def get_6dof_cst(D3, D2, D1, U1, U2, U3):
cur_cst = {
"distanceAB": [0.0, 0.2, 80.0, 0, 0],
"angle_A": [0.0, 5.0, 10.0, 360, 0],
"angle_B": [0.0, 5.0, 10.0, 360, 0],
"torsion_A": [0.0, 10.0, 10.0, 360, 0],
"torsion_AB": [0.0, 10.0, 10.0, 360, 0],
"torsion_B": [0.0, 10.0, 10.0, 360, 0]
}
if U1.split("/")[-1] == "NZ" and U2.split("/")[-1] == "CE" and U3.split(
"/")[-1] == "2HZ": #means processing constraint for LYS
cur_cst = {
"distanceAB": [
0.0, 0.1, 80.0, 1, 0
], #the only difference is periodicity will be set at 1 indicating covalent interaction in the cst file
"angle_A": [0.0, 5.0, 10.0, 360, 0],
"angle_B": [0.0, 5.0, 10.0, 360, 0],
"torsion_A": [0.0, 10.0, 10.0, 360, 0],
"torsion_AB": [0.0, 10.0, 10.0, 360, 0],
"torsion_B": [0.0, 10.0, 10.0, 360, 0]
}
cur_cst["distanceAB"][0] = round(cmd.get_distance(D1, U1), 1)
cur_cst["angle_A"][0] = round(cmd.get_angle(D2, D1, U1), 1)
cur_cst["angle_B"][0] = round(cmd.get_angle(D1, U1, U2), 1)
cur_cst["torsion_A"][0] = round(cmd.get_dihedral(D3, D2, D1, U1), 1)
cur_cst["torsion_AB"][0] = round(cmd.get_dihedral(D2, D1, U1, U2), 1)
cur_cst["torsion_B"][0] = round(cmd.get_dihedral(D1, U1, U2, U3), 1)
return cur_cst
def check_disulphide_criteria(pdb, resnum_i, resnum_j, f):
selection_i = "resi " + str(resnum_i)
selection_j = "resi " + str(resnum_j)
for frame_i in [1, 2]:
rotamer_i_pymol_prefix = "/" + "rotamer_" + str(resnum_i) + "_" + str(frame_i) + "///" + resnum_i + "/"
chi1_i = cmd.get_dihedral(rotamer_i_pymol_prefix + "N", rotamer_i_pymol_prefix + "CA", rotamer_i_pymol_prefix + "CB", rotamer_i_pymol_prefix + "SG")
theta_i = cmd.get_angle(rotamer_i_pymol_prefix + "CA", rotamer_i_pymol_prefix + "CB", rotamer_i_pymol_prefix + "SG")
for frame_j in [1, 2]:
rotamer_j_pymol_prefix = "/" + "rotamer_" + str(resnum_j) + "_" + str(frame_j) + "///" + resnum_j + "/"
chi1_j = cmd.get_dihedral(rotamer_j_pymol_prefix + "N", rotamer_j_pymol_prefix + "CA", rotamer_j_pymol_prefix + "CB", rotamer_j_pymol_prefix + "SG")
theta_j = cmd.get_angle(rotamer_j_pymol_prefix + "CA", rotamer_j_pymol_prefix + "CB", rotamer_j_pymol_prefix + "SG")
chi3 = cmd.get_dihedral(rotamer_i_pymol_prefix + "CB", rotamer_i_pymol_prefix + "SG", rotamer_j_pymol_prefix + "SG", rotamer_j_pymol_prefix + "CB")
#Energy = compute_energy(chi1_i, chi1_j, theta_i, theta_j, chi3)
s_gamma_distance = cmd.get_distance(rotamer_i_pymol_prefix + "SG", rotamer_j_pymol_prefix + "SG")
if (s_gamma_distance < 3 and ((chi3 > -110 and chi3 < -60) or (chi3 > 70 and chi3 < 130))):
print rotamer_i_pymol_prefix, rotamer_j_pymol_prefix, s_gamma_distance, chi3
f.write("%s\t%s\t%f\t%f\n" % (rotamer_i_pymol_prefix, rotamer_j_pymol_prefix, s_gamma_distance, chi3))
rotamer_i = "rotamer_" + str(resnum_i) + "_" + str(frame_i)
rotamer_j = "rotamer_" + str(resnum_j) + "_" + str(frame_j)
cmd.enable(rotamer_i)
cmd.enable(rotamer_j)
cmd.distance(rotamer_i_pymol_prefix + "SG", rotamer_j_pymol_prefix + "SG")
cmd.create(rotamer_i + rotamer_j, rotamer_i_pymol_prefix + "or" + rotamer_j_pymol_prefix)
def test_torsion(self):
cmd.fragment('ala')
delta = 10
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
d1 = cmd.get_dihedral(*atoms)
cmd.edit(*atoms[1:3])
cmd.torsion(delta)
d2 = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(d1 + delta, d2, 4)
def test_torsion(self):
cmd.fragment('ala')
delta = 10
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
d1 = cmd.get_dihedral(*atoms)
cmd.edit(*atoms[1:3])
cmd.torsion(delta)
d2 = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(d1 + delta, d2, 4)
def start(self,sel):
# Get selection model
model = cmd.get_model(sel)
residues = ['dummy']
resnames = ['dummy']
phi = []
psi = []
dummy = []
i = 0
# Loop through each atom
for at in model.atom:
# Only plot once per residue
if at.chain+":"+at.resn+":"+at.resi not in residues:
residues.append(at.chain+":"+at.resn+":"+at.resi)
resnames.append(at.resn+at.resi)
dummy.append(i)
i += 1
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if at.chain != "":
unit_select = "chain "+str(at.chain)+" and "
# Define selections for residue i-1, i and i+1
residue_def = unit_select+'resi '+str(at.resi)
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
try:
# Store phi,psi residue definitions to pass on to plot routine
phi_psi = [
# Phi angles
residue_def_prev+' and name C',
residue_def+' and name N',
residue_def+' and name CA',
residue_def+' and name C',
# Psi angles
residue_def+' and name N',
residue_def+' and name CA',
residue_def+' and name C',
residue_def_next+' and name N']
# Compute phi/psi angle
phi = cmd.get_dihedral(phi_psi[0],phi_psi[1],phi_psi[2],phi_psi[3])
psi = cmd.get_dihedral(phi_psi[4],phi_psi[5],phi_psi[6],phi_psi[7])
print "Plotting Phi,Psi: "+str(phi)+","+str(psi)
ramaplot(phi,psi,meta=phi_psi)
except:
continue
def set_phipsi(sel, phi, psi):
# Get atoms from selection
atoms = cmd.get_model("byres (" + sel + ")")
# Loop through atoms in selection
for at in atoms.atom: # pylint: disable=E1103
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain " + str(at.chain) + " and "
# end if
try:
# Define residue selections
rdef_prev = unit_select + 'resi ' + str(int(at.resi) - 1)
rdef = unit_select + 'resi ' + str(at.resi)
# print "rdef_prev: [%s]" % rdef_prev
# print "rdef : [%s]" % rdef
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(rdef_prev + ' and name C',
rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C')
cmd.set_dihedral(rdef_prev + ' and name C',
rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C', phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (
at.resn, at.resi, old_phi, float(phi))
except:
print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
rdef = unit_select + 'resi ' + str(at.resi)
residue_def_next = unit_select + 'resi ' + str(
int(at.resi) + 1)
# print "rdef : [%s]" % rdef
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C',
residue_def_next + ' and name N')
cmd.set_dihedral(rdef + ' and name N', rdef + ' and name CA',
rdef + ' and name C',
residue_def_next + ' and name N', psi) # pylint: disable=C0301
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (
at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"
def main():
args = parse_args()
pep_pdbs = read_rmsd(args)
for i in range(0, 7):
outputfilehandler = open('phi_psi_' + str(i + 2) + '.csv', 'w')
outputfilehandler.write("pdb,chain,pep_seq,index,phi,psi\n")
outputfilehandler.close()
for key in pep_pdbs:
phi = []
psi = []
model_name = key + '_reordered'
pdbfile = key + '_reordered.pdb'
targetfile = args.dir + '/' + pdbfile
cmd.load(targetfile)
chains = cmd.get_chains(model_name)
try:
#psi.append(cmd.get_dihedral(chains[1]+"/1/N,",chains[1]+"/1/ca,",chains[1]+"/1/c,",chains[1]+"/2/n"))
#phi_psi = cmd.phi_psi(model_name+ " and chain "+chains[1])
for i in range(2, 9):
phi.append(
cmd.get_dihedral(chains[1] + "/" + str(i - 1) + "/c,",
chains[1] + "/" + str(i) + "/n,",
chains[1] + "/" + str(i) + "/ca,",
chains[1] + "/" + str(i) + "/c"))
psi.append(
cmd.get_dihedral(chains[1] + "/" + str(i) + "/N,",
chains[1] + "/" + str(i) + "/ca,",
chains[1] + "/" + str(i) + "/c,",
chains[1] + "/" + str(i + 1) + "/n"))
#phi.append(cmd.get_dihedral(chains[1]+"/8/c,",chains[1]+"/9/n,",chains[1]+"/9/ca,",chains[1]+"/9/c"))
except:
print("Found exception, ignoring")
if len(phi) == 7 and len(psi) == 7:
for i in range(0, len(phi)):
outputfilehandler = open('phi_psi_' + str(i + 2) + '.csv', 'a')
print(pep_pdbs[key] + ',' + chains[1] + ',' + str(i + 2) +
',' + str(phi[i]) + ',' + str(psi[i]))
outputfilehandler.write(key + ',' + chains[1] + ',' +
pep_pdbs[key] + ',' + str(i + 2) +
',' + str(phi[i]) + ',' + str(psi[i]) +
'\n')
outputfilehandler.close()
pymol.cmd.do("delete all")
def doFinish(self):
r_aA = cmd.get_distance(atom1="pw2", atom2="pw3", state=0)
cmd.distance(self.params_str[0], "pw2", "pw3")
th_a = cmd.get_angle(atom1="pw1", atom2="pw2", atom3="pw3", state=0)
cmd.angle(self.params_str[1], "pw1", "pw2", "pw3")
th_A = cmd.get_angle(atom1="pw2", atom2="pw3", atom3="pw4", state=0)
cmd.angle(self.params_str[2], "pw2", "pw3", "pw4")
if not (r_aA and th_a and th_A):
showerror(self.parent, "Error!",
"Maybe you made a mistake when choosing atoms!")
self.reset()
phi_ba = cmd.get_dihedral(atom1="pw0",
atom2="pw1",
atom3="pw2",
atom4="pw3",
state=0)
cmd.dihedral(self.params_str[3], "pw0", "pw1", "pw2", "pw3")
phi_aA = cmd.get_dihedral(atom1="pw1",
atom2="pw2",
atom3="pw3",
atom4="pw4",
state=0)
cmd.dihedral(self.params_str[4], "pw1", "pw2", "pw3", "pw4")
phi_AB = cmd.get_dihedral(atom1="pw2",
atom2="pw3",
atom3="pw4",
atom4="pw5",
state=0)
cmd.dihedral(self.params_str[5], "pw2", "pw3", "pw4", "pw5")
index_c = cmd.id_atom("pw0")
index_c_name = getAtomString('pw0')
index_b = cmd.id_atom("pw1")
index_b_name = getAtomString('pw1')
index_a = cmd.id_atom("pw2")
index_a_name = getAtomString('pw2')
index_A = cmd.id_atom("pw3")
index_A_name = getAtomString('pw3')
index_B = cmd.id_atom("pw4")
index_B_name = getAtomString('pw4')
index_C = cmd.id_atom("pw5")
index_C_name = getAtomString('pw5')
self.setBondForceParam(r_aA, th_a, th_A, phi_ba, phi_aA, phi_AB,
index_c, index_b, index_a, index_A, index_B,
index_C)
self.setAtomsDef(index_c_name, index_b_name, index_a_name,
index_A_name, index_B_name, index_C_name)
top = Toplevel(
self.parent) # <- freeze when open gro file in pymol 1.X
Output(top, self.bondForceParams, self.atoms_def)
cmd.set_wizard()
def test_set_dihedral(self):
cmd.fragment('ala')
angle = 45.0
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
cmd.set_dihedral(*atoms, angle=angle)
v = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(v, angle, 4)
def measure_all_torsions(sele,prot_dict):
id_list = cmd.identify("((%s) and name ca)"%sele)
for a in id_list:
res_sele = "(alt '' and (byres id %d) and (%s))"%(a,sele)
lst = find_torsions(res_sele)
if len(lst):
cmd.iterate("(%s and n;ca)"%res_sele,"stored.resn=resn")
resn = pymol.stored.resn
print(resn)
name_list = []
for a in lst:
pymol.stored.names = []
for b in a:
cmd.iterate("(%s and id %d)"%(res_sele,b),"stored.names.append(name)")
name_list.append(tuple(pymol.stored.names))
res_dict = {}
for a in name_list:
dihe = cmd.get_dihedral("(%s and name %s)"%(res_sele,a[0]),
"(%s and name %s)"%(res_sele,a[1]),
"(%s and name %s)"%(res_sele,a[2]),
"(%s and name %s)"%(res_sele,a[3]))
res_dict[a]=dihe
if resn not in prot_dict:
prot_dict[resn]=[]
prot_dict[resn].append(res_dict)
def measure_all_torsions(sele,prot_dict):
id_list = cmd.identify("((%s) and name ca)"%sele)
for a in id_list:
res_sele = "(alt '' and (byres id %d) and (%s))"%(a,sele)
lst = find_torsions(res_sele)
if len(lst):
cmd.iterate("(%s and n;ca)"%res_sele,"stored.resn=resn")
resn = pymol.stored.resn
print resn
name_list = []
for a in lst:
pymol.stored.names = []
for b in a:
cmd.iterate("(%s and id %d)"%(res_sele,b),"stored.names.append(name)")
name_list.append(tuple(pymol.stored.names))
res_dict = {}
for a in name_list:
dihe = cmd.get_dihedral("(%s and name %s)"%(res_sele,a[0]),
"(%s and name %s)"%(res_sele,a[1]),
"(%s and name %s)"%(res_sele,a[2]),
"(%s and name %s)"%(res_sele,a[3]))
res_dict[a]=dihe
if not prot_dict.has_key(resn):
prot_dict[resn]=[]
prot_dict[resn].append(res_dict)
def get_psi_angle(pymol_object, chainID, aa_number):
"""Get Psi dihedral angle of a given residue.
Parameters
----------
pymol_object : String
Name of Pymol object in the session.
chainID : String
ChainID of residue.
aa_number : Integer
Residue number.
Returns
-------
angle : Float
Value of Psi angle.
"""
# Atom selection for each atom that participates in the angle
# Ni
atom1 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/N'
# CAi
atom2 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/CA'
# Ci
atom3 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/C'
# Ni+1
atom4 = pymol_object + '//' + chainID + '/' + str(aa_number+1) + '/N'
angle = cmd.get_dihedral(atom1, atom2, atom3, atom4)
return angle
def updateSels(self,event):
if (event.widget.widgetName == "toplevel"):
selections = self.getSels()
#set objects in box for adding Hs
objects = cmd.get_names_of_type("object:molecule");
if list(self.h_sel.get()) != list(objects):
self.h_sel.setlist(objects)
selections = objects+selections
for cBox in self.cBoxes:
listEles = cBox.component('scrolledlist').get()
#listEles = cBox.get()
if list(selections) != list(listEles):
cBox.setlist(selections)
#Rotamer Dihedral Code
if('pkresi' in cmd.get_names("public_selections")):
cmd.select('_kropkresi','pkresi')
myspace = {'resName': [], 'resNum': []}
cmd.iterate('_kropkresi and name CA', 'resName.append(resn);resNum.append(resi)', space=myspace)
if(list(myspace['resName']) != list(self.rotResList) or list(myspace['resNum']) != list(self.rotResIList)):
self.rotResList = myspace['resName']
self.rotResIList = myspace['resNum']
if(len(self.rotResList) == 1):
resn = self.rotResList[0].upper()
if(resn in self.AAtypes):
aa = self.AAtypes[resn]
self.curAAtype = aa
numDih = len(aa.dihAtomNames)
#set orig dihVals
self.origRotVals = []
for atoms in self.AAtypes[resn].dihAtomNames:
self.origRotVals.append(cmd.get_dihedral('_kropkresi and name ' + atoms[0], '_kropkresi and name ' + atoms[1], '_kropkresi and name ' + atoms[2],
'_kropkresi and name ' + atoms[3]))
for i,val in enumerate(self.origRotVals):
self.dihScale[i].grid()
self.dihScale[i].set(val)
for i in range(numDih,4):
self.dihScale[i].grid_remove()
self.rotsToAdd = []
self.rotsToAdd.append("orig")
for vals in self.AAtypes[resn].dihVals:
self.rotsToAdd.append(vals)
self.rotBox.setlist(self.rotsToAdd)
resStr = self.rotResList[0] + " " + str(self.rotResIList[0])
self.resLabel.config(text=resStr)
self.dotCheckCB()
else:
self.clearRot()
else:
self.clearRot()
def test_set_dihedral(self):
cmd.fragment('ala')
angle = 45.0
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
cmd.set_dihedral(*atoms, angle=angle)
v = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(v, angle, 4)
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 is_pro_cis_or_trans(obj, resi, chain=None):
gen_sel = '%s and chain %s and resi %s ' % (obj, chain, resi)
cmd.select(
'temp_O',
'%s and chain %s and resi %i and name O' % (obj, chain, int(resi) - 1))
cmd.select(
'temp_C',
'%s and chain %s and resi %i and name C' % (obj, chain, int(resi) - 1))
cmd.select('temp_N', '%s and name N' % gen_sel)
cmd.select('temp_CD', '%s and name CD' % gen_sel)
dihedral = cmd.get_dihedral('temp_O',
'temp_C',
'temp_N',
'temp_CD',
state=0)
if -170 <= dihedral <= 190:
cis_or_trans = 'trans'
elif -10 <= dihedral <= +10:
cis_or_trans = 'cis'
else:
cis_or_trans = 'unknown'
print('the dihedral is %.2f, I think it is %s' % (dihedral, cis_or_trans))
for atom in ['O', 'C', 'N', 'CD']:
cmd.delete('temp_%s' % atom)
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 DihedralFromPKSelection (selections = []):
""" Function doc """
dihedral = {}
if 'pk4' in selections:
dihedral['pk1pk2pk3pk4'] = str(cmd.get_dihedral ('pk1','pk2','pk3','pk4'))
else:
dihedral['pk1pk2pk3pk4'] = None
return dihedral
def getdihedral(selection, resids, atomnames):
# first check if all atoms are present and unique:
for an, resi in zip(atomnames, resids):
presentandunique(selection, resi, an)
return cmd.get_dihedral(*[
'({0}) and (resi {1}) and (name {2})'.format(selection, resi, an)
for resi, an in zip(resids, atomnames)
],
quiet=True)
def get_dihedral(modelname, nameandresi1, nameandresi2, nameandresi3,
nameandresi4):
"""A safer version of cmd.get_dihedral(): doesn't choke on non-singleton selections"""
selections = [
'({}) and name {} and resi {}'.format(modelname, *nr)
for nr in [nameandresi1, nameandresi2, nameandresi3, nameandresi4]
]
if not all([cmd.count_atoms(s) == 1 for s in selections]):
return None
return cmd.get_dihedral(*selections)
def get_chi(obj, resi, state):
"""
Get the dihedral angle chi (C1-O'x-C'x-C'x-1)
"""
atom1 = '%s and resi %s and name N' % (obj, resi)
atom2 = '%s and resi %s and name CA'% (obj, resi)
atom3 = '%s and resi %s and name CB' % (obj, resi)
atom4 = '%s and resi %s and name CG' % (obj, resi)
value = cmd.get_dihedral(atom1, atom2, atom3, atom4, state=state)
return value
def get_phi(res_num, state):
"""Computes the phi torsional angle"""
if res_num != 0:
cmd.select('A', 'resi %s and name C' % (res_num-1))
cmd.select('B', 'resi %s and name N' % res_num)
cmd.select('C', 'resi %s and name CA' % res_num)
cmd.select('D', 'resi %s and name C' % res_num)
return cmd.get_dihedral('A', 'B', 'C', 'D', state)
else:
return float('nan')
def get_omega(obj, bond, state=1):
"""
Get the dihedral angle omega (O6-C6-C5-C4)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
atom1 = '%s and resi %s and name O6' % (obj, resi_j)
atom2 = '%s and resi %s and name C6' % (obj, resi_j)
atom3 = '%s and resi %s and name C5' % (obj, resi_j)
atom4 = '%s and resi %s and name C4' % (obj, resi_j)
value = cmd.get_dihedral(atom1, atom2, atom3, atom4, state=state)
return value
def get_omega(obj, bond, state=1):
"""
Get the dihedral angle omega (O6-C6-C5-C4)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
atom1 = '%s and resi %s and name O6' % (obj, resi_j)
atom2 = '%s and resi %s and name C6' % (obj, resi_j)
atom3 = '%s and resi %s and name C5' % (obj, resi_j)
atom4 = '%s and resi %s and name C4' % (obj, resi_j)
value = cmd.get_dihedral(atom1, atom2, atom3, atom4, state=state)
return value
def get_chi2(res_num, res_name, state):
"""Computes the chi2 torsional angle"""
if res_name not in ['ALA', 'GLY', 'PRO', 'SER', 'THR', 'VAL', 'CYS']:
cmd.select('A', 'resi %s and name CA' % res_num)
cmd.select('B', 'resi %s and name CB' % res_num)
cmd.select('C', 'resi %s and (name CG or name CG1 or name OG1 or name OG)' % res_num)
cmd.select('D', 'resi %s and (name CD or name CD1 or name OD1 or name ND1 or name SD)' % res_num)
chi2 = cmd.get_dihedral('A', 'B', 'C', 'D', state)
return chi2
else:
return float('nan')
def get_chi1(res_num, res_name, state):
"""Computes the chi1 torsional angle"""
if res_name not in ['ALA', 'GLY', 'PRO']:
cmd.select('A', 'resi %s and name N' % res_num)
cmd.select('B', 'resi %s and name CA' % res_num)
cmd.select('C', 'resi %s and name CB' % res_num)
cmd.select('D', 'resi %s and (name CG or name CG1 or name OG1 or name OG or name SG)' % res_num)
chi1 = cmd.get_dihedral('A', 'B', 'C', 'D', state)
return chi1
else:
return float('nan')
def get_omega(res_num, state, total_residues):
"""Computes the omega torsional angle"""
if res_num != total_residues-1:
cmd.select('A', 'resi %s and name CA' % res_num)
cmd.select('B', 'resi %s and name C' % res_num)
cmd.select('C', 'resi %s and name N' % (res_num+1))
cmd.select('D', 'resi %s and name CA' % (res_num+1))
omega = cmd.get_dihedral('A', 'B', 'C', 'D', state)
return omega
else:
return float('nan')
def hw3(model):
cmd.remove(model + ' and resn hoh')
cmd.remove(model + ' and not alt a+""')
cmd.remove(model + ' and not chain A')
resis = []
cmd.iterate('/{}//A//CA'.format(model),
'resis.append(resi)',
space={'resis': resis})
resis_int = map(int, resis)
resis = map(sm, resis)
#Pro
resP = []
cmd.iterate('/{}//A//CA'.format(model),
'resP.append(resn == "PRO")',
space={'resP': resP})
angs_phi = []
angs_psi = []
for i in range(1, len(resis) - 1):
if (resis_int[i - 1] + 1
== resis_int[i]) and (resis_int[i] + 1
== resis_int[i + 1]) and resP[i]:
angs_phi.append(cmd.get_dihedral('/{}//A/{}/C'.format(model, resis[i-1]), \
'/{}//A/{}/N'.format(model, resis[i]), \
'/{}//A/{}/CA'.format(model, resis[i]), \
'/{}//A/{}/C'.format(model, resis[i]))),
angs_psi.append(cmd.get_dihedral('/{}//A/{}/N'.format(model, resis[i]), \
'/{}//A/{}/CA'.format(model, resis[i]), \
'/{}//A/{}/C'.format(model, resis[i]), \
'/{}//A/{}/N'.format(model, resis[i+1])))
fname = 'C:\\Users\\Nick\\Desktop\\Bank\\PhystechStuding\\Buslaev\\project3\\hw3_{}_Pro.dat'.format(
model)
open(fname, 'w').close()
np.savetxt(fname, np.transpose([angs_phi, angs_psi]))
def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")
# Loop through atoms in selection
for at in atoms.atom: # pylint: disable=E1103
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "
# end if
try:
# Define residue selections
rdef_prev = unit_select+'resi '+str(int(at.resi)-1)
rdef = unit_select+'resi '+str(at.resi)
# print "rdef_prev: [%s]" % rdef_prev
# print "rdef : [%s]" % rdef
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(rdef_prev+' and name C',rdef+' and name N', rdef+' and name CA',rdef+' and name C')
cmd.set_dihedral( rdef_prev+' and name C',rdef+' and name N', rdef+' and name CA',rdef+' and name C',phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (at.resn, at.resi, old_phi, float(phi))
except:
print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
rdef = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "rdef : [%s]" % rdef
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(rdef +' and name N',rdef+' and name CA',rdef+' and name C', residue_def_next+' and name N')
cmd.set_dihedral( rdef +' and name N',rdef+' and name CA',rdef+' and name C', residue_def_next+' and name N',psi) # pylint: disable=C0301
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"
def get_psi(obj, bond, state=1):
"""
Get the dihedral angle psi (C1-O'x-C'x-C'x-1)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
if atom_i > atom_j:
atom_j = atom_i
resi_i, resi_j = resi_j, resi_i
atom1 = '%s and resi %s and name C1' % (obj, resi_i)
atom2 = '%s and resi %s and name O%s' % (obj, resi_j, atom_j)
atom3 = '%s and resi %s and name C%s' % (obj, resi_j, atom_j)
atom4 = '%s and resi %s and name C%s' % (obj, resi_j, (atom_j - 1))
value = cmd.get_dihedral(atom1, atom2, atom3, atom4, state=state)
return value
def get_psi(obj, bond, state=1):
"""
Get the dihedral angle psi (C1-O'x-C'x-C'x-1)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
if atom_i > atom_j:
atom_j = atom_i
resi_i, resi_j = resi_j, resi_i
atom1 = '%s and resi %s and name C1' % (obj, resi_i)
atom2 = '%s and resi %s and name O%s' % (obj, resi_j, atom_j)
atom3 = '%s and resi %s and name C%s' % (obj, resi_j, atom_j)
atom4 = '%s and resi %s and name C%s' % (obj, resi_j, (atom_j-1))
value = cmd.get_dihedral(atom1, atom2, atom3, atom4, state=state)
return value
def calculateAlphaHelicalPhaseYieldPerResidue(caPositions, helixAxisPoints,correct):
alphaHelicalPhaseYieldPerResidue=[]
alphaHelicalPhaseYieldPerResidue.append(0)
#alphaHelicalPhaseYieldPerResidue.append(0)
for i in range (1,len(helixAxisPoints)-1):
#generate pseudoatoms for dihedral calculation
id=random.random()*1000
cmd.pseudoatom(pos=str([caPositions[i-1].item(0),caPositions[i-1].item(1),caPositions[i-1].item(2)]), object="ca_i-1"+str(id))
cmd.pseudoatom(pos=str([caPositions[i].item(0),caPositions[i].item(1),caPositions[i].item(2)]), object="ca_i"+str(id))
cmd.pseudoatom(pos=str([caPositions[i+1].item(0),caPositions[i+1].item(1),caPositions[i+1].item(2)]), object="ca_i+1"+str(id))
cmd.pseudoatom(pos=str([helixAxisPoints[i-1].item(0),helixAxisPoints[i-1].item(1),helixAxisPoints[i-1].item(2)]), object="axis_i-1"+str(id))
cmd.pseudoatom(pos=str([helixAxisPoints[i].item(0),helixAxisPoints[i].item(1),helixAxisPoints[i].item(2)]), object="axis_i"+str(id))
cmd.pseudoatom(pos=str([helixAxisPoints[i+1].item(0),helixAxisPoints[i+1].item(1),helixAxisPoints[i+1].item(2)]), object="axis_i+1"+str(id))
a=cmd.get_dihedral("ca_i-1"+str(id),"axis_i-1"+str(id),"axis_i"+str(id),"ca_i"+str(id),state=0)
b=cmd.get_dihedral("ca_i"+str(id),"axis_i"+str(id),"axis_i+1"+str(id),"ca_i+1"+str(id),state=0)
#print i,a,b, (a+b)/2
cmd.delete("ca_i-1"+str(id))
cmd.delete("ca_i"+str(id))
cmd.delete("ca_i+1"+str(id))
cmd.delete("axis_i-1"+str(id))
cmd.delete("axis_i"+str(id))
cmd.delete("axis_i+1"+str(id))
alphaHelicalPhaseYieldPerResidue.append(correct+(a+b)/2)
return alphaHelicalPhaseYieldPerResidue
def flip_by_atoms(self, atmA, atmB, atmC, atmD):
from pymol import CmdException, cmd
sele = self.selector()
a, b, c, d = map(lambda a: '{}/{}'.format(sele, a),
[atmA, atmB, atmC, atmD])
try:
dh = cmd.get_dihedral(a, b, c, d)
except CmdException:
print "Error on '{}'.".format(self.selector())
pass
else:
cmd.set_dihedral(a, b, c, d, dh + 180)
cmd.unpick()
def fix_gln_hydrogens(selection):
"""Fix the naming of cis and trans hydrogens in glutamine"""
# HZ21 is the cis, HZ22 is the trans
for hindex in iterate_indices(
'({}) and (name HZ21+HZ22)'.format(selection)):
if abs(
cmd.get_dihedral(
'(idx {}) and ({})'.format(hindex, selection),
'(name NZ2) and ({})'.format(selection),
'(name CE) and ({})'.format(selection),
'(name OZ1) and ({})'.format(selection))) < 90:
cmd.alter('(idx {}) and ({})'.format(hindex, selection),
'name="HZ21"')
else:
cmd.alter('(idx {}) and ({})'.format(hindex, selection),
'name="HZ22"')
def get_zmat_ext_freeze_torsion(self,flag=3):
# requires PYMOL to read dihedrals from structure
# requires list of dihedrals from tinker.amber
#
from pymol import cmd
from .tinker.amber import Topology
cmd.load_model(self.model,'_gamess1')
model = self.model
# get mapping of model ordering to zmat ordering
m2z = {}
z2m = {}
c = 1 # GAMESS is one-based
for a in self.get_zmat_ordering():
m2z[a] = c
z2m[c] = a
c = c + 1
# get all torsions in the molecule
topo = Topology(self.model)
# find those where flag is set in all atoms
mask = 2 ** flag
frozen_list = []
for a in list(topo.torsion.keys()):
if (model.atom[a[0]].flags&
model.atom[a[1]].flags&
model.atom[a[2]].flags&
model.atom[a[3]].flags)&mask:
frozen_list.append(a)
print(" freeze-torsion: %d torsions will be frozen."%len(frozen_list))
irzmat = []
ifzmat = []
fvalue = []
if len(frozen_list):
for frozen in frozen_list:
# find additional torsions which need to be removed
remove = []
for a in list(topo.torsion.keys()):
if (((a[1]==frozen[1])and(a[2]==frozen[2])) or
((a[2]==frozen[1])and(a[1]==frozen[2]))):
if a!=frozen:
remove.append(a)
# convert to internal coordinate ordering
frozen_z = (m2z[frozen[0]],m2z[frozen[1]],
m2z[frozen[2]],m2z[frozen[3]])
remove_z = []
for a in remove:
remove_z.append(m2z[a[0]],m2z[a[1]],m2z[a[2]],m2z[a[3]])
# now reorder atoms in torsions to reflect z_matrix ordering
# (not sure this is necessary)
if frozen_z[0]>frozen_z[3]:
frozen_z = (frozen_z[3],frozen_z[2],frozen_z[1],frozen_z[0])
tmp_z = []
for a in remove_z:
if a[0]>a[3]:
tmp_z.append((a[3],a[2],a[1],a[0]))
else:
tmp_z.append(a)
remove_z = tmp_z
# get value of the fixed torsion
fixed = (z2m[frozen_z[0]],z2m[frozen_z[1]],
z2m[frozen_z[2]],z2m[frozen_z[3]])
dihe = cmd.get_dihedral("(_gamess1 and id %d)"%fixed[0],
"(_gamess1 and id %d)"%fixed[1],
"(_gamess1 and id %d)"%fixed[2],
"(_gamess1 and id %d)"%fixed[3])
# write out report for user edification
print(" freeze-torsion: fixing freeze-torsion:")
print(" freeze-torsion: %d-%d-%d-%d (pymol), %d-%d-%d-%d (gamess)"%(
fixed[0],fixed[1],fixed[2],fixed[3],
frozen_z[0],frozen_z[1],frozen_z[2],frozen_z[3]))
print(" freeze-torsion: at %5.3f"%dihe)
print(" freeze-torsion: removing redundant torsions:")
for a in remove_z[1:]:
print(" freeze-torsion: %d-%d-%d-%d (pymol), %d-%d-%d-%d (gamess)"%(
z2m[a[0]],z2m[a[1]],z2m[a[2]],z2m[a[3]],
a[0],a[1],a[2],a[3]))
# add parameters for this torsion into the list
ifzmat.append((3,frozen_z[0],frozen_z[1],frozen_z[2],frozen_z[3]))
fvalue.append(dihe)
if len(remove_z):
for a in remove_z[1:]:
irzmat.append((3,a[0],a[1],a[2],a[3]))
# generate restrained dihedral information
zmat_ext = []
if len(ifzmat):
zmat_ext.append(" IFZMAT(1)=\n")
comma = ""
for a in ifzmat:
zmat_ext.append(comma+"%d,%d,%d,%d,%d\n"%a)
comma = ","
if len(fvalue):
zmat_ext.append(" FVALUE(1)=\n")
comma = ""
for a in fvalue:
zmat_ext.append(comma+"%1.7f\n"%a)
comma = ","
if len(irzmat):
zmat_ext.append(" IRZMAT(1)=\n")
comma = ""
for a in irzmat:
zmat_ext.append(comma+"%d,%d,%d,%d,%d\n"%a)
comma = ","
cmd.delete("_gamess1") # important
if len(zmat_ext):
return zmat_ext
else:
return None
def do_library(self):
cmd = self.cmd
pymol = cmd._pymol
if not (
(cmd.count_atoms("(%s) and name n" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name c" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name o" % src_sele) == 1)
):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable", "selector", "everythin")
cmd.feedback("disable", "editor", "actions")
self.prompt = ["Loading rotamers..."]
pymol.stored.name = "residue"
cmd.iterate("first (%s)" % src_sele, 'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight", src_sele)
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele, animate=-1)
self.lib_mode = self.mode
if self.lib_mode == "current":
pymol.stored.resn = ""
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn, pymol.stored.resn)
if (self.c_cap != "none") or (self.n_cap != "none") or (self.hyd != "auto"):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name, src_sele, 1, 1)
if self.c_cap == "open":
cmd.remove("%s and name OXT" % frag_name)
if self.lib_mode != "current":
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == "posi") and (frag_type[0:3] != "NT_"):
if not (cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) &! r. ace" % (src_sele, src_sele))):
# use N-terminal fragment
frag_type = "NT_" + frag_type
if (self.c_cap == "nega") and (frag_type[0:3] != "CT_"):
if not (cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele))):
# use C-terminal fragment
frag_type = "CT_" + frag_type
if rot_type[0:3] in ["NT_", "CT_"]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(string.lower(frag_type), frag_name)
# trim off hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# copy identifying information
cmd.iterate("(%s and n;ca)" % src_sele, "stored.chain=chain")
cmd.alter("(%s)" % frag_name, "chain=stored.chain")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resi=resi")
cmd.alter("(%s)" % frag_name, "resi=stored.resi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.segi=segi")
cmd.alter("(%s)" % frag_name, "segi=stored.segi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.ss=ss")
cmd.alter("(%s)" % frag_name, "ss=stored.ss")
# move the fragment
if (cmd.count_atoms("(%s and n;cb)" % frag_name) == 1) and (
cmd.count_atoms("(%s and n;cb)" % src_sele) == 1
):
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;cb)" % frag_name,
"(%s and n;cb)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
else:
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
# fix the carbonyl position...
cmd.iterate_state(1, "(%s and n;o)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;o)" % frag_name, "(x,y,z)=stored.list")
if cmd.count_atoms("(%s and n;oxt)" % src_sele):
cmd.iterate_state(1, "(%s and n;oxt)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;oxt)" % frag_name, "(x,y,z)=stored.list")
elif cmd.count_atoms("(%s and n;oxt)" % frag_name): # place OXT if no template exists
angle = cmd.get_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;o)" % frag_name,
)
cmd.protect("(%s and n;o)" % frag_name)
cmd.set_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;oxt)" % frag_name,
180.0 + angle,
)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % frag_name) == 1:
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % src_sele) == 1:
cmd.iterate_state(1, "(elem h and bound_to (n;n and (%s)))" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(elem h and bound_to (n;n and (%s)))" % frag_name, "(x,y,z)=stored.list")
elif cmd.select(tmp_sele1, "(n;c and bound_to (%s and e;n))" % src_sele) == 1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral(
"(%s and n;c)" % frag_name, "(%s and n;ca)" % frag_name, "(%s and n;n)" % frag_name, tmp_sele1
)
cmd.set_dihedral(
"(%s and n;c)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;n)" % frag_name,
"(%s and n;h)" % frag_name,
180.0 + angle,
)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in ["amin", "nmet"]:
if not cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele)):
if cmd.count_atoms("n;c & (%s)" % (frag_name)) == 1:
if self.c_cap == "amin":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nhh")
elif self.c_cap == "nmet":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nme")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & bound_to (n;c & (%s))" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# add n-cap (if appropriate)
if self.n_cap in ["acet"]:
if not cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) & !r. ace " % (src_sele, src_sele)):
if cmd.count_atoms("n;n & (%s)" % (frag_name)) == 1:
if self.n_cap == "acet":
editor.attach_amino_acid("n;n & (%s)" % (frag_name), "ace")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & (%s)" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
cartoon = cmd.count_atoms("(%s and n;ca and rep cartoon)" % src_sele) > 0
sticks = cmd.count_atoms("(%s and n;ca and rep sticks)" % src_sele) > 0
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == "dep":
try:
result = cmd.phi_psi("%s" % src_sele)
if len(result) == 1:
(phi, psi) = result[result.keys()[0]]
(phi, psi) = (int(10 * round(phi / 10)), int(10 * (round(psi / 10))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(20 * round(phi / 20)), int(20 * (round(psi / 20))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(60 * round(phi / 60)), int(60 * (round(psi / 60))))
key = (rot_type, phi, psi)
lib = self.dep_library.get(key, None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key, None)
if (lib != None) and self.dep == "dep":
print " Mutagenesis: no phi/psi, using backbone-independent rotamers."
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name, frag_name, 1, state)
if state == 1:
cmd.select(mut_sele, "(byres (%s like %s))" % (obj_name, src_sele))
if rot_type == "PRO":
cmd.unbond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
for b in a.keys():
if b != "FREQ":
cmd.set_dihedral(
"(%s & n;%s)" % (mut_sele, b[0]),
"(%s & n;%s)" % (mut_sele, b[1]),
"(%s & n;%s)" % (mut_sele, b[2]),
"(%s & n;%s)" % (mut_sele, b[3]),
a[b],
state=state,
)
else:
cmd.set_title(obj_name, state, "%1.1f%%" % (a[b] * 100))
if rot_type == "PRO":
cmd.bond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
state = state + 1
cmd.delete(frag_name)
print " Mutagenesis: %d rotamers loaded." % len(lib)
if self.bump_check:
cmd.delete(bump_name)
cmd.create(
bump_name,
"(((byobj %s) within 6 of (%s and not name n+c+ca+o+h+ha)) and (not (%s)))|(%s)"
% (src_sele, mut_sele, src_sele, mut_sele),
singletons=1,
)
cmd.color("gray50", bump_name + " and elem c")
cmd.set("seq_view", 0, bump_name, quiet=1)
cmd.hide("everything", bump_name)
if (cmd.select(tmp_sele1, "(n;N and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;C and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
if (cmd.select(tmp_sele1, "(n;C and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;N and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name n+c+ca+o+h+ha))" % (bump_name, bump_name, mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo", bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode", 1, bump_name)
state = 1
for a in lib:
cmd.sculpt_iterate(bump_name, state=state)
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name, frag_name, 1, 1)
print " Mutagenesis: no rotamers found in library."
cmd.set("seq_view", 0, obj_name, quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("(" + obj_name + ")")
cmd.show(self.rep, obj_name)
cmd.show("lines", obj_name) # neighbor always show lines
if cartoon:
cmd.show("cartoon", obj_name)
if sticks:
cmd.show("sticks", obj_name)
cmd.set("auto_zoom", auto_zoom, quiet=1)
cmd.delete(frag_name)
cmd.frame(0)
cmd.unpick()
cmd.feedback("pop")
def print_dihedrals(selection='sele',
state=1,
quiet=1,
ss='',
fc=10.0,
chi=0,
label='ID'):
'''
DESCRIPTION
"print_dihedrals" return the phi, psi, and chi1 angles for a protein atom
selection.
ARGUMENTS
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
amber = integer: generate AMBER rst file {default: 1;ON}
label = string: label type ('ID' or 'index') {default: ID}
fc = float: force constant for the dihedral angles {default: 10.0}
chi = 0: Do not print chi angles (default)
chi = 1: print chi1 dihedral angle (if exists)
chi = 2: print chi1 and chi2 dihedral angles (if exists) (not implemented yet)
SEE ALSO
phipsi
'''
# selectionからCalpha原子のIDリストを取得
chi = int(chi)
caindex = []
cmd.iterate('bycalpha (%s)' % selection,
'caindex.append(ID)',
space=locals())
# Calpha原子が属する残基ごとに処理を行う
for ca in caindex:
# resinameに残基名のみ取得
n_sele = "((byres ID %s) & name N)" % ca
c_sele = "((byres ID %s) & name C)" % ca
ca_sele = "((byres ID %s) & name CA)" % ca
cb_sele = "((byres ID %s) & name CB)" % ca
resiname_sele = []
cmd.iterate(ca_sele, "resiname_sele.append(resn)", space=locals())
resiname = str(resiname_sele[0])
if resiname == 'ILE' or resiname == 'VAL':
cg_sele = "((byres ID %s) & name CG1)" % ca
elif resiname == 'THR':
cg_sele = "((byres ID %s) & name OG1)" % ca
elif resiname == 'CYS' or resiname == 'CYX':
cg_sele = "((byres ID %s) & name SG)" % ca
else:
cg_sele = "((byres ID %s) & name CG)" % ca
cm_sele = "((neighbor (%s)) and not (byres (%s)))" % (n_sele, n_sele
) #前の残基のC
np_sele = "((neighbor (%s)) and not (byres (%s)))" % (c_sele, c_sele
) #次の残基のN
cmd.feedback("push")
cmd.feedback("disable", "selector", "everything")
cm_cnt = cmd.select("_pp_cm", cm_sele)
n_cnt = cmd.select("_pp_n", n_sele)
c_cnt = cmd.select("_pp_c", c_sele)
ca_cnt = cmd.select("_pp_ca", ca_sele)
cb_cnt = cmd.select("_pp_cb", cb_sele)
cg_cnt = cmd.select("_pp_cg", cg_sele)
np_cnt = cmd.select("_pp_np", np_sele)
# 残基名＋残基番号取得(ASP704みたいな)
rname = []
cmd.iterate(ca_sele, "rname.append(resn+resi)", space=locals())
if (cm_cnt and n_cnt and ca_cnt and c_cnt):
phi = cmd.get_dihedral("_pp_c", "_pp_ca", "_pp_n", "_pp_cm")
else:
phi = None
if (n_cnt and ca_cnt and c_cnt and np_cnt):
psi = cmd.get_dihedral("_pp_np", "_pp_c", "_pp_ca", "_pp_n")
else:
psi = None
if (n_cnt and ca_cnt and cb_cnt and cg_cnt):
chi1 = cmd.get_dihedral("_pp_cg", "_pp_cb", "_pp_ca", "_pp_n")
else:
chi1 = None
atomdict = {}
strings = [
"_pp_cm", "_pp_n", "_pp_c", "_pp_ca", "_pp_cb", "_pp_np", "_pp_cg"
]
for i in strings:
temp = cmd.identify(i)
# tempが空リストでなければatomdictに追加
if temp:
atomdict[i] = temp[0]
# phi, psi用に制限を設ける
# 引数でssが指定されている場合、その範囲になるよう設定
def phir2limit(x, sigma, ss):
if ss == '':
val = x - sigma
if val <= -180.0:
val = -180.0
return val
elif ss == 'alpha':
val = -80.0
return val
elif ss == 'beta':
val = -155.0
return val
def phir3limit(x, sigma, ss):
if ss == '':
val = x + sigma
if val >= 180.0:
val = 180.0
return val
elif ss == 'alpha':
val = -50.0
return val
elif ss == 'beta':
val = -125.0
return val
def psir2limit(x, sigma, ss):
if ss == '':
val = x - sigma
if val <= -180.0:
val = -180.0
return val
elif ss == 'alpha':
val = -55.0
return val
elif ss == 'beta':
val = 115.0
return val
def psir3limit(x, sigma, ss):
if ss == '':
val = x + sigma
if val >= 180.0:
val = 180.0
return val
elif ss == 'alpha':
val = -25.0
return val
elif ss == 'beta':
val = 145.0
return val
def r2limit(x, sigma):
val = x - sigma
if val <= -180.0:
val = -180.0
return val
def r3limit(x, sigma):
val = x + sigma
if val >= 180.0:
val = 180.0
return val
if phi is not None:
print('''# {6} phi
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_c']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']),
int(atomdict['_pp_cm']),
phir2limit(phi, 10.0, ss),
phir3limit(phi, 10.0, ss), str(rname[0]),
float(fc)))
if psi is not None:
print('''# {6} psi
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_np']),
int(atomdict['_pp_c']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']),
psir2limit(psi, 10.0, ss),
psir3limit(psi, 10.0, ss), str(rname[0]),
float(fc)))
if (chi > 0) and (chi1 is not None):
print('''# {6} chi1
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_cg']),
int(atomdict['_pp_cb']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']), r2limit(chi1, 10.0),
r3limit(chi1,
10.0), str(rname[0]), float(fc)))
def ens_measure(pk1 = None,
pk2 = None,
pk3 = None,
pk4 = None,
name = None,
log = None,
verbose = True):
'''
DESCRIPTION
Statistics from ensemble structure measurements. If:
2 selections give = distance
3 selections give = angle
4 selections give = dihedral angle
USAGE
ens_measure pk1, pk2, pk3, pk4, name, log, verbose
ARGUMENTS
log = name of log file
verbose = prints individual measurements
EXAMPLE
ens_measure atom1, atom2, name = 'measure', log 'ens.log'
'''
print >> log, '\nEnsemble measurement'
if [pk1, pk2, pk3, pk4].count(None) > 2:
print '\nERROR: Please supply at least 2 seletions'
return
number_models = cmd.count_states(pk1)
measurements = []
# distance
if [pk1, pk2, pk3, pk4].count(None) == 2:
print >> log, 'Distance'
if name == None: name = 'ens_distance'
# display as object
cmd.distance(name = name,
selection1 = pk1,
selection2 = pk2)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_distance(pk1, pk2, n+1) )
assert len(measurements) == number_models
# angle
if [pk1, pk2, pk3, pk4].count(None) == 1:
print >> log, 'Angle'
# display as object
if name == None: name = 'ens_angle'
cmd.angle(name = name,
selection1 = pk1,
selection2 = pk2,
selection3 = pk3)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_angle(atom1 = pk1,
atom2 = pk2,
atom3 = pk3,
state = n+1) )
assert len(measurements) == number_models
# Dihedral angle
if [pk1, pk2, pk3, pk4].count(None) == 0:
print >> log, 'Dihedral angle'
# display as object
if name == None: name = 'ens_dihedral'
cmd.dihedral(name = name,
selection1 = pk1,
selection2 = pk2,
selection3 = pk3,
selection4 = pk4)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_dihedral(atom1 = pk1,
atom2 = pk2,
atom3 = pk3,
atom4 = pk4,
state = n+1) )
assert len(measurements) == number_models
# print stats
if verbose:
print >> log, ' State Value'
for n, measurement in enumerate(measurements):
print >> log, ' %4d %3.3f '%(n+1, measurement)
print >> log, '\nMeasurement statistics'
print_array_stats(array = measurements,
log = log)
def get_zmat_ext_freeze_torsion(self, flag=3):
# requires PYMOL to read dihedrals from structure
# requires list of dihedrals from tinker.amber
#
from pymol import cmd
from tinker.amber import Topology
cmd.load_model(self.model, '_gamess1')
model = self.model
# get mapping of model ordering to zmat ordering
m2z = {}
z2m = {}
c = 1 # GAMESS is one-based
for a in self.get_zmat_ordering():
m2z[a] = c
z2m[c] = a
c = c + 1
# get all torsions in the molecule
topo = Topology(self.model)
# find those where flag is set in all atoms
mask = 2**flag
frozen_list = []
for a in topo.torsion.keys():
if (model.atom[a[0]].flags & model.atom[a[1]].flags
& model.atom[a[2]].flags & model.atom[a[3]].flags) & mask:
frozen_list.append(a)
print " freeze-torsion: %d torsions will be frozen." % len(frozen_list)
irzmat = []
ifzmat = []
fvalue = []
if len(frozen_list):
for frozen in frozen_list:
# find additional torsions which need to be removed
remove = []
for a in topo.torsion.keys():
if (((a[1] == frozen[1]) and (a[2] == frozen[2]))
or ((a[2] == frozen[1]) and (a[1] == frozen[2]))):
if a != frozen:
remove.append(a)
# convert to internal coordinate ordering
frozen_z = (m2z[frozen[0]], m2z[frozen[1]], m2z[frozen[2]],
m2z[frozen[3]])
remove_z = []
for a in remove:
remove_z.append(m2z[a[0]], m2z[a[1]], m2z[a[2]], m2z[a[3]])
# now reorder atoms in torsions to reflect z_matrix ordering
# (not sure this is necessary)
if frozen_z[0] > frozen_z[3]:
frozen_z = (frozen_z[3], frozen_z[2], frozen_z[1],
frozen_z[0])
tmp_z = []
for a in remove_z:
if a[0] > a[3]:
tmp_z.append((a[3], a[2], a[1], a[0]))
else:
tmp_z.append(a)
remove_z = tmp_z
# get value of the fixed torsion
fixed = (z2m[frozen_z[0]], z2m[frozen_z[1]], z2m[frozen_z[2]],
z2m[frozen_z[3]])
dihe = cmd.get_dihedral("(_gamess1 and id %d)" % fixed[0],
"(_gamess1 and id %d)" % fixed[1],
"(_gamess1 and id %d)" % fixed[2],
"(_gamess1 and id %d)" % fixed[3])
# write out report for user edification
print " freeze-torsion: fixing freeze-torsion:"
print " freeze-torsion: %d-%d-%d-%d (pymol), %d-%d-%d-%d (gamess)" % (
fixed[0], fixed[1], fixed[2], fixed[3], frozen_z[0],
frozen_z[1], frozen_z[2], frozen_z[3])
print " freeze-torsion: at %5.3f" % dihe
print " freeze-torsion: removing redundant torsions:"
for a in remove_z[1:]:
print " freeze-torsion: %d-%d-%d-%d (pymol), %d-%d-%d-%d (gamess)" % (
z2m[a[0]], z2m[a[1]], z2m[a[2]], z2m[a[3]], a[0], a[1],
a[2], a[3])
# add parameters for this torsion into the list
ifzmat.append(
(3, frozen_z[0], frozen_z[1], frozen_z[2], frozen_z[3]))
fvalue.append(dihe)
if len(remove_z):
for a in remove_z[1:]:
irzmat.append((3, a[0], a[1], a[2], a[3]))
# generate restrained dihedral information
zmat_ext = []
if len(ifzmat):
zmat_ext.append(" IFZMAT(1)=\n")
comma = ""
for a in ifzmat:
zmat_ext.append(comma + "%d,%d,%d,%d,%d\n" % a)
comma = ","
if len(fvalue):
zmat_ext.append(" FVALUE(1)=\n")
comma = ""
for a in fvalue:
zmat_ext.append(comma + "%1.7f\n" % a)
comma = ","
if len(irzmat):
zmat_ext.append(" IRZMAT(1)=\n")
comma = ""
for a in irzmat:
zmat_ext.append(comma + "%d,%d,%d,%d,%d\n" % a)
comma = ","
cmd.delete("_gamess1") # important
if len(zmat_ext):
return zmat_ext
else:
return None
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib is None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib is not None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib is not None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
# pymol -qc mutate.py pdb selection new_residue
# example: pymol -qc mutate.py 0.pdb C/1/ ALA 0_mutated.pdb
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")
resi_num = selection.split("/")[1]
#prefix = "chain B & resi " + resi_num + " & name "
prefix = "chain A & resi " + resi_num + " & name "
orig_dihedral = cmd.get_dihedral(prefix + "C", prefix + "CA", prefix + "CB", prefix + "CG")
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.set_dihedral(prefix + "C", prefix + "CA", prefix + "CB", prefix + "1HB", orig_dihedral)
cmd.save(output_name, "file")
(float(vdw) + float(Elec)))
### only args.distance atom is considered
if args.distance:
if number == str(args.distance):
model_dict.setdefault(
model,
distance(center, tuple(map(float, (x, y, z)))))
else:
model_dict.setdefault(model, 0)
### only args.angle atom is considered
if args.angle:
if number in args.angle:
angle.setdefault(
model, abs(cmd.get_dihedral('1', '2', '3', '4')))
else:
angle.setdefault(model, 0)
### only args.catalytic atoms are considered
if args.catalytic:
if number in args.catalytic:
cat.setdefault(model, []).append(
(float(vdw) + float(Elec)))
else:
cat.setdefault(model, [0])
### only args.prova atoms are considered
if args.catalytic:
if number in args.catalytic:
oh.setdefault(model,
def ens_measure(pk1=None,
pk2=None,
pk3=None,
pk4=None,
name=None,
log=None,
verbose=True):
'''
DESCRIPTION
Statistics from ensemble structure measurements. If:
2 selections give = distance
3 selections give = angle
4 selections give = dihedral angle
USAGE
ens_measure pk1, pk2, pk3, pk4, name, log, verbose
ARGUMENTS
log = name of log file
verbose = prints individual measurements
EXAMPLE
ens_measure atom1, atom2, name = 'measure', log 'ens.log'
'''
print('\nEnsemble measurement', file=log)
if [pk1, pk2, pk3, pk4].count(None) > 2:
print('\nERROR: Please supply at least 2 seletions')
return
number_models = cmd.count_states(pk1)
measurements = []
# distance
if [pk1, pk2, pk3, pk4].count(None) == 2:
print('Distance', file=log)
if name == None: name = 'ens_distance'
# display as object
cmd.distance(name=name, selection1=pk1, selection2=pk2)
# get individual values
for n in range(number_models):
measurements.append(cmd.get_distance(pk1, pk2, n + 1))
assert len(measurements) == number_models
# angle
if [pk1, pk2, pk3, pk4].count(None) == 1:
print('Angle', file=log)
# display as object
if name == None: name = 'ens_angle'
cmd.angle(name=name, selection1=pk1, selection2=pk2, selection3=pk3)
# get individual values
for n in range(number_models):
measurements.append(
cmd.get_angle(atom1=pk1, atom2=pk2, atom3=pk3, state=n + 1))
assert len(measurements) == number_models
# Dihedral angle
if [pk1, pk2, pk3, pk4].count(None) == 0:
print('Dihedral angle', file=log)
# display as object
if name == None: name = 'ens_dihedral'
cmd.dihedral(name=name,
selection1=pk1,
selection2=pk2,
selection3=pk3,
selection4=pk4)
# get individual values
for n in range(number_models):
measurements.append(
cmd.get_dihedral(atom1=pk1,
atom2=pk2,
atom3=pk3,
atom4=pk4,
state=n + 1))
assert len(measurements) == number_models
# print stats
if verbose:
print(' State Value', file=log)
for n, measurement in enumerate(measurements):
print(' %4d %3.3f ' % (n + 1, measurement), file=log)
print('\nMeasurement statistics', file=log)
print_array_stats(array=measurements, log=log)
def dihe(selection, a1, a2, a3, a4, state=-1): atm1=selection + " and name %s" %a1; atm2=selection + " and name %s" %a2; atm3=selection + " and name %s" %a3; atm4=selection + " and name %s" %a4; return cmd.get_dihedral(atm1,atm2,atm3,atm4, state=state);
def find_peptide_bonds(selection):
logger.debug('Finding peptide bonds in selection {}:'.format(selection))
for idx in iterate_indices('({}) and (e. N)'.format(selection)):
logger.debug('Candidate N: {}'.format(idx))
# this nitrogen should have:
# - at least one hydrogen neighbour
# - one carbon neighbour such as it has exactly one oxygen
# neighbour which has no other neighbours
hydrogens = list(
iterate_indices('(neighbor (idx {})) and (e. H) and ({})'.format(
idx, selection)))
if not hydrogens:
# check if idx is part of a proline ring
if not (
(cmd.count_atoms('(e. C) and (byring idx {}) and ({})'.format(
idx, selection)) == 4) and
(cmd.count_atoms('(byring idx {}) and ({})'.format(
idx, selection)) == 5)):
# idx is not part of a 5-ring with 4 other carbon atoms
continue
logger.debug('Idx {} is a proline nitrogen'.format(idx))
hydrogens = list(
iterate_indices(
'(neighbor (idx {0})) and (byring idx {0}) and ({1})'.
format(idx, selection)))
# now hydrogens contains two CARBON atoms!!!
carbon = None
oxygen = None
for c in iterate_indices(
'(neighbor (idx {})) and (e. C) and ({})'.format(
idx, selection)):
logger.debug('Candidate C: {}'.format(c))
for o in iterate_indices(
'(neighbor (idx {})) and (e. O) and ({})'.format(
c, selection)):
logger.debug('Candidate O: {}'.format(o))
oneighbours = list(iterate_neighbours(o, selection))
if len(oneighbours) == 1:
logger.debug('Carbon is {}, oxygen is {}'.format(c, o))
carbon = c
oxygen = o
break
else:
logger.debug('No good oxygens for this C')
continue
break
else:
logger.debug('No good carbons for this N.')
continue
if carbon is None or oxygen is None:
logger.debug('No carbon or no oxygen -> no N')
continue
for h in hydrogens:
dih = cmd.get_dihedral(
'(idx {}) and ({})'.format(h, selection),
'(idx {}) and ({})'.format(idx, selection),
'(idx {}) and ({})'.format(carbon, selection),
'(idx {}) and ({})'.format(oxygen, selection))
if abs(dih) > 140 or abs(dih) < 40:
hydrogen = h
break
else:
logger.debug(
'No appropriate (planar) hydrogens for this nitrogen, oxygen and carbon.'
)
continue
if (len(hydrogens) > 1) and not cmd.count_atoms(
'(e. C) and (idx {}) and ({})'.format(hydrogen, selection)):
# if the nitrogen has more than one hydrogens and the trans hydrogen is not a carbon
# (i.e. this peptide bond does not belong to a proline)
continue
logger.debug('Found peptide bond: {}, {}, {}, {}'.format(
hydrogen, idx, carbon, oxygen))
yield (hydrogen, idx, carbon, oxygen)
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib!= None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
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
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
for filename in filenames:
with open(filename, 'r') as f:
lines = f.readlines()
lines = list(filter(filter_func , lines))
dih_pairs.extend(list(map(map_func, lines)))
restraints.extend(list(map(map_func2, lines)))
out_lines = []
for dih_pair,restraint in zip(dih_pairs, restraints):
group1 = "(id %d)" % dih_pair[0]
group2 = "(id %d)" % dih_pair[1]
group3 = "(id %d)" % dih_pair[2]
group4 = "(id %d)" % dih_pair[3]
cmd.dihedral("%d-%d-%d-%d" % dih_pair, group1, group2, group3, group4)
resns = []
resis = []
atoms = []
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "resns.append(resn)")
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "resis.append(resi)")
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "atoms.append(name)")
dihedral = cmd.get_dihedral(group1, group2, group3, group4)
out_lines.append("[ %s%s(%s)-%s%s(%s)-%s%s(%s)-%s%s(%s) ~ %.2f degree (%s, %s, %s)]\n" % ((resns[0], resis[0], atoms[0], resns[1], resis[1], atoms[1], resns[2], resis[2], atoms[2],resns[3], resis[3], atoms[3], dihedral) + restraint))
out_lines.append("%d %d %d %d\n" % dih_pair)
# write dis_pairs to distance_pairs.ndx for analysis
with open("dihedral_out.ndx", 'w') as f:
for line in out_lines:
f.write(line)
print(line)
def color_abego( opt_enabled_only=True ):
pdb_list = PDB_list()
# make a namespace for iterate()
myspace = { 'pdb_list' : pdb_list }
cmd.iterate( 'n. ca', 'pdb_list.add_res( model, chain, resv )', space=myspace )
# loop over each object
for key, pdb in pdb_list.pdbs.iteritems():
if pdb.name in cmd.get_names( 'objects', enabled_only=opt_enabled_only ):
# list of residues for each ABEGO type
bb_a = []
bb_b = []
bb_e = []
bb_g = []
bb_o = []
# loop over each residue and calculate ABEGO type
for res in pdb.residues:
if ( res[0], res[1] - 1 ) in pdb.residues and ( res[0], res[1] + 1 ) in pdb.residues:
a1 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] - 1, 'C' )
a2 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] , 'N' )
a3 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] , 'CA' )
a4 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] , 'C' )
a5 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] + 1, 'N' )
a6 = '{0} and chain {1} and resi {2} and name {3}'.format( pdb, res[0], res[1] + 1, 'CA' )
phi = cmd.get_dihedral( a1, a2, a3, a4 )
psi = cmd.get_dihedral( a2, a3, a4, a5 )
omega = cmd.get_dihedral( a3, a4, a5, a6 )
if abs( omega ) < 90 or abs( omega ) > 270:
bb_o.append( res )
continue
if phi > 0:
if psi < 100 and psi > -100:
bb_g.append( res )
continue
else:
bb_e.append( res )
continue
else:
if psi < 50 and psi > -72:
bb_a.append( res )
continue
else:
bb_b.append( res )
continue
# color carbons based on residue ABEGO type
cmd.color( 'gray', '{0} and e. c'.format( pdb ) )
if bb_a:
cmd.select( 'bb_a', ' OR '.join( '{0} and chain {1[0]} and resi {1[1]} and e. c'.format( pdb, x ) for x in bb_a ) )
cmd.color( 'red', 'bb_a' )
if bb_b:
cmd.select( 'bb_b', ' OR '.join( '{0} and chain {1[0]} and resi {1[1]} and e. c'.format( pdb, x ) for x in bb_b ) )
cmd.color( 'blue', 'bb_b' )
if bb_e:
cmd.select( 'bb_e', ' OR '.join( '{0} and chain {1[0]} and resi {1[1]} and e. c'.format( pdb, x ) for x in bb_e ) )
cmd.color( 'yellow', 'bb_e' )
if bb_g:
cmd.select( 'bb_g', ' OR '.join( '{0} and chain {1[0]} and resi {1[1]} and e. c'.format( pdb, x ) for x in bb_g ) )
cmd.color( 'green', 'bb_g' )
if bb_o:
cmd.select( 'bb_o', ' OR '.join( '{0} and chain {1[0]} and resi {1[1]} and e. c'.format( pdb, x ) for x in bb_o ) )
cmd.color( 'orange', 'bb_o' )
# delete selections
cmd.delete( 'bb_a' )
cmd.delete( 'bb_b' )
cmd.delete( 'bb_e' )
cmd.delete( 'bb_g' )
cmd.delete( 'bb_o' )