (len(ys))) +
                           " out of {} steps. Chi2: {}".format(len(xs) * len(ys), 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['x-offset'] = x
                    res['y-offset'] = y
                    best = modelName
                    fitBest = fit
                else:
                    cmd.delete(modelName)
        tmpdir.move_out(best + ".pdb")
        tmpdir.move_out(fitBest)
    print("Best model: Offset coordinates in XY plane : ({},{})".format(res['x-offset'], res['y-offset']))
    print("Chi^2 : {} Best model name : {}".format(res['chi2'], best))
    return best, fitBest, counter1*counter2
Example #29
0
def extractStrain(residues):
    cmd.hide("everything")
    cmd.show("sticks")
    for resi in residues:
        for caa in residues[resi]:
            filename = "residue" + str(resi) + "to" + caa + ".csv"
            outfile = open(filename, "w")
            print(resi, caa)
            cmd.wizard("mutagenesis")
            cmd.do("refresh_wizard")
            cmd.get_wizard().set_mode(caa)
            sel = "/test//A/" + str(resi)
            cmd.get_wizard().do_select(sel)
            bump_name = "_bump_check"
            cmd.sculpt_activate(bump_name)
            cmd.set("sculpt_vdw_vis_mode", 1, bump_name)
            for rotamer in range(1, 1 + cmd.count_states(bump_name)):
                score = cmd.sculpt_iterate(bump_name, rotamer, 1)
                row = (str(rotamer) + "," + str(score) + "\n")
                outfile.write(row)
            outfile.close()
            cmd.get_wizard().clear()
def thread_onto_backbone(backbone_object, backbone_selection, aaString):
#
# 
#  
# create a new temporary dictionary
  stored.tmp_res_dict = {}
  
# store residue indices(=key) and chain(=value)
  cmd.iterate(backbone_selection, "stored.tmp_res_dict[resi] = chain")
  
# create a sorted list of all indices as integers  
  sorted_keys_list = []
  for index_string in stored.tmp_res_dict.keys(): 
    sorted_keys_list.append(int(index_string))
  sorted_keys_list.sort()
  
# set up the mutagenesis wizard
  cmd.wizard("mutagenesis")
  cmd.refresh_wizard()
  
  count = 0
 
  for residue_index in range(sorted_keys_list[0], sorted_keys_list[0] + len(sorted_keys_list) ):
    # get a selection string representation of our current residue
    # e.g. /HPG-3//A/12
    index_string = "%d" %(residue_index)
    selection_str = "/" + backbone_object + "//"+ stored.tmp_res_dict[index_string] + "/%d/" %(residue_index)
    
    # perform the desired mutagenesis
    cmd.get_wizard().do_select(selection_str)
    cmd.get_wizard().set_mode(aaName(aaString[count]))
    cmd.get_wizard().apply()
    
    count = count + 1
    
# close up the mutagenesis wizard    
  cmd.set_wizard()
Example #31
0
 def test_CanInit(self):
     cmd.wizard("nucmutagenesis")
     self.assertTrue(cmd.get_wizard() != None)
Example #32
0
 def test1232(self):
     with testing.mktemp('.pse') as filename:
         cmd.save(filename)
         cmd.wizard('message', 'foo')
         cmd.load(filename)
    def _create_model_from_template_pymol(self,
                                          savepath,
                                          mhcseq,
                                          pepseq,
                                          pdb,
                                          add_polar_h=False):
        """
        This doesn't work properly
        """
        raise NotImplementedError()

        table = self.pdb_table
        row = table[table.pdb == pdb].iloc[0, :]
        resi_list = row['resi_orig'].split(',')
        tplseq = row['seq_orig']
        pepseq_orig = row['peptide']

        aln = Bio.pairwise2.align.globalds(mhcseq, tplseq, matlist.blosum62,
                                           -14.0, -4.0)[0]
        aln1 = aln[0]
        aln2 = aln[1]

        logger.info('Alignment:')
        logger.info('new sequence: ' + aln1)
        logger.info('old sequence: ' + aln2)
        logger.info('')
        logger.info('new peptide: ' + pepseq)
        logger.info('old peptide: ' + pepseq_orig)

        mhc_mutations = []
        for anew, aold, resi in zip(list(aln1), list(aln2), resi_list):
            if anew != aold:
                if anew != '-' and anew != 'X' and aold != '-' and aold != 'X':
                    mhc_mutations.append((seq3(anew), seq3(aold), resi))
        logger.info('Found %i mutations in MHC' % len(mhc_mutations))

        pep_mutations = []
        pep_resi = map(str, range(1, len(pepseq_orig) + 1))
        for anew, aold, resi in zip(list(pepseq), list(pepseq_orig), pep_resi):
            if anew != aold:
                if anew != '-' and anew != 'X' and aold != '-' and aold != 'X':
                    pep_mutations.append((anew, aold, resi))

        logger.info('Found %i mutations in peptide' % len(pep_mutations))

        cmd.delete('all')
        cmd.load(self._get_mhc_path(pdb), 'mhc')
        cmd.load(self._get_pep_path(pdb), 'pep')

        cmd.wizard('mutagenesis')
        cmd.refresh_wizard()
        cmd.remove("not alt ''+A")
        cmd.alter('all', "alt=''")

        for new, old, resi in mhc_mutations:
            logger.info(resi, old, new)
            cmd.get_wizard().do_select("A/" + resi + "/")
            cmd.get_wizard().set_mode(seq3(new).upper())
            cmd.get_wizard().apply()

        for new, old, resi in pep_mutations:
            logger.info(resi, old, new)
            cmd.get_wizard().do_select("B/" + resi + "/")
            cmd.get_wizard().set_mode(seq3(new).upper())
            cmd.get_wizard().apply()

        cmd.set_wizard()

        if add_polar_h:
            cmd.h_add('donors or acceptors')

        cmd.save(savepath, "all")
        cmd.delete("all")
Example #34
0
def mutate(selection, new_resn, inplace=0, sculpt=0, hydrogens='auto', mode=0, quiet=1):
    '''
DESCRIPTION

    Mutate a single residue. Does call the mutagenesis wizard non-interactively
    and tries to select the best rotamer. Can do some sculpting in the end to
    the best rotamer.

USAGE

    mutate selection, new_resn [, inplace [, sculpt [, hydrogens]]]

ARGUMENTS

    selection = string: atom selection of single residue

    new_resn = string: new residue name (3-letter or 1-letter)

    inplace = 0 or 1: work on copy of input object if 0 {default: 0}

    sculpt = 0: no sculpting {default}
    sculpt = 1: do sculpting on best rotamer
    sculpt = 2: do sculpting with neighbors

    hydrogens = string: keep, auto or none {default: auto}

    mode = 0: select rotamer with best clash score {default}
    mode = 1: take chi angles from original residue
    mode = 2: first rotamer

EXAMPLE

    fetch 2x19, async=0
    select x, A/CYS`122/
    zoom x
    mutate x, LYS
    '''
    from pymol.wizard import mutagenesis
    from . import three_letter

    inplace, sculpt = int(inplace), int(sculpt)
    mode = int(mode)
    quiet = int(quiet)
    org = cmd.get_object_list(selection)[0]
    tmp = cmd.get_unused_name()
    new_resn = new_resn.upper()
    new_resn = three_letter.get(new_resn, new_resn)

    if inplace:
        cpy = org
    else:
        cpy = cmd.get_unused_name(org + '_cpy')
        cmd.create(cpy, org, -1, 1, zoom=0)

    scr = []
    cmd.iterate('first (%s)' % selection, 'scr[:] = (segi,chain,resi,resn)', space={'scr': scr})
    res = '/%s/%s/%s/%s' % tuple([cpy] + scr[:3])

    if mode == 1:
        old_resn = scr[3]
        chi_atoms = {
            'ALA': [],
            'ARG': ['C','CA','CB','CG','CD','NE','CZ'],
            'ASN': ['C','CA','CB','CG','OD1'],
            'ASP': ['C','CA','CB','CG','OD1'],
            'CYS': ['C','CA','CB','SG'],
            'GLN': ['C','CA','CB','CG','CD','OE1'],
            'GLU': ['C','CA','CB','CG','CD','OE1'],
            'GLY': [],
            'HIS': ['C','CA','CB','CG','ND1'],
            'ILE': ['C','CA','CB','CG1','CD1'],
            'LEU': ['C','CA','CB','CG','CD1'],
            'LYS': ['C','CA','CB','CG','CD','CE','NZ'],
            'MET': ['C','CA','CB','CG','SD','CE'],
            'MSE': ['C','CA','CB','CG','SE','CE'],
            'PHE': ['C','CA','CB','CG','CD1'],
            'PRO': [],
            'SER': ['C','CA','CB','OG'],
            'THR': ['C','CA','CB','OG1'],
            'TRP': ['C','CA','CB','CG','CD2'],
            'TYR': ['C','CA','CB','CG','CD1'],
            'VAL': ['C','CA','CB','CG2'],
        }
        atoms = [res + '/' + name for name in chi_atoms.get(old_resn, [])]
        old_chi = []
        for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:]):
            try:
                old_chi.append(cmd.get_dihedral(*args))
            except:
                break

    cmd.remove('%s and not name CA+C+N+O+OXT' % (res))

    # start the wizard to count the number of rotamers for this residue
    cmd.wizard("mutagenesis")
    cmd.get_wizard().set_mode(new_resn)
    cmd.get_wizard().set_hyd(hydrogens)
    cmd.get_wizard().do_select("("+res+")")

    def get_best_state_bump():
        best_state = (1, 1e9)
        cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
                (mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
        cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
                'name CA and %s in %s' % (tmp, res))
        cmd.sculpt_activate(tmp)
        for i in range(1, cmd.count_states(tmp)+1):
            score = cmd.sculpt_iterate(tmp, state=i)
            if not quiet:
                print('Frame %d Score %.2f' % (i, score))
            if score < best_state[1]:
                best_state = (i, score)
        cmd.delete(tmp)
        if not quiet:
            print(' Best: Frame %d Score %.2f' % best_state)
        return best_state

    if cmd.count_states(mutagenesis.obj_name) < 2 or mode > 0:
        best_state = (1, -1.0)
    else:
        best_state = get_best_state_bump()
    cmd.frame(best_state[0])
    cmd.get_wizard().apply()
    cmd.wizard()

    if mode == 1:
        atoms = [res + '/' + name for name in chi_atoms.get(new_resn, [])]
        for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:], old_chi):
            cmd.set_dihedral(*args)
        cmd.unpick()

    if sculpt > 0:
        sculpt_relax(res, 0, sculpt == 2, cpy)

    return cpy
Example #35
0
def mutate(selection, new_resn, inplace=0, sculpt=0, hydrogens='auto', mode=0, quiet=1):
    '''
DESCRIPTION

    Mutate a single residue. Does call the mutagenesis wizard non-interactively
    and tries to select the best rotamer. Can do some sculpting in the end to
    the best rotamer.

USAGE

    mutate selection, new_resn [, inplace [, sculpt [, hydrogens]]]

ARGUMENTS

    selection = string: atom selection of single residue

    new_resn = string: new residue name (3-letter or 1-letter)

    inplace = 0 or 1: work on copy of input object if 0 {default: 0}

    sculpt = 0: no sculpting {default}
    sculpt = 1: do sculpting on best rotamer
    sculpt = 2: do sculpting with neighbors

    hydrogens = string: keep, auto or none {default: auto}

    mode = 0: select rotamer with best clash score {default}
    mode = 1: take chi angles from original residue
    mode = 2: first rotamer

EXAMPLE

    fetch 2x19, async=0
    select x, A/CYS`122/
    zoom x
    mutate x, LYS
    '''
    from pymol.wizard import mutagenesis
    from . import three_letter

    inplace, sculpt = int(inplace), int(sculpt)
    mode = int(mode)
    quiet = int(quiet)
    org = cmd.get_object_list(selection)[0]
    tmp = cmd.get_unused_name()
    new_resn = new_resn.upper()
    new_resn = three_letter.get(new_resn, new_resn)

    if inplace:
        cpy = org
    else:
        cpy = cmd.get_unused_name(org + '_cpy')
        cmd.create(cpy, org, -1, 1, zoom=0)

    scr = []
    cmd.iterate('first (%s)' % selection, 'scr[:] = (segi,chain,resi,resn)', space={'scr': scr})
    res = '/%s/%s/%s/%s' % tuple([cpy] + scr[:3])

    if mode == 1:
        old_resn = scr[3]
        chi_atoms = {
            'ALA': [],
            'ARG': ['C','CA','CB','CG','CD','NE','CZ'],
            'ASN': ['C','CA','CB','CG','OD1'],
            'ASP': ['C','CA','CB','CG','OD1'],
            'CYS': ['C','CA','CB','SG'],
            'GLN': ['C','CA','CB','CG','CD','OE1'],
            'GLU': ['C','CA','CB','CG','CD','OE1'],
            'GLY': [],
            'HIS': ['C','CA','CB','CG','ND1'],
            'ILE': ['C','CA','CB','CG1','CD1'],
            'LEU': ['C','CA','CB','CG','CD1'],
            'LYS': ['C','CA','CB','CG','CD','CE','NZ'],
            'MET': ['C','CA','CB','CG','SD','CE'],
            'MSE': ['C','CA','CB','CG','SE','CE'],
            'PHE': ['C','CA','CB','CG','CD1'],
            'PRO': [],
            'SER': ['C','CA','CB','OG'],
            'THR': ['C','CA','CB','OG1'],
            'TRP': ['C','CA','CB','CG','CD2'],
            'TYR': ['C','CA','CB','CG','CD1'],
            'VAL': ['C','CA','CB','CG2'],
        }
        atoms = [res + '/' + name for name in chi_atoms.get(old_resn, [])]
        old_chi = []
        for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:]):
            try:
                old_chi.append(cmd.get_dihedral(*args))
            except:
                break

    cmd.remove('%s and not name CA+C+N+O+OXT' % (res))

    # start the wizard to count the number of rotamers for this residue
    cmd.wizard("mutagenesis")
    cmd.get_wizard().set_mode(new_resn)
    cmd.get_wizard().set_hyd(hydrogens)
    cmd.get_wizard().do_select("("+res+")")

    def get_best_state_bump():
        best_state = (1, 1e9)
        cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
                (mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
        cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
                'name CA and %s in %s' % (tmp, res))
        cmd.sculpt_activate(tmp)
        for i in range(1, cmd.count_states(tmp)+1):
            score = cmd.sculpt_iterate(tmp, state=i)
            if not quiet:
                print('Frame %d Score %.2f' % (i, score))
            if score < best_state[1]:
                best_state = (i, score)
        cmd.delete(tmp)
        if not quiet:
            print(' Best: Frame %d Score %.2f' % best_state)
        return best_state

    if cmd.count_states(mutagenesis.obj_name) < 2 or mode > 0:
        best_state = (1, -1.0)
    else:
        best_state = get_best_state_bump()
    cmd.frame(best_state[0])
    cmd.get_wizard().apply()
    cmd.wizard()

    if mode == 1:
        atoms = [res + '/' + name for name in chi_atoms.get(new_resn, [])]
        for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:], old_chi):
            cmd.set_dihedral(*args)
        cmd.unpick()

    if sculpt > 0:
        sculpt_relax(res, 0, sculpt == 2, cpy)

    return cpy
Example #36
0
    def run(self):
        my_view = cmd.get_view()
        #mark Search
        if self.mode == 'Search':
            #show message
            cmd.wizard("message", "Searching conformers...")
            cmd.refresh()
            if self.currentLabel.uid != "Rx":
                self.search()
                print "Creating Rotamers in PyMOL...",
                for aRotamer in self.currentLabel.ensembles["mW"].rotamers:
                    self.createRotamerInPymol(aRotamer, "mW")
# 				if self.thoroughness == "painstaking" and self.currentLabel.uid == "R1":
# 					scoringWeights = {"totalContactWeight": 0.0, "typeOfContactWeight": 1.0}
# 					for aRotamer in self.currentLabel.ensembles["mW"].rotamers:
# 						aRotamer.score(scoringWeights)
# 					self.currentLabel.ensembles["mW"].sortRotamers("chi2")
# 					numberOfRotamers = len(self.currentLabel.ensembles["mW"].rotamers)
# 					newEnsemble = ensemble.Ensemble()
# 					newEnsemble.name = "contactFit"
# 					newEnsemble.rotamers = self.currentLabel.ensembles["mW"].rotamers[0:20]
# 					self.currentLabel.ensembles["contactFit"] = newEnsemble
# 					for aRotamer in self.currentLabel.ensembles["contactFit"].rotamers:
# 						self.createRotamerInPymol(aRotamer, "contactFit")
                print "done!"

            elif self.currentLabel.uid == "Rx":
                ca1 = numpy.array(
                    cmd.get_model(self.residue1Name + " & name CA",
                                  1).get_coord_list()[0])
                ca2 = numpy.array(
                    cmd.get_model(self.residue2Name + " & name CA",
                                  1).get_coord_list()[0])
                try:
                    cb1 = numpy.array(
                        cmd.get_model(self.residue1Name + " & name CB",
                                      1).get_coord_list()[0])
                except:
                    cb1 = ca1
                try:
                    cb2 = numpy.array(
                        cmd.get_model(self.residue2Name + " & name CB",
                                      1).get_coord_list()[0])
                except:
                    cb2 = ca2

                environmentatoms = numpy.array(cmd.get_model("(%s within 10 of %s or %s) and not (%s or %s)" \
                     %(self.pickedObject1, \
                      self.residue1Name, \
                      self.residue2Name, \
                      self.residue1Name, \
                      self.residue2Name), 1).get_coord_list())
                anchor1rotamers = self.currentLabel.calculateCone(
                    ca1, cb1, environmentatoms, numberOfAtoms=8000)
                anchor2rotamers = self.currentLabel.calculateCone(
                    ca2, cb2, environmentatoms, numberOfAtoms=8000)
                solutions1 = []
                solutions2 = []
                for anchor1rotamer in anchor1rotamers:
                    anAtom = anchor1rotamer.atoms["N1"]
                    solutions1.append(anAtom.coordinate)
                for anchor2rotamer in anchor2rotamers:
                    anAtom = anchor2rotamer.atoms["N1"]
                    solutions2.append(anAtom.coordinate)

                #determine common accessible volume
                distances1 = self.currentLabel.quick_map(solutions1, cb2)
                distances2 = self.currentLabel.quick_map(solutions2, cb1)
                indices1 = numpy.where(numpy.any(distances1 > 6, axis=1))
                indices2 = numpy.where(numpy.any(distances2 > 6, axis=1))
                solutions1 = numpy.delete(solutions1, indices1, 0)
                solutions2 = numpy.delete(solutions2, indices2, 0)
                solutions = numpy.concatenate((solutions1, solutions2))

                #create resulting ensemble
                newEnsemble = ensemble.Ensemble()
                newEnsemble.name = "mW"
                id = 0
                newRotamers = []
                if len(solutions) > 0:
                    for solution in solutions:
                        newRotamer = rotamer.Rotamer()
                        thisAtom = atom.Atom()
                        thisAtom.coordinate = solution
                        thisAtom.name = "N1"
                        thisAtom.element = "N"
                        newRotamer.id = id
                        newRotamer.atoms["N1"] = thisAtom
                        id += 1
                        newRotamers.append(newRotamer)
                else:
                    print "Did not find any possible N1 locations. Are the two anchorpoints too far apart?"
                newEnsemble.rotamers = newRotamers
                self.currentLabel.ensembles[newEnsemble.name] = newEnsemble
                cmd.load(
                    "%s/labels/%s" % (self.path, self.currentLabel.pdbFile),
                    "currentLabel")
                for aRotamer in self.currentLabel.ensembles["mW"].rotamers:
                    self.createRotamerInPymol(aRotamer, "mW")
            self.numberOfLabel += 1
            self.finalCosmetics()
            #dismiss message
            cmd.wizard()

        #mark Measure
        elif self.mode == "Measure":
            cmd.wizard("message", "Calculating distances...")
            cmd.refresh()
            print "\n\n\nDistance calculation:\n"
            print "The dashed lines are the c-beta distance (green),\nand the distance between the geometric averages\nof the two ensembles (yellow).\n"
            print "The following statistics refer to the distribution\nof the individual distances between all conformers (may take a while):\n"

            #find out what the selections are
            stored.label1 = []
            stored.label2 = []
            stored.label1Coordinates = []
            stored.label2Coordinates = []
            stored.atomNames1 = []
            stored.atomNames2 = []

            #extract label info
            cmd.iterate(self.residue1Name, 'stored.label1.append(segi)')
            cmd.iterate(self.residue2Name, 'stored.label2.append(segi)')
            cmd.iterate(self.residue1Name, 'stored.atomNames1.append(name)')
            cmd.iterate(self.residue2Name, 'stored.atomNames2.append(name)')
            try:
                label1 = label.Label.fromfile("labels/%s.txt" %
                                              stored.label1[0])
                cmd.iterate_state(
                    0,
                    "%s & name %s" % (self.residue1Name, label1.spinLocation),
                    'stored.label1Coordinates.append((x,y,z))')
            except:
                cmd.iterate_state(0, "%s" % (self.residue1Name),
                                  'stored.label1Coordinates.append((x,y,z))')
            try:
                label2 = label.Label.fromfile("labels/%s.txt" %
                                              stored.label2[0])
                cmd.iterate_state(
                    0,
                    "%s & name %s" % (self.residue2Name, label2.spinLocation),
                    'stored.label2Coordinates.append((x,y,z))')
            except:
                cmd.iterate_state(0, "%s" % (self.residue2Name),
                                  'stored.label2Coordinates.append((x,y,z))')
            #calculate distances
            distances = distanceDistribution.DistanceDistribution()
            dist = distances.calculateDistanceDistribution(
                stored.label1Coordinates, stored.label2Coordinates)

            #create pseudoatom at average coordinate of each ensemble and display the distance between them
            atoms1 = numpy.array(stored.label1Coordinates)
            atoms2 = numpy.array(stored.label2Coordinates)
            avgAtoms1 = numpy.average(atoms1, axis=0)
            avgAtoms2 = numpy.average(atoms2, axis=0)
            self.createPseudoatom(avgAtoms1, "tmp_average1", 1)
            self.createPseudoatom(avgAtoms2, "tmp_average2", 1)
            cmd.distance(self.object_prefix + "avg", "tmp_average1 & name PS1",
                         "tmp_average2 & name PS1")
            cmd.delete("tmp_average1")
            cmd.delete("tmp_average2")

            #cbeta distance if cbeta is present in both selections
            #cBetaDistance = 0.0
            if any("CB" in atom for atom in stored.atomNames1) and any(
                    "CB" in atom for atom in stored.atomNames2):
                cmd.distance(self.object_prefix + "cBeta",
                             self.residue1Name + " & name CB",
                             self.residue2Name + " & name CB")
                #for some reason, cmd.distance does not return the correct distance. Although it is shown in the viewer...
                #get_distance gives the correct distance, but does not create the object in the viewer.
                cBetaDistance = cmd.get_distance(
                    self.residue1Name + " & name CB",
                    self.residue2Name + " & name CB")
                cmd.set("dash_color", "green", self.object_prefix + "cBeta")

            histogram = numpy.histogram(dist, numpy.arange(100))
            envelopePlot = numpy.zeros((100, 2))
            envelopePlot[0:99] = numpy.column_stack(
                (histogram[1][0:len(histogram[1]) - 1], histogram[0]))

            #put point in mid of bin
            envelopePlot[:, 0] += 0.5
            normEnvelopePlot = numpy.copy(envelopePlot)
            normEnvelopePlot[:, 1] = normEnvelopePlot[:, 1] / numpy.amax(
                histogram[0])

            #combine dist and histogram to single array before output
            output = numpy.column_stack((envelopePlot, normEnvelopePlot[:, 1]))
            averageDistance = numpy.average(dist)

            #make graph dictionary for mtsslPlotter
            graphtitle = "%s-%s" % (self.residue1Name, self.residue2Name)
            xlim = [0, 100]
            ylim = [0, 1]
            plotDictionary = self.makeGraphDataDictionary(
                graphtitle, "DistanceDistribution", "Distance (Angstrom)",
                "Relative Probability", output[:, 0], output[:,
                                                             2], 0, xlim, ylim)
            stored.plots.append(plotDictionary)
            print "Distribution plot added to memory. Inspect it with mtsslPlotter."

            #Copy to clipboard
            header = "Dist.   Count   Norm.Count\n"
            outputStr = header + numpy.array_str(output)
            outputStr = outputStr.replace("[", "")
            outputStr = outputStr.replace("]", "")
            self.copyStringToClipboard(outputStr)

            #Write to file
            if self.writeToFile:
                try:
                    filename = "%s-%s" % (self.residue1Name, self.residue2Name)
                    numpy.savetxt(filename + ".txt", output, delimiter='\t')
                    print "Written to file:"
                    print "%s/%s" % (os.getcwd(), filename)
                except:
                    print "Writing to file failed!"
            print self.calculateStatistics2(dist)
            try:
                if cBetaDistance > 0.0:
                    print "Cbeta distance: %3.1f" % cBetaDistance
            except:
                print "No Cbeta distance."
            cmd.wizard()

        #mark Distance Map
        elif self.mode == "Distance Map":
            #show message
            cmd.wizard("message",
                       "Calculating distance maps. Please be patient...")
            cmd.refresh()
            dm = distanceMap.DistanceMap(self.writeToFile, self.currentLabel,
                                         self.homoOligomerMode)
            if self.pickedObject1 == self.pickedObject2:
                dm.intraDistanceMap(self.pickedObject1)
            else:
                dm.interDistanceMap(self.pickedObject1, self.pickedObject2)
            print "Done!"
            cmd.wizard()

        self.cleanupAfterRun()
        cmd.set_view(my_view)
Example #37
0
 def test1232(self):
     with testing.mktemp('.pse') as filename:
         cmd.save(filename)
         cmd.wizard('message', 'foo')
         cmd.load(filename)
Example #38
0
def dis(event):
    cmd.wizard('Distance')
Example #39
0
def dis(event):
    cmd.wizard('Distance')
Example #40
0
        elif mutation_list[x][-1] == 'F':
            residue_list[x] = 'PHE'
        elif mutation_list[x][-1] == 'P':
            residue_list[x] = 'PRO'
        elif mutation_list[x][-1] == 'S':
            residue_list[x] = 'SER'
        elif mutation_list[x][-1] == 'T':
            residue_list[x] = 'THR'
        elif mutation_list[x][-1] == 'W':
            residue_list[x] = 'TRP'
        elif mutation_list[x][-1] == 'Y':
            residue_list[x] = 'TYR'
        elif mutation_list[x][-1] == 'V':
            residue_list[x] = 'VAL'
    cmd.load('D:/autodock_automation/tmafc.pdb')  #Replace with your directory
    cmd.wizard('mutagenesis')
    for x in range(len(mutation_list)):
        cmd.get_wizard().do_select('/tmafc//A/%s' % (position_list[x]))
        cmd.get_wizard().set_mode("%s" % (residue_list[x]))
        cmd.get_wizard().apply()
    cmd.save('D:/autodock_automation/PDB_Files/mutant_%s.pdb' % (mutation))
    cmd.reinitialize('everything')
cmd.quit()

for pdbFile in os.listdir('D:/autodock_automation/PDB_FILES'):
    subprocess.run(
        'cmd /c "python D:/autodock_automation/prepare_receptor4.py -r D:/autodock_automation/PDB_Files/'
        + pdbFile + ' -o D:/autodock_automation/PDBQT_Files/' + pdbFile +
        'qt -U waters"')

for pdbqtFile in os.listdir('D:/autodock_automation/PDBQT_FILES'):
# pymol -qc mutate.py pdb selection new_residue
# example: pymol -qc mutate.py 0.pdb C/1/ ALA 0_mutated.pdb

# run for all the confs in the ensemble
# append all to one using mdconvert

from pymol import cmd
import sys

pdb, selection, mutant, output_name = sys.argv[-4:]
print("file:", pdb)
print("selection:", selection)
print("mutating to:", mutant)
print("output name:", output_name)

cmd.load(pdb, "file")

cmd.wizard("mutagenesis")
cmd.refresh_wizard()
cmd.get_wizard().do_select(selection)
cmd.get_wizard().set_mode(mutant)
cmd.get_wizard().apply()
cmd.set_wizard()

cmd.save(output_name, "file")
 def test_CanInit(self):
     cmd.wizard("nucmutagenesis")
     self.assertTrue(cmd.get_wizard() != None)