def show_rep(tag):
try:
sel = glb.SELE
if tag == 'Lines':
cmd.show('lines', sel)
elif tag == 'Sticks':
cmd.show('sticks', sel)
elif tag == 'Ribbons':
cmd.show('ribbon', sel)
elif tag == 'Cartoon':
cmd.show('cartoon', sel)
elif tag == 'Dots':
cmd.show('dots', sel)
elif tag == 'Spheres':
cmd.show('spheres', sel)
elif tag == 'Mesh':
cmd.show('mesh', sel)
elif tag == 'Surface':
cmd.show('surface', sel)
elif tag == 'Water':
cmd.show('spheres', '(resn HOH)')
elif tag == 'Ball and Stick':
preset.ball_and_stick(sel)
elif tag == 'Polar Contacts':
cmd.dist(sel+"_polar_conts", sel, sel, quiet = 1, mode = 2, label = 0,
reset = 1)
cmd.enable(sel+"1CHO_polar_conts")
except:
showinfo('Error', 'Update Selection!')
def fSumWMCFirst(molecule, SGNameAngle, chain, residue, MCNeighbour, DieElecMC,
MCchargeC, MCchargeO, printMC):
# print "First", MCNeighbour
SumWMCFirst = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
NBnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
# print NBnameselect, residueName
# Mainchain C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distFirstC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMCFirst = SumWMCFirst + WMC
if printMC == 'yes':
print("MC C ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain O
Onameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distFirstO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMCFirst = SumWMCFirst + WMC
if printMC == 'yes':
print("MC O ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ",
ResDist, " ", WMC)
cmd.delete(residue + 'distFirstC')
cmd.delete(residue + 'distFirstO')
cmd.delete("MC")
return SumWMCFirst
def show_ligand_interactions(recsel="not hetatm", ligsel="hetatm", cutoff=5):
"""
DESCRIPTION
Visualize interactions between receptor and ligand.
ARGUMENTS
recsel = string: atom selection of the receptor {default: "not hetatm"}
ligsel = string: atom selections of the ligand {default: "hetatm"}
cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0}
"""
cmd.select('ligand', ligsel)
cmd.select('receptor', recsel)
cmd.bg_color('white')
cmd.show_as('cartoon')
cmd.show_as('sticks', 'hetatm')
cmd.set('cartoon_transparency', 0.2)
cmd.spectrum(selection=recsel+" or "+ligsel,byres=1)
util.cbag('not elem C')
cmd.set('cartoon_fancy_helices', 1);
cmd.show("sticks", "(hydro)");
cmd.select("pocket", "byres (receptor within %s of ligand)" % cutoff);
cmd.show("sticks", "pocket")
cmd.hide('(h. and (e. c extend 1))')
cmd.set('h_bond_max_angle', 30)
cmd.set('h_bond_cutoff_center', 3.6)
cmd.set('h_bond_cutoff_edge', 3.2)
cmd.dist('ligand_Hbonds', 'ligand', 'receptor', 3.5, mode=2)
cmd.set('dash_radius', 0.15)
# now set the label options
cmd.set('label_size', 20)
cmd.set('label_position', [0,0,10])
def show_rep(tag):
try:
sel = glb.SELE
if tag == 'Lines':
cmd.show('lines', sel)
elif tag == 'Sticks':
cmd.show('sticks', sel)
elif tag == 'Ribbons':
cmd.show('ribbon', sel)
elif tag == 'Cartoon':
cmd.show('cartoon', sel)
elif tag == 'Dots':
cmd.show('dots', sel)
elif tag == 'Spheres':
cmd.show('spheres', sel)
elif tag == 'Mesh':
cmd.show('mesh', sel)
elif tag == 'Surface':
cmd.show('surface', sel)
elif tag == 'Water':
cmd.show('spheres', '(resn HOH)')
elif tag == 'Ball and Stick':
preset.ball_and_stick(sel)
elif tag == 'Polar Contacts':
cmd.dist(sel + "_polar_conts",
sel,
sel,
quiet=1,
mode=2,
label=0,
reset=1)
cmd.enable(sel + "1CHO_polar_conts")
except:
showinfo('Error', 'Update Selection!')
def bonds(recsel="clean*", ligsel="vina*", cutoff=3.5):
"""
DESCRIPTION
Visualize interactions between receptor and ligand.
ARGUMENTS
recsel = string: atom selection of the receptor {default: "not hetatm"}
ligsel = string: atom selections of the ligand {default: "hetatm"}
cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0}
"""
cmd.select('ligand', ligsel)
cmd.select('receptor', recsel)
cmd.select(
"pocket",
"byres (receptor within %s of ligand and not resn HEM)" % cutoff)
cmd.show("sticks", "pocket")
cmd.set('stick_transparency', 0.5, 'clean*')
cmd.set('stick_radius', 0.05, 'clean*')
cmd.hide('(h. and (e. c extend 1))')
cmd.set('h_bond_max_angle', 30)
cmd.set('h_bond_cutoff_center', 3.6)
cmd.set('h_bond_cutoff_edge', 3.2)
cmd.dist('ligand_Hbonds', 'ligand', 'receptor', 3.5, mode=2)
#cmd.dist('pipi','ligand','receptor',2.5,mode=5)
cmd.set('dash_radius', 0.09)
def fSumWMCFirst(molecule, SGNameAngle, chain, residue, MCNeighbour, DieElecMC, MCchargeC, MCchargeO, printMC):
# print "First", MCNeighbour
SumWMCFirst = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
NBnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
# print NBnameselect, residueName
# Mainchain C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distFirstC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMCFirst = SumWMCFirst + WMC
if printMC == 'yes':
print("MC C ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ", ResDist, " ", WMC)
# Mainchain O
Onameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distFirstO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMCFirst = SumWMCFirst + WMC
if printMC == 'yes':
print("MC O ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ", ResDist, " ", WMC)
cmd.delete(residue + 'distFirstC')
cmd.delete(residue + 'distFirstO')
cmd.delete("MC")
return SumWMCFirst
def fSumWMCresidue(molecule, SGNameAngle, chain, residue, MCNeighbour,
DieElecMC, MCchargeC, MCchargeO, MCchargeN, MCchargeH,
AmideName, printMC):
# print "residue", MCNeighbour
SumWMCresidue = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
NBnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
# print NBnameselect, residueName
AmideProt = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/H01"
Hnameselect = "/" + AmideName + "//" + chain + "/" + str(
MCNeighbour) + "/H01"
if cmd.count_atoms(AmideProt) == 0 and cmd.count_atoms(Hnameselect) == 0:
HbuildSelect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/N"
cmd.h_add(HbuildSelect)
cmd.create(AmideName, AmideName + " + " + AmideProt)
cmd.remove(AmideProt)
# Mainchain AmideH
ResDist = cmd.dist(residue + 'distResH', SGnameselect, Hnameselect)
WMC = fWMC(MCchargeH, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC H ", MCNeighbour, " ", MCchargeH, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distResC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC C ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain O
Onameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distResO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC O ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain N
Nnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/N"
ResDist = cmd.dist(residue + 'distResN', SGnameselect, Nnameselect)
WMC = fWMC(MCchargeN, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC N ", MCNeighbour, " ", MCchargeN, " ", DieElecMC, " ",
ResDist, " ", WMC)
cmd.delete(residue + 'distResH')
cmd.delete(residue + 'distResC')
cmd.delete(residue + 'distResO')
cmd.delete(residue + 'distResN')
cmd.show("nb_spheres", AmideName)
cmd.delete("MC")
return SumWMCresidue
def fSumWMCLast(molecule, SGNameAngle, chain, residue, MCNeighbour, DieElecMC, MCchargeN, MCchargeH, MCchargeProCA, MCchargeProCD, MCchargeProN, AmideName, printMC):
#print "Last", MCNeighbour
SumWMCLast = 0.0
SGnameselect = "/"+SGNameAngle+"//"+"/"+"/SG"
NBnameselect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
#print NBnameselect, residueName
if residueName == "PRO":
### Proline CA
CAnameselect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/CA"
ResDist = cmd.dist(residue+'distLastProCA', SGnameselect,CAnameselect)
WMC = fWMC(MCchargeProCA, DieElecMC, ResDist)
SumWMCLast = SumWMCLast + WMC
if printMC == 'yes': print "MC ProCA ", MCNeighbour, " ", MCchargeProCA, " ", DieElecMC, " ", ResDist, " ", WMC
### Proline CD
CDnameselect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/CD"
ResDist = cmd.dist(residue+'distLastProCD', SGnameselect,CDnameselect)
WMC = fWMC(MCchargeProCD, DieElecMC, ResDist)
SumWMCLast = SumWMCLast + WMC
if printMC == 'yes': print "MC ProCD ", MCNeighbour, " ", MCchargeProCD, " ", DieElecMC, " ", ResDist, " ", WMC
### Proline N
Nnameselect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/N"
ResDist = cmd.dist(residue+'distLastProN', SGnameselect,Nnameselect)
WMC = fWMC(MCchargeProN, DieElecMC, ResDist)
SumWMCLast = SumWMCLast + WMC
if printMC == 'yes': print "MC ProN ", MCNeighbour, " ", MCchargeProN, " ", DieElecMC, " ", ResDist, " ", WMC
else:
AmideProt = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/H01"
Hnameselect = "/"+AmideName+"//"+chain+"/"+str(MCNeighbour)+"/H01"
if cmd.count_atoms(AmideProt) == 0 and cmd.count_atoms(Hnameselect) == 0:
HbuildSelect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/N"
cmd.h_add(HbuildSelect)
cmd.create(AmideName, AmideName+" + "+AmideProt)
cmd.remove(AmideProt)
### Mainchain AmideH
ResDist = cmd.dist(residue+'distLastH', SGnameselect,Hnameselect)
WMC = fWMC(MCchargeH, DieElecMC, ResDist)
SumWMCLast = SumWMCLast + WMC
if printMC == 'yes': print "MC H ", MCNeighbour, " ", MCchargeH, " ", DieElecMC, " ", ResDist, " ", WMC
### Mainchain N
Nnameselect = "/"+molecule+"//"+chain+"/"+str(MCNeighbour)+"/N"
ResDist = cmd.dist(residue+'distLastN', SGnameselect,Nnameselect)
WMC = fWMC(MCchargeN, DieElecMC, ResDist)
SumWMCLast = SumWMCLast + WMC
if printMC == 'yes': print "MC N ", MCNeighbour, " ", MCchargeN, " ", DieElecMC, " ", ResDist, " ", WMC
cmd.delete(residue+'distLastProCA')
cmd.delete(residue+'distLastProCD')
cmd.delete(residue+'distLastProN')
cmd.delete(residue+'distLastH')
cmd.delete(residue+'distLastN')
cmd.show("nb_spheres", AmideName)
cmd.delete("MC")
return SumWMCLast
def do_pick(self, bondFlag):
global dist_count
if bondFlag:
self.error = "Error: please select an atom, not a bond."
print(self.error)
else:
if self.mode == 'pairs':
if self.status == 0:
name = sele_prefix
cmd.select(name, "(pk1)")
self.status = 1
self.error = None
elif self.status == 1:
if ((self.object_mode == 'append') or (not dist_count)):
dist_count = dist_count + 1
else:
cmd.delete(dist_prefix + "%2d" % dist_count)
name = dist_prefix + "%02d" % dist_count
cmd.dist(name, sele_prefix, "(pk1)")
cmd.delete(sele_prefix)
cmd.unpick()
cmd.enable(name)
self.status = 0
elif self.mode in ['neigh', 'polar', 'heavy']:
if ((self.object_mode == 'append') or (not dist_count)):
dist_count = dist_count + 1
else:
cmd.delete(dist_prefix + "%2d" % dist_count)
name = dist_prefix + "%02d" % dist_count
cnt = 0
if self.mode == 'neigh':
cnt = cmd.select(
sele_prefix,
"(v. and (pk1 a; %f) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"
% self.__class__.cutoff)
elif self.mode == 'polar':
cnt = cmd.select(
sele_prefix,
"(v. and (pk1 a; %f) and (e. n,o) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"
% self.__class__.cutoff)
elif self.mode == 'heavy':
cnt = cmd.select(
sele_prefix,
"(v. and (pk1 a; %f) and (not h.) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"
% self.__class__.cutoff)
cmd.delete(name)
if cnt:
cmd.dist(name, "(pk1)", sele_prefix)
else:
print(" Wizard: No neighbors found.")
cmd.delete(sele_prefix)
cmd.unpick()
cmd.enable(name)
cmd.refresh_wizard()
def fSumWMCresidue(molecule, SGNameAngle, chain, residue, MCNeighbour, DieElecMC, MCchargeC, MCchargeO, MCchargeN, MCchargeH, AmideName, printMC):
# print "residue", MCNeighbour
SumWMCresidue = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
NBnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
# print NBnameselect, residueName
AmideProt = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/H01"
Hnameselect = "/" + AmideName + "//" + chain + "/" + str(MCNeighbour) + "/H01"
if cmd.count_atoms(AmideProt) == 0 and cmd.count_atoms(Hnameselect) == 0:
HbuildSelect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/N"
cmd.h_add(HbuildSelect)
cmd.create(AmideName, AmideName + " + " + AmideProt)
cmd.remove(AmideProt)
# Mainchain AmideH
ResDist = cmd.dist(residue + 'distResH', SGnameselect, Hnameselect)
WMC = fWMC(MCchargeH, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC H ", MCNeighbour, " ", MCchargeH, " ", DieElecMC, " ", ResDist, " ", WMC)
# Mainchain C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distResC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC C ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ", ResDist, " ", WMC)
# Mainchain O
Onameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distResO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC O ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ", ResDist, " ", WMC)
# Mainchain N
Nnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour) + "/N"
ResDist = cmd.dist(residue + 'distResN', SGnameselect, Nnameselect)
WMC = fWMC(MCchargeN, DieElecMC, ResDist)
SumWMCresidue = SumWMCresidue + WMC
if printMC == 'yes':
print("MC N ", MCNeighbour, " ", MCchargeN, " ", DieElecMC, " ", ResDist, " ", WMC)
cmd.delete(residue + 'distResH')
cmd.delete(residue + 'distResC')
cmd.delete(residue + 'distResO')
cmd.delete(residue + 'distResN')
cmd.show("nb_spheres", AmideName)
cmd.delete("MC")
return SumWMCresidue
def interface_analyser(name, dist_cuoff=10, animate=True):
'''
DESCRIPTION
displays the chains in different colors, showas cavity surfaces, and h.bonds with an interface cutoff
of 10 (default)
'''
# cmd.hide("lines")
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cuoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.show("surface", "all")
cmd.set('surface_cavity_mode', 1)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def interface_analyser_with_surface(name='all',
chain_sur='A',
dist_cutoff=10,
animate=True):
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cutoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.create("chain%s" % chain_sur,
name + " and chain %s" % chain_sur,
zoom=0)
cmd.show("surface", "chain%s" % chain_sur)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def update_dashes(self):
cmd.delete(dist_prefix+"*")
lst = self.get_sele_list()
c = 0
while 1:
if not len(lst): break
a = lst.pop()
if not len(lst): break
b = lst.pop()
name = dist_prefix+str(c)
cmd.dist(name,a,b,width=7,length=0.05,gap=0.05)
cmd.hide('label',name)
cmd.enable(name)
c = c + 1
def update_dashes(self):
cmd.delete(dist_prefix + "*")
lst = self.get_sele_list()
c = 0
while 1:
if not len(lst): break
a = lst.pop()
if not len(lst): break
b = lst.pop()
name = dist_prefix + str(c)
cmd.dist(name, a, b, width=7, length=0.05, gap=0.05)
cmd.hide('label', name)
cmd.enable(name)
c = c + 1
def zn_interface():
cmd.show( 'cartoon' )
cmd.hide( 'lines', 'elem H' )
util.cbc("elem C")
cmd.show( 'sticks', 'resn znx')
cmd.set('cartoon_transparency','0.5')
cmd.hide( 'sticks', 'elem H' )
loaded_objs = cmd.get_names('objects')
print loaded_objs
for obj in loaded_objs :
cmd.dist( '"'+obj+'_polar_conts"','"'+obj+'"','"'+obj+'"',quiet=1,mode=2,label=0,reset=1)
cmd.enable("'"+obj+'_polar_conts"')
def do_pick(self,bondFlag):
global dist_count
if bondFlag:
self.error = "Error: please select an atom, not a bond."
print self.error
else:
if self.mode == 'pairs':
if self.status==0:
name = sele_prefix
cmd.select(name,"(pk1)")
self.status = 1
self.error = None
elif self.status==1:
if ((self.object_mode=='append') or (not dist_count)):
dist_count = dist_count + 1
else:
cmd.delete(dist_prefix+"%2d"%dist_count)
name = dist_prefix + "%02d"%dist_count
cmd.dist(name,sele_prefix,"(pk1)")
cmd.delete(sele_prefix)
cmd.unpick()
cmd.enable(name)
self.status = 0
elif self.mode in ['neigh','polar','heavy']:
if ((self.object_mode=='append') or (not dist_count)):
dist_count = dist_count + 1
else:
cmd.delete(dist_prefix+"%2d"%dist_count)
name = dist_prefix + "%02d"%dist_count
cnt = 0
if self.mode == 'neigh':
cnt = cmd.select(sele_prefix,"(v. and (pk1 a; %f) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"%self.__class__.cutoff)
elif self.mode == 'polar':
cnt = cmd.select(sele_prefix,"(v. and (pk1 a; %f) and (e. n,o) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"%self.__class__.cutoff)
elif self.mode == 'heavy':
cnt = cmd.select(sele_prefix,"(v. and (pk1 a; %f) and (not h.) and (not (nbr. pk1)) and (not (nbr. (nbr. pk1))) and (not (nbr. (nbr. (nbr. pk1)))))"%self.__class__.cutoff)
cmd.delete(name)
if cnt:
cmd.dist(name,"(pk1)",sele_prefix)
else:
print " Wizard: No neighbors found."
cmd.delete(sele_prefix)
cmd.unpick()
cmd.enable(name)
cmd.refresh_wizard()
def print_hb(selection):
hb = cmd.find_pairs("((byres "+selection+") and n;n)","((byres "+selection+") and n;o)",mode=1,cutoff=3.7,angle=55)
pair1_list = []
pair2_list = []
dist_list = []
for pairs in hb:
cmd.iterate("%s and ID %s" % (pairs[0][0],pairs[0][1]), 'print "%s/%3s`%s/%s " % (chain,resn,resi,name),')
cmd.iterate("%s and ID %s" % (pairs[1][0],pairs[1][1]), 'print "%s/%3s`%s/%s " % (chain,resn,resi,name),')
print "%.2f" % cmd.dist("%s and ID %s" % (pairs[0][0],pairs[0][1]),"%s and ID %s" % (pairs[1][0],pairs[1][1]))
def rep_old(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("pept")
cmd.delete("pept_dist")
cmd.load("$PYMOL_DATA/demo/pept.pdb")
cmd.show("sticks","(pept and not i;5:7)")
cmd.show("surface","(pept and i;5,6)")
cmd.show("mesh","(pept and i;1,11,12,13)")
cmd.show("spheres","(?pept & resi 2+12+9+4 &! name C+N+O+CA)")
cmd.show("dots","(i;8)")
cmd.dist("pept_dist","(pept and i;1&n;OD2)","(pept and i;13&n;OG1)")
cmd.set("dot_width","2");
finally:
cmd.set("suspend_updates",0,quiet=1)
else:
cmd.delete("pept")
cmd.delete("pept_dist")
def rep_old(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("pept")
cmd.delete("pept_dist")
cmd.load("$PYMOL_DATA/demo/pept.pdb")
cmd.show("sticks","(pept and not i;5:7)")
cmd.show("surface","(pept and i;5,6)")
cmd.show("mesh","(pept and i;1,11,12,13)")
cmd.show("spheres","(?pept & resi 2+12+9+4 &! name C+N+O+CA)")
cmd.show("dots","(i;8)")
cmd.dist("pept_dist","(pept and i;1&n;OD2)","(pept and i;13&n;OG1)")
cmd.set("dot_width","2");
finally:
cmd.set("suspend_updates",0,quiet=1)
else:
cmd.delete("pept")
cmd.delete("pept_dist")
receptor = receptor_pdb.replace(".pdb", "")
cmd.load(WORKDIR + "/" + receptor_pdb)
ligname_pattern = receptor.replace("receptor1",
"ligand[0-9]+") + ".pdb"
ligpdb_list = list_files(WORKDIR, ligname_pattern, full_path=False)
ligmol_list = [m.replace(".pdb", "") for m in ligpdb_list]
cmd.set('h_bond_max_angle', 30)
cmd.set('h_bond_cutoff_center', 3.6)
cmd.set('h_bond_cutoff_edge', 3.2)
for ligpdb in ligpdb_list:
cmd.load(WORKDIR + "/" + ligpdb)
ligmol = ligpdb.replace(".pdb", "")
# contacts = cmd.dist('contacts', ligmol, receptor + " resid " + resids, 3.5, mode=2)
cont399 = cmd.dist('cont399',
ligmol,
receptor + " and resid 399",
3.5,
mode=2)
cont402 = cmd.dist('cont402',
ligmol,
receptor + " and resid 402",
3.5,
mode=2)
cont403 = cmd.dist('cont403',
ligmol,
receptor + " and resid 403",
3.5,
mode=2)
cont404 = cmd.dist('cont404',
ligmol,
receptor + " and resid 404",
def fSumWSC(molecule, SGNameAngle, chain, residue, DieElecSC, SCchargeASP, SCchargeGLU, SCchargeOXT, SCchargeARG, SCchargeHIS, SCchargeLYS, SCchargeMET1, printSC):
SumWSC = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
# Sidechain ASP
nameselect = "/" + molecule + " and resn ASP and name CG and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distASP', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeASP, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC ASP ", str(SClist[i]), " ", SCchargeASP, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distASP')
# Sidechain GLU
nameselect = "/" + molecule + " and resn GLU and name CD and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distGLU', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeGLU, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC GLU ", str(SClist[i]), " ", SCchargeGLU, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distGLU')
# print "GLU", cmd.count_atoms("SC"), SumWSC
# Sidechain OXT
nameselect = "/" + molecule + " and byres name OXT and not resi " + residue
cmd.select("SC", nameselect)
cmd.select("SC", "SC and name C")
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distOXT', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeOXT, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC OXT ", str(SClist[i]), " ", SCchargeOXT, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distOXT')
# print "OXT", cmd.count_atoms("SC"), SumWSC
# Sidechain ARG
nameselect = "/" + molecule + " and resn ARG and name CZ and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distARG', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeARG, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC ARG ", str(SClist[i]), " ", SCchargeARG, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distARG')
# print "ARG", cmd.count_atoms("SC"), SumWSC
# Sidechain HIS
nameselect = "/" + molecule + " and resn HIS and name CD2 and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distHIS', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeHIS, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC HIS ", str(SClist[i]), " ", SCchargeHIS, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distHIS')
# print "HIS", cmd.count_atoms("SC"), SumWSC
# Sidechain LYS
nameselect = "/" + molecule + " and resn LYS and name NZ and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distLYS', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeLYS, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC LYS ", str(SClist[i]), " ", SCchargeLYS, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distLYS')
# print "LYS", cmd.count_atoms("SC"), SumWSC
# Sidechain MET1
nameselect = "/" + molecule + " and resn MET and res 1 and not resi " + residue
cmd.select("SC", nameselect)
cmd.select("SC", "SC and name N")
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distMET1', SGnameselect, molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeMET1, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC MET1 ", str(SClist[i]), " ", SCchargeMET1, " ", DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distMET1')
# print "MET1", cmd.count_atoms("SC"), SumWSC
cmd.delete("SC")
return SumWSC
#cmd.delete("all")
#cmd.load("2bem.pdb")
#cmd.color("white") # Pro jistotu
#cmd.show("lines")
cmd.select("cis", "resn CYS")
cmd.color("yellow", "cis")
list_of_bonds = []
# Projdi atom po atomu
for a_mol in cmd.index("CYS/SG", "cis"):
for b_mol in cmd.index("CYS/SG", "cis"):
if a_mol[1] < b_mol[1]: # Neprchazej molekuly ktere uz mam
if cmd.dist("tmp", a_mol, b_mol) < MAX_DIST: # Seber Vzdalenost
print "dist(" + str(b_mol[1]) + ", " + str(
a_mol[1]) + ") = " + str(cmd.dist("result", a_mol, b_mol))
list_of_bonds.append(a_mol[1])
list_of_bonds.append(b_mol[1])
cmd.select(
"sulfidy",
"?sulfidy | (" + a_mol[0] + "`" + str(a_mol[1]) + ")")
cmd.select(
"sulfidy",
"?sulfidy | (" + b_mol[0] + "`" + str(b_mol[1]) + ")")
cmd.delete("tmp")
if len(list_of_bonds) > 0:
cmd.color("orange", "sulfidy")
# Jsem prase and i know it
0.399889141, -0.795006156, -0.456119299,\
-0.090745762, -0.529538393, 0.843419492,\
0.000087761, -0.000581503, -183.590560913,\
8.321296692, -66.967765808, -33.590000153,\
-36.799331665, 403.937011719, -20.000000000' )
# constants
cutoff = 2
# Load the edges from file
with open(edgepath, 'r') as fin:
data = fin.readlines()
edges = [line.strip().split() for line in data]
for n, e in enumerate(edges):
t = cmd.dist('dist'+str(n),'3H4E//A/'+e[0]+'/CA',\
'3H4E//A/'+e[1]+'/CA')
if t < cutoff:
cmd.delete('dist' + str(n))
else:
cmd.color('blue', 'dist' + str(n))
cmd.hide('labels', 'dist' + str(n))
cmd.show('spheres', '3H4E//A/' + e[0] + '/CA')
cmd.show('spheres', '3H4E//A/' + e[1] + '/CA')
cmd.color('yellow', '3H4E//A/' + e[0] + '/CA')
cmd.color('yellow', '3H4E//A/' + e[1] + '/CA')
cmd.set('dash_radius', '0.2')
cmd.set('dash_gap', '0.0')
cmd.set('sphere_scale', '0.3')
#cmd.set('sphere_scale','0.8','retinal');
# PRESKOC TO CO UZ MAME
if (int(atom_a.resi)) <= (int(atom_b.resi) + 1): # +1 PRESKOC SUSEDA
continue
dist = sqrt((atom_a.coord[0] - atom_b.coord[0])**2 +
(atom_a.coord[1] - atom_b.coord[1])**2 +
(atom_a.coord[2] - atom_b.coord[2])**2)
if maximal < dist:
maximal = dist
max_atom_a = atom_a
max_atom_b = atom_b
if dist < minimal:
minimal = dist
min_atom_a = atom_a
min_atom_b = atom_b
print "MAX distance: " + str(maximal) + " " + "[" + str(
max_atom_a.index) + ", " + str(max_atom_b.index) + "]"
print "MIN distance: " + str(minimal) + " " + "[" + str(
min_atom_a.index) + ", " + str(min_atom_b.index) + "]"
cmd.dist("MAX_DISTANCE",
cmd.index("index " + str(max_atom_a.index))[0],
cmd.index("index " + str(max_atom_b.index))[0])
cmd.dist("MIN_DISTANCE",
cmd.index("index " + str(min_atom_a.index))[0],
cmd.index("index " + str(min_atom_b.index))[0])
cmd.color("orange", "MIN_DISTANCE")
cmd.color("white", "MAX_DISTANCE")
#"""
-0.090745762, -0.529538393, 0.843419492,\
0.000087761, -0.000581503, -183.590560913,\
8.321296692, -66.967765808, -33.590000153,\
-36.799331665, 403.937011719, -20.000000000' )
# constants
cutoff = 2
# Load the edges from file
with open(edgepath,'r') as fin :
data = fin.readlines();
edges = [line.strip().split() for line in data]
for n,e in enumerate(edges) :
t = cmd.dist('dist'+str(n),'3H4E//A/'+e[0]+'/CA',\
'3H4E//A/'+e[1]+'/CA')
if t < cutoff :
cmd.delete('dist'+str(n))
else :
cmd.color('blue','dist'+str(n))
cmd.hide('labels','dist'+str(n))
cmd.show('spheres','3H4E//A/'+e[0]+'/CA')
cmd.show('spheres','3H4E//A/'+e[1]+'/CA')
cmd.color('yellow','3H4E//A/'+e[0]+'/CA')
cmd.color('yellow','3H4E//A/'+e[1]+'/CA')
cmd.set('dash_radius','0.2');
cmd.set('dash_gap','0.0');
cmd.set('sphere_scale','0.3')
#cmd.set('sphere_scale','0.8','retinal');
def fSumWSC(molecule, SGNameAngle, chain, residue, DieElecSC, SCchargeASP,
SCchargeGLU, SCchargeOXT, SCchargeARG, SCchargeHIS, SCchargeLYS,
SCchargeMET1, printSC):
SumWSC = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
# Sidechain ASP
nameselect = "/" + molecule + " and resn ASP and name CG and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distASP', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeASP, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC ASP ", str(SClist[i]), " ", SCchargeASP, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distASP')
# Sidechain GLU
nameselect = "/" + molecule + " and resn GLU and name CD and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distGLU', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeGLU, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC GLU ", str(SClist[i]), " ", SCchargeGLU, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distGLU')
# print "GLU", cmd.count_atoms("SC"), SumWSC
# Sidechain OXT
nameselect = "/" + molecule + " and byres name OXT and not resi " + residue
cmd.select("SC", nameselect)
cmd.select("SC", "SC and name C")
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distOXT', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeOXT, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC OXT ", str(SClist[i]), " ", SCchargeOXT, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distOXT')
# print "OXT", cmd.count_atoms("SC"), SumWSC
# Sidechain ARG
nameselect = "/" + molecule + " and resn ARG and name CZ and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distARG', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeARG, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC ARG ", str(SClist[i]), " ", SCchargeARG, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distARG')
# print "ARG", cmd.count_atoms("SC"), SumWSC
# Sidechain HIS
nameselect = "/" + molecule + " and resn HIS and name CD2 and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distHIS', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeHIS, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC HIS ", str(SClist[i]), " ", SCchargeHIS, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distHIS')
# print "HIS", cmd.count_atoms("SC"), SumWSC
# Sidechain LYS
nameselect = "/" + molecule + " and resn LYS and name NZ and not resi " + residue
cmd.select("SC", nameselect)
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distLYS', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeLYS, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC LYS ", str(SClist[i]), " ", SCchargeLYS, " ", DieElecSC,
" ", ResDist, " ", WSC)
cmd.delete(residue + 'distLYS')
# print "LYS", cmd.count_atoms("SC"), SumWSC
# Sidechain MET1
nameselect = "/" + molecule + " and resn MET and res 1 and not resi " + residue
cmd.select("SC", nameselect)
cmd.select("SC", "SC and name N")
SClist = cmd.identify("SC")
for i in range(len(SClist)):
ResDist = cmd.dist(residue + 'distMET1', SGnameselect,
molecule + " and id " + str(SClist[i]))
WSC = fWSC(SCchargeMET1, DieElecSC, ResDist)
SumWSC = SumWSC + WSC
if printSC == 'yes':
print("SC MET1 ", str(SClist[i]), " ", SCchargeMET1, " ",
DieElecSC, " ", ResDist, " ", WSC)
cmd.delete(residue + 'distMET1')
# print "MET1", cmd.count_atoms("SC"), SumWSC
cmd.delete("SC")
return SumWSC
fname = sys.argv[1]
with open(fname) as fin :
lines = fin.readlines()
tuples_list = []
for line in lines :
tuples_list.append((line.split()[0],line.split()[2:]))
#lines = [(line.split()[0],line.split()[2:]) for line in lines ]
row = ('ASD00280000',
['subtilis',
'site,339,Lys@@range,251,257,loop@@site,316,Lys@@site,318,Arg@@site,317,Asn'])
site_line = row[1][1]
nums = re.findall('\d+',site_line)
nicks_nums = [13,127,29,45]
#----------------------------------------------------------------------
# Pymol specific code
cmd.load('ASD00250000_3.pdb')
cmd.dist('resi '+str(nicks_nums[0]),', resi '+str(nicks_nums[1]))
cmd.spectrum(palette = 'green_red', selection = '1F88 and chain A')
cmd.select('retinal','1F88 and het and chain A and resn ret')
cmd.show('spheres','retinal')
cmd.color('magenta','retinal')
# constants
cutoff = 2
# Load the edges from file
with open(edgepath,'r') as fin :
data = fin.readlines();
edges = [line.strip().split() for line in data]
for n,e in enumerate(edges) :
t = cmd.dist('dist'+str(n),'1F88//A/'+e[0]+'/CA',\
'1F88//A/'+e[1]+'/CA')
if t < cutoff :
cmd.delete('dist'+str(n))
else :
cmd.color('blue','dist'+str(n))
cmd.hide('labels','dist'+str(n))
cmd.show('spheres','1F88//A/'+e[0]+'/CA')
cmd.show('spheres','1F88//A/'+e[1]+'/CA')
cmd.color('yellow','1F88//A/'+e[0]+'/CA')
cmd.color('yellow','1F88//A/'+e[1]+'/CA')
cmd.set('dash_radius','0.2');
cmd.set('dash_gap','0.0');
cmd.set('sphere_scale','0.3')
cmd.set('sphere_scale','0.8','retinal');
# constants
cutoff = 2
# Load the edges from file
with open(edgepath,'r') as fin :
data = fin.readlines();
edges = [line.strip().split() for line in data]
chains = ['A','B','C','D','E','F']
for n,e in enumerate(edges) :
for ch in chains :
t = cmd.dist('dist'+ch+str(n),'3H4E//'+ch+'/'+e[0]+'/CA',\
'3H4E//'+ch+'/'+e[1]+'/CA')
if t < cutoff :
cmd.delete('dist'+ch+str(n))
else :
cmd.color('blue','dist'+ch+str(n))
cmd.hide('labels','dist'+ch+str(n))
cmd.show('spheres','3H4E//'+ch+'/'+e[0]+'/CA')
cmd.show('spheres','3H4E//'+ch+'/'+e[1]+'/CA')
cmd.color('yellow','3H4E//'+ch+'/'+e[0]+'/CA')
cmd.color('yellow','3H4E//'+ch+'/'+e[1]+'/CA')
# Create a set of residues
set_res = []
for e_tup in edges :
set_res.extend(e_tup)
continue
cmd.select("polar_atoms", "e. O or e. N or e. S")
model_halogen = cmd.get_model(
"halogen") # create model for halogen selection
for halo in model_halogen.atom:
cmd.select("current_halogen", "id %s" % (halo.id))
#cmd.select("current_neighbor", "current_halogen extend 1")
#cmd.select("current_neighbor", "current_neighbor and not current_halogen")
cmd.select("current_neighbor", "neighbor current_halogen")
cmd.select("current_surroundings", "current_halogen expand 5.0")
cmd.select("current_surroundings",
"current_surroundings and bindingsite")
cmd.select("current_polar", "current_surroundings and polar_atoms")
polar_distance = cmd.dist("polar_contacts",
"ligand",
"polar_atoms",
mode=2)
print("Polar contact: ")
print polar_distance, halo.name, halo.resn, halo.resi
model_polar = cmd.get_model("current_polar")
for pol in model_polar.atom:
cmd.select("current_polar", "id %s" % (pol.id))
# check for halogen bonds, distances 5.0, angles: > 140
current_distance = cmd.distance("current_distance",
"current_halogen", "current_polar")
current_angle = cmd.angle("current_angle", "current_neighbor",
"current_halogen", "current_polar")
if (current_angle >= 140) and (current_distance <= 5.0):
print("Halogen bond: ")
print current_distance, current_angle, pol.name, pol.resn, pol.resi
from pymol import cmd
from glob import glob
for file in glob("*.pdb"):
print file
cmd.load(file,'prot')
for a in cmd.index("elem s and bound_to elem s"):
if cmd.select("s1","%s`%d"%a) and \
cmd.select("s2","elem s and bound_to %s`%d"%a):
if cmd.select("(s1|s2) and not ?skip"):
cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")
print ' ',round(cmd.dist("tmp","s1","s2"),3)
cmd.select("skip","s1|s2|?skip")
cmd.delete("all")
def fSumWMC(molecule, SGNameAngle, chain, residue, MCNeighbour, DieElecMC,
MCchargeC, MCchargeO, MCchargeN, MCchargeH, MCchargeProCA,
MCchargeProCD, MCchargeProN, AmideName, printMC):
# print "chain", MCNeighbour
SumWMC = 0.0
SGnameselect = "/" + SGNameAngle + "//" + "/" + "/SG"
NBnameselect = "/" + molecule + "//" + chain + "/" + str(MCNeighbour)
cmd.select("MC", NBnameselect)
MCpdbstr = cmd.get_pdbstr("MC")
MCsplit = MCpdbstr.split()
residueName = MCsplit[3]
# print NBnameselect, residueName
if residueName == "PRO":
# Proline CA
CAnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/CA"
ResDist = cmd.dist(residue + 'distProCA', SGnameselect, CAnameselect)
WMC = fWMC(MCchargeProCA, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC ProCA ", MCNeighbour, " ", MCchargeProCA, " ", DieElecMC,
" ", ResDist, " ", WMC)
# Proline CD
CDnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/CD"
ResDist = cmd.dist(residue + 'distProCD', SGnameselect, CDnameselect)
WMC = fWMC(MCchargeProCD, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC ProCD ", MCNeighbour, " ", MCchargeProCD, " ", DieElecMC,
" ", ResDist, " ", WMC)
# Proline N
Nnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/N"
ResDist = cmd.dist(residue + 'distProN', SGnameselect, Nnameselect)
WMC = fWMC(MCchargeProN, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC ProN ", MCNeighbour, " ", MCchargeProN, " ", DieElecMC,
" ", ResDist, " ", WMC)
# Proline C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distProC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC ProC ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Proline O
Onameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distProO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC ProO ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ",
ResDist, " ", WMC)
else:
AmideProt = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/H01"
Hnameselect = "/" + AmideName + "//" + chain + "/" + str(
MCNeighbour) + "/H01"
if cmd.count_atoms(AmideProt) == 0 and cmd.count_atoms(
Hnameselect) == 0:
HbuildSelect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/N"
cmd.h_add(HbuildSelect)
cmd.create(AmideName, AmideName + " + " + AmideProt)
cmd.remove(AmideProt)
# Mainchain AmideH
ResDist = cmd.dist(residue + 'distH', SGnameselect, Hnameselect)
WMC = fWMC(MCchargeH, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC H ", MCNeighbour, " ", MCchargeH, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain C
Cnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/C"
ResDist = cmd.dist(residue + 'distC', SGnameselect, Cnameselect)
WMC = fWMC(MCchargeC, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC C ", MCNeighbour, " ", MCchargeC, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain O
Onameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/O"
ResDist = cmd.dist(residue + 'distO', SGnameselect, Onameselect)
WMC = fWMC(MCchargeO, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC O ", MCNeighbour, " ", MCchargeO, " ", DieElecMC, " ",
ResDist, " ", WMC)
# Mainchain N
Nnameselect = "/" + molecule + "//" + chain + "/" + str(
MCNeighbour) + "/N"
ResDist = cmd.dist(residue + 'distN', SGnameselect, Nnameselect)
WMC = fWMC(MCchargeN, DieElecMC, ResDist)
SumWMC = SumWMC + WMC
if printMC == 'yes':
print("MC N ", MCNeighbour, " ", MCchargeN, " ", DieElecMC, " ",
ResDist, " ", WMC)
cmd.delete(residue + 'distProCA')
cmd.delete(residue + 'distProCD')
cmd.delete(residue + 'distProN')
cmd.delete(residue + 'distProC')
cmd.delete(residue + 'distProO')
cmd.delete(residue + 'distH')
cmd.delete(residue + 'distC')
cmd.delete(residue + 'distO')
cmd.delete(residue + 'distN')
cmd.show("nb_spheres", AmideName)
cmd.delete("MC")
return SumWMC
# customize these lines to your protein.
cmd.fetch("6NEC")
cmd.select("prot","not resn XIN and not resn HOH and not chain C")
cmd.select("lig", "resn XIN and not chain C")
dist_list = {
pro_atoms = cmd.get_model("prot")
lig_atoms = cmd.get_model("lig")
for l_at in lig_atoms.atom:
for p_at in pro_atoms.atom:
dist_list[str(l_at.resn) +
":" +
str(l_at.resi) +
" " +
l_at.name +
" ---- " +
str(p_at.resn) +
":" +
str(p_at.resi) +
" " +
p_at.name] = cmd.dist("foo",
"index " +
str(l_at.index),"index " + str(p_at.index))
cmd.delete("foo")
print("List of all pairwise ligand--protein atom-atom distances:")
# [print("Distance of " + d + " is " + str(dist_list[d])) for d in dist_list.keys()]
# More compact print statement. Need an f-string format statement.
[print( d + " " + str(dist_list[d])) for d in dist_list.keys()]