# Pucker

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
```from pymol.cgo import *    # get constants
from math import *
from pymol import cmd

def pucker(selection):

# Author: Sean Law
# Institute: Michigan State University
# E-mail: slaw@msu.edu

obj_name = selection
objects = cmd.get_names(selection)
for obj in objects:
if (obj == selection):
obj_name=obj
sel=cmd.get_model(selection)
first=1
old=" "
oldchain=" "
residue={}
theta={}
count=0
for atom in sel.atom:
new=atom.chain+" "+str(atom.resi)
newchain=atom.chain+" "+atom.segi
if (not (oldchain == newchain) and first):
print " " #Blank line to separate chain output
print "%6s  %6s  %8s  Residue" % ("Phase", "Amp", "Pucker")
if (not(new == old) and (not first)):
#Check that all 5 atoms exist
if(len(residue) == 15):
#Construct planes
get_dihedrals(residue,theta)
#Calculate pucker
info = pseudo(residue,theta)
print info+"  "+old
else:
print "There is no sugar in this residue"
if (not (oldchain == newchain)):
print " " #Blank line to separate chain output
print "%6s  %6s  %8s  Residue" % ("Phase", "Amp", "Pucker")
#Clear values
residue={}
dihedrals={}
theta={}
#Store new value
store_atom(atom,residue)
else:
store_atom(atom,residue)
first=0
old=new
oldchain=newchain
#Final Residue
#Calculate dihedrals for final residue
if (len(residue) == 15):
#Construct planes
get_dihedrals(residue,theta)
#Calculate pucker for final residue
info = pseudo(residue,theta)
print info+"  "+old
else:
print "There is no sugar in this residue"
return

def sele_exists(sele):
return sele in cmd.get_names("selections");

def pseudo(residue,theta):

phase=atan2((theta['4']+theta['1'])-(theta['3']+theta['0']),theta['2']*other)
amplitude=theta['2']/cos(phase)
phase=math.degrees(phase)
if (phase < 0):
phase=phase+360 # 0 <= Phase < 360
#Determine pucker
if (phase < 36):
pucker = "C3'-endo"
elif (phase < 72):
pucker = "C4'-exo"
elif (phase <108):
pucker = "O4'-endo"
elif (phase < 144):
pucker = "C1'-exo"
elif (phase < 180):
pucker = "C2'-endo"
elif (phase < 216):
pucker = "C3'-exo"
elif (phase < 252):
pucker = "C4'-endo"
elif (phase < 288):
pucker = "O4'-exo"
elif (phase < 324):
pucker = "C1'-endo"
elif (phase < 360):
pucker = "C2'-exo"
else:
pucker = "Phase is out of range"
info = "%6.2f  %6.2f  %8s" % (phase, amplitude, pucker)
return info

def store_atom(atom,residue):
if (atom.name == "O4'" or atom.name == "O4*"):
residue['O4*X'] = atom.coord[0]
residue['O4*Y'] = atom.coord[1]
residue['O4*Z'] = atom.coord[2]
elif (atom.name == "C1'" or atom.name == "C1*"):
residue['C1*X'] = atom.coord[0]
residue['C1*Y'] = atom.coord[1]
residue['C1*Z'] = atom.coord[2]
elif (atom.name == "C2'" or atom.name == "C2*"):
residue['C2*X'] = atom.coord[0]
residue['C2*Y'] = atom.coord[1]
residue['C2*Z'] = atom.coord[2]
elif (atom.name == "C3'" or atom.name == "C3*"):
residue['C3*X'] = atom.coord[0]
residue['C3*Y'] = atom.coord[1]
residue['C3*Z'] = atom.coord[2]
elif (atom.name == "C4'" or atom.name == "C4*"):
residue['C4*X'] = atom.coord[0]
residue['C4*Y'] = atom.coord[1]
residue['C4*Z'] = atom.coord[2]
return

def get_dihedrals(residue,theta):

C = []
ribose = residue.keys()
ribose.sort()

shift_up(ribose,6)
for i in range (0,12):
C.append(residue[ribose[i]])
theta['0']=dihedral(C)

C = []
shift_down(ribose,3)
for i in range (0,12):
C.append(residue[ribose[i]])
theta['1']=dihedral(C)

C = []
shift_down(ribose,3)
for i in range (0,12):
C.append(residue[ribose[i]])
theta['2']=dihedral(C)

C = []
shift_down(ribose,3)
for i in range (0,12):
C.append(residue[ribose[i]])
theta['3']=dihedral(C)

C = []
shift_down(ribose,3)
for i in range (0,12):
C.append(residue[ribose[i]])
theta['4']=dihedral(C)

return

def shift_up(list,value):
for i in range (0,value):
list.insert(0,list.pop())
return

def shift_down(list,value):
for i in range (0,value):
list.insert(len(list),list.pop(0))
return

def dihedral(C):

DX12=C[0]-C[3]
DY12=C[1]-C[4]
DZ12=C[2]-C[5]

DX23=C[3]-C[6]
DY23=C[4]-C[7]
DZ23=C[5]-C[8]

DX43=C[9]-C[6];
DY43=C[10]-C[7];
DZ43=C[11]-C[8];

#Cross product to get normal

PX1=DY12*DZ23-DY23*DZ12;
PY1=DZ12*DX23-DZ23*DX12;
PZ1=DX12*DY23-DX23*DY12;

NP1=sqrt(PX1*PX1+PY1*PY1+PZ1*PZ1);

PX1=PX1/NP1
PY1=PY1/NP1
PZ1=PZ1/NP1

PX2=DY43*DZ23-DY23*DZ43;
PY2=DZ43*DX23-DZ23*DX43;
PZ2=DX43*DY23-DX23*DY43;

NP2=sqrt(PX2*PX2+PY2*PY2+PZ2*PZ2);

PX2=PX2/NP2
PY2=PY2/NP2
PZ2=PZ2/NP2

DP12=PX1*PX2+PY1*PY2+PZ1*PZ2

TS=1.0-DP12*DP12

if (TS < 0):
TS=0
else:
TS=sqrt(TS)

ANGLE=math.pi/2.0-atan2(DP12,TS)

PX3=PY1*PZ2-PY2*PZ1
PY3=PZ1*PX2-PZ2*PX1
PZ3=PX1*PY2-PX2*PY1

DP233=PX3*DX23+PY3*DY23+PZ3*DZ23

if (DP233 > 0):
ANGLE=-ANGLE

ANGLE=math.degrees(ANGLE)

if (ANGLE > 180):
ANGLE=ANGLE-360
if (ANGLE < -180):
ANGLE=ANGLE+360

return ANGLE

cmd.extend("pucker",pucker)```