Pucker

DESCRIPTION

pucker.py is a PyMol script that returns the sugar pucker information (phase, amplitude, pucker) for a given selection.

This script uses its own dihedral calculation scheme rather than the get_dihedral command. Thus, it is lightning fast!

If a selection does not contain any ribose sugars then an error message is returned.

USAGE

load the script using the run command

pucker selection

EXAMPLES

pucker all

PYMOL API

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_(at)_msu_dot_edu
	
	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):
	other=2*(sin(math.radians(36.0))+sin(math.radians(72.0)))
	
	#phase=atan2((theta4+theta1)-(theta3+theta0),2*theta2*(sin(math.radians(36.0))+sin(math.radians(72.0))))
	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)