def testLabel(self, func):
cmd.pseudoatom('m1')
for expr in expr_list + ['resn + " " + resi']:
func('*', expr)
self.assertEqualIterate('label', expr)
func()
self.assertTrueIterate('label == ""')
def createPseudoatom (coordinates, objectName):
x=float(coordinates[0])
y=float(coordinates[1])
z=float(coordinates[2])
#print x,y,z,objectName
posString="[%3.2f,%3.2f,%3.2f]" % (x,y,z)
cmd.pseudoatom(pos=posString, object=objectName)
def testLabelPositionZ(self, use_shaders, ray):
'''
Test label z position for regular labels
'''
if not ray and invocation.options.no_gui:
self.skipTest('no gui')
cmd.set('use_shaders', use_shaders)
cmd.viewport(200, 200)
cmd.pseudoatom('m1', vdw=10, label='X')
cmd.zoom(buffer=12)
cmd.show('spheres')
cmd.color('blue')
cmd.set('label_color', 'red')
cmd.set('label_size', 20)
cmd.set('label_font_id', 7) # bold
self.ambientOnly()
# label outside of sphere
cmd.set('label_position', [0, 0, 11.1])
img = self.get_imagearray(ray=ray)
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img, delta=20)
# label inside of sphere
cmd.set('label_position', [0, 0, 10.5])
img = self.get_imagearray(ray=ray)
self.assertImageHasColor('blue', img)
self.assertImageHasNotColor('red', img, delta=20)
def test_atom_state_settings_3f(self, f, data):
m1 = "pseudo01"
lp1, lp2 = lp = map(f, data)
cmd.pseudoatom(m1)
cmd.pseudoatom(m1)
cmd.create(m1, m1, 1, 2)
stored.pos = {}
stored.lp1 = lp1
stored.lp2 = lp2
stored.origp = None
# get origp (should be 0.,0.,0.
cmd.alter("(index 1)", "stored.origp = s['label_placement_offset']")
# change atom-state setting to lp1 for atom in both states
cmd.alter_state(0, "(index 1)", "s['label_placement_offset']=stored.lp1")
# change atom-level setting for all atoms to something else
cmd.alter("all", "s['label_placement_offset']=stored.lp2")
# get atom-state settings
cmd.iterate_state(0, "all", "stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']")
# atom-state setting should be lp1 for atom 1
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
# atom setting should override to lp2 for atom 2 in both states
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 2, 2)])
# unset all atom-level settings, atom-state settings should still exist
cmd.alter("all", "s['label_placement_offset']=None")
stored.pos = {}
cmd.iterate_state(0, "all", "stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']")
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
self.assertEqual(tuple(stored.origp), stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(stored.origp), stored.pos['%s-%s-%s' % (m1, 2, 2)])
def test(self):
cmd.set('suspend_updates')
cmd.set('depth_cue', 0)
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('stereo_angle', 10)
cmd.pseudoatom()
cmd.show_as('sphere')
cmd.zoom()
cmd.stereo('anaglyph')
cmd.set('suspend_updates', 0)
wh = (40, 40)
cmd.draw(*wh, antialias=0)
cmd.sync()
img = self.get_imagearray(prior=1)
self.assertEqual(wh, img.shape[:2])
# ray tracing and shaders in PyMOL 1.7.6+:
# 0xe50000
# 0x00e5e5
# -> delta=26 (0x1a)
self.assertImageHasColor('0xff0000', img, delta=0x1a)
self.assertImageHasColor('0x00ffff', img, delta=0x1a)
def testLabelRelativeMode(self):
# +-----+-----+
# | | |
# +-----+-----+
# | XYZ | |
# +-----+-----|
self.ambientOnly()
cmd.set('opaque_background')
cmd.set('label_font_id', 7) # bold
cmd.set('label_color', 'white')
cmd.set('label_size', -1) # Angstrom sized
cmd.pseudoatom('m1', label="XYZ")
cmd.zoom()
width = 400
height = 200
w4 = width // 4
h4 = height // 4
cmd.viewport(width, height)
for x in (-1, 1):
for y in (-1, 1):
# relative position
cmd.set('label_relative_mode', 1)
cmd.set('label_screen_point', (0.5 * x, 0.5 * y, 0))
self.assertColorInQuadrant(x, y, width, height)
# absolute position in pixels
cmd.set('label_relative_mode', 2)
cmd.set('label_screen_point', ((2 + x) * w4, (2 + y) * h4, 0))
self.assertColorInQuadrant(x, y, width, height)
def test_wildcard_sets_ranges(self):
for i in range(10): cmd.pseudoatom('m%d' % i, chain=chr(65 + i))
cmd.alter('m5', 'chain = "AB"')
cmd.alter('m6', 'chain = "BA"')
cmd.alter('m7', 'chain = "CC"')
cmd.alter('m8', 'chain = "ZA"')
cmd.alter('m9', 'chain = "ABA"')
# A patterns
self.assertEqual(1, cmd.count_atoms('chain A'))
self.assertEqual(3, cmd.count_atoms('chain A*'))
self.assertEqual(4, cmd.count_atoms('chain *A'))
self.assertEqual(5, cmd.count_atoms('chain *A*'))
self.assertEqual(1, cmd.count_atoms('chain A*A'))
# B patterns
self.assertEqual(2, cmd.count_atoms('chain B*'))
self.assertEqual(2, cmd.count_atoms('chain *B'))
self.assertEqual(4, cmd.count_atoms('chain *B*'))
# X patterns (no matches)
self.assertEqual(0, cmd.count_atoms('chain X*'))
self.assertEqual(0, cmd.count_atoms('chain *X'))
self.assertEqual(0, cmd.count_atoms('chain *X*'))
# list with wildcards
self.assertEqual(5, cmd.count_atoms('chain B*+A*'))
self.assertEqual(3, cmd.count_atoms('chain B*+A*A'))
self.assertEqual(3, cmd.count_atoms('chain B*+A*A+*X'))
# lexicographical alpha ranges, A:C, will match AB (A <= AB <= C) but not CC (C < CC)
# no wildcards in alpha ranges possible
self.assertEqual(6, cmd.count_atoms('chain A:C'))
self.assertEqual(6, cmd.count_atoms('chain A:CA'))
self.assertEqual(7, cmd.count_atoms('chain A:CX')) # include CC
self.assertEqual(6, cmd.count_atoms('chain A:C+Z'))
self.assertEqual(7, cmd.count_atoms('chain A:C+Z*'))
def DisplaySphere(self):
try:
# Display the Sphere
cmd.delete(self.SphereDisplay)
cmd.refresh()
except:
pass
try:
cmd.pseudoatom(self.SphereDisplay,
pos=self.SphereView.Center,
vdw=self.SphereView.Radius,
state=self.State)
cmd.refresh()
cmd.color('oxygen', self.SphereDisplay)
cmd.refresh()
cmd.hide('everything', self.SphereDisplay)
cmd.refresh()
cmd.show('spheres', self.SphereDisplay)
cmd.refresh()
except:
self.ErrorCode = 1
return self.ErrorCode
def testDoNotDuplicateGroup(self):
cmd.pseudoatom("m3")
cmd.group("g1", "m3")
cmd.load("PYMOL-772-example.pse.gz", partial=1)
v = cmd.get_names()
self.assertEqual(v, ["m3", "g1", "m1", "m2"])
def show_points(points, color = [1.0, 0.0, 0.0], selection='all', name = 'samples', labels=[]):
view = cmd.get_view(quiet=not DEBUG)
# adjust radius to size of bounding box
bb = cmd.get_extent(selection, quiet=not DEBUG)
ll = vec3(bb[0])
tr = vec3(bb[1])
diag = tr - ll
r = diag.length() / 2.0
# origin of rotation in model space
#o = vec3(view[12:15])
c = com.COM(selection)
o = vec3(c)
#spheres = [BEGIN, TRIANGLE_STRIP]
spheres = [COLOR]
spheres.extend(color)
i = 0.0
j = 0
for p in points:
#spheres.extend([COLOR, 1.0, 1 - scaled_value, 1 - scaled_value])
spheres.extend([SPHERE, o[0]+r*p[0], o[1]+r*p[1], o[2]+r*p[2], 1.25])
#drawVector(o, o + r * vec3(p))
#spheres.extend([VERTEX, o[0]+r*p[0], o[1]+r*p[1], o[2]+r*p[2]])
#i += 1.0/len(values)
l = 1.1
if (len(labels) > j):
cmd.pseudoatom(labels[j] + "_label", pos = [o[0]+l * r*p[0], o[1]+l*r*p[1], o[2]+l*r*p[2], 1.25], label = labels[j])
j += 1
#spheres.extend([END])
cmd.load_cgo(spheres, name, 1)
def com(selection,state=None,mass=None,object=None, quiet=1, **kwargs):
"""
DESCRIPTION
Places a pseudoatom at the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
SEE ALSO
pseudoatom, get_com
"""
quiet = int(quiet)
if (object == None):
object = cmd.get_legal_name(selection)
object = cmd.get_unused_name(object + "_COM", 0)
cmd.delete(object)
if (state != None):
x, y, z=get_com(selection,mass=mass, quiet=quiet)
if not quiet:
print "%f %f %f" % (x, y, z)
cmd.pseudoatom(object,pos=[x, y, z], **kwargs)
cmd.show("spheres",object)
else:
for i in range(cmd.count_states()):
x, y, z=get_com(selection,mass=mass,state=i+1, quiet=quiet)
if not quiet:
print "State %d:%f %f %f" % (i+1, x, y, z)
cmd.pseudoatom(object,pos=[x, y, z],state=i+1, **kwargs)
cmd.show("spheres", 'last ' + object)
def load_net():
file_coors = open_it()
i = 0
for line in open(file_coors, "r"):
coors_net = map(float, line.split())
i = i + 1
cmd.pseudoatom("net", pos=coors_net, name="node", resi=i, chain="A")
def testDel(self):
cmd.pseudoatom('m1')
stored.keys = []
cmd.alter('all', 'p.foo = 123')
cmd.alter('all', 'p.bar = "Hello World"')
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, ['bar', 'foo'])
stored.keys = []
cmd.alter('all', "del p['foo']")
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, ['bar'])
stored.keys = []
cmd.alter('all', "p.bar = None")
cmd.iterate('all', 'stored.keys = list(sorted(p.all))')
self.assertEqual(stored.keys, [])
# object-level
cmd.set_property('bla', 456, 'm1')
stored.keys = cmd.get_property_list('m1')
self.assertEqual(stored.keys, ['bla'])
cmd.set_property('bla', None, 'm1')
stored.keys = cmd.get_property_list('m1')
self.assertEqual(stored.keys, [])
def test_sort(self):
cmd.pseudoatom('m1', name='PS2')
cmd.pseudoatom('m1', name='PS1')
v = [a.name for a in cmd.get_model().atom]
self.assertEqual(['PS2', 'PS1'], v)
cmd.sort()
v = [a.name for a in cmd.get_model().atom]
self.assertEqual(['PS1', 'PS2'], v)
def test_attach(self):
cmd.pseudoatom()
cmd.edit('first all')
cmd.attach('C', 1, 1)
self.assertEqual(2, cmd.count_atoms())
cmd.attach('C', 1, 1)
self.assertEqual(3, cmd.count_atoms())
self.assertEqual(['C01', 'C02', 'PS1'], sorted(get_atom_names()))
def test_set_object_ttt(self):
M = [1.0, 0.0, 0.0, 0.0,
0.0, 0.0,-1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.pseudoatom('m1')
cmd.set_object_ttt('m1', M)
self.assertArrayEqual(M, cmd.get_object_matrix('m1'), 1e-4)
def test_sort(self):
cmd.pseudoatom('m1', name='PS2')
cmd.pseudoatom('m1', name='PS1')
cmd.alter('all', 'name = name_list.pop()', space={'name_list': ['PS1', 'PS2']})
v = [a.name for a in cmd.get_model().atom]
self.assertEqual(['PS2', 'PS1'], v)
cmd.sort()
v = [a.name for a in cmd.get_model().atom]
self.assertEqual(['PS1', 'PS2'], v)
def testDirtyDelete(self):
cmd.pseudoatom('m1')
cmd.pseudoatom('m2')
cmd.group('g1', 'm1 m2')
cmd.set_wizard(MockWizard())
cmd.draw()
v = cmd.get_object_list('(g1)')
self.assertEqual(v, ['m1', 'm2'])
def highlight_Atom(self, atom):
try:
cmd.pseudoatom(self.AtomDisplay, pos=atom[5:], vdw=0.30, color='white')
cmd.hide('nonbonded', self.AtomDisplay)
cmd.show('spheres', self.AtomDisplay)
cmd.mask(self.AtomDisplay)
except:
self.FlexAID.DisplayMessage("Failed to highlight atom upon selecting atom", 1)
return
def testAlter(self):
cmd.pseudoatom('m1')
for ptype, names in self.alter_names_atomic.items():
stored.v_mock = tuple(map(ptype, range(len(names))))
names_fmt = '(' + ','.join(names) + ',)'
if not (cmd.alter('all', names_fmt + ' = stored.v_mock') and
cmd.iterate('all', 'stored.v_names = ' + names_fmt)):
raise UserWarning('iterate failed')
self.assertEqual(stored.v_names, stored.v_mock)
def testPngExists(self):
'''
Save a PNG image with width/height specified and
check if the file exists.
'''
cmd.pseudoatom('m1')
cmd.show('spheres')
with testing.mktemp('.png') as filename:
cmd.png(filename, width=100, height=100, ray=0)
cmd.draw()
self.assertTrue(os.path.exists(filename), 'png file not written')
def drawAnnote(self, axis, x, y, annote):
# EDIT: remove last markers
for markers in self.drawnAnnotations.itervalues():
for m in markers: # tuple
#m.set_visible(not m.get_visible())
m.remove()
self.axis.figure.canvas.draw()
self.drawnAnnotations = {}
if (x,y) in self.drawnAnnotations:
markers = self.drawnAnnotations[(x,y)]
for m in markers:
m.set_visible(not m.get_visible())
self.axis.figure.canvas.draw()
else:
"""
Mark data point and show data
"""
t = axis.text(x,y, "(%3.2f, %3.2f)"%(x,y), )
m = axis.scatter([x],[y], marker='d', c='r', zorder=100)
self.drawnAnnotations[(x,y)] =(t,m)
self.axis.figure.canvas.draw()
"""Your code here!"""
cmd.delete('all')
# load pdb files
pdb_ext = '.pdb'
cmd.load(self.native)
cmd.load(os.path.join(self.pdb_dir, annote + pdb_ext))
# label
cmd.pseudoatom('foo')
cmd.hide('all')
#cmd.label('foo', '"'+annote+'"')
# color
native_name = os.path.splitext(os.path.basename(self.native))[0]
cmd.color('green', native_name)
cmd.set('label_color', 'green', native_name)
cmd.color('blue', annote)
cmd.set('label_color', 'blue', annote)
cmd.set('label_color', 'blue', 'foo')
# background
cmd.bg_color("white")
cmd.set("depth_cue", 0)
cmd.set("ray_trace_fog", 0)
# view
cmd.show(representation='cartoon')
# alignment
cmd.super(annote, native_name)
# zoom
cmd.zoom()
def test_set_object_settings_3f(self, f, data):
m1 = "pseudo01"
m2 = "pseudo02"
cmd.pseudoatom(m1)
cmd.pseudoatom(m2)
lp1, lp2 = lp = map(f, data)
cmd.set("label_position", lp1, m1)
cmd.set("label_position", lp2, m2)
stored.pos = {}
cmd.iterate("all", "stored.pos[model]=s['label_position']")
self.assertEqual(tuple(lp1), stored.pos[m1])
self.assertEqual(tuple(lp2), stored.pos[m2])
def testIterate(self):
cmd.pseudoatom('m1')
for ptype, names in (
list(self.alter_names_atomic.items()) +
list(self.alter_names_atomic_special.items())):
stored.v_names = None
cmd.iterate('all', 'stored.v_names = [' + ','.join(names) + ']')
self.assertNotEqual(stored.v_names, None)
for v in stored.v_names:
self.assertTrue(isinstance(v, ptype))
def test_unsetting_atom_setting(self, f, data):
m1 = "pseudo01"
lp = f(data)
cmd.pseudoatom(m1)
stored.lp = lp
stored.pos = {}
cmd.iterate("all", "stored.pos['%s-%s' % (model, index)] = s['label_placement_offset']")
cmd.alter("all", "s['label_placement_offset']=stored.lp")
stored.pos2 = {}
cmd.alter("all", "s['label_placement_offset']=None")
cmd.iterate("all", "stored.pos2['%s-%s' % (model, index)] = s['label_placement_offset']")
self.assertEqual(stored.pos, stored.pos2)
def test_set_symmetry(self):
sym = [68.7, 126.8, 184.0, 90.0, 90.0, 90.0, 'P 21 21 21']
cmd.pseudoatom('m1')
cmd.set_symmetry('m1', *sym)
v = cmd.get_symmetry('m1')
self.assertEqual(v[-1], sym[-1])
self.assertArrayEqual(v[:-1], sym[:-1], 1e-4)
cmd.pseudoatom('m2')
cmd.symmetry_copy('m1', 'm2')
v = cmd.get_symmetry('m2')
self.assertEqual(v[-1], sym[-1])
self.assertArrayEqual(v[:-1], sym[:-1], 1e-4)
def test_protect(self):
cmd.pseudoatom('m1', pos=[0.,0.,0.])
cmd.pseudoatom('m1', pos=[1.,0.,0.])
cmd.protect('m1`1')
cmd.translate([0.,1.,0.])
self.assertEqual([0.,0.,0.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1.,1.,0.], cmd.get_atom_coords('m1`2'))
cmd.deprotect()
cmd.translate([0.,0.,1.])
self.assertEqual([0.,0.,1.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1.,1.,1.], cmd.get_atom_coords('m1`2'))
def test(self):
for i in range(100):
cmd.pseudoatom('xxxxxxxxxx%04d' % i)
setting = 'sphere_color'
color = 'blue'
name = 'xxxxxxxxxx0005'
cmd.set(setting, color, name)
self.assertEqual(cmd.get(setting, name), color)
# crashes in 1.7.6.0 to 1.7.6.6
util.color_deep('red', 'all')
self.assertEqual(cmd.get(setting, name), 'default')
def test(self):
names_ungrouped = ['a0', 'a1', 'b0', 'b1', 'c0', 'c1', 'g1']
names_grouped = ['a0', 'a1', 'c0', 'c1', 'b0', 'g1', 'b1']
for name in names_ungrouped[:-1]:
cmd.pseudoatom(name)
cmd.group(names_ungrouped[-1])
self.assertEqual(cmd.get_names(), names_ungrouped)
cmd.group('g1', 'b*')
cmd.order('b0 g1', location="upper")
self.assertEqual(cmd.get_names(), names_grouped)
def load_net():
file_coors= open_it()
net=network(file_coors)
for ii in range(net.num_nodes):
cmd.pseudoatom('net',pos=net.node[ii].coors,resi=ii,chain='A')
selec='resi '+str(ii)
cmd.alter(selec,'resn='+'"'+net.node[ii].label+'"')
cmd.label(selec,'"'+net.node[ii].label+'"')
cmd.alter(selec,'b='+str(net.node[ii].weight))
cmd.alter(selec,'q='+str(net.node[ii].cluster))
for ii in range(net.num_nodes):
for jj in net.node[ii].link.keys():
cmd.bond('resi '+str(ii),'resi '+str(jj))
cmd.spectrum('b','blue_red')
##cmd.show ('spheres', 'clauc2h2')
cmd.load('this.cube')
cmd.isosurface('sp', 'this', 0.005)
cmd.color('gray90', 'sp')
cmd.isosurface('sm', 'this', -0.005)
cmd.color('red', 'sm')
#cmd.set ('label_font_id', 16)
#cmd.set ('label_size', 24)
#cmd.pseudoatom('xatom', pos=[1,0,0], label="x")
#cmd.pseudoatom('yatom', pos=[0,1,0], label="y")
#cmd.pseudoatom('zatom', pos=[0,0,2], label="z")
cmd.set('label_font_id', 16)
cmd.set('label_size', 20)
cmd.pseudoatom('xatom', pos=[2.5, 0, 0], label="x")
cmd.pseudoatom('yatom', pos=[0, 2.5, 0], label="y")
cmd.pseudoatom('zatom', pos=[0, 0, 5.5], label="z")
cmd.set('ray_opaque_background', 'off')
cmd.set('transparency', 0.50)
cmd.set_view('\
-0.086753346, 0.836276770, 0.541441798,\
0.670052588, -0.353231400, 0.652936995,\
0.737265468, 0.419426382, -0.529700875,\
0.000000000, 0.000000000, -34.167503357,\
0.108778238, 0.131587982, 2.662951946,\
26.937919617, 41.397087097, -20.000000000')
cmd.pseudoatom('latom', pos=[3.5, -2.5, 0], label=" ")
def angle_between_domains(selection1,
selection2,
method='align',
state1=STATE,
state2=STATE,
visualize=1,
quiet=1):
'''
DESCRIPTION
Angle by which a molecular selection would be rotated when superposing
on a selection2.
Do not use for measuring angle between helices, since the alignment of
the helices might involve a rotation around the helix axis, which will
result in a larger angle compared to the angle between helix axes.
USAGE
angle_between_domains selection1, selection2 [, method ]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: alignment command like "align" or "super" {default: align}
EXAMPLE
fetch 3iplA 3iplB, async=0
select domain1, resi 1-391
select domain2, resi 392-475
align 3iplA and domain1, 3iplB and domain1
angle_between_domains 3iplA and domain2, 3iplB and domain2
SEE ALSO
align, super, angle_between_helices
'''
import math
try:
import numpy
except ImportError:
print(' Error: numpy not available')
raise CmdException
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
if cmd.is_string(method):
try:
method = cmd.keyword[method][0]
except KeyError:
print('no such method:', method)
raise CmdException
mobile_tmp = get_unused_name('_')
cmd.create(mobile_tmp, selection1, state1, 1, zoom=0)
try:
method(mobile=mobile_tmp,
target=selection2,
mobile_state=1,
target_state=state2,
quiet=quiet)
mat = cmd.get_object_matrix(mobile_tmp)
except:
print(' Error: superposition with method "%s" failed' %
(method.__name__))
raise CmdException
finally:
cmd.delete(mobile_tmp)
try:
# Based on transformations.rotation_from_matrix
# Copyright (c) 2006-2012, Christoph Gohlke
R33 = [mat[i:i + 3] for i in [0, 4, 8]]
R33 = numpy.array(R33, float)
# direction: unit eigenvector of R33 corresponding to eigenvalue of 1
w, W = numpy.linalg.eig(R33.T)
i = w.real.argmax()
direction = W[:, i].real
# rotation angle depending on direction
m = direction.argmax()
i, j, k, l = [[2, 1, 1, 2], [0, 2, 0, 2], [1, 0, 0, 1]][m]
cosa = (R33.trace() - 1.0) / 2.0
sina = (R33[i, j] +
(cosa - 1.0) * direction[k] * direction[l]) / direction[m]
angle = math.atan2(sina, cosa)
angle = abs(math.degrees(angle))
except:
print(' Error: rotation from matrix failed')
raise CmdException
if not quiet:
try:
# make this import optional to support running this script standalone
from .querying import centerofmass, gyradius
except (ValueError, ImportError):
gyradius = None
try:
# PyMOL 1.7.1.6+
centerofmass = cmd.centerofmass
except AttributeError:
centerofmass = lambda s: cpv.scale(cpv.add(*cmd.get_extent(s)),
0.5)
center1 = centerofmass(selection1)
center2 = centerofmass(selection2)
print(' Angle: %.2f deg, Displacement: %.2f angstrom' %
(angle, cpv.distance(center1, center2)))
if visualize:
center1 = numpy.array(center1, float)
center2 = numpy.array(center2, float)
center = (center1 + center2) / 2.0
if gyradius is not None:
rg = numpy.array(gyradius(selection1), float)
else:
rg = 10.0
h1 = numpy.cross(center2 - center1, direction)
h2 = numpy.dot(R33, h1)
h1 *= rg / cpv.length(h1)
h2 *= rg / cpv.length(h2)
for pos in [center1, center2, center1 + h1, center1 + h2]:
cmd.pseudoatom(mobile_tmp, pos=list(pos), state=1)
# measurement object for angle and displacement
name = get_unused_name('measurement')
cmd.distance(name, *['%s`%d' % (mobile_tmp, i) for i in [1, 2]])
cmd.angle(name, *['%s`%d' % (mobile_tmp, i) for i in [3, 1, 4]])
# CGO arrow for axis of rotation
visualize_orientation(direction, center1, rg, color='blue')
cmd.delete(mobile_tmp)
return angle
def test_unpick(self):
cmd.pseudoatom('m1')
cmd.edit('m1')
cmd.unpick()
self.assertTrue('pk1' not in cmd.get_names('selections'))
#get coordinates from ligand and mol file complex
pos_halligand = get_pos("halligand")
pos_halcomplex = get_pos("halcomplex")
pos_halligand = np.array(pos_halligand)
#rotate the complex to fit the negative x axis
cmd.rotate("z", 180, "circ_complex", 0, 0, origin=[0, 0, 0])
cmd.rotate("x", 180, "circ_complex", 0, 0, origin=[0, 0, 0])
#do the same for the backbone of the complex
cmd.rotate("x", 180, "comp_back", 0, 0, origin=[0, 0, 0])
pos_c2ligand = get_pos("c2ligand")
#create pseudoatoms of the ligand for calculating rotation angles without moving the actual ligand
cmd.pseudoatom("pseudo_ciligand",
pos=[
pos_ciligand[0][0], pos_ciligand[0][1],
pos_ciligand[0][2]
])
cmd.pseudoatom("pseudo_c2ligand",
pos=[
pos_c2ligand[0][0], pos_c2ligand[0][1],
pos_c2ligand[0][2]
])
cmd.pseudoatom("pseudo_halligand",
pos=[
pos_halligand[0][0], pos_halligand[0][1],
pos_halligand[0][2]
])
cmd.select("pseudo_ligand", "pseudo_*ligand")
#ADD PSEUDO BACKBONE
def visualize_epistasis(file,
obj,
max_atom_scale=2,
min_atom_scale=0.5,
max_line_scale=2,
min_line_scale=0.5,
pos_color=[1, 0, 0],
neg_color=[0, 0, 1],
backbone_color=[0.8, 0.8, 0.8]):
'''
Inputs
file - data file of epistatic effects in csv format.
obj - model object to visualize on. Usually the structure has the same name as the pbd identifier.
max_atom_scale - maximum scale to size atoms by. Maximum size is assigned to the largest absolute value of epistatic effects.
min_atom_scale - minimum scale to size atoms by. Minimum size is assigned to the smallest absolute value of epistatic effects.
max_line_scale - maximum scale to size lines by. Maximum size is assigned to the largest absolute value of epistatic effects.
min_line_scale - minimum scale to size lines by. Minimum size is assigned to the smallest absolute value of epistatic effects.
pos_color - color for positive effects.
neg_color - color for negative effects.
backbone_color - color for the cartoon representation of the structure.
'''
# fetch the current vwd radius
vdw_space = {'vdw_list': []}
cmd.iterate_state(-1, "name CA", "vdw_list.append(vdw)", space=vdw_space)
CA_vdw = vdw_space['vdw_list'][0]
max_atom_scale = float(max_atom_scale)
min_atom_scale = float(min_atom_scale)
max_line_scale = float(max_line_scale)
min_line_scale = float(min_line_scale)
# house keeping
# make sure the file exists
p, s = read_csv(file)
if p is None or s is None:
print('Error: plotting failed, invalid data file.')
return
# make sure the chains exists
chains = cmd.get_chains(obj)
# program in colors
cmd.set_color("pos_color", pos_color)
cmd.set_color("neg_color", neg_color)
# make sure colors do not smear
cmd.set("cartoon_discrete_colors", "on")
# determine order of epistasis, first order is plotted on atoms while higher levels are lines connecting atoms
atom = [True if len(x) <= 1 else False for x in p]
# normalize scores
abs_score = [abs(x) for x in s]
upper = max(abs_score)
lower = min(abs_score)
score_range = upper - lower
# calculate scaling variables
atom_scale_range = float(max_atom_scale) - float(min_atom_scale)
line_scale_range = float(max_line_scale) - float(min_line_scale)
scales = [(abs_score[i] - lower) / score_range
for i in range(len(abs_score))]
# set to atom or line scaling, respectively
scales = [
scales[i] * atom_scale_range +
min_atom_scale if atom[i] else scales[i] * line_scale_range +
min_line_scale for i in range(len(scales))
]
# do some plotting
sel_temp = '{obj}//{chain}/{resi}/CA' # selection template
for chain in chains:
sel = sel_temp.format(obj=obj, chain=chain, resi="{resi}")
for i in range(len(p)):
scale = scales[i]
# decide color
score = s[i]
color = "pos_color"
if score < 0:
color = "neg_color"
# reset name
name = ""
# visualize
if atom[i]: # first order
name = p[i][0]
cmd.select(name, sel.format(resi=p[i][0]))
cmd.show("sphere", name)
cmd.set("sphere_scale", scale / CA_vdw, name)
elif len(p[i]) == 2: # second order
name = "{}_{}".format(p[i][0], p[i][1])
cmd.distance(name, sel.format(resi=p[i][0]),
sel.format(resi=p[i][1]))
cmd.set("dash_radius", scale, name)
elif len(p[i]) > 2: # higher order
# get all linked atoms and find the centroid
target_resi = ""
for j in range(len(p[i])):
if j == 0:
target_resi = p[i][j]
name = p[i][j]
else:
target_resi = target_resi + "+" + p[i][j]
name = name + "_" + p[i][j]
group_sel = sel.format(resi=target_resi) # make selection
coords = []
myspace = {'coords': coords}
cmd.iterate_state(-1,
group_sel,
"coords.append([x,y,z])",
space=myspace) # get list of xyz coordinates
xyz = centroid(coords) # calculate the centroid
# create a pseudoatom at the centroid, and link all atoms to it with lines
cmd.pseudoatom("pseudoatoms", name=name, chain=chain, pos=xyz)
for x in p[i]:
cmd.distance(name,
"pseudoatoms//{}//{}".format(chain, name),
sel.format(resi=x))
cmd.set("dash_radius", scale, name)
# clean up after each set of data
cmd.color(color, name)
# final clean up
cmd.set("dash_gap", 0)
cmd.hide("everything", "pseudoatoms")
cmd.hide('labels')
cmd.set('cartoon_color', backbone_color)
def runSurfStamp_(self):
import tempfile
tmpdir = tempfile.TemporaryDirectory()
tmp_outfile = tmpdir.name + "/tmpout.obj"
if len(re.sub("[\s]*", "", self.text_outprefix.text())) > 0:
tmp_outfile = self.text_outprefix.text()
my_view = cmd.get_view()
modelname = self.combo_model.currentText()
output_modelname = re.sub("[^A-Za-z0-9\\.\\-]", "_",
modelname) + "_obj"
output_modelname = cmd.get_unused_name(output_modelname)
surf_args = ["java", "-jar", surfstamp_jar]
surf_args.extend(["-out", tmp_outfile])
tmpmodel_created = ""
if self.check_cartoon.isChecked() or (
not self.check_builtin.isChecked()):
#Use .obj generated by PyMOL. If this step is skipped, built-in generator is used.
tmpmodel_created = cmd.get_unused_name("tmpmodel_")
cmd.load_model(cmd.get_model(modelname), tmpmodel_created)
cmd.set_view((0.9999905824661255, -0.00367919635027647,
-0.002306032460182905, 0.003680833615362644,
0.9999929666519165, 0.0007080769282765687,
0.0023034177720546722, -0.0007165365968830884,
0.999997079372406, 0.0, 0.0, -50.0, 0.0, 0.0, 0.0,
40.0, 100.0, -20.0))
activeobjects = cmd.get_names('public_objects', enabled_only=1)
for aa in list(activeobjects):
cmd.disable(aa)
cmd.enable(tmpmodel_created)
modelname = tmpmodel_created
cmd.hide("everything", modelname)
if self.check_cartoon.isChecked():
cmd.show("cartoon", modelname)
surf_args.extend(["-use_ca", "-force", "-sep_block"])
else:
cmd.show("surface", modelname)
surf_args.extend(["-force"])
cmd.reset()
cmd.origin(position=[0.0, 0.0, 0.0])
cmd.center(origin=0)
unusedname = cmd.get_unused_name("pseudo_")
unused_selectionname = cmd.get_unused_name("pseudo_sel_")
cmd.pseudoatom(unusedname, pos=[0, 0, 0])
cmd.select(unused_selectionname, "/pseudo_//P/PSD`1/PS1")
cmd.center(selection=unused_selectionname)
cmd.save(tmpdir.name + "/tmpin.obj", modelname)
cmd.delete(unusedname)
cmd.delete(unused_selectionname)
for aa in list(activeobjects):
cmd.enable(aa)
surf_args.extend(["-obj", tmpdir.name + "/tmpin.obj"])
cmd.hide("everything", modelname)
if self.check_mmcif.isChecked():
tmp_infile = tmpdir.name + "/tmpin.cif"
surf_args.extend(["-mmcif_use_label", "-mmcif", tmp_infile])
cmd.save(tmp_infile, modelname)
else:
tmp_infile = tmpdir.name + "/tmpin.pdb"
cmd.save(tmp_infile, modelname)
surf_args.extend(["-pdb", tmp_infile])
if len(tmpmodel_created) > 0:
cmd.delete(tmpmodel_created)
surf_args.extend(["-surface_resolution",
str(self.spin_reso.value())])
surf_args.extend(["-image_size",
str(self.spin_imagesize.value())])
if not self.check_outline.isChecked():
surf_args.extend(["-nooutline"])
if self.check_nowater.isChecked():
surf_args.extend(["-nowater"])
if self.check_oneletter.isChecked():
surf_args.extend(["-residue_oneletter"])
if self.check_nochainname.isChecked():
surf_args.extend(["-nochainname"])
if self.check_tile.isChecked():
if self.check_cartoon.isChecked():
surf_args.extend(
["-tile", "-font_size",
str(self.spin_fontsize.value())])
else:
surf_args.extend([
"-tile", "-no_sep", "-font_size",
str(self.spin_fontsize.value())
])
if self.check_colorall.isChecked():
surf_args.extend(["-color_missing", "-color_chainbreak"])
if self.check_ignore_occupancy.isChecked():
surf_args.extend(["-ignore_occupancy"])
surf_args.extend(["-quiet", "1"])
import subprocess
process = subprocess.run(surf_args,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
#process = subprocess.run(surf_args, stdout=None, stderr=subprocess.PIPE);
print(process.stdout.decode("utf-8"))
#os.system(" ".join(surf_args)+" >&2 ");
self.label_message.setText("Finished.")
print("Finished.")
self.text_outprefix.setText("")
self.button_ok.setEnabled(True)
self.update()
if not re.search("\.obj$", tmp_outfile):
tmp_outfile = tmp_outfile + ".obj"
cmd.load_callback(pymol_obj_loader.myOBJCallback(tmp_outfile),
output_modelname)
cmd.set_view(my_view)
def main(d1, d2):
## Make an output folder
outdir = 'output_dd/' + input_protein + '+' + d1 + '+' + d2 + '/'
#print (outdir)
if os.path.isdir(outdir) == False:
os.system('mkdir ' + outdir)
domains = d1 + '+' + d2
for pdb in dd[domains]:
download_pdb_cif(pdb)
for coordinates in dd[domains][pdb]:
#print (pdb, domains, dd[domains][pdb][coordinates])
chainA = coordinates.split('+')[0].split(':')[0]
chainA_res = coordinates.split('+')[0].split(':')[1]
chainB = coordinates.split('+')[1].split(':')[0]
chainB_res = coordinates.split('+')[1].split(':')[1]
cmd.load('pdbs/' + pdb.upper() + '.pdb')
cmd.hide('everything')
cmd.show('cartoon', 'chain ' + chainA + '+' + chainB)
cmd.set('cartoon_fancy_helices', 1)
print(pdb, chainA, chainA_res, chainB, chainB_res)
try:
x = cmd.centerofmass('chain ' + chainA)
print('Success chainA')
cmd.pseudoatom('chainA_label', pos=x)
global nameA
nameA = id_to_name[d1] + '(' + d1 + ')'
cmd.label('chainA_label', 'nameA')
except:
print('Failed chainA')
try:
x = cmd.centerofmass('chain ' + chainB)
print('Success chainB')
cmd.pseudoatom('chainB_label', pos=x)
global nameB
nameB = id_to_name[d2] + '(' + d2 + ')'
cmd.label('chainB_label', 'nameB')
x = cmd.centerofmass('chain ' + chainA + '+' + chainB)
cmd.origin(position=x)
cmd.center('origin')
except:
print('Failed chainB')
cmd.set('label_size', 7.5)
cmd.set('cartoon_fancy_helices', 1)
cmd.color('red', 'chain ' + chainA)
cmd.color('orange', 'chain ' + chainB)
for row in dd[domains][pdb][coordinates]:
res1 = row[2]
res2 = row[3]
#cmd.distance('chain '+chainA+' and i. '+res1+' and n. CB', 'chain '+chainB+' and i. '+res2+' and n. CB')
cutoff = 6.5
m = cmd.distance(
'dist',
'chain ' + chainA + ' and i. ' + res1 + ' and n. CB',
'chain ' + chainB + ' and i. ' + res2 + ' and n. CB',
cutoff, 0)
#m = cmd.get_distance(atom1='chain '+chainA+' and i. '+res1+' and n. CB',atom2='chain '+chainB+' and i. '+res2+' and n. CB',state=0)
#print (pdb, m, chainA, res1, chainB, res2)
cmd.select('res1', 'chain ' + chainA + ' and resi ' + res1)
cmd.select('res2', 'chain ' + chainB + ' and resi ' + res2)
if float(m) != 0.0:
cmd.show('sticks', 'res1')
cmd.show('sticks', 'res2')
cmd.color('cyan', 'res1')
cmd.color('yellow', 'res2')
cmd.save(outdir + pdb + '_' + input_protein + '_' + d1 + '_' +
d2 + '_' + coordinates.replace(':', '_').replace(
'+', '_').replace('-', '_') + '.pse')
cmd.save(outdir + pdb + '_' + input_protein + '_' + d1 + '_' +
d2 + '_' + coordinates.replace(':', '_').replace(
'+', '_').replace('-', '_') + '.pdb')
cmd.delete('all')
#break
'''
import math
from pymol import cmd, finish_launching, plugins
from pymol.cgo import *
finish_launching()
cmd.load("ligands.mol2", "ligands")
ring_point_0 = [COLOR, 0.33, 1.0, 0.0] + [ALPHA, 0.8] + [
SPHERE, float(18.0),
float(13.0), float(112.5),
float(2.0)
]
cmd.load_cgo(ring_point_0, "ring_point_0_obj", 1)
cmd.pseudoatom(object="ring_point_0_score",
pos=(18.0, 13.0, 112.5),
color=(1, 1, 1),
label=21.6)
cmd.group("ring_0", members="ring_point_0_obj")
cmd.group("ring_0", members="ring_point_0_score")
ring_point_1 = [COLOR, 0.33, 1.0, 0.0] + [ALPHA, 0.8] + [
SPHERE, float(18.5),
float(15.0), float(109.0),
float(2.0)
]
cmd.load_cgo(ring_point_1, "ring_point_1_obj", 1)
cmd.pseudoatom(object="ring_point_1_score",
pos=(18.5, 15.0, 109.0),
color=(1, 1, 1),
label=14.0)
def test_set_title(self):
text = 'foo'
cmd.pseudoatom('m1')
cmd.set_title('m1', 1, text)
self.assertEqual(cmd.get_title('m1', 1), text)
def test_wildcards(self):
cmd.pseudoatom('foo')
cmd.pseudoatom('foobar')
cmd.pseudoatom('foo_bar')
cmd.pseudoatom('foo_bar_bla')
cmd.pseudoatom('bar')
cmd.pseudoatom('_bar')
self.assertEqual(1, cmd.count_atoms('foo'))
self.assertEqual(1, cmd.count_atoms('*foo'))
self.assertEqual(4, cmd.count_atoms('*foo*'))
self.assertEqual(1, cmd.count_atoms('bar'))
self.assertEqual(4, cmd.count_atoms('*bar'))
self.assertEqual(5, cmd.count_atoms('*bar*'))
self.assertEqual(2, cmd.count_atoms('foo*bar'))
self.assertEqual(3, cmd.count_atoms('*foo*bar*'))
self.assertEqual(1, cmd.count_atoms('_*'))
self.assertEqual(6, cmd.count_atoms('*'))
self.assertEqual(6, cmd.count_atoms('*'))
cmd.alter('*', 'name = "ABCD"')
cmd.alter('foo', 'name = "ABED"')
cmd.alter('bar', 'name = "ABEC"')
self.assertEqual(6, cmd.count_atoms('name A*'))
self.assertEqual(2, cmd.count_atoms('name ABE*'))
self.assertEqual(1, cmd.count_atoms('name ABED*'))
self.assertEqual(1, cmd.count_atoms('name AB*C'))
self.assertEqual(5, cmd.count_atoms('name AB*C*'))
self.assertEqual(5, cmd.count_atoms('name AB*D'))
self.assertEqual(5, cmd.count_atoms('name AB*D*'))
def prune_grid(rna, score_file, outname, quantile=0.99, sasa_cutoff=20.0):
# make sure all atoms within an object occlude one another
cmd.flag("ignore", "none")
# use solvent-accessible surface with high sampling density
cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)
cmd.set('solvent_radius', 2.0)
k = 1
df = pd.read_csv(score_file, header=0, sep=",")
means = df[['pred_MLP', 'pred_XGB', 'pred_RF', 'pred_LR',
'pred_Extra']].apply(np.mean, 'columns')
cutoff = np.quantile(a=means, q=quantile)
for pred, pos in zip(
df[['pred_MLP', 'pred_XGB', 'pred_RF', 'pred_LR',
'pred_Extra']].values, df[['x', 'y', 'z']].values):
if np.mean(pred) > cutoff:
# create tmp complex
cmd.pseudoatom("tmpPoint3",
hetatm=1,
name="C",
resn="UNK",
pos=[pos[0], pos[1], pos[2]])
cmd.create("complextmp", "%s tmpPoint3" % rna)
sasa = cmd.get_area('resn UNK and not polymer and complextmp')
cmd.delete("complextmp tmpPoint3")
# remove really highly exposed points
if sasa < sasa_cutoff:
cmd.pseudoatom("tmpPoint",
hetatm=1,
b=np.mean(pred),
q=sasa,
name="C",
resn="UNK",
resi=k,
chain="ZZ",
pos=[pos[0], pos[1], pos[2]])
print(pred, pos, np.mean(pred), cutoff, sasa)
k += 1
# write out grid file
coor = "%s_pruned_grid.xyz" % (outname)
xyz = cmd.get_coords('tmpPoint', 1)
df = pd.DataFrame.from_records(xyz)
df.insert(0, "element", "C")
df.to_csv(coor, index=False, header=False, sep=" ")
# write out complex
cmd.create("complex", "%s tmpPoint" % rna)
coor = "%s_pruned_grid.pdb" % (outname)
cmd.save(coor, "complex")
coor = "cavity_pruned_grid.sd"
cmd.save(coor, "tmpPoint")
# remove isolated
remove_isolated()
# write out grid file
coor = "%s_pruned_grid_clusters.xyz" % (outname)
xyz = cmd.get_coords('tmpPoint', 1)
df = pd.DataFrame.from_records(xyz)
df.insert(0, "element", "C")
df.to_csv(coor, index=False, header=False, sep=" ")
# write out complex
cmd.create("complex", "%s tmpPoint" % rna)
coor = "%s_pruned_grid_clusters.pdb" % (outname)
cmd.save(coor, "complex")
coor = "cavity_pruned_grid.sd"
cmd.save(coor, "tmpPoint")
cmd.isosurface(name="surface_acceptor_hotspot",
map="acceptor_hotspot",
level="5")
cmd.color("red", "surface_acceptor_hotspot")
cmd.set("transparency", 0.2, "surface_acceptor_hotspot")
cmd.group("hotspot", members="apolar_hotspot")
cmd.group("hotspot", members="surface_apolar_hotspot")
cmd.group("hotspot", members="donor_hotspot")
cmd.group("hotspot", members="surface_donor_hotspot")
cmd.group("hotspot", members="acceptor_hotspot")
cmd.group("hotspot", members="surface_acceptor_hotspot")
cmd.group("hotspot", members="buriedness_hotspot")
cmd.group("hotspot", members="surface_buriedness_hotspot")
cmd.pseudoatom(object="PS_apolar_hotspot_0",
pos=(24.5, 1.0, 19.5),
color=(1, 1, 1),
label=12.8)
cmd.pseudoatom(object="PS_apolar_hotspot_1",
pos=(23.0, -6.0, 15.0),
color=(1, 1, 1),
label=16.5)
cmd.pseudoatom(object="PS_apolar_hotspot_2",
pos=(21.0, -1.0, 16.0),
color=(1, 1, 1),
label=6.4)
cmd.pseudoatom(object="PS_apolar_hotspot_3",
pos=(18.5, 1.0, 20.0),
color=(1, 1, 1),
import math
from pymol import cmd, finish_launching, plugins
from pymol.cgo import *
finish_launching()
cmd.load("ligands.mol2", "ligands")
ring_point_0 = [COLOR, 0.33, 1.0, 0.0] + [ALPHA, 0.8] + [
SPHERE, float(27.5),
float(5.0), float(64.5),
float(2.0)
]
cmd.load_cgo(ring_point_0, "ring_point_0_obj", 1)
cmd.pseudoatom(object="ring_point_0_score",
pos=(27.5, 5.0, 64.5),
color=(1, 1, 1),
label=191.4)
cmd.group("ring_0", members="ring_point_0_obj")
cmd.group("ring_0", members="ring_point_0_score")
acceptor_projected_point_1 = [COLOR, 1.0, 0.0, 0.0] + [ALPHA, 0.8] + [
SPHERE, float(28.5),
float(4.5), float(65.5),
float(1)
]
cmd.load_cgo(acceptor_projected_point_1, "acceptor_projected_point_1_obj", 1)
cmd.pseudoatom(object="acceptor_projected_point_1_score",
pos=(28.5, 4.5, 65.5),
color=(1, 1, 1),
label=190.6)
def elbow_angle(obj, light='L', heavy='H', limit_l=107, limit_h=113, draw=0):
"""
DESCRIPTION
Calculates the integer elbow angle of an antibody Fab complex and
optionally draws a graphical representation of the vectors used to
determine the angle.
ARGUMENTS
obj = string: object
light/heavy = strings: chain ID of light and heavy chains, respectively
limit_l/limit_h = integers: residue numbers of the last residue in the
light and heavy chain variable domains, respectively
draw = boolean: Choose whether or not to draw the angle visualization
REQUIRES: com.py, transformations.py, numpy (see above)
"""
# store current view
orig_view = cmd.get_view()
limit_l = int(limit_l)
limit_h = int(limit_h)
draw = int(draw)
# for temp object names
tmp_prefix = "tmp_elbow_"
prefix = tmp_prefix + obj + '_'
# names
vl = prefix + 'VL'
vh = prefix + 'VH'
cl = prefix + 'CL'
ch = prefix + 'CH'
# selections
vl_sel = 'polymer and %s and chain %s and resi 1-%i' % (obj, light, limit_l)
vh_sel = 'polymer and %s and chain %s and resi 1-%i' % (obj, heavy, limit_h)
cl_sel = 'polymer and %s and chain %s and not resi 1-%i' % (obj, light, limit_l)
ch_sel = 'polymer and %s and chain %s and not resi 1-%i' % (obj, heavy, limit_h)
v_sel = '((' + vl_sel + ') or (' + vh_sel + '))'
c_sel = '((' + cl_sel + ') or (' + ch_sel + '))'
# create temp objects
cmd.create(vl, vl_sel)
cmd.create(vh, vh_sel)
cmd.create(cl, cl_sel)
cmd.create(ch, ch_sel)
# superimpose vl onto vh, calculate axis and angle
Rv = calc_super_matrix(vl, vh)
angle_v, direction_v, point_v = transformations.rotation_from_matrix(Rv)
# superimpose cl onto ch, calculate axis and angle
Rc = calc_super_matrix(cl, ch)
angle_c, direction_c, point_c = transformations.rotation_from_matrix(Rc)
# delete temporary objects
cmd.delete(vl)
cmd.delete(vh)
cmd.delete(cl)
cmd.delete(ch)
# if dot product is positive, angle is acute
if (numpy.dot(direction_v, direction_c) > 0):
direction_c = direction_c * -1 # ensure angle is > 90 (need to standardize this)
# TODO: make both directions point away from the elbow axis.
elbow = int(numpy.degrees(numpy.arccos(numpy.dot(direction_v, direction_c))))
# while (elbow < 90):
# elbow = 180 - elbow # limit to physically reasonable range
# compare the direction_v and direction_c axes to the vector defined by
# the C-alpha atoms of limit_l and limit_h of the original fab
hinge_l_sel = "%s//%s/%s/CA" % (obj, light, limit_l)
hinge_h_sel = "%s//%s/%s/CA" % (obj, heavy, limit_h)
hinge_l = cmd.get_atom_coords(hinge_l_sel)
hinge_h = cmd.get_atom_coords(hinge_h_sel)
hinge_vec = numpy.array(hinge_h) - numpy.array(hinge_l)
test = numpy.dot(hinge_vec, numpy.cross(direction_v, direction_c))
if (test > 0):
elbow = 360 - elbow
print(" Elbow angle: %i degrees" % elbow)
if (draw == 1):
# there is probably a more elegant way to do this, but
# it works so I'm not going to mess with it for now
pre = obj + '_elbow_'
# draw hinge vector
cmd.pseudoatom(pre + "hinge_l", pos=hinge_l)
cmd.pseudoatom(pre + "hinge_h", pos=hinge_h)
cmd.distance(pre + "hinge_vec", pre + "hinge_l", pre + "hinge_h")
cmd.set("dash_gap", 0)
# draw the variable domain axis
com_v = COM(v_sel)
start_v = [a - 10 * b for a, b in zip(com_v, direction_v)]
end_v = [a + 10 * b for a, b in zip(com_v, direction_v)]
cmd.pseudoatom(pre + "start_v", pos=start_v)
cmd.pseudoatom(pre + "end_v", pos=end_v)
cmd.distance(pre + "v_vec", pre + "start_v", pre + "end_v")
# draw the constant domain axis
com_c = COM(c_sel)
start_c = [a - 10 * b for a, b in zip(com_c, direction_c)]
end_c = [a + 10 * b for a, b in zip(com_c, direction_c)]
cmd.pseudoatom(pre + "start_c", pos=start_c)
cmd.pseudoatom(pre + "end_c", pos=end_c)
cmd.distance(pre + "c_vec", pre + "start_c", pre + "end_c")
# customize appearance
cmd.hide("labels", pre + "hinge_vec")
cmd.hide("labels", pre + "v_vec")
cmd.hide("labels", pre + "c_vec")
cmd.color("green", pre + "hinge_l")
cmd.color("red", pre + "hinge_h")
cmd.color("black", pre + "hinge_vec")
cmd.color("black", pre + "start_v")
cmd.color("black", pre + "end_v")
cmd.color("black", pre + "v_vec")
cmd.color("black", pre + "start_c")
cmd.color("black", pre + "end_c")
cmd.color("black", pre + "c_vec")
# draw spheres
cmd.show("spheres", pre + "hinge_l or " + pre + "hinge_h")
cmd.show("spheres", pre + "start_v or " + pre + "start_c")
cmd.show("spheres", pre + "end_v or " + pre + "end_c")
cmd.set("sphere_scale", 2)
cmd.set("dash_gap", 0, pre + "hinge_vec")
cmd.set("dash_width", 5)
cmd.set("dash_radius", 0.3)
# group drawing objects
cmd.group(pre, pre + "*")
# restore original view
cmd.set_view(orig_view)
return 0
float(0.5)
]
cmd.load_cgo(donor_projected_point_0, "donor_projected_point_0_obj", 1)
donor_projected_projection_0 = [COLOR, 0.6, 0.6, 1.0] + [ALPHA, 1.0] + [
SPHERE,
float(6.60241953313495),
float(5.401737482286244),
float(5.986274419667637),
float(0.5)
]
cmd.load_cgo(donor_projected_projection_0, "donor_projected_projection_0_obj",
1)
cmd.pseudoatom(object="donor_projected_line_0pa1",
pos=(4.8497557616643245, 3.893318200000001, 4.407401095742814),
color=(1, 1, 1))
cmd.pseudoatom(object="donor_projected_line_0pa2",
pos=(6.60241953313495, 5.401737482286244, 5.986274419667637),
color=(1, 1, 1))
cmd.distance(name="donor_projected_line_0",
selection1="donor_projected_line_0pa1",
selection2="donor_projected_line_0pa2",
width=0.5,
gap=0.2,
label=0,
state=1)
cmd.set("dash_color", (0.6, 0.6, 1.0), selection="donor_projected_line_0")
def PiPi(pdb_file, lig_name, centroid_distance, dih_parallel, dih_tshape):
# Get ligand residue and print its name.
ligAtomList = []
ligAtomIdList = []
mol = pybel.readfile('pdb', pdb_file).next()
print "A total of %s residues" % mol.OBMol.NumResidues()
lig = None
for res in ob.OBResidueIter(mol.OBMol):
# print res.GetName()
if res.GetName() == lig_name:
lig = res
print "Ligand residue name is: ", lig.GetName()
break
if not lig:
print "No ligand residue %s found, please confirm." % lig_name
return 0
else:
for atom in ob.OBResidueAtomIter(lig):
# print atom.GetIdx()
ligAtomList.append(atom)
ligAtomIdList.append(atom.GetIdx())
# Set ring_id
i = 0
for ring in mol.sssr:
ring.ring_id = i
i += 1
# print ring.ring_id
# Determine which rings are from ligand.
ligRingList = []
ligAroRingList = []
ligRingIdList = []
recRingList = []
recAroRingList = []
for ring in mol.sssr:
for atom in ligAtomList:
if ring.IsMember(atom):
if ring not in ligRingList:
ligRingList.append(ring)
ligRingIdList.append(ring.ring_id)
print "ligand ring_ID: ", ring.ring_id,
if ring.IsAromatic():
print "Aromatic"
ligAroRingList.append(ring)
else:
print "Saturated"
for ring in mol.sssr:
if ring.ring_id not in ligRingIdList:
recRingList.append(ring)
if ring.IsAromatic():
recAroRingList.append(ring)
print "\nReceptor has ", len(recRingList), " rings,",
print " has ", len(recAroRingList), " aromatic rings."
# Find and show the rings
ligRingCenter = ob.vector3()
recRingCenter = ob.vector3()
ligNorm1 = ob.vector3()
ligNorm2 = ob.vector3()
recNorm1 = ob.vector3()
recNorm2 = ob.vector3()
coord1 = []
coord2 = []
pair = [] # Store the names of the objects
pairList = []
psObjectList = []
i = 0
for ligRing in ligAroRingList:
ligRing.findCenterAndNormal(ligRingCenter, ligNorm1, ligNorm2)
coord1 = [
ligRingCenter.GetX(),
ligRingCenter.GetY(),
ligRingCenter.GetZ()
]
# Create a pseudoatom for the centroid of each ring in the ligand
objectName1 = 'psCenter%.2d' % i
i += 1
cmd.pseudoatom(object=objectName1, pos=coord1)
psObjectList.append(objectName1)
for recRing in recAroRingList:
recRing.findCenterAndNormal(recRingCenter, recNorm1, recNorm2)
dist = ligRingCenter.distSq(recRingCenter)
angle = vecAngle(ligNorm1, recNorm1)
if (dist**0.5 < centroid_distance and
(angle < dih_parallel or angle > dih_tshape)): # the criteria
coord2 = [
recRingCenter.GetX(),
recRingCenter.GetY(),
recRingCenter.GetZ()
]
# Create pseudoatom for each lig ring center
objectName2 = 'psCenter%.2d' % i
i += 1
cmd.pseudoatom(object=objectName2, pos=coord2)
psObjectList.append(objectName2)
# pair=[coord1,coord2]
pair = [objectName1, objectName2]
# print "%.4f,%.4f,%.4f" % (pair[1][0],pair[1][1],pair[1][2])
pairList.append(pair)
cmd.distance('dist-' + objectName1 + '-' + objectName2,
pair[0], pair[1])
print objectName1, objectName2, " angle is : %.2f" % angle
from os.path import join
import tempfile
import zipfile
import math
from pymol import cmd, finish_launching
from pymol.cgo import *
finish_launching()
cmd.pseudoatom(object="myline1pa1", pos=(0, 0, 0), color=(1, 1, 1))
cmd.pseudoatom(object="myline1pa2", pos=(1, 1, 1), color=(1, 1, 1))
cmd.distance(name="myline1",
selection1="myline1pa1",
selection2="myline1pa2",
width=0.5,
gap=0.2,
label=0,
state=1)
cmd.set("dash_color",
(0.9411764705882353, 0.20392156862745098, 0.20392156862745098),
selection="myline1")
cmd.set("dash_width", 10)
cmd.delete("myline1pa1")
cmd.delete("myline1pa2")
cmd.pseudoatom(object="mypseudoatom1",
pos=(0, 0, 0),
color=(0.9411764705882353, 0.20392156862745098,
0.20392156862745098, 0.5))
# create N particle system [x,y,z,r,vx,vy,vz]
particle = []
for resi in range(0, particle_count):
particle.append([resi] +
map(lambda x: (random() - 0.5) * box_size / 2, [0] *
3) + # x,y,z
[random() + 0.5] + # r
map(lambda x: (random() - 0.5), [0] * 3) # vx,vy,vz
)
# create cloud object
for part in particle:
cmd.pseudoatom("cloud", resi=part[0], pos=part[1:4], vdw=part[4])
# draw spheres efficiently
cmd.show_as("spheres")
cmd.unset("cull_spheres")
# position the camera
cmd.zoom()
cmd.zoom("center", box_size)
# let there be color
cmd.spectrum()
# this is the main loop
def testIterateLocalVars(self, func):
cmd.pseudoatom('m1')
stored.v = None
func('all', 'foobar = model;stored.v = foobar')
self.assertEqual(stored.v, 'm1')
cmd.color('_colorm', 'sm')
#cmd.load('dif_B1.cube')
#cmd.isosurface('spp', 'dif_B1', 0.00008)
#cmd.color('blue', 'spp')
#cmd.isosurface('smp', 'dif_B1', -0.00008)
#cmd.color('red', 'smp')
#cmd.set ('label_font_id', 16)
#cmd.set ('label_size', 24)
#cmd.pseudoatom('xatom', pos=[1,0,0], label="x")
#cmd.pseudoatom('yatom', pos=[0,1,0], label="y")
#cmd.pseudoatom('zatom', pos=[0,0,2], label="z")
cmd.set('label_font_id', 16)
cmd.set('label_size', 20)
cmd.pseudoatom('xatom', pos=[2.5, 0, 0], label="x")
cmd.pseudoatom('yatom', pos=[0, 2.5, 0], label="y")
cmd.pseudoatom('zatom', pos=[0, 0, 4.0], label="z")
cmd.set('ray_opaque_background', 'off')
cmd.set('transparency', 0.30)
#cmd.set_view ('\
# -0.086753346, 0.836276770, 0.541441798,\
# 0.670052588, -0.353231400, 0.652936995,\
# 0.737265468, 0.419426382, -0.529700875,\
# 0.000000000, 0.000000000, -34.167503357,\
# 0.108778238, 0.131587982, 1.662951946,\
# 26.937919617, 41.397087097, -20.000000000' )
#
def test_set_name(self):
cmd.pseudoatom('m1')
cmd.set_name('m1', 'm2')
self.assertEqual(['m2'], cmd.get_names())
print("Translation vector: ")
print(translation_vector)
print([translation_vector[0][0],translation_vector[0][1],translation_vector[0][2]])
#translate molecule from mol file to 0,0,0
cmd.translate([translation_vector[0][0],translation_vector[0][1],translation_vector[0][2]],"circ_complex",-1,0)
#get coordinates from ligand and mol file complex
pos_halligand = []
pos_halcomplex = []
cmd.iterate_state(1, 'halligand', 'pos_halligand.append((x,y,z))')
cmd.iterate_state(1, 'halcomplex', 'pos_halcomplex.append((x,y,z))')
pos_halligand = np.array(pos_halligand)
#add pseudoatom on x axis to measure angle for rotation around y axis
cmd.pseudoatom("x-1",pos=[-1,0,0])
#measure angle for molfile rotation
angle = cmd.get_angle(atom1="cicomplex",atom2="halcomplex",atom3="x-1")
#rotate mol file
cmd.rotate("z",180,"circ_complex",0,0,origin=[0,0,0])
#cmd.pseudoatom("e",pos=[-2,0,z_temp])
print(angle)
print(pos_halligand[0][2])
cmd.pseudoatom("z1",pos=[0,0,1])
cmd.pseudoatom("pseudo_ciligand",pos=[pos_ciligand[0][0],pos_ciligand[0][1],pos_ciligand[0][2]])
cmd.pseudoatom("pseudo_c2ligand",pos=[pos_c2ligand[0][0],pos_c2ligand[0][1],pos_c2ligand[0][2]])
cmd.isosurface(name="surface_acceptor_hotspot",
map="acceptor_hotspot",
level="5")
cmd.color("red", "surface_acceptor_hotspot")
cmd.set("transparency", 0.2, "surface_acceptor_hotspot")
cmd.group("hotspot", members="apolar_hotspot")
cmd.group("hotspot", members="surface_apolar_hotspot")
cmd.group("hotspot", members="donor_hotspot")
cmd.group("hotspot", members="surface_donor_hotspot")
cmd.group("hotspot", members="acceptor_hotspot")
cmd.group("hotspot", members="surface_acceptor_hotspot")
cmd.group("hotspot", members="buriedness_hotspot")
cmd.group("hotspot", members="surface_buriedness_hotspot")
cmd.pseudoatom(object="PS_apolar_hotspot_0",
pos=(25.0, 7.5, 16.5),
color=(1, 1, 1),
label=11.5)
cmd.pseudoatom(object="PS_apolar_hotspot_1",
pos=(25.0, 6.5, 14.0),
color=(1, 1, 1),
label=10.0)
cmd.pseudoatom(object="PS_apolar_hotspot_2",
pos=(22.0, 5.5, 11.5),
color=(1, 1, 1),
label=18.1)
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_0")
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_0")
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_1")
def hs_gsimplifier(*args, **kwargs):
radius = form.radius1.value()
color = kwargs.get("color", "red")
selections = args
for selection in selections:
if not is_sele(selection):
raise RuntimeError(
"Selection \"{}\" does not exists.".format(selection))
states = cmd.count_states(selection=selections[0])
hs_values = []
all_coords = []
for state in range(1, states + 1):
stored.info = []
for selection in selections:
cmd.iterate_state(
state, selection,
"stored.info.append([ID, partial_charge, (x,y,z), \"{}\"])"
.format(selection))
for line in stored.info:
partial_charge = line[1]
coord = line[2]
hs_values.append(partial_charge)
all_coords.append(coord)
hs = np.array(copy.copy(stored.info))
n = dict()
for h in hs:
dists = np.linalg.norm(np.array(h[2]) - list(zip(*hs))[2],
axis=1)
# Convert to dict due to same hotspots IDs
n[(h[0], h[3])] = hs[dists <= radius]
exc_indexes = []
hs_id = free_hotspot_id(hs, exc_indexes=exc_indexes)
while hs_id is not None:
excluded, coords = find_all_coords(n,
hs_id,
exc_indexes=[],
coords=[])
exc_indexes.extend(excluded)
if form.geometric.isChecked():
middle_point = group_center(np.array(coords))
cmd.pseudoatom(object="simply",
color=color,
pos=middle_point,
state=state)
else:
middle_points = find_center(hs_values,
all_coords,
nbr=len(exc_indexes))
for point in middle_points:
cmd.pseudoatom(object="simply",
color=color,
pos=point,
state=state)
hs_id = free_hotspot_id(hs, exc_indexes=exc_indexes)
cmd.show(representation="spheres", selection="simply")
from os.path import join
import tempfile
import zipfile
import math
from pymol import cmd, finish_launching
from pymol.cgo import *
finish_launching()
cmd.pseudoatom(object="mylinepa1", pos=(1, 1, 1), color=(1, 1, 1))
cmd.pseudoatom(object="mylinepa2", pos=(2, 2, 2), color=(1, 1, 1))
cmd.distance(name="myline",
selection1="mylinepa1",
selection2="mylinepa2",
width=0.5,
gap=0.2,
label=0,
state=1)
cmd.set("dash_color",
(0.9411764705882353, 0.20392156862745098, 0.20392156862745098),
selection="myline")
cmd.set("dash_width", 4)
cmd.delete("mylinepa1")
cmd.delete("mylinepa2")
cmd.pseudoatom(object="myline2pa1", pos=(1, 1, 1), color=(1, 1, 1))
cmd.pseudoatom(object="myline2pa2", pos=(0, 0, 0), color=(1, 1, 1))
def show_cationpi(self):
"""Visualize cation-pi interactions."""
for i, p in enumerate(self.plcomplex.pication):
cmd.pseudoatom('ps-picat-1-%i' % i, pos=p.ring_center)
cmd.pseudoatom('ps-picat-2-%i' % i, pos=p.charge_center)
if p.protcharged:
cmd.pseudoatom('Chargecenter-P', pos=p.charge_center)
cmd.pseudoatom('Centroids-L', pos=p.ring_center)
pilig_ids = '+'.join(map(str, p.ring_atoms))
cmd.select('PiCatRing-L', 'PiCatRing-L or (id %s & %s)' % (pilig_ids, self.ligname))
for a in p.charge_atoms:
cmd.select('PosCharge-P', 'PosCharge-P or (id %i & %s)' % (a, self.protname))
else:
cmd.pseudoatom('Chargecenter-L', pos=p.charge_center)
cmd.pseudoatom('Centroids-P', pos=p.ring_center)
pires_ids = '+'.join(map(str, p.ring_atoms))
cmd.select('PiCatRing-P', 'PiCatRing-P or (id %s & %s)' % (pires_ids, self.protname))
for a in p.charge_atoms:
cmd.select('PosCharge-L', 'PosCharge-L or (id %i & %s)' % (a, self.ligname))
cmd.distance('PiCation', 'ps-picat-1-%i' % i, 'ps-picat-2-%i' % i)
if self.object_exists('PiCation'):
cmd.set('dash_color', 'orange', 'PiCation')
cmd.set('dash_gap', 0.3, 'PiCation')
cmd.set('dash_length', 0.6, 'PiCation')
cmd.isosurface(name="surface_acceptor_hotspot",
map="acceptor_hotspot",
level="5")
cmd.color("red", "surface_acceptor_hotspot")
cmd.set("transparency", 0.2, "surface_acceptor_hotspot")
cmd.group("hotspot", members="apolar_hotspot")
cmd.group("hotspot", members="surface_apolar_hotspot")
cmd.group("hotspot", members="donor_hotspot")
cmd.group("hotspot", members="surface_donor_hotspot")
cmd.group("hotspot", members="acceptor_hotspot")
cmd.group("hotspot", members="surface_acceptor_hotspot")
cmd.group("hotspot", members="buriedness_hotspot")
cmd.group("hotspot", members="surface_buriedness_hotspot")
cmd.pseudoatom(object="PS_apolar_hotspot_0",
pos=(31.0, 8.5, 65.5),
color=(1, 1, 1),
label=115.1)
cmd.pseudoatom(object="PS_apolar_hotspot_1",
pos=(27.5, 5.0, 64.5),
color=(1, 1, 1),
label=191.4)
cmd.pseudoatom(object="PS_apolar_hotspot_2",
pos=(25.0, 7.0, 61.5),
color=(1, 1, 1),
label=62.2)
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_0")
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_0")
cmd.group("label_apolar_hotspot", members="PS_apolar_hotspot_1")
def angle_between_helices(selection1,
selection2,
method='helix',
state1=STATE,
state2=STATE,
visualize=1,
quiet=1):
'''
DESCRIPTION
Calculates the angle between two helices
USAGE
angle_between_helices selection1, selection2 [, method [, visualize]]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: function to calculate orientation {default: helix_orientation}
visualize = 0 or 1: show fitted vector as arrow {default: 1}
EXAMPLE
fetch 2x19, bsync=0
select hel1, /2x19//B/23-36/
select hel2, /2x19//B/40-54/
angle_between_helices hel1, hel2
angle_between_helices hel1, hel2, cafit
SEE ALSO
helix_orientation, loop_orientation, cafit_orientation, angle_between_domains
'''
import math
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
try:
orientation = globals()[methods_sc[str(method)]]
except KeyError:
print('no such method:', method)
raise CmdException
if not int(quiet):
print(' Using method:', orientation.__name__)
cen1, dir1 = orientation(selection1, state1, visualize, quiet=1)
cen2, dir2 = orientation(selection2, state2, visualize, quiet=1)
angle = cpv.get_angle(dir1, dir2)
angle = math.degrees(angle)
if not quiet:
print(' Angle: %.2f deg' % (angle))
if visualize:
# measurement object for angle
center = cpv.scale(cpv.add(cen1, cen2), 0.5)
tmp = get_unused_name('_')
for pos in [
center,
cpv.add(center, cpv.scale(dir1, 5.0)),
cpv.add(center, cpv.scale(dir2, 5.0))
]:
cmd.pseudoatom(tmp, pos=list(pos), state=1)
name = get_unused_name('angle')
cmd.angle(name, *[(tmp, i) for i in [2, 1, 3]])
cmd.delete(tmp)
cmd.zoom('(%s) or (%s)' % (selection1, selection2), 2,
state1 if state1 == state2 else 0)
return angle
import zipfile
import math
from pymol import cmd, finish_launching, plugins
from pymol.cgo import *
finish_launching()
cmd.load("ligands.mol2", "ligands")
cmd.load("protein.mol2", "protein")
donor_projected_point_0 = [COLOR, 0.0, 0.0, 1.0] + [ALPHA, 1.0] + [SPHERE, float(27.308), float(3.547), float(65.078), float(0.5)]
cmd.load_cgo(donor_projected_point_0, "donor_projected_point_0_obj", 1)
donor_projected_projection_0 = [COLOR, 0.6, 0.6, 1.0] + [ALPHA, 1.0] + [SPHERE, float(26.877), float(0.821), float(65.99), float(0.5)]
cmd.load_cgo(donor_projected_projection_0, "donor_projected_projection_0_obj", 1)
cmd.pseudoatom(object="donor_projected_line_0pa1", pos=(27.308, 3.547, 65.078), color=(1, 1, 1))
cmd.pseudoatom(object="donor_projected_line_0pa2", pos=(26.877, 0.821, 65.99), color=(1, 1, 1))
cmd.distance(name="donor_projected_line_0", selection1="donor_projected_line_0pa1", selection2="donor_projected_line_0pa2", width=0.5, gap=0.2, label=0, state=1)
cmd.set("dash_color", (0.6, 0.6, 1.0), selection="donor_projected_line_0")
cmd.set("dash_width", 4.0)
cmd.delete("donor_projected_line_0pa1")
cmd.delete("donor_projected_line_0pa2")
cmd.group("donor_projected_0", members="donor_projected_point_0_obj")
cmd.group("donor_projected_0", members="donor_projected_projection_0")
cmd.group("donor_projected_0", members="donor_projected_line_0")
cmd.select("sele", "resi 81")
cmd.show("sticks", "sele")
acceptor_projected_point_1 = [COLOR, 1.0, 0.0, 0.0] + [ALPHA, 1.0] + [SPHERE, float(28.364), float(4.137), float(65.698), float(0.5)]
def testGetPdbstr(self):
cmd.pseudoatom()
lines = cmd.get_pdbstr().splitlines()
self.assertTrue(lines[0].startswith('HETATM'))
self.assertTrue(lines[1].startswith('END'))