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Difference between revisions of "SuperSymSource"

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(move code to Pymol-script-repo)
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==Source Code==
 
==Source Code==
  
−
File: SuperSymPlugin12.py
+
See https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/SuperSymPlugin.py
−
<source lang="python">
 
−
from Tkinter import *
 
−
import tkSimpleDialog
 
−
import tkMessageBox
 
−
import tkColorChooser
 
−
import tkFileDialog
 
−
import sys
 
−
import re
 
−
from pymol import stored, cmd, selector
 
−
import math
 
−
from pymol.cgo import *
 
−
from pymol.vfont import plain
 
−
try:
 
−
    from cctbx import sgtbx, uctbx
 
−
    import numpy as N
 
−
    from numpy.linalg import *
 
−
    from cctbx import uctbx, sgtbx
 
−
except:
 
−
    quit("Oops! SuperSym requires cctbx and numeric python to function. Please install these.")
 
−
 
 
−
 
 
−
def __init__(self):
 
−
    #MAIN
 
−
    self.menuBar.addcascademenu('Plugin','SuperSym')
 
−
    #DEFAULT SET BUILD
 
−
    self.menuBar.addmenuitem('SuperSym', 'command', 'Default Symmetry Partner Set',
 
−
                            label = 'Default Symmetry Partner Set',
 
−
                            command = lambda s = self: symDialog(s, 0))
 
−
    #UNIT CELL BUILD
 
−
    self.menuBar.addmenuitem('SuperSym', 'command', 'Draw Unit Cell',
 
−
                            label = 'Draw Unit Cell',
 
−
                            command = lambda s = self: cellDialog(s))
 
−
    #SYM SUBMENU
 
−
    self.menuBar.addcascademenu('SuperSym', 'Build Symmetry Partners')
 
−
 
 
−
    self.menuBar.addmenuitem('Build Symmetry Partners', 'command', 'Cell [0,0,0] (default)',
 
−
                            label = 'Cell [0,0,0] (default)',
 
−
                            command = lambda s = self: symDialog(s, 0))
 
−
 
 
−
    self.menuBar.addmenuitem('Build Symmetry Partners', 'command', 'Cell [x,y,z] (custom)',
 
−
                            label = 'Cell [x,y,z] (custom)',
 
−
                            command = lambda s = self: symDialog(s, 1))
 
−
 
 
−
    self.menuBar.addmenuitem('Build Symmetry Partners', 'command', '2x2x2 Block',
 
−
                            label = '2x2x2 Block',
 
−
                            command = lambda s = self: symDialog(s, 2))
 
−
 
 
−
    self.menuBar.addmenuitem('Build Symmetry Partners', 'command', '3x3x3 Block',
 
−
                            label = '3x3x3 Block',
 
−
                            command = lambda s = self: symDialog(s, 3))
 
−
 
 
−
    self.menuBar.addmenuitem('Build Symmetry Partners', 'command', 'By Partner',
 
−
                            label = 'By Partner',
 
−
                            command = lambda s = self: symDialog(s, 4))
 
−
    #COLOR SUBMENU
 
−
    self.menuBar.addcascademenu('SuperSym', 'Coloring')
 
−
 
 
−
    self.menuBar.addmenuitem('Coloring', 'command', 'Default Rainbow',
 
−
                            label = 'Default Rainbow',
 
−
                            command = lambda s = self: colorDialog(s, 0))
 
−
 
 
−
    self.menuBar.addmenuitem('Coloring', 'command', 'Select color for each operation',
 
−
                            label = 'Select color for each operation',
 
−
                            command = lambda s = self: colorDialog(s, 1))
 
−
 
 
−
    self.menuBar.addmenuitem('Coloring', 'command', 'Select one color for custom set of operations',
 
−
                            label = 'Select one color for custom set of operations',
 
−
                            command = lambda s = self: colorDialog(s, 2))
 
−
    #GRAPHICS SUBMENU
 
−
    self.menuBar.addcascademenu('SuperSym', 'Graphics')
 
−
 
 
−
    self.menuBar.addmenuitem('Graphics', 'command', 'Lines',
 
−
                            label = 'Lines',
 
−
                            command = lambda s = self: graphicsDialog(s, 0))
 
−
 
 
−
    self.menuBar.addmenuitem('Graphics', 'command', 'Ribbon',
 
−
                            label = 'Ribbon',
 
−
                            command = lambda s = self: graphicsDialog(s, 1))
 
−
    self.menuBar.addmenuitem('Graphics', 'command', 'Cartoon',
 
−
                            label = 'Cartoon',
 
−
                            command = lambda s = self: graphicsDialog(s, 2))
 
−
    self.menuBar.addmenuitem('Graphics', 'command', 'Sphere Surface (best for printing)',
 
−
                            label = 'Sphere Surface (best for printing)',
 
−
                            command = lambda s = self: graphicsDialog(s, 3))
 
−
 
 
−
    self.menuBar.addmenuitem('Graphics', 'command', 'Surface (high load render)',
 
−
                            label = 'Surface (high load render)',
 
−
                            command = lambda s = self: graphicsDialog(s, 4))
 
−
    #SYM AXES SUBMENU
 
−
    self.menuBar.addcascademenu('SuperSym', 'Symmetry Axes')
 
−
 
 
−
    self.menuBar.addmenuitem('Symmetry Axes', 'command', 'Build Axes',
 
−
                            label = 'Build Axes',
 
−
                            command = lambda s = self: axesDialog(s))
 
−
    #ADD OTHER SYMMETRY AXES OPTION HERE
 
−
    self.menuBar.addmenuitem('SuperSym', 'command', 'Move symmetry partners',
 
−
                            label = 'Move symmetry partners',
 
−
                            command = lambda s = self: cellShiftInfo(s))
 
−
    self.menuBar.addmenuitem('SuperSym', 'command', 'About',
 
−
                            label = 'About',
 
−
                            command = lambda s = self: aboutInfo(s))
 
−
    self.menuBar.addmenuitem('SuperSym', 'command', 'Help',
 
−
                            label = 'Help',
 
−
                            command = lambda s = self: helpInfo(s))
 
−
    cmd.cell_shift = cell_shift
 
−
    cmd.get_operations = get_operations
 
−
    cmd.get_matrix = get_orthogonalization_matrix
 
−
    cmd.symset = symset
 
−
    cmd.cell_shift_helper = cell_shift_helper
 
−
    cmd.set_key("ALT-6", cell_shift_proxyX1)
 
−
    cmd.set_key("ALT-4", cell_shift_proxyX2)
 
−
    cmd.set_key("ALT-8", cell_shift_proxyY1)
 
−
    cmd.set_key("ALT-2", cell_shift_proxyY2)
 
−
    cmd.set_key("ALT-5", cell_shift_proxyZ1)
 
−
    cmd.set_key("ALT-1", cell_shift_proxyZ2)
 
−
 
 
−
 
 
−
'''
 
−
symDialog: Dialog generator and command issuer for generating symmetry partners
 
−
 
 
−
This function is called by SuperSymMenu when any symmetry partner generating option is
 
−
selected. It creates dialog windows and receives user input for symmetry generation parameters.
 
−
 
 
−
@app -- identifies the GUI interface to build dialog boxes onto.
 
−
@mode -- determines specific treatment of symmetry building command
 
−
'''
 
−
def symDialog(app, mode):
 
−
    prefix = tkSimpleDialog.askstring('Prefix',
 
−
    'Enter desired prefix for these partners:', parent=app.root)
 
−
    object = tkSimpleDialog.askstring('Object',
 
−
    'Enter object to generate partners from:', parent=app.root)
 
−
    if mode == 0: #make default symmetry set in cell [0,0,0]
 
−
        symset(prefix, object)
 
−
    if mode == 1: #make symmetry set in custom cell
 
−
        cell = tkSimpleDialog.askstring('Cell',
 
−
        'Enter lattice cell coordinates separated by commas (ex:x,y,z):', parent = app.root)
 
−
        x,y,z = cell.split(',')
 
−
        x,y,z = int(x),int(y),int(z)
 
−
        symset(prefix, object, x, y, z)
 
−
    if mode == 2: #make 2x2x2 block of symmetry sets
 
−
        for i in range(2):
 
−
            for j in range(2):
 
−
                for k in range(2):
 
−
                    symset(prefix, object, i, j, k)
 
−
    if mode == 3: #make 3x3x3 block of symmetry sets
 
−
        for i in range(-1,2):
 
−
            for j in range(-1,2):
 
−
                for k in range(-1,2):
 
−
                    symset(prefix, object, i, j, k)
 
−
    if mode == 4: #select individual partners by operation and cell
 
−
        ops = get_operations(object)
 
−
        opString = ""
 
−
        for i,x in enumerate(ops):
 
−
            opString += str(i) + " : " + x + "\n"
 
−
        opIndeces = tkSimpleDialog.askstring("Symmetry Operations", opString +
 
−
        "Enter numbers of desired operations separated by commas (ex:0,2,9)", parent = app.root)
 
−
        opListStrings = opIndeces.split(",")
 
−
        opList = []
 
−
        for op in opListStrings:
 
−
            opList.append(int(op))
 
−
        cell = tkSimpleDialog.askstring('Cell',
 
−
        'Enter lattice cell coordinates separated by commas (ex:x,y,z):', parent = app.root)
 
−
        x,y,z = cell.split(',')
 
−
        x,y,z = int(x),int(y),int(z)
 
−
        symset(prefix, object, x,y,z, opList)
 
−
 
 
−
'''
 
−
colorDialog: Dialog generator for coloring commands
 
−
 
 
−
This function colors sets of symmetry partners defined by the user in the
 
−
dialog which it generates.
 
−
 
 
−
@app -- identifies root menu calling this function
 
−
@mode -- determines coloring scheme to execute
 
−
'''
 
−
def colorDialog(app, mode):
 
−
    prefix = tkSimpleDialog.askstring('Prefix',
 
−
    'Enter the prefix of symmetry partners to color', parent = app.root)
 
−
    if mode == 0: #standard rainbow by symmetry operation
 
−
        colors = ["red", "orange", "yellow", "green", "blue", "purple",
 
−
              "salmon", "grey", "pink", "teal", "brown", "br0", "aquamarine",
 
−
              "deepolive", "dirtyviolet", "slate", "br4", "darksalmon", "br7",
 
−
              "chocolate", "firebrick", "brightorange"]
 
−
        for i in range(20):
 
−
            try: #required because PyMOL inappropriately throws an exception
 
−
                #when the cmd.color() function colors no objects
 
−
                cmd.color(colors[i], "%s%02d*" % (prefix, i))
 
−
            except:
 
−
                pass #allows us to move on to next symmetry operator
 
−
    if mode == 1: #specify for each symmetry operation
 
−
        cmd.iterate_state(1, prefix + "*", "stored.tmpObject = model")
 
−
        ops = get_operations(stored.tmpObject)
 
−
        opString = ""
 
−
        for i,x in enumerate(ops):
 
−
            opString += str(i) + " : " + x + "\n"
 
−
        opIndeces = tkSimpleDialog.askstring("Symmetry Operations", opString +
 
−
        "Enter numbers of desired operations separated by commas (ex:0,2,9) or all", parent = app.root)
 
−
        if opIndeces == "all":
 
−
            opList = []
 
−
            for i in range(len(ops)):
 
−
                opList.append(i)
 
−
        else:
 
−
            opList = opIndeces.split(",")
 
−
        opStringList = opString.split("\n")
 
−
        for i in opList:
 
−
            try:
 
−
                cmd.color("white", "%s%02d*" % (prefix, i))
 
−
                cmd.center("%s%02d*" % (prefix, i))
 
−
               
 
−
            except:
 
−
                pass
 
−
            tempColor = tkColorChooser.askcolor(title = "Color for " + opStringList[int(i)] + " (currently white)",
 
−
                                                parent = app.root)[0]
 
−
            rgb = []
 
−
            for value in tempColor:
 
−
                value = float(value)
 
−
                value = value/255
 
−
                rgb.append(value)
 
−
            cmd.set_color("tempColor", rgb)
 
−
            try:
 
−
                cmd.color("tempColor", "%s%02d*" % (prefix, i))
 
−
            except:
 
−
                pass
 
−
    if mode == 2: #monochrome for a set of operations
 
−
        cmd.iterate_state(1, prefix + "*", "stored.tmpObject = model")
 
−
        ops = get_operations(stored.tmpObject)
 
−
        opString = ""
 
−
        for i,x in enumerate(ops):
 
−
            opString += str(i) + " : " + x + "\n"
 
−
        opIndeces = tkSimpleDialog.askstring("Symmetry Operations", opString +
 
−
        "Enter numbers of desired operations separated by commas (ex:0,2,9) or all", parent = app.root)
 
−
        if opIndeces == 'all':
 
−
            opList = []
 
−
            for i in range(len(ops)):
 
−
                opList.append(i)
 
−
        else:
 
−
            opList = opIndeces.split(",")
 
−
        opStringList = opString.split("\n")
 
−
        tempColor = tkColorChooser.askcolor(parent = app.root)[0]
 
−
        rgb = []
 
−
        for value in tempColor:
 
−
            value = float(value)
 
−
            value = value/255
 
−
            rgb.append(value)
 
−
        cmd.set_color("tempColor", rgb)
 
−
        for i in opList:
 
−
            try:
 
−
                cmd.color("tempColor", "%s%02d*" % (prefix, i))
 
−
            except:
 
−
                pass
 
−
'''
 
−
graphicsDialog: Dialog generator for graphics commands
 
−
 
 
−
This function sets visual representations for sets of symmetry partners.
 
−
 
 
−
@app -- identifies root menu
 
−
@mode -- determines type of representation to show
 
−
'''
 
−
def graphicsDialog(app, mode):
 
−
    prefix = tkSimpleDialog.askstring('Prefix',
 
−
    'Enter prefix of symmetry partners to display', parent = app.root)
 
−
    cmd.hide("everything", prefix + "*")
 
−
    if mode == 0: # show lines
 
−
        cmd.show("lines", prefix + "*")
 
−
    if mode == 1: # show ribbon
 
−
        cmd.show("ribbon", prefix + "*")
 
−
    if mode == 2: # show cartoon
 
−
        cmd.show("cartoon", prefix + "*")
 
−
    if mode == 3: # sphere surface
 
−
        objSel = prefix + "*"
 
−
        findSurfaceResidues(objSel, 3.5, "surface")
 
−
        cmd.set("sphere_scale", 1.8)
 
−
        cmd.show("spheres", "surface")
 
−
    if mode == 4: # regular surface
 
−
        cmd.show("surface", prefix + "*")
 
−
 
 
−
'''
 
−
cellDialog: dialog proxy for draw_cell
 
−
 
 
−
This function generates a unit cell representation
 
−
FUTURE IMPLEMENTATIONS: select which lattice coordinates to generate unit cell for
 
−
 
 
−
@app -- identifies root menu
 
−
'''
 
−
def cellDialog(app):
 
−
    object = tkSimpleDialog.askstring('Object',
 
−
    'Enter object to generate cell for:', parent = app.root)
 
−
    if tkMessageBox.askyesno('3D Printing', 'Going to print this model?', parent = app.root):
 
−
        draw_cell(object, 3.0)
 
−
    else:
 
−
        draw_cell(object)
 
−
 
 
−
'''
 
−
axesDialog: dialog proxy for draw_symops_cctbx
 
−
 
 
−
This function generates one set of symmetry axes for a given object
 
−
FUTURE IMPLEMENTATIONS: select individual axes to generate, attach to model for 3D printing,
 
−
                        generate axes for multiple unit cells
 
−
 
 
−
@app -- identifies root menu
 
−
'''
 
−
def axesDialog(app):
 
−
    object = tkSimpleDialog.askstring('Object',
 
−
    'Enter object to generate symmetry axes for:', parent = app.root)
 
−
    if tkMessageBox.askyesno('3D Printing', 'Going to print this model?', parent = app.root):
 
−
        draw_symops(object, 2.0)
 
−
    else:
 
−
        draw_symops(object)
 
−
 
 
−
'''
 
−
cellShiftInfo: displays info for using cell_shift hotkeys
 
−
 
 
−
@app -- identifies root menu
 
−
'''
 
−
def cellShiftInfo(app):
 
−
    tkMessageBox.showinfo('Cell Shifting',
 
−
    "To shift a symmetry partner, simply click to select any part of it (select only one partner at a time). \n\n" +
 
−
    "Next, hold ALT and press the numpad key corresponding to the axis direction you\'d like to move. \n\n" +
 
−
    "Key assignments:\n" +
 
−
    "A (x) axis: down--4, up--6 \n" +
 
−
    "B (y) axis: down--2, up--8 \n" +
 
−
    "C (z) axis: down--1, up--5", parent = app.root)
 
−
    tkMessageBox.showwarning('Caution', 'Only attempt to shift symmetry partners created by SuperSym.'+
 
−
                            'Attempting to shift any other object will result in errors.')
 
−
 
 
−
def aboutInfo(app):
 
−
    tkMessageBox.showinfo('About',
 
−
                          'SuperSym \nDeveloped by Stuart Ballard (srballard@wisc.edu)\nDepartment of Biochemistry\n'+
 
−
                          'University of Wisconsin-Madison', parent = app.root)
 
−
def helpInfo(app):
 
−
    tkMessageBox.showinfo('Help',
 
−
                          'For documentation see http://pymolwiki.org/index.php/SuperSym', parent = app.root)
 
−
 
 
−
'''
 
−
symset: generates up to one full set of symmetry partners for a given object in a given lattice position
 
−
 
 
−
1. Obtain all essential symmetry information from CCTBX. This includes the space group, unit cell parameters,
 
−
and fractional coordinates corresponding to symmetry operations.
 
−
2. Generate transformation matrices to translate coordinates from orthogonal to fractional, and back.
 
−
3.
 
−
'''
 
−
def symset(prefix = "sym", object = -1, x=0,y=0,z=0, opList = []):
 
−
    if object == -1:
 
−
        object = cmd.get_names()[0]
 
−
    cell = [float(x),float(y),float(z)]
 
−
    view = cmd.get_view()
 
−
    cmd.show("lines", object)
 
−
    sgInfo = cmd.get_symmetry(object)
 
−
    raw_ops = []
 
−
    for s in sgtbx.space_group_info(sgInfo[6]).group():
 
−
        raw_ops.append(str(s))
 
−
    if len(opList) == 0:
 
−
        for i in range(len(raw_ops)):
 
−
            opList.append(i)
 
−
    opMatrices = []
 
−
    vars = ["x","y","z"]
 
−
#CREATE 4X4 MATRICES FOR SYMMETRY OPERATORS
 
−
    for i,raw_op in enumerate(raw_ops):
 
−
        ops = raw_op.split(",")
 
−
        matrix = [[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]]
 
−
        for j in range(len(ops)):
 
−
            for k in range(len(vars)):
 
−
                index = ops[j].find(vars[k])
 
−
                if index != -1:
 
−
                    if index == 0:
 
−
                        matrix[k][j] = 1
 
−
                    elif ops[j][index - 1] == "-":
 
−
                        matrix[k][j] = -1
 
−
                    else:
 
−
                        matrix[k][j] = 1
 
−
            index = ops[j].find("/")
 
−
            if index != -1:
 
−
                matrix[3][j] = float(ops[j][index - 1]) / float(ops[j][index + 1])
 
−
        opMatrices.append(matrix)
 
−
    a,b,c,alpha,beta,gamma = sgInfo[0:6]
 
−
    ca = math.cos(math.radians(alpha))
 
−
    cb = math.cos(math.radians(beta))
 
−
    cg = math.cos(math.radians(gamma))
 
−
    sb = math.sin(math.radians(beta))
 
−
    sg = math.sin(math.radians(gamma))
 
−
    fracToOrt = N.array([[a, b * cg, c * cb, 0.0],
 
−
                                [0.0, b * sg, c * (ca - cb * cg) / sg, 0.0],
 
−
                                [0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2), 0.0],
 
−
                                [0.0,0.0,0.0,1.0]])
 
−
    fracToOrt = fracToOrt.transpose()
 
−
    ortToFrac = inv(fracToOrt)
 
−
    stored.atoms = []
 
−
    cmd.iterate_state(1,object,"stored.atoms.append([x,y,z,1])")
 
−
    stored.atoms = N.array(stored.atoms)
 
−
    fracCoords = N.dot(stored.atoms,ortToFrac)
 
−
    for i in opList:
 
−
        try:
 
−
            op = opMatrices[i]
 
−
        except:
 
−
            print "Bad symmetry partner numbers. Try again."
 
−
            quit()
 
−
        copy = "%s%02d_%d_%d_%d" % (prefix, i, x, y, z)
 
−
        cmd.copy(copy, object)
 
−
        newCoordsFrac = N.dot(fracCoords, op)
 
−
        stored.newCoords = N.dot(newCoordsFrac, fracToOrt)
 
−
        stored.j = 0
 
−
        cmd.alter_state(1,copy,"x,y,z = stored.newCoords[stored.j][0], stored.newCoords[stored.j][1], stored.newCoords[stored.j][2]; stored.j = stored.j + 1")
 
−
        xSum=ySum=zSum=0.0
 
−
        for a,b,c in newCoordsFrac:
 
−
            xSum += a
 
−
            ySum += b
 
−
            zSum += c
 
−
        center = N.array([xSum,ySum,zSum])
 
−
        center = center/len(stored.newCoords)
 
−
        shift = [cell[0]-math.floor(center[0]),
 
−
                cell[1]-math.floor(center[1]),
 
−
                cell[2]-math.floor(center[2])]
 
−
        cell_shift(copy,shift[0],shift[1],shift[2],0)
 
−
        '''
 
−
        #COPIES COORDINATES OF EACH ATOM TO CORRESPONDING ONE IN GIVEN SYMMETRY PARTNER
 
−
        #cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
 
−
        #MOVES SYMMETRY PARTNER TO PROPER LATTICE COORDINATES AND CORRECTS FOR NATIVE LATTICE POSITION ERROR
 
−
        #stored.xSum,stored.ySum,stored.zSum = 0.0,0.0,0.0
 
−
        #atoms = cmd.count_atoms(copy)
 
−
        #cmd.iterate_state(1, copy, "stored.xSum = stored.xSum + x; stored.ySum = stored.ySum + y; stored.zSum = stored.zSum + z")
 
−
        #xMean = stored.xSum / atoms
 
−
        #yMean = stored.ySum / atoms
 
−
        #zMean = stored.zSum / atoms
 
−
        #xError, yError, zError = N.dot(N.array([xMean,yMean,zMean]), stored.ortToFrac)
 
−
        #dX,dY,dZ = cell[0]-math.floor(xError), cell[1]-math.floor(yError), cell[2]-math.floor(zError)
 
−
        #cell_shift(copy,dX,dY,dZ, 0)
 
−
        '''
 
−
    cmd.hide("everything", object)
 
−
    cmd.set_view(view)
 
−
 
 
−
'''
 
−
def sym_partner(coords, op):
 
−
    fracCoords = N.dot(N.array(coords), stored.ortToFrac)
 
−
    op = op.replace("x", "(" + str(fracCoords[0]) + ")")
 
−
    op = op.replace("y", "(" + str(fracCoords[1]) + ")")
 
−
    op = op.replace("z", "(" + str(fracCoords[2]) + ")")
 
−
    op = op.split(",")
 
−
    for i in range(3):
 
−
        index = op[i].find("/")
 
−
        if index != -1:
 
−
            if len(op[i]) == index + 2:
 
−
                op[i] = op[i][0:index - 1] + str(float(op[i][index - 1]) / float(op[i][index + 1]))
 
−
            else:
 
−
                op[i] = op[i][0:index - 1] + str(float(op[i][index - 1]) / float(op[i][index + 1])) + op[i][index + 2:]
 
−
        op[i] = eval(op[i])
 
−
    return N.dot(N.array(op), stored.fracToOrt)
 
−
'''
 
−
 
 
−
 
 
−
def cell_shift_proxyX1():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, 1,0,0)
 
−
def cell_shift_proxyX2():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, -1,0,0)
 
−
def cell_shift_proxyY1():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, 0,1,0)
 
−
def cell_shift_proxyY2():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, 0,-1,0)
 
−
def cell_shift_proxyZ1():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, 0,0,1)
 
−
def cell_shift_proxyZ2():
 
−
    cmd.iterate_state(1, "sele", "stored.tmpObject = model")
 
−
    cell_shift(stored.tmpObject, 0,0,-1)
 
−
 
 
−
def cell_shift(object, dX, dY, dZ, rename = 1):
 
−
    if rename:
 
−
        oldName = object.split("_")
 
−
        oldPre = oldName[0]
 
−
        oldX = int(oldName[1])
 
−
        oldY = int(oldName[2])
 
−
        oldZ = int(oldName[3])
 
−
        newX = "_" + str(int(dX) + oldX)
 
−
        newY = "_" + str(int(dY) + oldY)
 
−
        newZ = "_" + str(int(dZ) + oldZ)
 
−
        newName = oldPre + newX + newY + newZ
 
−
        #if cmd.get_names().find(newName) != -1:
 
−
        #    print "Symmetry partner already exists in destination position!"
 
−
        #    quit()
 
−
        cmd.set_name(object, newName)
 
−
object = newName
 
−
    stored.shift = [float(dX),float(dY),float(dZ)]
 
−
    stored.sgInfo = cmd.get_symmetry(object)
 
−
    a,b,c,alpha,beta,gamma = stored.sgInfo[0:6]
 
−
    ca = math.cos(math.radians(alpha))
 
−
    cb = math.cos(math.radians(beta))
 
−
    cg = math.cos(math.radians(gamma))
 
−
    sb = math.sin(math.radians(beta))
 
−
    sg = math.sin(math.radians(gamma))
 
−
    stored.fracToOrt = N.array([[a, b * cg, c * cb],
 
−
                                [0.0, b * sg, c * (ca - cb * cg) / sg],
 
−
                                [0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2)]])
 
−
    stored.fracToOrt = stored.fracToOrt.transpose()
 
−
    stored.ortToFrac = inv(stored.fracToOrt)
 
−
    cmd.cell_shift_helper = cell_shift_helper
 
−
    cmd.alter_state(1, object, "x,y,z = cmd.cell_shift_helper([x,y,z],stored.shift)")
 
−
 
 
−
def cell_shift_helper(coords, shift):
 
−
    fracCoords = N.dot(N.array(coords), stored.ortToFrac)
 
−
    for i in range(3):
 
−
        fracCoords[i] += shift[i]
 
−
    coords = N.dot(N.array(fracCoords), stored.fracToOrt)
 
−
    return coords[0], coords[1], coords[2]
 
−
 
 
−
def get_operations(object):
 
−
    raw_ops = []
 
−
    sgInfo = cmd.get_symmetry(object)
 
−
    for s in sgtbx.space_group_info(sgInfo[6]).group():
 
−
        raw_ops.append(str(s))
 
−
    return raw_ops 
 
−
 
 
−
def get_orthogonalization_matrix(object, quiet = 0):
 
−
    a,b,c,alpha,beta,gamma = cmd.get_symmetry(object)[0:6]
 
−
    ca = math.cos(math.radians(alpha))
 
−
    cb = math.cos(math.radians(beta))
 
−
    cg = math.cos(math.radians(gamma))
 
−
    sb = math.sin(math.radians(beta))
 
−
    sg = math.sin(math.radians(gamma))
 
−
    fracToOrt = N.array([[a, b * cg, c * cb],
 
−
                                [0.0, b * sg, c * (ca - cb * cg) / sg],
 
−
                                [0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2)]])
 
−
    if not quiet:
 
−
        print fracToOrt
 
−
        print inv(fracToOrt)
 
−
    return fracToOrt
 
−
 
 
−
# -*- coding: utf-8 -*-
 
−
def findSurfaceResidues(objSel="(all)", cutoff=2.5, selName = 0):
 
−
"""
 
−
findSurfaceResidues
 
−
finds those residues on the surface of a protein
 
−
that have at least 'cutoff' exposed A**2 surface area.
 
−
 
−
PARAMS
 
−
objSel (string)
 
−
the object or selection in which to find
 
−
exposed residues
 
−
DEFAULT: (all)
 
−
 
−
cutoff (float)
 
−
your cutoff of what is exposed or not.
 
−
DEFAULT: 2.5 Ang**2
 
−
 
−
asSel (boolean)
 
−
make a selection out of the residues found
 
−
 
−
RETURNS
 
−
(list: (chain, resv ) )
 
−
A Python list of residue numbers corresponding
 
−
to those residues w/more exposure than the cutoff.
 
−
 
−
"""
 
−
tmpObj="__tmp"
 
−
cmd.create( tmpObj, objSel + " and polymer");
 
−
cmd.set("dot_solvent");
 
−
cmd.get_area(selection=tmpObj, load_b=1)
 
−
 
−
# threshold on what one considers an "exposed" atom (in A**2):
 
−
cmd.remove( tmpObj + " and b < " + str(cutoff) )
 
−
 
−
stored.tmp_dict = {}
 
−
cmd.iterate(tmpObj, "stored.tmp_dict[(chain,resv)]=1")
 
−
exposed = stored.tmp_dict.keys()
 
−
exposed.sort()
 
−
 
−
cmd.select(selName, objSel + " in " + tmpObj )
 
−
cmd.delete(tmpObj)
 
−
 
−
return exposed
 
−
 
 
−
#CELL DRAWING
 
−
 
 
−
def set_to_zero(a):
 
−
  if abs(a) < 1e-10:
 
−
    a=0
 
−
  return a
 
−
 
 
−
def draw_cell(obj,radius=1.0,mode=0):
 
−
  """
 
−
  From pymol issue the "run draw_cell.py" command to load the script,
 
−
  then issue the "draw_cell(object,<optional radius>)" command
 
−
  to actually run it and create the cgo object showing the unit cell
 
−
  border for the space group specified by molecular object 'object'.
 
−
 
 
−
  e.g. load 1avv.pdb
 
−
      run draw_cell.py
 
−
      draw_cell 1avv 0.5  (or draw_cell('1avv',.5))
 
−
 
 
−
  see also help(draw_cell_param) to draw the cell border for
 
−
  user-defined cell dimensions (i.e. not loaded from a pdb file)
 
−
 
 
−
  See also "help(draw_cell_param) to draw the cell border by
 
−
  specifying the unit cell parameters directly (i.e. not loaded from
 
−
  a pdb file).
 
−
  """
 
−
  radius=float(radius)
 
−
  cell_info=cmd.get_symmetry(obj)
 
−
  draw_cell_param(cell_info[0:6],radius,mode)
 
−
 
 
−
def draw_cell_param(cell_param_list,radius=1.0,mode=0):
 
−
  """
 
−
  If you wish to draw the unit cell border for any cell without the
 
−
  need to load a pdb file, then do this:
 
−
 
 
−
  e.g. run draw_cell.py
 
−
      draw_cell_param((45.2,45.2,70.8,90.,90.,120.),0.5)
 
−
 
 
−
  to generate the cell border for this trigonal space group "p 31 2 1"
 
−
  with a radius of 0.5A.  Labels for the origin, and A, B and C axes
 
−
  will appear as well.  The perimeter of the cell is colored with the
 
−
  RGB components corresponding to the A,B,C components.
 
−
  """
 
−
 
 
−
  U=uctbx.unit_cell((cell_param_list))
 
−
 
 
−
  vert_000 = map(set_to_zero,U.orthogonalize((0.,0.,0)))
 
−
  vert_100 = map(set_to_zero,U.orthogonalize((1.,0.,0)))
 
−
  vert_010 = map(set_to_zero,U.orthogonalize((0.,1.,0)))
 
−
  vert_001 = map(set_to_zero,U.orthogonalize((0.,0.,1)))
 
−
  vert_110 = map(set_to_zero,U.orthogonalize((1.,1.,0)))
 
−
  vert_011 = map(set_to_zero,U.orthogonalize((0.,1.,1)))
 
−
  vert_101 = map(set_to_zero,U.orthogonalize((1.,0.,1)))
 
−
  vert_111 = map(set_to_zero,U.orthogonalize((1.,1.,1)))
 
−
 
 
−
#  vert_000 = map(None,U.orthogonalize((0.,0.,0)))
 
−
#  vert_100 = map(None,U.orthogonalize((1.,0.,0)))
 
−
#  vert_010 = map(None,U.orthogonalize((0.,1.,0)))
 
−
#  vert_001 = map(None,U.orthogonalize((0.,0.,1)))
 
−
#  vert_110 = map(None,U.orthogonalize((1.,1.,0)))
 
−
#  vert_011 = map(None,U.orthogonalize((0.,1.,1)))
 
−
#  vert_101 = map(None,U.orthogonalize((1.,0.,1)))
 
−
#  vert_111 = map(None,U.orthogonalize((1.,1.,1)))
 
−
 
 
−
  #print vert_000
 
−
 
 
−
  #CYLINDER = ['CYLINDER']
 
−
  #radius = [0.2]
 
−
  #print radius
 
−
  cell = []
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_000 + vert_100 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_000 + vert_010 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_000 + vert_001 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_100 + vert_110 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_100 + vert_101 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_010 + vert_110 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_010 + vert_011 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_001 + vert_101 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_001 + vert_011 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_110 + vert_111 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_101 + vert_111 + [radius] + [1,1,1] + [1,1,1])
 
−
  cell.append(CYLINDER)
 
−
  cell.extend(vert_011 + vert_111 + [radius] + [1,1,1] + [1,1,1]
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_000 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_001 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_010 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_011 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_100 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_101 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_110 + [radius])
 
−
  cell.append(SPHERE)
 
−
  cell.extend(vert_111 + [radius])
 
−
 
 
−
  cmd.load_cgo(cell,"cell")
 
−
  #return cell
 
−
 
 
−
  if mode == 1:
 
−
    text = [COLOR, 1.0, 0.0, 1.0,]
 
−
 
 
−
  #wire_text(text,plain,[-5.,-5.,-1],'Origin',[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
 
−
  #wire_text(text,plain,map(None,U.orthogonalize((1.05,0.0,0.0))),'A',[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
 
−
  #wire_text(text,plain,map(None,U.orthogonalize((0.0,1.05,0.0))),'B',[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
 
−
  #wire_text(text,plain,map(None,U.orthogonalize((0.0,0.0,1.05))),'C',[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
 
−
 
 
−
    cyl_text(text,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]],color=[1.0,0.0,1.0])
 
−
    cyl_text(text,plain,map(None,U.orthogonalize((1.05,0.0,0.0))),'A',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]],color=[1.0,0.0,0.0])
 
−
    cyl_text(text,plain,map(None,U.orthogonalize((0.0,1.05,0.0))),'B',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]],color=[0.0,1.0,0.0])
 
−
    cyl_text(text,plain,map(None,U.orthogonalize((0.0,0.0,1.05))),'C',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]],color=[0.0,0.0,1.0])
 
−
 
 
−
    cmd.load_cgo(text,'text')
 
−
 
 
−
 
 
−
#AXES DRAWING
 
−
#! /usr/bin/env python
 
−
# Copyright (c) 2004 Robert L. Campbell
 
−
 
 
−
#import math
 
−
 
 
−
def set_to_zero(a):
 
−
  if abs(a) < 1e-10:
 
−
    a=0
 
−
  return a
 
−
 
 
−
def draw_symbol(start,end,symb,color,radius=0.2):
 
−
  degtorad = N.pi/180.
 
−
  costhirty = N.cos(30.0*degtorad)
 
−
  sinthirty = N.sin(30.0*degtorad)
 
−
  symb_obj = []
 
−
 
 
−
  if symb in ('2', '2^1'):
 
−
    pass
 
−
 
 
−
  elif symb in ('3', '3^1', '3^2'):
 
−
    symb_obj = [ BEGIN, TRIANGLES, COLOR ] + color
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([radius, 0, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([-radius*sinthirty, radius*costhirty, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([-radius*sinthirty, -radius*costhirty, 0]))[0].tolist())
 
−
 
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([radius, 0, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([-radius*sinthirty, radius*costhirty, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([-radius*sinthirty, -radius*costhirty, 0]))[0].tolist())
 
−
    symb_obj.append(END)
 
−
 
 
−
  elif symb in ('4', '4^1', '4^2', '4^3'):
 
−
    symb_obj = [ BEGIN, TRIANGLES, COLOR ] + color
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([-radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([-radius, -radius, 0]))[0].tolist())
 
−
 
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([radius, -radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([start]) + N.array([-radius, -radius, 0]))[0].tolist())
 
−
 
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([-radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([-radius, -radius, 0]))[0].tolist())
 
−
 
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([radius, radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([radius, -radius, 0]))[0].tolist())
 
−
    symb_obj.append(VERTEX)
 
−
    symb_obj.extend((N.array([end]) + N.array([-radius, -radius, 0]))[0].tolist())
 
−
    symb_obj.append(END)
 
−
 
 
−
  elif symb in ('6', '6^1', '6^2', '6^3', '6^4', '6^5'):
 
−
    # hexagons still need to be created :)
 
−
    pass
 
−
 
 
−
  return symb_obj
 
−
 
 
−
def draw_symops(obj,radius=0.2,extension=0):
 
−
  """
 
−
  From pymol issue the "run draw_symops_cctbx.py" command to load the script,
 
−
  then issue the "draw_symops(object,<optional radius>,<optional extension>)" command
 
−
  to actually run it and create the cgo object.
 
−
 
 
−
  e.g. load 1avv.pdb
 
−
      run draw_symops_cctbx.py
 
−
      draw_symops 1avv, 0.5, .2 
 
−
        or draw_symops('1avv',.5,.2)
 
−
        or draw_symops 1avv, radius=.5, extension=.2
 
−
 
 
−
  The different axis types appear as different objects on the PyMOL menu so they can be turned
 
−
  on and off individually.
 
−
 
 
−
  See also help(draw_symops_param) to draw operators by specifying the space group
 
−
  and cell dimensions directly (i.e. not loaded from a pdb file)
 
−
 
 
−
  The 'extension' parameter is a fractional increase in the length of each symmetry
 
−
  operator axis drawn.  i.e. a value of 0 is the default and a value of .2 increases
 
−
  the length by 20% at each end
 
−
  """
 
−
  radius=float(radius)
 
−
  extension=float(extension)
 
−
  cell_info=cmd.get_symmetry(obj)
 
−
  draw_symops_param(cell_info[0:6],cell_info[6],radius,extension)
 
−
 
 
−
def draw_symops_param(cell_param_list,sg,radius=0.2,extension=0):
 
−
  """
 
−
  If you wish to draw the symmetry operators for any cell without the need to load a
 
−
  pdb file, then do this:
 
−
 
 
−
  e.g. run draw_symops_cctbx.py
 
−
      draw_symops_param((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5,0.1)
 
−
 
 
−
  to generate the symmetry operators for this trigonal space group "p 31 2 1"
 
−
  of radius .5 with 10% added as an extension at each end.
 
−
  """
 
−
  radius=float(radius)
 
−
  extension=float(extension)
 
−
 
 
−
  U=uctbx.unit_cell((cell_param_list))
 
−
 
 
−
#rotation axes
 
−
#    "2" "yellow",
 
−
#    "3" "orange",
 
−
#    "4" "mauve",
 
−
#    "6" "purple",
 
−
 
 
−
#screw axes (all sub_1 axes are green)
 
−
#    "21" "green",
 
−
#    "31" "green",
 
−
#    "32" "lime",
 
−
#    "41" "green",
 
−
#    "42" "cyan",
 
−
#    "43" "iceblue",
 
−
#    "61" "green",
 
−
#    "62" "silver",
 
−
#    "63" "cyan",
 
−
#    "64" "iceblue",
 
−
#    "65" "blue",
 
−
 
 
−
  color = {
 
−
    "2" : [1.0, 1.0, 0.0],
 
−
    "3" : [1.0, 0.5, 0.0],
 
−
    "4" : [1.0, 0.5, 1.0],
 
−
    "6" : [1.0, 0.0, 1.0],
 
−
    "2^1" : [0.0, 1.0, 0.0],
 
−
    "3^1" : [0.0, 1.0, 0.0],
 
−
    "3^2" : [0.5, 1.0, 0.5],
 
−
    "4^1" : [0.0, 1.0, 0.0],
 
−
    "4^2" : [0.0, 1.0, 1.0],
 
−
    "4^3" : [0.5, 0.5, 1.0],
 
−
    "6^1" : [0.0, 1.0, 0.0],
 
−
    "6^2" : [0.8, 0.8, 0.8],
 
−
    "6^3" : [0.0, 1.0, 1.0],
 
−
    "6^4" : [0.5, 0.5, 1.0],
 
−
    "6^5" : [0.0, 0.0, 1.0],
 
−
    }
 
−
 
 
−
  sg = sg.upper()
 
−
  symop_axes = get_all_axes(sg,extension=extension)
 
−
 
 
−
  #CYLINDER = 'CYLINDER'
 
−
  ax_obj = {}
 
−
  #vert_obj = []
 
−
 
 
−
  #debug_out = open('debug.log','w')
 
−
 
 
−
  if symop_axes:
 
−
    for ax in symop_axes:
 
−
      #print ax
 
−
      start = map(set_to_zero,U.orthogonalize(list(ax['start'])))
 
−
      end = map(set_to_zero,U.orthogonalize(list(ax['end'])))
 
−
###############################################################################
 
−
# Tried rounding off start and end values in order to understand why axes go
 
−
# missing in the drawing, but seem to be present in the cgo.  Doesn't help!
 
−
# e.g. for space group 'p23' one of the 3-fold rotations is missing (0,0,0 -> x,-x,x)
 
−
# changing one cell axis to something ever so slightly different recovers the axis
 
−
# e.g. set cell to be (30.00001,30.,30.,90.,90.,90) and it works!
 
−
#    start = map(lambda x: round(x,3),U.orthogonalize(ax['start']))
 
−
#    end = map(lambda x: round(x,3),U.orthogonalize(ax['end']))
 
−
###############################################################################
 
−
      symb_ax = ax['symb']
 
−
      color_ax = color[symb_ax]
 
−
 
 
−
      #print "axis: ",symb_ax, start, end
 
−
      if symb_ax in ax_obj:
 
−
        ax_obj[symb_ax].append(CYLINDER)
 
−
      else:
 
−
        ax_obj[symb_ax] = [CYLINDER]
 
−
 
 
−
      ax_obj[symb_ax].extend(start + end + [radius])
 
−
      ax_obj[symb_ax].extend(color[symb_ax] + color[symb_ax])
 
−
      ax_obj[symb_ax].extend(draw_symbol(start,end,symb_ax,color[symb_ax],radius*6.))
 
−
 
 
−
#  #######################################################################################
 
−
#    # Debugging output to try to understand why some axes go missing in the drawing.
 
−
#    # They don't appear to be missing from the cgo object, though!
 
−
#    for xxx in ax_obj[symb_ax]:
 
−
#      if xxx == 9.0:
 
−
#        #print "\n\n",xxx
 
−
#        xxx = "\n\n" + str(xxx) + " "
 
−
#        debug_out.write(xxx)
 
−
#      else:
 
−
#        #print xxx
 
−
#        #xxx = "\n" + str(xxx) + " "
 
−
#        xxx = str(xxx) + " "
 
−
#        debug_out.write(xxx)
 
−
#      #print ax_obj[symb_ax]
 
−
#  debug_out.write("\n\n")
 
−
#  big_string = str(ax_obj)
 
−
#  debug_out.write(big_string)
 
−
#  # End of debugging output
 
−
#  #######################################################################################
 
−
 
 
−
  else:
 
−
    print "\nNo symmetry axes found for this space group: %s\n" % sg
 
−
 
 
−
  for key,val in ax_obj.items():
 
−
    name=sg + "_" + key
 
−
    cmd.load_cgo(val,name)
 
−
    #debug_out.write("\n\n" + key + "\n" + str(val))
 
−
  #return ax_obj
 
−
 
 
−
#cmd.extend("draw_symops_param",draw_symops_param)
 
−
 
 
−
#! /usr/bin/env python
 
−
# List all axes in the unit cell.
 
−
 
 
−
# usage:
 
−
#  python all_axes.py     - show axes for the 230 reference settings.
 
−
#  python all_axes.py P2  - show axes for (e.g.) space group P2
 
−
 
 
−
# RWGK = Ralf W. Grosse-Kunstleve
 
−
# RWGK Some further refinement is required:
 
−
# RWGK  - List only the axes of highest order (e.g. only 4, not 4 and 2).
 
−
# RWGK  - List only the axes with the smallest intrinsic component
 
−
# RWGK    (e.g. list only 3(1), not both 3(1) and 3(2)).
 
−
# RWGK See also: comment regarding shift_range below.
 
−
 
 
−
def list_plus(lhs, rhs):
 
−
  return [l + r for l, r in zip(lhs, rhs)]
 
−
 
 
−
def list_minus(lhs, rhs):
 
−
  return [l - r for l, r in zip(lhs, rhs)]
 
−
 
 
−
def list_multiplies(lhs, rhs):
 
−
  return [l * r for l, r in zip(lhs, rhs)]
 
−
 
 
−
def list_divides(lhs, rhs):
 
−
  return [l / r for l, r in zip(lhs, rhs)]
 
−
 
 
−
def list_modulus(lhs, rhs):
 
−
  return [l % r for l, r in zip(lhs, rhs)]
 
−
 
 
−
def list_dot_product(lhs, rhs=0):
 
−
  if rhs == 0: rhs = lhs
 
−
  result = 0
 
−
  for l, r in zip(lhs, rhs): result += l * r
 
−
  return result
 
−
 
 
−
def str_ev(EV):
 
−
  return "[%d,%d,%d]" % EV
 
−
 
 
−
###def fract_2_dec(fraction):
 
−
###  list = fraction.split('/')
 
−
###  if len(list) == 2 and list[1] != 0:
 
−
###    decimal = float(list[0])/float(list[1])
 
−
###  else:
 
−
###    decimal = float(fraction)
 
−
###  return decimal
 
−
 
 
−
def rlc_RTMxAnalysis(M):
 
−
  r_info = sgtbx.rot_mx_info(M.r())
 
−
  t_info = sgtbx.translation_part_info(M)
 
−
  t_intrinsic = t_info.intrinsic_part().mod_positive().as_double()
 
−
  t_shift = t_info.origin_shift().mod_positive().as_double()
 
−
 
 
−
  #End = list_plus(Start + map(None,r_info.ev()))
 
−
####debug
 
−
###  trans = 0
 
−
###  length = 0
 
−
####debug
 
−
 
 
−
  #if r_info.type() == 1:
 
−
  if r_info.type() < 2:
 
−
    #(rt, start, end) = ('1',(0,0,0),(0,0,0))
 
−
    return None
 
−
  #elif r_info.type() == -1:
 
−
  #  (rt, start, end) = (str(r_info.type()),t_shift,())
 
−
  elif abs(r_info.type()) == 2:
 
−
    trans = sum(t_intrinsic)
 
−
    if trans == 0:
 
−
      maxr = max([abs(x) for x in r_info.ev()])
 
−
      r = [float(x)/maxr for x in r_info.ev()]
 
−
      (rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
 
−
      #(rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r_info.ev())))
 
−
    else:
 
−
      maxr = max([abs(x) for x in r_info.ev()])
 
−
      r = [float(x)/maxr for x in r_info.ev()]
 
−
      (rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r)))
 
−
      #(rt, start, end) = (str(r_info.type())+"^1",t_shift,tuple(list_plus(t_shift,r_info.ev())))
 
−
  elif r_info.type() == 3:
 
−
    if r_info.sense() >= 0 :
 
−
      # ignore opposite sense of rotation axes since they superimpose
 
−
      trans = N.sqrt(sum((map(lambda x,y:(y-x)*(y-x),(0,0,0),t_intrinsic))))
 
−
#      trans = N.sqrt(t_intrinsic[0]**2 + t_intrinsic[1]**2 + t_intrinsic[2]**2)
 
−
      if trans == 0:
 
−
        maxr = max([abs(x) for x in r_info.ev()])
 
−
        r = [float(x)/maxr for x in r_info.ev()]
 
−
# fudge to make sure that PyMOL actually draws the axis (move it slightly off [1,-1,1]) !!!
 
−
        r[0] = r[0]*1.000001
 
−
        (rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
 
−
        #(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
 
−
      else:
 
−
        maxr = max([abs(x) for x in r_info.ev()])
 
−
        r = [float(x)/maxr for x in r_info.ev()]
 
−
        #(rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
 
−
        (start, end) = (t_shift,tuple(list_plus(t_shift,r)))
 
−
        length = N.sqrt(sum((map(lambda x,y:(y-x)*(y-x),start, end))))
 
−
 
 
−
#  r_info.sense() for 3^1 and 3^2 seems always to be "1" ???
 
−
#        if r_info.sense() < 0:
 
−
#          subscript = str(1-r_info.sense())
 
−
#        else:
 
−
#          subscript = str(r_info.sense())
 
−
 
 
−
# use ratio of trans to length to get the correct axis symbol:
 
−
# fudged the value to get the right numbers. (using length/2., rather than length/3.)
 
−
        if trans < length*0.5 :
 
−
          subscript = '1'
 
−
        else:
 
−
          subscript = '2'
 
−
 
 
−
        rt = str(r_info.type())+ "^" + subscript
 
−
        #(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
 
−
###        print "Type, sense, Start, End, length, trans", rt, r_info.sense(), start, end, length, trans
 
−
#        print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length)
 
−
#        print "(rt, start, end)", (rt,start,end)
 
−
    else:
 
−
      return None
 
−
  #return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
 
−
  elif r_info.sense() > 0:
 
−
    # ignore opposite sense of rotation axes since they superimpose
 
−
    trans = sum(t_intrinsic)
 
−
    if trans == 0:
 
−
      maxr = max([abs(x) for x in r_info.ev()])
 
−
      r = [float(x)/maxr for x in r_info.ev()]
 
−
      (rt, start, end) = (str(r_info.type()),t_shift,tuple(list_plus(t_shift,r)))
 
−
      #(rt, start, end) = (str(r_info.type()),t_shift, tuple(list_plus(t_shift,r_info.ev())))
 
−
    else:
 
−
      maxr = max([abs(x) for x in r_info.ev()])
 
−
      r = [float(x)/maxr for x in r_info.ev()]
 
−
      subscript =  str(int(trans*r_info.type()+.5))  # add 0.5 to fix rounding errors
 
−
      (rt, start, end) = (str(r_info.type())+ "^" + subscript ,t_shift,tuple(list_plus(t_shift,r)))
 
−
      #(rt, start, end) = (str(r_info.type()) + "^" + subscript,t_shift, tuple(list_plus(t_shift,r_info.ev())))
 
−
  #return (r_info.type(),r_info.ev(), t_intrinsic, t_shift)
 
−
  else:
 
−
    return None
 
−
#  print "type: %s, sense: %s, trans: %s, length: %s," % (r_info.type(), r_info.sense(), trans, length),
 
−
#  print "(rt, start, end)", (rt,start,end)
 
−
  return (rt, start, end)
 
−
 
 
−
def get_all_axes(space_group_symbol=None, space_group_info=None, extension=0):
 
−
  assert space_group_symbol is None or space_group_info is None
 
−
  shift_range = 1 # RWGK Works for the 230 reference settings; it is not
 
−
          # RWGK clear to me (rwgk) what value is needed in general.
 
−
  if space_group_symbol is not None:
 
−
    space_group_info = sgtbx.space_group_info(symbol=space_group_symbol)
 
−
  #space_group_info.show_summary()
 
−
 
 
−
  axes_dict = {}
 
−
  for smx in space_group_info.group():
 
−
    r = smx.r()
 
−
    t = smx.t()
 
−
    shift = [0,0,0]
 
−
    for shift[0] in range(-shift_range,shift_range+1):
 
−
      for shift[1] in range(-shift_range,shift_range+1):
 
−
        for shift[2] in range(-shift_range,shift_range+1):
 
−
          ts = t.plus(sgtbx.tr_vec(shift, 1)).new_denominator(t.den())
 
−
          m = sgtbx.rt_mx(r, ts)
 
−
          #print m
 
−
          rtmxanal = rlc_RTMxAnalysis(m)
 
−
          #print r, t, shift, ts, m
 
−
          if rtmxanal:
 
−
            #print rtmxanal
 
−
            axes_dict[rtmxanal] = 0
 
−
  axes_list = axes_dict.keys()
 
−
  axes_list.sort()
 
−
 
 
−
  # reject nonenantiomorphic space groups
 
−
  if len(axes_list) > 0 and not re.compile("[A-z]").search(space_group_symbol[1:]):
 
−
    try:
 
−
      sgtbx.space_group_info(space_group_symbol).show_summary(),
 
−
      #print len(axes_list), space_group_symbol
 
−
    except:
 
−
      print space_group, space_group_symbol
 
−
      print
 
−
      sys.exit(1)
 
−
    axes = []
 
−
    for a in axes_list:
 
−
      if len(a) == 3 and len(a[1]) == 3 and len(a[2]) == 3:
 
−
        tmp_dict = {}
 
−
        print "%4s %7.4f %7.4f %7.4f    %7.4f %7.4f %7.4f " % (a[0],a[1][0],a[1][1],a[1][2],a[2][0],a[2][1],a[2][2])
 
−
        tmp_dict['symb'] = a[0]
 
−
        start_array = N.asarray(a[1])
 
−
        end_array = N.asarray(a[2])
 
−
        start_vec = start_array - (end_array - start_array)*extension
 
−
        end_vec = end_array + (end_array - start_array)*extension
 
−
        tmp_dict['start'] = start_vec
 
−
        tmp_dict['end'] = end_vec
 
−
#rlc#        tmp_dict['start'] = a[1]
 
−
#rlc#        tmp_dict['end'] = a[2]
 
−
        axes.append(tmp_dict)
 
−
      else:
 
−
        print a
 
−
  else:
 
−
    return None
 
−
 
 
−
  return axes
 
−
 
 
−
if __name__ == "__main__":
 
−
  import sys
 
−
  if len(sys.argv) == 1:
 
−
    for i in range(230):
 
−
      get_all_axes(i + 1)
 
−
  else:
 
−
    for symbol in sys.argv[1:]:
 
−
      get_all_axes(symbol)
 
−
</source>
 
  
 
[[Category:Electron_Density]]
 
[[Category:Electron_Density]]
 
[[Category:Maps]]
 
[[Category:Maps]]
 
[[Category:Plugins]]
 
[[Category:Plugins]]

Revision as of 09:35, 1 July 2020

This page contains source files for the SuperSym plugin. For documentation and use instructions, see SuperSym.

Source Code

See https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/SuperSymPlugin.py

Retrieved from "http://wiki.pymol.org/index.php?title=SuperSymSource&oldid=14772"