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| − | <gallery perrow=2 heights=250px widths=191px> | + | {{Infobox script-repo |
| | + | |type = Python Module |
| | + | |filename = anglebetweenhelices.py |
| | + | |author = [[User:Speleo3|Thomas Holder]] |
| | + | |license = BSD |
| | + | }} |
| | + | |
| | + | {{Infobox psico |
| | + | |module = psico.orientation |
| | + | }} |
| | + | |
| | + | <gallery perrow=1 heights=191px widths=250px style="float:right; clear: right"> |
| | Image:Helix_orientation1.png|Orientation of a helix | | Image:Helix_orientation1.png|Orientation of a helix |
| | Image:Helix_orientation2.png|Orientation of two helices, their angle that separates the two is 145.08 degrees as reported by the script | | Image:Helix_orientation2.png|Orientation of two helices, their angle that separates the two is 145.08 degrees as reported by the script |
| | </gallery> | | </gallery> |
| | + | |
| | Calculate angle between alpha-helices or beta-sheets. | | Calculate angle between alpha-helices or beta-sheets. |
| | There are four different methods implemented to fit a helix, two of them also work for sheets or loops. | | There are four different methods implemented to fit a helix, two of them also work for sheets or loops. |
| | | | |
| | = Commands = | | = Commands = |
| − | <source lang="python">
| |
| − | helix_orientation selection [, visualize [, sigma_cutoff [, quiet ]]]
| |
| | | | |
| − | helix_orientation_hbond selection [, visualize [, cutoff [, quiet ]]]
| + | angle_between_helices selection1, selection2 [, method [, visualize ]] |
| | | | |
| − | loop_orientation selection [, visualize [, quiet ]]
| + | helix_orientation selection [, visualize [, sigma_cutoff ]] |
| | | | |
| − | cafit_orientation selection [, visualize [, quiet ]]
| + | helix_orientation_hbond selection [, visualize [, cutoff ]] |
| | | | |
| − | angle_between_helices selection1, selection2 [, method [, visualize [, quiet ]]]
| + | loop_orientation selection [, visualize ] |
| − | </source>
| + | |
| | + | cafit_orientation selection [, visualize ] |
| | | | |
| | = Example = | | = Example = |
| | | | |
| − | <source lang="python"> | + | <syntaxhighlight lang="python"> |
| − | fetch 2x19 | + | import anglebetweenhelices |
| | + | |
| | + | fetch 2x19, async=0 |
| | select hel1, /2x19//B/23-36/ | | select hel1, /2x19//B/23-36/ |
| | select hel2, /2x19//B/40-54/ | | select hel2, /2x19//B/40-54/ |
| − | | + | |
| | # just calculate/visualize orientation of single alpha-helix | | # just calculate/visualize orientation of single alpha-helix |
| | helix_orientation_hbond hel1 | | helix_orientation_hbond hel1 |
| − | | + | |
| | # get angle between two helices | | # get angle between two helices |
| | angle_between_helices hel1, hel2 | | angle_between_helices hel1, hel2 |
| | angle_between_helices hel1, hel2, method=1 | | angle_between_helices hel1, hel2, method=1 |
| | angle_between_helices hel1, hel2, method=2 | | angle_between_helices hel1, hel2, method=2 |
| − | | + | |
| | # get angle between beta-sheets | | # get angle between beta-sheets |
| | select sheet1, A/47-54/ | | select sheet1, A/47-54/ |
| Line 39: |
Line 52: |
| | angle_between_helices sheet1, sheet6, method=loop_orientation | | angle_between_helices sheet1, sheet6, method=loop_orientation |
| | angle_between_helices sheet1, sheet6, method=cafit_orientation | | angle_between_helices sheet1, sheet6, method=cafit_orientation |
| − | </source> | + | </syntaxhighlight> |
| | | | |
| | Output: | | Output: |
| − | <source lang="python"> | + | <syntaxhighlight lang="python"> |
| | PyMOL>angle_between_helices hel1, hel2, method=cafit_orientation | | PyMOL>angle_between_helices hel1, hel2, method=cafit_orientation |
| | Using method: cafit_orientation | | Using method: cafit_orientation |
| | Angle: 145.08 deg | | Angle: 145.08 deg |
| − | </source> | + | </syntaxhighlight> |
| − | | |
| − | = The Script =
| |
| − | <source lang="python">
| |
| − | '''
| |
| − | (c) 2010 Thomas Holder
| |
| − | '''
| |
| − | | |
| − | from pymol import cmd, stored, CmdException
| |
| − | from chempy import cpv
| |
| − | import math
| |
| − | | |
| − | def _vec_sum(vec_list):
| |
| − | # this is the same as
| |
| − | # return numpy.array(vec_list).sum(0).tolist()
| |
| − | vec = cpv.get_null()
| |
| − | for x in vec_list:
| |
| − | vec = cpv.add(vec, x)
| |
| − | return vec
| |
| − | | |
| − | def _mean_and_std(x):
| |
| − | # this is the same as
| |
| − | # return (numpy.mean(x), numpy.std(x, ddof=1))
| |
| − | N = len(x)
| |
| − | if N < 2:
| |
| − | return (x[0], 0.0)
| |
| − | mu = sum(x)/float(N)
| |
| − | var = sum((i - mu)**2 for i in x) / float(N - 1)
| |
| − | return (mu, var**0.5)
| |
| − | | |
| − | def _common_orientation(selection, vec, visualize=1, quiet=0):
| |
| − | '''
| |
| − | Common part of different helix orientation functions. Does calculate
| |
| − | the center of mass and does the visual feedback.
| |
| − | '''
| |
| − | stored.x = []
| |
| − | cmd.iterate_state(-1, '(%s) and name CA' % (selection),
| |
| − | 'stored.x.append([x,y,z])')
| |
| − | if len(stored.x) < 2:
| |
| − | print 'warning: count(CA) < 2'
| |
| − | raise CmdException
| |
| − | center = cpv.scale(_vec_sum(stored.x), 1./len(stored.x))
| |
| − | if visualize:
| |
| − | scale = cpv.distance(stored.x[0], stored.x[-1])
| |
| − | visualize_orientation(vec, center, scale, True)
| |
| − | cmd.zoom(selection, buffer=2)
| |
| − | if not quiet:
| |
| − | print 'Center: (%.2f, %.2f, %.2f) Direction: (%.2f, %.2f, %.2f)' % tuple(center + vec)
| |
| − | return center, vec
| |
| − | | |
| − | def visualize_orientation(direction, center=[0,0,0], scale=1.0, symmetric=False, color='green', color2='red'):
| |
| − | '''
| |
| − | Draw an arrow. Helper function for "helix_orientation" etc.
| |
| − | '''
| |
| − | from pymol import cgo
| |
| − | color_list = cmd.get_color_tuple(color)
| |
| − | color2_list = cmd.get_color_tuple(color2)
| |
| − | if symmetric:
| |
| − | scale *= 0.5
| |
| − | end = cpv.add(center, cpv.scale(direction, scale))
| |
| − | radius = 0.3
| |
| − | obj = [cgo.SAUSAGE]
| |
| − | obj.extend(center)
| |
| − | obj.extend(end)
| |
| − | obj.extend([
| |
| − | radius,
| |
| − | 0.8, 0.8, 0.8,
| |
| − | ])
| |
| − | obj.extend(color_list)
| |
| − | if symmetric:
| |
| − | start = cpv.sub(center, cpv.scale(direction, scale))
| |
| − | obj.append(cgo.SAUSAGE)
| |
| − | obj.extend(center)
| |
| − | obj.extend(start)
| |
| − | obj.extend([
| |
| − | radius,
| |
| − | 0.8, 0.8, 0.8,
| |
| − | ])
| |
| − | obj.extend(color2_list)
| |
| − | coneend = cpv.add(end, cpv.scale(direction, 4.0*radius))
| |
| − | obj.append(cgo.CONE)
| |
| − | obj.extend(end)
| |
| − | obj.extend(coneend)
| |
| − | obj.extend([
| |
| − | radius * 1.75,
| |
| − | 0.0,
| |
| − | ])
| |
| − | obj.extend(color_list * 2)
| |
| − | obj.extend([
| |
| − | 1.0, 1.0, # Caps
| |
| − | ])
| |
| − | cmd.load_cgo(obj, cmd.get_unused_name('oriVec'), zoom=0)
| |
| − | | |
| − | def cafit_orientation(selection, visualize=1, quiet=0):
| |
| − | '''
| |
| − | DESCRIPTION
| |
| − | | |
| − | Get the center and direction of a peptide by least squares
| |
| − | linear fit on CA atoms.
| |
| − | | |
| − | USAGE
| |
| − | | |
| − | cafit_orientation selection [, visualize]
| |
| − | | |
| − | NOTES
| |
| − | | |
| − | Requires python module "numpy".
| |
| − | | |
| − | SEE ALSO
| |
| − | | |
| − | helix_orientation
| |
| − | '''
| |
| − | visualize, quiet = int(visualize), int(quiet)
| |
| − | import numpy
| |
| − | stored.x = list()
| |
| − | cmd.iterate_state(-1, '(%s) and name CA' % (selection),
| |
| − | 'stored.x.append([x,y,z])')
| |
| − | x = numpy.array(stored.x)
| |
| − | U,s,Vh = numpy.linalg.svd(x - x.mean(0))
| |
| − | vec = cpv.normalize(Vh[0])
| |
| − | if cpv.dot_product(vec, x[-1] - x[0]) < 0:
| |
| − | vec = cpv.negate(vec)
| |
| − | return _common_orientation(selection, vec, visualize, quiet)
| |
| − | | |
| − | def loop_orientation(selection, visualize=1, quiet=0):
| |
| − | '''
| |
| − | DESCRIPTION
| |
| − | | |
| − | Get the center and approximate direction of a peptide. Works for any
| |
| − | secondary structure.
| |
| − | Averages direction of N(i)->C(i) pseudo bonds.
| |
| − | | |
| − | USAGE
| |
| − | | |
| − | loop_orientation selection [, visualize]
| |
| − | | |
| − | SEE ALSO
| |
| − | | |
| − | helix_orientation
| |
| − | '''
| |
| − | visualize, quiet = int(visualize), int(quiet)
| |
| − | stored.x = dict()
| |
| − | cmd.iterate_state(-1, '(%s) and name N+C' % (selection),
| |
| − | 'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
| |
| − | vec = cpv.get_null()
| |
| − | count = 0
| |
| − | for x in stored.x.itervalues():
| |
| − | if 'C' in x and 'N' in x:
| |
| − | vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
| |
| − | count += 1
| |
| − | if count == 0:
| |
| − | print 'warning: count == 0'
| |
| − | raise CmdException
| |
| − | vec = cpv.normalize(vec)
| |
| − | return _common_orientation(selection, vec, visualize, quiet)
| |
| − | | |
| − | def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
| |
| − | '''
| |
| − | DESCRIPTION
| |
| − | | |
| − | Get the center and direction of a helix as vectors. Will only work
| |
| − | for helices and gives slightly different results than loop_orientation.
| |
| − | Averages direction of C(i)->O(i) bonds.
| |
| − | | |
| − | USAGE
| |
| − | | |
| − | helix_orientation selection [, visualize [, sigma_cutoff]]
| |
| − | | |
| − | ARGUMENTS
| |
| − | | |
| − | selection = string: atom selection of helix
| |
| − | | |
| − | visualize = 0 or 1: show fitted vector as arrow {default: 1}
| |
| − | | |
| − | sigma_cutoff = float: drop outliers outside
| |
| − | (standard_deviation * sigma_cutoff) {default: 1.5}
| |
| − | | |
| − | SEE ALSO
| |
| − | | |
| − | angle_between_helices, helix_orientation_hbond, loop_orientation, cafit_orientation
| |
| − | '''
| |
| − | visualize, quiet, sigma_cutoff = int(visualize), int(quiet), float(sigma_cutoff)
| |
| − | stored.x = dict()
| |
| − | cmd.iterate_state(-1, '(%s) and name C+O' % (selection),
| |
| − | 'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
| |
| − | vec_list = []
| |
| − | count = 0
| |
| − | for x in stored.x.itervalues():
| |
| − | if 'C' in x and 'O' in x:
| |
| − | vec_list.append(cpv.sub(x['O'], x['C']))
| |
| − | count += 1
| |
| − | if count == 0:
| |
| − | print 'warning: count == 0'
| |
| − | raise CmdException
| |
| − | vec = _vec_sum(vec_list)
| |
| − | if count > 2 and sigma_cutoff > 0:
| |
| − | angle_list = [cpv.get_angle(vec, x) for x in vec_list]
| |
| − | angle_mu, angle_sigma = _mean_and_std(angle_list)
| |
| − | vec_list = [vec_list[i] for i in range(len(vec_list))
| |
| − | if abs(angle_list[i] - angle_mu) < angle_sigma * sigma_cutoff]
| |
| − | if not quiet:
| |
| − | print 'Dropping %d outlier(s)' % (len(angle_list) - len(vec_list))
| |
| − | vec = _vec_sum(vec_list)
| |
| − | vec = cpv.normalize(vec)
| |
| − | return _common_orientation(selection, vec, visualize, quiet)
| |
| − | | |
| − | def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
| |
| − | '''
| |
| − | DESCRIPTION
| |
| − | | |
| − | Get the center and direction of a helix as vectors. Will only work
| |
| − | for alpha helices and gives slightly different results than
| |
| − | helix_orientation. Averages direction of O(i)->N(i+4) hydrogen bonds.
| |
| − | | |
| − | USAGE
| |
| − | | |
| − | helix_orientation selection [, visualize [, cutoff]]
| |
| − | | |
| − | ARGUMENTS
| |
| − | | |
| − | cutoff = float: maximal hydrogen bond distance {default: 3.5}
| |
| − | | |
| − | SEE ALSO
| |
| − | | |
| − | helix_orientation
| |
| − | '''
| |
| − | visualize, quiet, cutoff = int(visualize), int(quiet), float(cutoff)
| |
| − | stored.x = dict()
| |
| − | cmd.iterate_state(-1, '(%s) and name N+O' % (selection),
| |
| − | 'stored.x.setdefault(resv, dict())[name] = x,y,z')
| |
| − | vec_list = []
| |
| − | for resi in stored.x:
| |
| − | resi_other = resi + 4
| |
| − | if 'O' in stored.x[resi] and resi_other in stored.x:
| |
| − | if 'N' in stored.x[resi_other]:
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| − | vec = cpv.sub(stored.x[resi_other]['N'], stored.x[resi]['O'])
| |
| − | if cpv.length(vec) < cutoff:
| |
| − | vec_list.append(vec)
| |
| − | if len(vec_list) == 0:
| |
| − | print 'warning: count == 0'
| |
| − | raise CmdException
| |
| − | vec = _vec_sum(vec_list)
| |
| − | vec = cpv.normalize(vec)
| |
| − | return _common_orientation(selection, vec, visualize, quiet)
| |
| − | | |
| − | def angle_between_helices(selection1, selection2, method='helix_orientation', visualize=1, quiet=0):
| |
| − | '''
| |
| − | 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}
| |
| − | or int: 0: helix_orientation, 1: helix_orientation_hbond,
| |
| − | 2: loop_orientation, 3: cafit_orientation
| |
| − | | |
| − | visualize = 0 or 1: show fitted vector as arrow {default: 1}
| |
| − | | |
| − | SEE ALSO
| |
| | | | |
| − | helix_orientation, helix_orientation_hbond, loop_orientation, cafit_orientation
| + | == See Also == |
| − | '''
| |
| − | visualize, quiet = int(visualize), int(quiet)
| |
| − | methods = {
| |
| − | '0': helix_orientation,
| |
| − | '1': helix_orientation_hbond,
| |
| − | '2': loop_orientation,
| |
| − | '3': cafit_orientation,
| |
| − | }
| |
| − | methods.update((x.__name__, x) for x in methods.values())
| |
| − | try:
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| − | orientation = methods[str(method)]
| |
| − | except KeyError:
| |
| − | print 'no such method:', method
| |
| − | raise CmdException
| |
| − | if not quiet:
| |
| − | print 'Using method:', orientation.__name__
| |
| − | cen1, dir1 = orientation(selection1, visualize, quiet=1)
| |
| − | cen2, dir2 = orientation(selection2, visualize, quiet=1)
| |
| − | angle = cpv.get_angle(dir1, dir2)
| |
| − | angle_deg = math.degrees(angle)
| |
| − | if not quiet:
| |
| − | print 'Angle: %.2f deg' % (angle_deg)
| |
| − | if visualize:
| |
| − | cmd.zoom('(%s) or (%s)' % (selection1, selection2), buffer=2)
| |
| − | return angle_deg
| |
| | | | |
| − | cmd.extend('helix_orientation', helix_orientation)
| + | * [[angle_between_domains]] |
| − | cmd.extend('helix_orientation_hbond', helix_orientation_hbond)
| |
| − | cmd.extend('loop_orientation', loop_orientation)
| |
| − | cmd.extend('cafit_orientation', cafit_orientation)
| |
| − | cmd.extend('angle_between_helices', angle_between_helices)
| |
| − | </source>
| |
| | | | |
| − | [[Category:Plugins]]
| |
| | [[Category:Structural_Biology_Scripts]] | | [[Category:Structural_Biology_Scripts]] |
| | + | [[Category:Pymol-script-repo]] |
