RE: [PyMOL] H-bond display

Warren,

Great - that's what I needed.  For those who are interested, I've
attached code below which draws a dashed line between two atoms, with an
arrow on it.  It's called with pretty much the same syntax as the
'distance' command.

Gareth


#------------------------------------------------------------------------

from pymol.cgo import *
from pymol import cmd
from math import *


#-------------------------------------------------
# Draw a hydrogen bond
#---------------------------------

def hbond(name,s1,s2,r=1.0,g=1.0,b=0.2):

      '''
DESCRIPTION

   "hbond" creates a dashed line between two selections, marked with an
arrow.

USAGE

   distance name, (selection1), (selection1) , [, r, [, g, [, b] ] ]

   name = name of distance object 
   selection1,selection2 = atom selections
   r, g, b = colour

   '''	


	# Convert arguments into floating point values
	rr = float(r)
	gg = float(g)
	bb = float(b)

	# Get dash length, gap length and dash radius from PyMOL
	# settings
	dl = float(cmd.get_setting_tuple("dash_length")[1][0])
	gl = float(cmd.get_setting_tuple("dash_gap")[1][0])
	dr = float(cmd.get_setting_tuple("dash_radius")[1][0])

	# Get tuple containing object and index of atoms in these
	# selections
	x1 = cmd.index(s1,1)	
	x2 = cmd.index(s2,1)

	# Get number of atoms in each selection	
	n1 = len(x1)
	n2 = len(x2)
	if(n1 < 1):
		print "Error: selection " + s1 + " has no atoms"
		return
	if(n2 < 1):
		print "Error: selection " + s2 + " has no atoms"
		return

	# Get objects and atom indices
	o1 = x1[0][0]
	i1 = x1[0][1]
	o2 = x2[0][0]
	i2 = x2[0][1]

	# Get ChemPy models
	m1 = cmd.get_model(o1)
	m2 = cmd.get_model(o2)

	# Get atoms
	a1 = m1.atom[i1-1]
	a2 = m2.atom[i2-1]

	# Get coords
	x1 = a1.coord[0]
	y1 = a1.coord[1]
	z1 = a1.coord[2]
	x2 = a2.coord[0]
	y2 = a2.coord[1]
	z2 = a2.coord[2]

	# Make some nice strings for user feedback
	s1 = o1 + "/" + a1.chain + "/" + a1.resn + "." + a1.resi + "/" 
		+ a1.name
	print s1 + "(" + str(x1) + "," + str(y1) + "," + str(z1) + ")"
	s2 = o2 + "/" + a2.chain + "/" + a2.resn + "." + a2.resi + "/" 
		+ a2.name
	print s2 + "(" + str(x2) + "," + str(y2) + "," + str(z2) + ")"

	# Calculate distances 
	dx = x2 - x1
	dy = y2 - y1
	dz = z2 - z1
	d  = math.sqrt((dx*dx) + (dy*dy) + (dz*dz))
	print "distance = " + str(d) + "A"

	# Work out how many times (dash_len + gap_len) fits into d
	dash_tot = dl + gl
	n_dash = math.floor(d / dash_tot)

	# Work out step lengths
	dx1 = (dl / dash_tot) * (dx / n_dash)
	dy1 = (dl / dash_tot) * (dy / n_dash)
	dz1 = (dl / dash_tot) * (dz / n_dash)
	dx2 = (dx / n_dash)
	dy2 = (dy / n_dash)
	dz2 = (dz / n_dash)


	# Empty CGO object
	obj = []


	# Generate dashes
	x = x1
	y = y1
	z = z1
	for i in range(n_dash):
		
		# Generate a dash cylinder
		obj.extend( [ CYLINDER, x, y, z, x+dx1, y+dy1, z+dz1,
			dr, rr, gg, bb, rr, gg, bb ] )

		# Move to start of next dash
		x = x + dx2
		y = y + dy2
		z = z + dz2


	# Add an arrow half way along
	# Calculate midpoint
	xm = (x1 + x2) / 2	
	ym = (y1 + y2) / 2
	zm = (z1 + z2) / 2

	# Vector pointing along the bond
	xv = (3.5 * dr / d) * dx
	yv = (3.5 * dr / d) * dy
	zv = (3.5 * dr / d) * dz

	# Rotate step vector 90deg around X axis
	xxv = xv
	yyv = -1 * zv
	zzv = yv

	# Add lines
	obj.extend( [ CYLINDER, xm-xv-xxv, ym-yv-yyv, zm-zv-zzv,
		xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )
	obj.extend( [ CYLINDER, xm-xv+xxv, ym-yv+yyv, zm-zv+zzv,
		xm+xv, ym+yv, zm+zv, dr, rr, gg, bb, rr, gg, bb ] )


	# Load the object into PyMOL
	cmd.load_cgo(obj, name)


# Add to PyMOL API
cmd.extend("hbond",hbond)

#------------------------------------------------------------------------




On Fri, 2003-07-18 at 18:25, Warren L. DeLano wrote:
> Gareth,
> 
> 	cmd.identify returns the input indexing, which will correspond
> to the PDB file.
> 
> 	cmd.index returns the internal indexing, which will correspond
> to cmd.get_model
> 
> help identify
> help index
> 
> Cheers,
> Warren
> 
> 
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -----Original Message-----
> > From: Gareth Stockwell [mailto:ga...@eb...]
> > Sent: Friday, July 18, 2003 8:50 AM
> > To: Warren L. DeLano
> > Cc: 'pymol-users'
> > Subject: RE: [PyMOL] H-bond display
> > 
> > Warren,
> > 
> > I started having a look at this, but I am getting stuck with atom 
> > indices.  If I make two selections, (lb) and (rb), by clicking on 
> > atoms in an object called 'x', then I can get the indices and objects 
> > of those atoms by doing
> > 
> > x1 = cmd.identify("lb",1)
> > x2 = cmd.identify("rb",1)
> > 
> > In my example, printing out x1 and x2 gives the following: [('x', 2)]
> > [('x', 16)]
> > 
> > As I clicked on these atoms, the GUI told me that they were,
> > respectively:
> > VAL: /x/1ATP/E/15/CA
> > LYS: /x/1ATP/E/16/NZ
> > 
> > But now, if I dump out the contents of the model.atom array, using 
> > this
> > code:
> > 
> > m = cmd.get_model("x")
> > 	i = 1
> > 	for a in m.atom:
> > 		print str(i) + " -> " + a.chain + "/" + a.resn + "." \
> > 			 + a.resi + "/" + a.name
> > 		i = i+1
> > 
> > Then I see the following
> > 1 -> E/VAL.15/N
> > 2 -> E/VAL.15/CA
> > 3 -> E/VAL.15/CB
> > 4 -> E/VAL.15/CG1
> > 5 -> E/VAL.15/CG2
> > 6 -> E/VAL.15/C
> > 7 -> E/VAL.15/O
> > 8 -> E/LYS.16/N
> > 9 -> E/LYS.16/CA
> > 10 -> E/LYS.16/CB
> > 11 -> E/LYS.16/CG
> > 12 -> E/LYS.16/CD
> > 13 -> E/LYS.16/CE
> > 14 -> E/LYS.16/NZ
> > 15 -> E/LYS.16/C
> > 16 -> E/LYS.16/O
> > 17 -> E/GLU.17/N
> > 18 -> E/GLU.17/CA
> > 19 -> E/GLU.17/C
> > 20 -> E/GLU.17/O
> > 
> > So atom number 2 is correct (VAL.15/CA), but in this array, atom 16 is
> 
> > the O, not NZ in LYS.16.  I presume that ChemPy is re-ordering the 
> > atoms some time during the get_model call - how do I resolve this?
> > 
> > Gareth
> > 
> > 
> > On Fri, 2003-07-18 at 16:36, Warren L. DeLano wrote:
> > > Gareth,
> > >
> > > 	CGO is currently the way to go...
> > >
> > > Cheers,
> > > Warren
> > >
> > >
> > > --
> > > mailto:wa...@de...
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax   (650)-593-4020
> > >
> > > > -----Original Message-----
> > > > From: pym...@li... [mailto:pymol-users-
> 
> > > > ad...@li...] On Behalf Of Gareth Stockwell
> > > > Sent: Friday, July 18, 2003 2:46 AM
> > > > To: pymol-users
> > > > Subject: [PyMOL] H-bond display
> > > >
> > > >
> > > > I am using distance objects at the moment, to display h-bonding 
> > > > contacts.  My question is ... is there any easy way to display the
> 
> > > > direction of an h-bond using distances (i.e. putting a little 
> > > > arrow on the dashed line)?
> > > >
> > > > I am prepared to bash out some functions which do this using CGOs,
> 
> > > > but of course I won't if it's already implemented!
> > > >
> > > > Gareth
> > > >
> > > >
> > > > --
> > > > Gareth Stockwell <ga...@eb...>
> > > > European Bioinformatics Institute
> > > >
> > > >
> > > >
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> > >
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> > --
> > Gareth Stockwell <ga...@eb...>
> > European Bioinformatics Institute
> 
> 
> 
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-- 
Gareth Stockwell <ga...@eb...>
European Bioinformatics Institute