def object_tfm_interpolate(object_properties, number_of_frames, frameno):
tmpnames = []
for objnm, properties in object_properties.items():
[source_tfm, target_tfm, reverse, color,
small_molecule] = properties[:5]
transparency_range = properties[5] if len(properties) > 5 else None
frame = frameno
if reverse: frame = number_of_frames - frame
tfm = intermediate_tfm(source_tfm, target_tfm, number_of_frames, frame)
if objnm == "lipid": lipid_decimate(number_of_frames, frameno)
tmpnm = objnm + str(frameno)
cmd.copy(tmpnm, objnm, zoom=0)
cmd.transform_selection(tmpnm, tfm)
transparency = -1
if transparency_range:
transparency = transparency_range[0] \
+ float(frameno)/number_of_frames*(transparency_range[1]-transparency_range[0])
if small_molecule:
if objnm == "lipid":
style_lipid(tmpnm)
else:
style_substrate(tmpnm, mol_color[objnm], transparency)
else:
clump_representation([tmpnm],
color,
tmpnm,
small_molecule=small_molecule,
transparency=transparency)
tmpnames.append(tmpnm)
return tmpnames
def rotateline(Pos1,Pos2,degangle,molecule): diffvector = vector(Pos1,Pos2) uvector = unitvector(diffvector)[0] xyz = getxyz(Pos2)[0] rmat = rotmat(radangle(float(degangle)),uvector,xyz) cmd.transform_selection(molecule,rmat) return(None)
def rotateline(Pos1, Pos2, degangle, molecule):
diffvector = vector(Pos1, Pos2)
uvector = unitvector(diffvector)[0]
xyz = getxyz(Pos2)[0]
rmat = rotmat(radangle(float(degangle)), uvector, xyz)
cmd.transform_selection(molecule, rmat)
return (None)
def alpraxin(sel):
"""run alpraxin and apply transformation matrix"""
with TemporaryDirectory():
pdbfn = writePdb(sel, "in_")
outfn = sel + ".pdb"
systemCommand(["alpraxin", "-o", outfn, pdbfn])
tmat = readTransformationMatrixFromPdbRemark(outfn)
cmd.transform_selection(sel, tmat)
def transform_by_camera_rotation():
view = list(cmd.get_view())
M = view[0:3] + [-view[12]] + \
view[3:6] + [-view[13]] + \
view[6:9] + [-view[14]] + \
view[12:15] + [1.]
cmd.transform_selection('(all)', M, transpose=1)
cmd.set_view([1,0,0,0,1,0,0,0,1] + view[9:])
def orient_origin(selection):
shift_to_center(selection)
cmd.orient(selection)
cv = list(cmd.get_view(quiet=1))
#cmd.origin(selection, position=origin1)
cmd.transform_selection(selection,
cv[0:3] + [0.0] + cv[3:6] + [0.0] + cv[6:9] +
[0.0] + cv[12:15] + [1.0],
transpose=1)
cmd.reset()
def toline(Pos1, Pos2, atom, molecule, dist=1):
dist = float(dist)
diffvector = vector(atom, Pos2)
move = transmat(diffvector)
cmd.transform_selection("%s" % molecule, move)
diffvector = vector(Pos1, Pos2)
uvector = unitvector(diffvector)[0]
move = transmat(uvector, dist)
cmd.transform_selection("%s" % molecule, move)
return (None)
def toline(Pos1,Pos2,atom,molecule,dist=1):
dist = float(dist)
diffvector = vector(atom,Pos2)
move = transmat(diffvector)
cmd.transform_selection("%s"%molecule,move)
diffvector = vector(Pos1,Pos2)
uvector = unitvector(diffvector)[0]
move = transmat(uvector,dist)
cmd.transform_selection("%s"%molecule,move)
return(None)
def supalm(template, toalign):
"""run supalm and apply transformation matrix"""
if(toalign == template):
message("ERROR Please choose different models for superimposition\n")
return
with TemporaryDirectory('supalm'):
f1 = writePdb(template)
f2 = writePdb(toalign, "in_")
outfn = toalign + ".pdb"
systemCommand(['supalm', '-o', outfn, '--prog2=crysol'] + [f1, f2])
tmat = readTransformationMatrixFromPdbRemark(outfn)
nsd = readNSDFromSupalmPdb(outfn)
cmd.transform_selection(toalign, tmat)
message("SUPALM NSD = " + repr(nsd))
def rdkitalign(mobile, target, mobile_state=-1, target_state=-1,
reflect=0, max_iters=500):
"""
DESCRIPTION
Align two molecules using RDKit.
USAGE
rdkitalign mobile, target, [, target_state [, mobile_state [, reflect [,
max_iters ]]]]
NOTES
"rdkitalign" uses RDKit's alignment interface. "target_state"
and "mobile_state" indicate the states of the molecules that will be used
the alignment, though all states will be transformed accordingly. These
default to -1, the use of the currently visible states.
"reflect" reflects the conformation of the mobile molecule (defaults to 0).
EXAMPLES
# align molA onto molB
rdkitalign molA, molB
"""
print("Aligning %s to %s with RDKit" % (mobile, target))
mobile_mol = obj_to_rdmol(mobile, int(mobile_state))
target_mol = obj_to_rdmol(target, int(target_state))
try:
rmsd, trans_matrix = rdMolAlign.GetAlignmentTransform(
mobile_mol, target_mol, reflect=bool(int(reflect)),
maxIters=int(max_iters))
except RuntimeError:
print " RDKitAlign-Error: alignment failed."
return False
cmd.transform_selection(mobile, trans_matrix.flatten().tolist(),
homogenous=1)
if HAS_NP:
inv_array_string = "["+", ".join(
["%.4g" % x for x
in np.linalg.inv(trans_matrix).flatten().tolist()])+"]"
print("Molecules are aligned. To reverse the alignment, run:")
print('cmd.transform_selection("%s", %s, homogenous=1)' % (
mobile, inv_array_string))
print("RMSD: %.4f" % rmsd)
def open3dalign(mobile, target, mobile_state=-1, target_state=-1,
options=0, max_iters=500):
"""
DESCRIPTION
Align two molecules using Open3DAlign.
USAGE
open3dalign mobile, target, [, target_state [, mobile_state [, options [,
max_iters ]]]]
NOTES
"open3dalign" uses RDKit's interface for Open3DAlign. "target_state"
and "mobile_state" indicate the states of the molecules that will be used
the alignment, though all states will be transformed accordingly. These
default to -1, the use of the currently visible states.
For description of other parameters, see RDKit's Open3DAlign documentation:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolAlign-module.html#GetO3A
EXAMPLES
# align molA onto molB
open3dalign molA, molB
"""
print("Aligning %s to %s with Open3DAlign" % (mobile, target))
mobile_mol = obj_to_rdmol(mobile, int(mobile_state))
target_mol = obj_to_rdmol(target, int(target_state))
alignment = rdMolAlign.GetO3A(mobile_mol, target_mol, options=int(options),
maxIters=int(max_iters))
rmsd, trans_matrix = alignment.Trans()
cmd.transform_selection(mobile, trans_matrix.flatten().tolist(),
homogenous=1)
if HAS_NP:
inv_array_string = "["+", ".join(
["%.4g" % x for x
in np.linalg.inv(trans_matrix).flatten().tolist()])+"]"
print("Molecules are aligned. To reverse the alignment, run:")
print('cmd.transform_selection("%s", %s, homogenous=1)' % (
mobile, inv_array_string))
score = alignment.Score()
print("RMSD: %.4f" % rmsd)
print("Score: %.4f" % score)
def supalm(template, toalign):
"""run supalm and apply transformation matrix"""
if(toalign == template):
message("ERROR Please choose different models for superimposition\n")
return
with TemporaryDirectory('supalm'):
f1 = writePdb(template)
f2 = writePdb(toalign, "in_")
outfn = toalign + ".pdb"
systemCommand(['supalm', '-o', outfn, '--prog2=crysol'] + [f1, f2])
#reloading file approach, needed for ATSAS 2.7.1
#cmd.delete(toalign)
#cmd.load(outfn)
#and the following works properly for ATSAS 2.7.2
tmat = readTransformationMatrixFromPdbRemark(outfn)
nsd = readNSDFromSupalmPdb(outfn)
cmd.transform_selection(toalign, tmat)
message("SUPALM NSD = " + repr(nsd))
def supalm(template, toalign):
"""run supalm and apply transformation matrix"""
if (toalign == template):
message("ERROR Please choose different models for superimposition\n")
return
with TemporaryDirectory('supalm'):
f1 = writePdb(template)
f2 = writePdb(toalign, "in_")
outfn = toalign + ".pdb"
sargs = ['supalm', '-o', outfn]
sargs.append('--prog2=crysol')
sargs.append('--enantiomorphs=N')
sargs.append(f1)
sargs.append(f2)
systemCommand(sargs)
tmat = readTransformationMatrixFromPdbRemark(outfn)
nsd = readNSDFromSupalmPdb(outfn)
cmd.transform_selection(toalign, tmat)
message("SUPALM NSD = " + repr(nsd))
def transformar(selection): ''' DESCRIPTION Rotate the molecule and draw the inertia axis. ''' rotacion_orig(selection) model_rot = cmd.transform_selection(selection, transf_array, homogenous=0, transpose=1); draw_inertia_axis(selection)
def alpraxin(models, enantiomode):
"""run alpraxin and apply transformation matrix"""
sel = " or ".join(models)
with TemporaryDirectory():
pdbfn = writePdb(sel, "in_")
outfn = sel + ".pdb"
outfn = outfn.replace(" ", "")
aargs = ["alpraxin", pdbfn]
if ('yes' == enantiomode):
message("ALPRAXIN will create enantiomer as new model")
aargs.append("--enantiomorph=Y")
aargs.append("-o")
aargs.append(outfn)
systemCommand(aargs)
if ('no' == enantiomode):
tmat = readTransformationMatrixFromPdbRemark(outfn)
cmd.transform_selection(sel, tmat)
if ('yes' == enantiomode):
cmd.load(outfn, "enantiomorph_" + sel)
def princ_align(selection='(all)'):
model = cmd.get_model(f"{selection} and name CA")
coords = np.array([at.coord for at in model.atom])
try:
center = np.mean(coords, axis=0)
except NameError:
print(
"This command will not work without numpy.\nConsider installing numpy (or anaconda, provides numpy)."
)
return
coords -= center
eig_vec = get_principal_axes(coords)
# Now i have to calculate angles...
# largest should be aligned with Z-axis
x0 = np.array([1, 0, 0])
y0 = np.array([0, 1, 0])
z0 = np.array([0, 0, 1])
# Transform everything such that it is centered around
# selection's center, and rotated
# Such that the principal axes of the selection
# align with those of the frame of reference
# For some reason x0 is the right one to align with the z-axis
rot_mat = rotation_matrix_from_vectors(eig_vec[0], x0)
TTT = [
*rot_mat[0], -center[0], *rot_mat[1], -center[1], *rot_mat[2],
-center[2], 0, 0, 0, 1
]
cmd.transform_selection('(all)', TTT, transpose=1)
# Finally center all
cmd.center()
return eig_vec # Just in case i need them later
def tx(obj_name=None,
tran_before=[0, 0, 0],
rot=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
tran_after=[0, 0, 0]):
"""Transforms an object.
Args:
- obj_name - string
- tran_before - a 3x1 translation vector applied before rotation
- rot - a 3x3 rotation matrix
- tran_after - a 3x1 translation vector applied after rotation
"""
if obj_name is None:
print(tx.__doc__)
else:
rot_tran_mat = np.array(rot)
rot_tran_mat = np.append(rot_tran_mat,
np.transpose([tran_after]),
axis=1)
rot_tran_mat = np.append(rot_tran_mat, [tran_before + [1]], axis=0)
pymol_rot_tran_vals = [v for row in rot_tran_mat for v in row]
cmd.transform_selection(obj_name,
matrix=pymol_rot_tran_vals,
homogenous=0)
def translacion_cM(selection): ''' DESCRIPTION Translate the center of mass of the molecule to the origin. ''' model = cmd.get_model(selection) totmass = 0.0 x,y,z = 0,0,0 for a in model.atom: m = a.get_mass() x += a.coord[0]*m y += a.coord[1]*m z += a.coord[2]*m totmass += m cM = numpy.array([x/totmass, y/totmass, z/totmass]) trans_array = ([1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, -cM[0], -cM[1], -cM[2], 1]) model_trans = cmd.transform_selection(selection, trans_array)
def affine(selection, sh_x=0.1, sh_y=0.1):
"""
Perform distortion from circular geometry on scaffold
Peform rotation-translation-rotation on a PDB
1. load scaffold
2. apply transfromation
sh_x,sh_y = shear factors (x,y)
"""
# set-up transformation
shift0 = 0.0
shift1 = 0.0
shift2 = 0.0
# sh_x = 0.1 # shear factor for transformation in x
# sh_y = 0.1 # shear factor for transformation in y
rotMat = [
1.0, sh_x, 0.0, shift0, sh_y, 1.0, 0.0, shift1, 0.0, 0.0, 1.0, shift2,
0.0, 0.0, 0.0, 1.0
]
# perform the transformation
return cmd.transform_selection(selection, rotMat)
def sasref(SaxsDataFileName, models = [], mode = 'local', viewer='sasplot'):
'''Execute SASREF and apply obtained transformations to subunits'''
global modelingRuns
#parameter configuration
#local refinment (to reproduce MASSHA behaviour):
confp = {'spst':'1.0', # spatial step, SASREF default is 5.0 Angstrom
'anst':'5.0', #angular step, SASREF default is 20 degrees
'init':'1.0', # Initial annealing temperature (def= 10)
'sche':'0.9', # Annealing schedule factor
'iter':'500', # Max # of iterations at each T (def = 10000)
'maxs':' 50', # Max # of successes at each T (def = 1000)
'mins':' 10', # Min # of successes to continue (def = 100)
'maxa':' 10', # Max # of annealing steps (def = 100)
'msol':' 1', # Max # of solutions to store (def = 1)
'shft':' '} #xyz init shift, blank for local
#0.0 for global search
if 'global' == mode: #settings for default global search
confp['spst'] = '5.0'
confp['anst'] = '20.0'
confp['init'] = '10.0'
confp['sche'] = '0.9'
confp['iter'] = '10000'
confp['maxs'] = '1000'
confp['mins'] = '100'
confp['maxa'] = '100'
confp['msol'] = '1'
confp['shft'] = '0.0'
if False == os.path.isfile(SaxsDataFileName):
message("SAXS .dat file \'"+SaxsDataFileName+"\' not found")
return 113
fileFullPath = os.path.abspath(SaxsDataFileName)
prefix = 'sasref'
modelingRuns += 1
prefix = prefix + repr(modelingRuns)
numberOfSubunits = len(models);
with TemporaryDirectory(prefix) as tmpdir:
#sasref can not deal with long path/names
tmpsaxsfn = os.path.basename(SaxsDataFileName)
tmpdir.copy_in(fileFullPath, tmpsaxsfn);
sc = ""
sc += "Expert ! Configuration mode\n"
sc += prefix + " ! logfilename\n"
sc += prefix + " ! projectDescription\n"
sc += " ! initRandomSeed\n"
sc += repr(numberOfSubunits) + " ! totalNumberOfSubunits\n"
sc += "P1 ! Symmetry\n"
sc += "1 ! totalNumberOfScatteringCurves\n"
sc += "N ! KratkyGeometry\n"
sc += "1,2 ! Input first & last subunits in 1-st construct\n"
sc += tmpsaxsfn+ " ! Enter file name, 1-st experimental data\n"
sc += " ! Angular units input file\n"
sc += "1.0 ! Fitting range in fractions of Smax\n"
count = 1
for m in models:
pdbtmpfn = writePdb(m)
pdbtmpfn = os.path.basename(pdbtmpfn)
fid = os.path.splitext(pdbtmpfn)[0]
#print "abs: " + m + " and temp: "+pdbtmpfn + "while id: "+fid;
#tmpdir.copy_in(m, pdbtmpfn);
#compute amplitudes
systemCommand(["crysol"] + ["-p"] + [fid] + [pdbtmpfn])
print "computed alm for : "+ fid +"\n"
sc += fid+".alm"+"! subunit " +repr(count)+" amplitudes\n"
sc += "0.0 ! Initial rotation by alpha\n"
sc += "0.0 ! Initial rotation by beta\n"
sc += "0.0 ! Initial rotation by gamma\n"
sc += confp['shft']+" ! Initial shift along X\n"
sc += confp['shft']+" ! Initial shift along Y\n"
sc += confp['shft']+" ! Initial shift along Z\n"
sc += "N ! Movements limitations of subunit: N/F/X/Y/Z/D\n"
sc += confp['spst'] + " ! Spatial step in Angstrom\n"
sc += confp['anst'] + " ! Angular step in degrees\n"
#continue with rest of commands
sc += " ! Cross penalty weight\n"
sc += " ! Disconnectivity penalty weight\n"
sc += " ! Docking penalty weight\n"
sc += " ! File name, contacts conditions, CR for none\n"
sc += "U ! Expected particle shape: <P>rolate, <O>blate or <U>nknown\n"
sc += " ! Shift penalty weight \n"
sc += confp['init'] + " ! Initial annealing temperature (def= 10) \n"
sc += confp['sche'] + " ! Annealing schedule factor\n"
sc += confp['iter'] + " ! Max # of iterations at each T (def = 10000)\n"
sc += confp['maxs'] + " ! Max # of successes at each T (def = 1000)\n"
sc += confp['mins'] +" ! Min # of successes to continue (def = 100)\n"
sc += confp['maxa'] +" ! Max # of annealing steps (def = 100)\n"
sc += confp['msol']+" ! Max # of solutions to store (def = 1)\n"
comfn = 'setup_sasref.com'
with open(comfn, 'w') as commandfile:
commandfile.write(sc)
with open(comfn, 'r') as commandfile:
systemCommand(['sasref'], stdin=commandfile)
outpdb = prefix + ".pdb"
#read and apply movements
moves = parseEulerAngles(outpdb);
idx = 0
for mov in moves:
tmat = anglesToTTTMat(mov)
cmd.transform_selection(models[idx], tmat)
idx = idx+1
outpdbfn = tmpdir.move_out_numbered(prefix + ".pdb", prefix, '.pdb')
message( ".pdb file written to " + outpdbfn)
cf = tmpdir.move_out_numbered(prefix + "-1.fit", prefix, '.fit')
message( ".fit file written to " + cf)
openSingleDatFile(viewer, cf)
return
def sasref(SaxsDataFileName, models=[], mode='local', viewer='primus'):
'''Execute SASREF and apply obtained transformations to subunits'''
global modelingRuns
#parameter configuration
#local refinment (to reproduce MASSHA behaviour):
confp = {
'spst': '1.0', # spatial step, SASREF default is 5.0 Angstrom
'anst': '5.0', #angular step, SASREF default is 20 degrees
'init': '1.0', # Initial annealing temperature (def= 10)
'sche': '0.9', # Annealing schedule factor
'iter': '500', # Max # of iterations at each T (def = 10000)
'maxs': ' 50', # Max # of successes at each T (def = 1000)
'mins': ' 10', # Min # of successes to continue (def = 100)
'maxa': ' 10', # Max # of annealing steps (def = 100)
'msol': ' 1', # Max # of solutions to store (def = 1)
'shft': ' '
} #xyz init shift, blank for local
#0.0 for global search
if 'global' == mode: #settings for default global search
confp['spst'] = '5.0'
confp['anst'] = '20.0'
confp['init'] = '10.0'
confp['sche'] = '0.9'
confp['iter'] = '10000'
confp['maxs'] = '1000'
confp['mins'] = '100'
confp['maxa'] = '100'
confp['msol'] = '1'
confp['shft'] = '0.0'
if False == os.path.isfile(SaxsDataFileName):
message("SAXS .dat file \'" + SaxsDataFileName + "\' not found")
return 113
fileFullPath = os.path.abspath(SaxsDataFileName)
prefix = 'sasref'
modelingRuns += 1
prefix = prefix + repr(modelingRuns)
numberOfSubunits = len(models)
with TemporaryDirectory(prefix) as tmpdir:
#sasref can not deal with long path/names
tmpsaxsfn = os.path.basename(SaxsDataFileName)
tmpdir.copy_in(fileFullPath, tmpsaxsfn)
sc = ""
sc += "Expert ! Configuration mode\n"
sc += prefix + " ! logfilename\n"
sc += prefix + " ! projectDescription\n"
sc += " ! initRandomSeed\n"
sc += repr(numberOfSubunits) + " ! totalNumberOfSubunits\n"
sc += "P1 ! Symmetry\n"
sc += "1 ! totalNumberOfScatteringCurves\n"
sc += "N ! KratkyGeometry\n"
sc += "1,2 ! Input first & last subunits in 1-st construct\n"
sc += tmpsaxsfn + " ! Enter file name, 1-st experimental data\n"
sc += " ! Angular units input file\n"
sc += "1.0 ! Fitting range in fractions of Smax\n"
count = 1
for m in models:
pdbtmpfn = writePdb(m)
pdbtmpfn = os.path.basename(pdbtmpfn)
fid = os.path.splitext(pdbtmpfn)[0]
#print "abs: " + m + " and temp: "+pdbtmpfn + "while id: "+fid;
#tmpdir.copy_in(m, pdbtmpfn);
#compute amplitudes
systemCommand(["crysol"] + ["-p"] + [fid] + [pdbtmpfn])
print "computed alm for : " + fid + "\n"
sc += fid + ".alm" + "! subunit " + repr(count) + " amplitudes\n"
sc += "0.0 ! Initial rotation by alpha\n"
sc += "0.0 ! Initial rotation by beta\n"
sc += "0.0 ! Initial rotation by gamma\n"
sc += confp['shft'] + " ! Initial shift along X\n"
sc += confp['shft'] + " ! Initial shift along Y\n"
sc += confp['shft'] + " ! Initial shift along Z\n"
sc += "N ! Movements limitations of subunit: N/F/X/Y/Z/D\n"
sc += confp['spst'] + " ! Spatial step in Angstrom\n"
sc += confp['anst'] + " ! Angular step in degrees\n"
#continue with rest of commands
sc += " ! Cross penalty weight\n"
sc += " ! Disconnectivity penalty weight\n"
sc += " ! Docking penalty weight\n"
sc += " ! File name, contacts conditions, CR for none\n"
sc += "U ! Expected particle shape: <P>rolate, <O>blate or <U>nknown\n"
sc += " ! Shift penalty weight \n"
sc += confp[
'init'] + " ! Initial annealing temperature (def= 10) \n"
sc += confp['sche'] + " ! Annealing schedule factor\n"
sc += confp[
'iter'] + " ! Max # of iterations at each T (def = 10000)\n"
sc += confp[
'maxs'] + " ! Max # of successes at each T (def = 1000)\n"
sc += confp[
'mins'] + " ! Min # of successes to continue (def = 100)\n"
sc += confp['maxa'] + " ! Max # of annealing steps (def = 100)\n"
sc += confp['msol'] + " ! Max # of solutions to store (def = 1)\n"
comfn = 'setup_sasref.com'
with open(comfn, 'w') as commandfile:
commandfile.write(sc)
if "win32" != platform:
with open(comfn, 'r') as commandfile:
systemCommand(['sasref'], stdin=commandfile)
#somehow this doesn't work on Windows with PyMOL 2.0
#there's an issue with the underlying libraries...
else:
os.system('sasref < setup_sasref.com')
outpdb = prefix + ".pdb"
#read and apply movements
moves = parseEulerAngles(outpdb)
idx = 0
for mov in moves:
tmat = anglesToTTTMat(mov)
cmd.transform_selection(models[idx], tmat)
idx = idx + 1
outpdbfn = tmpdir.move_out_numbered(prefix + ".pdb", prefix, '.pdb')
message(".pdb file written to " + outpdbfn)
cf = tmpdir.move_out_numbered(prefix + "-1.fit", prefix, '.fit')
message(".fit file written to " + cf)
openSingleDatFile(viewer, cf)
return
def tmalign(mobile,
target,
args='',
exe='TMalign',
ter=0,
transform=1,
object=None,
quiet=0):
"""
DESCRIPTION
TMalign wrapper
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
USAGE
tmalign mobile, target [, args [, exe ]]
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign executable {default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
SEE ALSO
tmscore, mmalign
"""
import subprocess
import tempfile
import os
import re
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
matrix_filename = tempfile.mktemp('.txt', 'matrix')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % mobile
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % target
if ter:
save = cmd.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele)
save(target_filename, target_ca_sele)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename, '-m', matrix_filename
] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
lines = process.stdout.readlines()
except OSError:
print('Cannot execute "%s", please provide full path to TMscore or '
'TMalign executable' % exe)
raise CmdException
finally:
os.remove(mobile_filename)
os.remove(target_filename)
# TMalign >= 2012/04/17
if os.path.exists(matrix_filename):
lines += open(matrix_filename).readlines()
os.remove(matrix_filename)
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(lines)
alignment = []
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = list(map(float, line.split()))
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = []
for i in range(3):
alignment.append(line_it.next().rstrip())
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print(line.rstrip())
if not quiet:
for i in range(0, len(alignment[0]) - 1, 78):
for line in alignment:
print(line[i:i + 78])
print('')
assert len(matrix) == 3 * 4
matrix.extend([0, 0, 0, 1])
if int(transform):
cmd.transform_selection('byobject (%s)' % mobile, matrix, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
cmd.iterate(mobile_ca_sele,
'mobile_idx.append("%s`%d" % (model, index))',
space=space)
cmd.iterate(target_ca_sele,
'target_idx.append("%s`%d" % (model, index))',
space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if len(mobile_idx) == len(target_idx) == len(alignment[2]):
cmd.rms_cur(' '.join(idx
for (idx, m) in zip(mobile_idx, alignment[1])
if m in ':.'),
' '.join(idx
for (idx, m) in zip(target_idx, alignment[1])
if m in ':.'),
matchmaker=4,
object=object)
else:
print('Could not load alignment object')
if not quiet and r is not None:
print('Found in output TM-score = %.4f' % r)
return r
def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object=None, quiet=0):
'''
DESCRIPTION
TMalign wrapper
Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
http://zhanglab.ccmb.med.umich.edu/TM-align/
USAGE
tmalign mobile, target [, args [, exe ]]
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d0 5 -L 100
exe = string: Path to TMalign executable {default: TMalign}
ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
at first TER record {default: 0}
SEE ALSO
tmscore, mmalign
'''
import subprocess
import tempfile
import os
import re
ter, quiet = int(ter), int(quiet)
mobile_filename = tempfile.mktemp('.pdb', 'mobile')
target_filename = tempfile.mktemp('.pdb', 'target')
matrix_filename = tempfile.mktemp('.txt', 'matrix')
mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
if ter:
save = cmd.save
else:
save = save_pdb_without_ter
save(mobile_filename, mobile_ca_sele)
save(target_filename, target_ca_sele)
exe = cmd.exp_path(exe)
args = [exe, mobile_filename, target_filename, '-m', matrix_filename] + args.split()
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
lines = process.stdout.readlines()
except OSError:
print('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe))
raise CmdException
finally:
os.remove(mobile_filename)
os.remove(target_filename)
# TMalign >= 2012/04/17
if os.path.exists(matrix_filename):
lines += open(matrix_filename).readlines()
os.remove(matrix_filename)
r = None
re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
rowcount = 0
matrix = []
line_it = iter(lines)
alignment = []
for line in line_it:
if 4 >= rowcount > 0:
if rowcount >= 2:
a = list(map(float, line.split()))
matrix.extend(a[2:5])
matrix.append(a[1])
rowcount += 1
elif line.lower().startswith(' -------- rotation matrix'):
rowcount = 1
elif line.startswith('(":" denotes'):
alignment = [line_it.next().rstrip() for i in range(3)]
else:
match = re_score.search(line)
if match is not None:
r = float(match.group(1))
if not quiet:
print(line.rstrip())
if not quiet:
for i in range(0, len(alignment[0]) - 1, 78):
for line in alignment:
print(line[i:i + 78])
print('')
assert len(matrix) == 3 * 4
matrix.extend([0, 0, 0, 1])
if int(transform):
cmd.transform_selection('byobject (%s)' % (mobile), matrix, homogenous=1)
# alignment object
if object is not None:
mobile_idx, target_idx = [], []
space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
cmd.iterate(mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
cmd.iterate(target_ca_sele, 'target_idx.append("%s`%d" % (model, index))', space=space)
for i, aa in enumerate(alignment[0]):
if aa == '-':
mobile_idx.insert(i, None)
for i, aa in enumerate(alignment[2]):
if aa == '-':
target_idx.insert(i, None)
if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
cmd.rms_cur(
' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
cycles=0, matchmaker=4, object=object)
else:
print('Could not load alignment object')
if not quiet and r is not None:
print('Found in output TM-score = %.4f' % (r))
return r
obj.extend( [ VERTEX ] + v1 + [ VERTEX ] + v0 )
obj.extend( [END] )
# then we load it into PyMOL
cmd.load_cgo(obj,'cgo06')
# position haemolysin through pore
if 1:
cmd.fetch("7ahl")
cmd.transform_selection("7ahl",
(0.70349078502033213, 0.19033556773811347, -0.68474258132841503, -11.993190038310882,
-0.15869362855324043, 0.98121371667870472, 0.10970571819737528, -29.939406659327624,
0.69276001846262825, 0.03148755047390385, 0.72048024614206196, -26.250180846754432,
0.0, 0.0, 0.0, 1.0))
cmd.show_as("cartoon","7ahl")
cmd.do("util.cbc")
cmd.set_view((\
-0.589197695, -0.440498680, 0.677344978,\
0.574851871, -0.817646086, -0.031699535,\
0.567794442, 0.370693058, 0.734975874,\
0.000004128, -0.000099868, -651.343872070,\
-4.874452114, 8.360315323, 11.387301445,\
528.689147949, 773.963684082, 0.000000000 ))
def alignZ(selection, name="tensor", state=1, scaling=0, quiet=1):
"""
DESCRIPTION
This script will draw the inertia tensor of the selection.
ARGUMENTS
selection = string: selection for the atoms included in the tensor calculation
name = string: name of the tensor object to be created {default: "tensor"}
state = int: state/model in the molecule object used in the tensor calculation
scaling = int {0, 1, or 2}: 0 for no scaling of the inertia axes, 1 for scaling
according to the molecular shape, 2 for scaling according to the eigenvalues
{default: 0}
EXAMPLE
PyMOL> run inertia_tensor.py
PyMOL> tensor molecule_object & i. 2-58+63-120 & n. n+ca+c, "tensor_model5_dom2", 5, 1
NOTES
Requires numpy.
"""
import numpy
totmass = 0.0
x_com, y_com, z_com = 0, 0, 0
model = cmd.get_model(selection, state)
for a in model.atom:
x_com += a.coord[0] * a.get_mass()
y_com += a.coord[1] * a.get_mass()
z_com += a.coord[2] * a.get_mass()
totmass += a.get_mass()
x_com /= totmass
y_com /= totmass
z_com /= totmass
if not int(quiet):
print()
print("Center of mass: ")
print()
print(x_com, y_com, z_com)
cmd.translate([-x_com, -y_com, -z_com], selection)
# Go back and rewrite the COM section to be a function, then it can
# be called again to ensure the translation was correct
x_com = 0.0
y_com = 0.0
z_com = 0.0
I = []
for index in range(9):
I.append(0)
for a in model.atom:
temp_x, temp_y, temp_z = a.coord[0], a.coord[1], a.coord[2]
temp_x -= x_com
temp_y -= y_com
temp_z -= z_com
I[0] += a.get_mass() * (temp_y ** 2 + temp_z ** 2)
I[4] += a.get_mass() * (temp_x ** 2 + temp_z ** 2)
I[8] += a.get_mass() * (temp_x ** 2 + temp_y ** 2)
I[1] -= a.get_mass() * temp_x * temp_y
I[3] -= a.get_mass() * temp_x * temp_y
I[2] -= a.get_mass() * temp_x * temp_z
I[6] -= a.get_mass() * temp_x * temp_z
I[5] -= a.get_mass() * temp_y * temp_z
I[7] -= a.get_mass() * temp_y * temp_z
tensor = numpy.array([(I[0:3]), (I[3:6]), (I[6:9])])
vals, vects = numpy.linalg.eig(tensor) # they come out unsorted, so the command below is needed
eig_ord = numpy.argsort(vals) # a thing to note is that here COLUMN i corrensponds to eigenvalue i.
ord_vals = vals[eig_ord]
ord_vects = vects[:, eig_ord].T
if not int(quiet):
print()
print("Inertia tensor z, y, x eigenvalues:")
print()
print(ord_vals)
print()
print("Inertia tensor z, y, x eigenvectors:")
print()
print(ord_vects)
if int(scaling) == 0:
norm_vals = [sum(numpy.sqrt(ord_vals / totmass)) / 3 for i in range(3)]
elif int(scaling) == 1:
normalizer = numpy.sqrt(max(ord_vals) / totmass)
norm_vals = normalizer / numpy.sqrt(ord_vals / totmass) * normalizer
norm_vals = norm_vals / (max(norm_vals) / min(norm_vals))
elif int(scaling) == 2:
normalizer = numpy.sqrt(max(ord_vals) / totmass)
norm_vals = numpy.sqrt(ord_vals / totmass)
start = [x_com, y_com, z_com]
ends = [[(norm_vals[0] - 1) * ord_vects[0][0], (norm_vals[0] - 1) * ord_vects[0][1], (norm_vals[0] - 1) * ord_vects[0][2]],
[(norm_vals[1] - 1) * ord_vects[1][0], (norm_vals[1] - 1) * ord_vects[1][1], (norm_vals[1] - 1) * ord_vects[1][2]],
[(norm_vals[2] - 1) * ord_vects[2][0], (norm_vals[2] - 1) * ord_vects[2][1], (norm_vals[2] - 1) * ord_vects[2][2]]]
import numpy as np
zvec = np.array([[0],[0],[1]])
newvec = np.array([[(norm_vals[0]-1) * ord_vects[0][2]],
[(norm_vals[1]-1) * ord_vects[1][2]],
[(norm_vals[2]-1) * ord_vects[2][2]]])
print(newvec)
norm = np.linalg.norm(newvec)
newvecnorm = np.divide(newvec, norm)
newvec = newvecnorm
print(newvec)
#create the rotation matrix, cross product, and dot prduct
rotmat = np.zeros((3,3))
cross = np.cross(newvec, zvec, axis=0)
crossnorm = np.linalg.norm(cross)
dot = np.dot(np.transpose(newvec), zvec)
vxmat = np.zeros((3,3))
vxmat[0,1] = -cross[2]
vxmat[0,2] = cross[1]
vxmat[1,0] = cross[2]
vxmat[1,2] = -cross[0]
vxmat[2,0] = -cross[1]
vxmat[2,1] = cross[0]
thirdterm = np.matmul(vxmat, vxmat) * (1/(1+dot))
rotmat = np.diag((1,1,1)) + vxmat + thirdterm
newvectrans = np.matmul(rotmat, newvec)
print("New vector after alignment: %s" % newvectrans)
cmd.transform_selection(selection, ([rotmat[0,0], rotmat[0,1], rotmat[0,2], 0.0,
rotmat[1,0], rotmat[1,1], rotmat[1,2], 0.0,
rotmat[2,0], rotmat[2,1], rotmat[2,2], 0.0,
0.0, 0.0, 0.0, 1.0]))
obj.extend([VERTEX] + v1 + [VERTEX] + v0)
obj.extend([END])
# then we load it into PyMOL
cmd.load_cgo(obj, 'cgo06')
# position haemolysin through pore
if 1:
cmd.fetch("7ahl")
cmd.transform_selection(
"7ahl",
(0.70349078502033213, 0.19033556773811347, -0.68474258132841503,
-11.993190038310882, -0.15869362855324043, 0.98121371667870472,
0.10970571819737528, -29.939406659327624, 0.69276001846262825,
0.03148755047390385, 0.72048024614206196, -26.250180846754432, 0.0,
0.0, 0.0, 1.0))
cmd.show_as("cartoon", "7ahl")
cmd.do("util.cbc")
cmd.set_view((\
-0.589197695, -0.440498680, 0.677344978,\
0.574851871, -0.817646086, -0.031699535,\
0.567794442, 0.370693058, 0.734975874,\
0.000004128, -0.000099868, -651.343872070,\
-4.874452114, 8.360315323, 11.387301445,\
528.689147949, 773.963684082, 0.000000000 ))
def align_to_axis(obj, atom_sel=None, axis="y", axes_dict=AXES):
"""
DESCRIPTION
Align protein to arbitrary axis with atom selection at origin.
USAGE
align_to_axis obj [, atom_sel [, axis ]]
NOTES
"atom_sel" must contain a single atom in "obj". If not specified, defaults
to N-terminal nitrogen. "axis" must be either x, y, or z, or coordinates
for an axis (e.g. [1, 2, 3]).
EXAMPLES
# align to y-axis with N-terminus at origin
align_to_axis obj
# align to x-axis
align_to_axis obj, axis=x
# align to y-axis with C-terminus at origin
cmd.select("cterm", "index %d:%d" % cmd.get_model("obj and not het", 1).get_residues()[-1])
align_to_axis obj, cterm and n. c
"""
if atom_sel is None:
stored.list = []
cmd.iterate("%s and not hetatm and n. n" % obj, "stored.list.append(resi)")
atom_sel = "%s and resi %s and n. n" % (obj, stored.list[0])
if axis.lower() in axes_dict:
target_vect = np.asarray(axes_dict[axis], dtype=np.float)
else:
try:
target_vect = np.asarray(ast.literal_eval(axis), dtype=np.float)
except (ValueError, TypeError):
print ("AlignToAxisError: Provided axis is of unknown format: %s." % (repr(axis)))
return False
target_vect = as_unit(target_vect)
cmd.reset()
origin_coord_list = cmd.get_model(atom_sel, 1).get_coord_list()
if len(origin_coord_list) != 1:
print (
"AlignToAxisError: atom selection should contain exactly 1 atom. Selection contains %d atoms."
% (len(origin_coord_list))
)
return False
origin_coord = np.asarray(origin_coord_list[0], dtype=np.float)
com_coord = np.asarray(get_com(obj), dtype=np.float)
com_vect = com_coord - origin_coord
pre_trans_vect = -com_coord
post_trans_vect = target_vect * np.linalg.norm(com_vect)
rot_matrix = create_rot_matrix(com_vect, target_vect)
trans_matrix = create_trans_matrix(rot_matrix, pre_trans_vect, post_trans_vect)
cmd.transform_selection(obj, trans_matrix.flatten().tolist(), homogenous=0)
cmd.reset()
