def writeDeformProfile(stiffness, pdb, filename='dp_out', \
select='protein and name CA', \
pdb_selstr='protein', loadToVMD=False):
"""Calculate deformability (plasticity) profile of molecule based on mechanical
stiffness matrix (see [EB08]_).
:arg model: this is an 3-dimensional NMA instance from a :class:`.ANM
calculations
:type model: :class:`.ANM`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`numpy.ndarray`
Note: selection can be done using ``select`` and ``pdb_selstr``.
``select`` defines ``model`` selection (used for building :class:`.ANM` model)
and ``pdb_selstr`` will be used in VMD program for visualization.
By default files are saved as *filename* and loaded to VMD program. To change
it use ``loadToVMD=False``.
Mean value of mechanical stiffness for molecule can be found in occupancy column
in PDB file.
"""
_, pdb = sliceAtoms(pdb, pdb_selstr)
_, coords = sliceAtoms(pdb, select)
meanStiff = np.mean(stiffness, axis=0)
out_mean = open(filename+'_mean.txt','w') # mean value of Kij for each residue
for nr_i, i in enumerate(meanStiff):
out_mean.write("{} {}\n".format(nr_i, i))
out_mean.close()
from collections import Counter
aa_counter = Counter(pdb.getResindices())
meanStiff_all = []
for i in range(coords.numAtoms()):
meanStiff_all.extend(list(aa_counter.values())[i]*[round(meanStiff[i], 2)])
writePDB(filename, pdb, occupancy=meanStiff_all)
LOGGER.info('PDB file with deformability profile has been saved.')
LOGGER.info('Creating TCL file.')
out_tcl = open(filename+'.tcl','w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./'+filename+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write('display depthcue off \ndisplay rendermode GLSL \naxes location Off \n')
out_tcl.write('color Display Background white \n')
out_tcl.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modmaterial 0 0 Diffuse \nmol modcolor 0 0 Occupancy \n')
out_tcl.write('menu colorscalebar on \n')
out_tcl.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
def writeDeformProfile(stiffness, pdb, filename='dp_out', \
select='protein and name CA', \
pdb_selstr='protein', loadToVMD=False):
"""Calculate deformability (plasticity) profile of molecule based on mechanical
stiffness matrix (see [EB08]_).
:arg stiffness: mechanical stiffness matrix
:type stiffness: :class:`~numpy.ndarray
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`~numpy.ndarray`
Note: selection can be done using ``select`` and ``pdb_selstr``.
``select`` defines ``model`` selection (used for building :class:`.ANM` model)
and ``pdb_selstr`` will be used in VMD program for visualization.
By default files are saved as *filename* and loaded to VMD program. To change
it use ``loadToVMD=False``.
Mean value of mechanical stiffness for molecule can be found in occupancy column
in PDB file.
"""
_, pdb = sliceAtoms(pdb, pdb_selstr)
_, coords = sliceAtoms(pdb, select)
meanStiff = np.mean(stiffness, axis=0)
out_mean = open(filename+'_mean.txt','w') # mean value of Kij for each residue
for nr_i, i in enumerate(meanStiff):
out_mean.write("{} {}\n".format(nr_i, i))
out_mean.close()
from collections import Counter
aa_counter = Counter(pdb.getResindices())
meanStiff_all = []
for i in range(coords.numAtoms()):
meanStiff_all.extend(list(aa_counter.values())[i]*[round(meanStiff[i], 2)])
writePDB(filename, pdb, occupancy=meanStiff_all)
LOGGER.info('PDB file with deformability profile has been saved.')
LOGGER.info('Creating TCL file.')
out_tcl = open(filename+'.tcl','w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./'+filename+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write('display depthcue off \ndisplay rendermode GLSL \naxes location Off \n')
out_tcl.write('color Display Background white \n')
out_tcl.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modmaterial 0 0 Diffuse \nmol modcolor 0 0 Occupancy \n')
out_tcl.write('menu colorscalebar on \n')
out_tcl.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
def writeVMDstiffness(model, pdb, indices, k_range, filename='vmd_out', \
selstr='protein and name CA', loadToVMD=True):
"""Returns three *filename* files: (1) PDB file with coordinates.
(2) TCL file containing vmd commands for loading PDB file with accurate
vmd representation. Pair of residues with selected *k_range* of
effective spring constant are shown in VMD respresentation with
solid line between them.
If more than one residue will be selected in *indices*, different pair
for each residue will be colored in the different colors.
(3) TXT file contains pair of residues with effective spring constant in
selected range *k_range*.
The effective spring constant calculation using ``buildSM`` method
from :class:`.ANM`.
.. note::
#. This function skips modes with zero eigenvalues.
#. If a :class:`.Vector` instance is given, it will be normalized
before it is written. It's length before normalization will be
written as the scaling factor of the vector.
:arg model: this is an 3-dimensional NMA instance from a :class:`.ANM
calculations
:type model: :class:`.ANM`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`numpy.ndarray`.
:arg indices: amino acid number.
:type indices: ``[int, int]`` or ``[int]`` for one amino acid
:arg k_range: effective force constant value.
:type k_range: int or float, ``[int, int]``
By default files are saved as *filename* and loaded to VMD program and
*selstr* is a selection from :class:`.Select`
"""
try:
coords_sel = pdb.select(selstr)
resnum_list = coords_sel.getResnums()
coords = (coords_sel._getCoords() if hasattr(coords_sel, '_getCoords')
else coords_sel.getCoords())
except AttributeError:
try:
checkCoords(coords_sel)
except TypeError:
raise TypeError('pdb must be a Numpy array or an object '
'with `getCoords` method')
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance')
elif not model.is3d():
raise TypeError('model must be a 3-dimensional NMA instance')
elif len(model) == 0:
raise ValueError('model must have normal modes calculated')
elif model.getStiffness() is None:
raise ValueError('model must have stiffness matrix calculated')
elif len(indices) == 0:
raise ValueError('indices cannot be an empty array')
if len(indices) == 1:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[0] - resnum_list[0]
elif len(indices) == 2:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[1] - resnum_list[0]
out = openFile(addext(filename, '.tcl'), 'w')
out_txt = openFile(addext(filename, '.txt'), 'w')
writePDB(filename + '.pdb', pdb)
LOGGER.info('Creating VMD file.')
out.write('display rendermode GLSL \n')
out.write('display projection orthographic\n')
out.write('color Display Background white\n')
out.write('display shadows on\n')
out.write('display depthcue off\n')
out.write('axes location off\n')
out.write('stage location off\n')
out.write('light 0 on\n')
out.write('light 1 on\n')
out.write('light 2 off\n')
out.write('light 3 on\n')
out.write('mol addrep 0\n')
out.write('display resetview\n')
out.write('mol new {./' + str(filename) +
'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1\n')
out.write('mol modselect 0 0 protein\n')
out.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol modcolor 0 0 Structure\n')
out.write('mol color Structure\n')
out.write('mol representation NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol selection protein\n')
out.write('mol material Opaque\n')
colors = ['blue', 'red', 'gray', 'orange','yellow', 'tan','silver', 'green', \
'white', 'pink', 'cyan', 'purple', 'lime', 'mauve', 'ochre', 'iceblue', 'black', \
'yellow2','yellow3','green2','green3','cyan2','cyan3','blue2','blue3','violet', \
'violet2','magenta','magenta2','red2','red3','orange2','orange3']*50
color_nr = 1 # starting from red color in VMD
ResCounter = []
for r in xrange(indices0, indices1 + 1):
baza_col = [] # Value of Kij is here for each residue
nr_baza_col = [] # Resid of aa are here
out.write("draw color " + str(colors[color_nr]) + "\n")
for nr_i, i in enumerate(model.getStiffness()[r]):
if k_range[0] < float(i) < k_range[1]:
baza_col.append(i)
nr_baza_col.append(nr_i + resnum_list[0])
resid_r = str(
coords_sel.getResnames()[r]) + str(r + resnum_list[0])
resid_r2 = str(
coords_sel.getResnames()[nr_i]) + str(nr_i +
resnum_list[0])
if len(
baza_col
) == 0: # if base is empty then it will not change the color
color_nr = 0
else:
out.write("draw line "+'{'+str(coords[r])[1:-1]+'} {'+\
str(coords[nr_i])[1:-1]+'} width 3 style solid \n')
out_txt.write(
str(resid_r) + '\t' + resid_r2 + '\t' + str(i) + '\n')
ResCounter.append(len(baza_col))
else:
pass
if len(baza_col) != 0:
out.write('mol addrep 0\n')
out.write('mol modselect '+str(color_nr+1)+' 0 protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol modcolor ' + str(color_nr + 1) + ' 0 ColorID ' +
str(color_nr) + '\n')
out.write('mol modstyle ' + str(color_nr + 1) +
' 0 VDW 0.600000 12.000000\n')
out.write('mol color ColorID ' + str(color_nr) + '\n')
out.write('mol representation VDW 1.000000 12.000000 \n')
out.write('mol selection protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol material Opaque \n')
color_nr = color_nr + 1
out.write('mol addrep 0\n')
out.close()
out_txt.close()
if (loadToVMD == True):
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD() + " -e " + str(filename) + ".tcl")
if len(ResCounter) > 0:
return out
elif len(ResCounter) == 0:
LOGGER.info('There is no residue pair in this Kij range.')
return 'None'
def calcChainsNormDistFluct(coords, ch1, ch2, cutoff=10., percent=5, rangeAng=5, \
filename='ch_ndf_out', loadToVMD=True):
'''Calculate protein-protein interaction using getNormDistFluct() from
:class:`.GNM` model. It is assigned to protein complex.
:arg coords: a coordinate set or an object with ``getCoords`` method.
:type coords: :class:`numpy.ndarray`.
:arg ch1: first chain name
:type ch1: 'A' or other letter as a string
:arg ch2: second chain name
:type ch2: string
:arg cutoff: cutoff distance (Å) for pairwise interactions
in Kirchhoff matrix, default is 10.0 Å
:type cutoff: float
:arg percent: percent of the highest and lowest results displayed in _VMD
program, default is 5%
:type percent: int or float
:arg rangeAng: cutoff range of protein-protein interactions, default is 5 Å
:type rangeAng: int or float
:arg filename: name of tcl file from _VMD program
:type filename: str
By default files are saved as *filename* and loaded to VMD program.
To change it use ``loadToVMD=False``.
UNDER PREPARATION.. problems with not complete structures
'''
sele1 = coords.select('name CA and same residue as exwithin '+str(rangeAng) \
+' of chain '+str(ch1))
sele2 = coords.select('name CA and same residue as exwithin '+str(rangeAng) \
+' of chain '+str(ch2))
num1 = len(list(set(sele1.getResnums())))
num2 = len(list(set(sele2.getResnums())))
LOGGER.info('Analized chains: {0}, {1}'.format(ch1, ch2))
LOGGER.info(
'Number of selected amino acids: chain {0}-{1}aa, chain {2}-{3}aa'.
format(ch1, num2, ch2, num1))
seleALL = sele1 + sele2
seleALL_ca = seleALL.select('protein and name CA')
from .gnm import GNM
model = GNM('prot analysis')
model.buildKirchhoff(seleALL_ca, cutoff)
model.calcModes()
ndf_matrix0 = model.getNormDistFluct(seleALL_ca)
ndf_c1 = np.delete(ndf_matrix0, np.s_[0:num1], axis=0) # rows
ndf_matrix = np.delete(ndf_c1, np.s_[num1:(num1 + num2)], axis=1)
perc = (np.amax(ndf_matrix) - np.min(ndf_matrix)) * percent * 0.01
maxRange = np.amax(ndf_matrix) - perc
minRange = np.min(ndf_matrix) + perc
writePDB(filename, coords)
out_tcl = open(filename + '.tcl', 'w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./' + filename +
'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write(
'display depthcue off \ndisplay rendermode GLSL \naxes location Off \n'
)
out_tcl.write('color Display Background white \n')
out_tcl.write(
'mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modselect 0 0 protein \nmol modcolor 0 0 Chain \n')
out_tcl.write('mol modmaterial 0 0 BrushedMetal\n')
out_tcl.write('m')
mmRange = {'minRange': minRange, 'maxRange': maxRange}
ch = [ch2, ch1]
color = ['1', '7'] # red-maxRange, red-minRange
out_pairs = open(filename + '_pairs.txt', 'w')
for nr_j, j in enumerate(mmRange):
if j == 'minRange':
x, y = np.where(ndf_matrix < mmRange[j])
out_pairs.write(j + ' (< ' + str(mmRange[j]) + ') \n')
elif j == 'maxRange':
x, y = np.where(ndf_matrix > mmRange[j])
out_pairs.write(j + ' (> ' + str(mmRange[j]) + ') \n')
vmd_ch_list = [[], []]
for i in range(len(x)):
out_pairs.write("{}{} {}{} {}\n".format(sele1.select('protein and name \
CA' ).getResnames()[y[i]], sele1.select('protein and name CA').getResnums()[y[i]], \
sele2.select('protein and name CA').getResnames()[x[i]], sele2.select('protein and \
name CA' ).getResnums()[x[i]], ndf_matrix[x[i],y[i]]))
vmd_ch_list[0].append(
sele1.select('protein and name CA').getResnums()[y[i]])
vmd_ch_list[1].append(
sele2.select('protein and name CA').getResnums()[x[i]])
out_pairs.write('\n')
for k in range(len(vmd_ch_list)):
out_tcl.write('mol addrep 0\n')
out_tcl.write('mol modselect '+color[nr_j]+' 0 protein and name chain '+ch[k]+\
' and resid '+str(list(set(vmd_ch_list[k]))).replace(',','')[1:-1]+'\n')
out_tcl.write('mol modcolor ' + color[nr_j] + ' 0 ColorID ' +
color[nr_j] + '\n')
out_tcl.write('mol modstyle ' + color[nr_j] +
' 0 CPK 1.000000 0.300000 12.000000 12.000000\n')
out_tcl.write('mol color ColorID ' + color[nr_j] + '\n')
out_tcl.write(
'mol representation CPK 1.000000 0.300000 12.000000 12.000000\n'
)
out_tcl.write('mol selection protein and chain '+ch[k]+' and resid '\
+str(list(set(vmd_ch_list[k]))).replace(',','')[1:-1]+'\n')
out_tcl.write('mol material Opaque \n')
#out_tcl.write('mol addrep 0\n')
LOGGER.info('Finded residues in {0}: {1}'.format(mmRange.keys()[nr_j],\
len(list(set(vmd_ch_list[1])))+len(list(set(vmd_ch_list[0])))))
LOGGER.info('chain {0} and resid {1}'.format(ch[0], \
str(list(set(vmd_ch_list[0]))).replace(',','')[1:-1]))
LOGGER.info('chain {0} and resid {1}'.format(ch[1], \
str(list(set(vmd_ch_list[1]))).replace(',','')[1:-1]))
out_tcl.write('mol addrep 0\n')
LOGGER.info('Created TCL file.')
out_tcl.close()
out_pairs.close()
if (loadToVMD == True):
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD() + " -e " + str(filename) + ".tcl")
return ndf_matrix
def writeVMDstiffness(model, pdb, indices, k_range, filename='vmd_out', \
selstr='protein and name CA', loadToVMD=True):
"""Returns three *filename* files: (1) PDB file with coordinates.
(2) TCL file containing vmd commands for loading PDB file with accurate
vmd representation. Pair of residues with selected *k_range* of
effective spring constant are shown in VMD respresentation with
solid line between them.
If more than one residue will be selected in *indices*, different pair
for each residue will be colored in the different colors.
(3) TXT file contains pair of residues with effective spring constant in
selected range *k_range*.
The effective spring constant calculation using ``buildSM`` method
from :class:`.ANM`.
.. note::
#. This function skips modes with zero eigenvalues.
#. If a :class:`.Vector` instance is given, it will be normalized
before it is written. It's length before normalization will be
written as the scaling factor of the vector.
:arg model: this is an 3-dimensional NMA instance from a :class:`.ANM
calculations
:type model: :class:`.ANM`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`numpy.ndarray`.
:arg indices: amino acid number.
:type indices: ``[int, int]`` or ``[int]`` for one amino acid
:arg k_range: effective force constant value.
:type k_range: int or float, ``[int, int]``
By default files are saved as *filename* and loaded to VMD program and
*selstr* is a selection from :class:`.Select`
"""
try:
coords_sel = pdb.select(selstr)
resnum_list = coords_sel.getResnums()
coords = (coords_sel._getCoords() if hasattr(coords_sel, '_getCoords') else
coords_sel.getCoords())
except AttributeError:
try:
checkCoords(coords_sel)
except TypeError:
raise TypeError('pdb must be a Numpy array or an object '
'with `getCoords` method')
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance')
elif not model.is3d():
raise TypeError('model must be a 3-dimensional NMA instance')
elif len(model) == 0:
raise ValueError('model must have normal modes calculated')
elif model.getStiffness() is None:
raise ValueError('model must have stiffness matrix calculated')
elif len(indices)==0:
raise ValueError('indices cannot be an empty array')
if len(indices)==1:
indices0=indices[0]-resnum_list[0]
indices1=indices[0]-resnum_list[0]
elif len(indices)==2:
indices0=indices[0]-resnum_list[0]
indices1=indices[1]-resnum_list[0]
out = openFile(addext(filename, '.tcl'), 'w')
out_txt = openFile(addext(filename,'.txt'), 'w')
writePDB(filename + '.pdb', pdb)
LOGGER.info('Creating VMD file.')
out.write('display rendermode GLSL \n')
out.write('display projection orthographic\n')
out.write('color Display Background white\n')
out.write('display shadows on\n')
out.write('display depthcue off\n')
out.write('axes location off\n')
out.write('stage location off\n')
out.write('light 0 on\n')
out.write('light 1 on\n')
out.write('light 2 off\n')
out.write('light 3 on\n')
out.write('mol addrep 0\n')
out.write('display resetview\n')
out.write('mol new {./'+str(filename)+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1\n')
out.write('mol modselect 0 0 protein\n')
out.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol modcolor 0 0 Structure\n')
out.write('mol color Structure\n')
out.write('mol representation NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol selection protein\n')
out.write('mol material Opaque\n')
colors = ['blue', 'red', 'gray', 'orange','yellow', 'tan','silver', 'green', \
'white', 'pink', 'cyan', 'purple', 'lime', 'mauve', 'ochre', 'iceblue', 'black', \
'yellow2','yellow3','green2','green3','cyan2','cyan3','blue2','blue3','violet', \
'violet2','magenta','magenta2','red2','red3','orange2','orange3']*50
color_nr = 1 # starting from red color in VMD
ResCounter = []
for r in xrange(indices0, indices1+1):
baza_col = [] # Value of Kij is here for each residue
nr_baza_col = [] # Resid of aa are here
out.write("draw color "+str(colors[color_nr])+"\n")
for nr_i, i in enumerate(model.getStiffness()[r]):
if k_range[0] < float(i) < k_range[1]:
baza_col.append(i)
nr_baza_col.append(nr_i+resnum_list[0])
resid_r = str(coords_sel.getResnames()[r])+str(r+resnum_list[0])
resid_r2 = str(coords_sel.getResnames()[nr_i])+str(nr_i+resnum_list[0])
if len(baza_col) == 0: # if base is empty then it will not change the color
color_nr = 0
else:
out.write("draw line "+'{'+str(coords[r])[1:-1]+'} {'+\
str(coords[nr_i])[1:-1]+'} width 3 style solid \n')
out_txt.write(str(resid_r)+'\t'+resid_r2+'\t'+str(i)+'\n')
ResCounter.append(len(baza_col))
else: pass
if len(baza_col) != 0:
out.write('mol addrep 0\n')
out.write('mol modselect '+str(color_nr+1)+' 0 protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol modcolor '+str(color_nr+1)+' 0 ColorID '+str(color_nr)+'\n')
out.write('mol modstyle '+str(color_nr+1)+' 0 VDW 0.600000 12.000000\n')
out.write('mol color ColorID '+str(color_nr)+'\n')
out.write('mol representation VDW 1.000000 12.000000 \n')
out.write('mol selection protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol material Opaque \n')
color_nr = color_nr + 1
out.write('mol addrep 0\n')
out.close()
out_txt.close()
if (loadToVMD == True):
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
if len(ResCounter) > 0:
return out
elif len(ResCounter) == 0:
LOGGER.info('There is no residue pair in this Kij range.')
return 'None'
def calcChainsNormDistFluct(coords, ch1, ch2, cutoff=10., percent=5, rangeAng=5, \
filename='ch_ndf_out', loadToVMD=True):
'''Calculate protein-protein interaction using getNormDistFluct() from
:class:`.GNM` model. It is assigned to protein complex.
:arg coords: a coordinate set or an object with ``getCoords`` method.
:type coords: :class:`numpy.ndarray`.
:arg ch1: first chain name
:type ch1: 'A' or other letter as a string
:arg ch2: second chain name
:type ch2: string
:arg cutoff: cutoff distance (Å) for pairwise interactions
in Kirchhoff matrix, default is 10.0 Å
:type cutoff: float
:arg percent: percent of the highest and lowest results displayed in _VMD
program, default is 5%
:type percent: int or float
:arg rangeAng: cutoff range of protein-protein interactions, default is 5 Å
:type rangeAng: int or float
:arg filename: name of tcl file from _VMD program
:type filename: str
By default files are saved as *filename* and loaded to VMD program.
To change it use ``loadToVMD=False``.
UNDER PREPARATION.. problems with not complete structures
'''
sele1 = coords.select('name CA and same residue as exwithin '+str(rangeAng) \
+' of chain '+str(ch1))
sele2 = coords.select('name CA and same residue as exwithin '+str(rangeAng) \
+' of chain '+str(ch2))
num1 = len(list(set(sele1.getResnums())))
num2 = len(list(set(sele2.getResnums())))
LOGGER.info('Analized chains: {0}, {1}'.format(ch1, ch2))
LOGGER.info('Number of selected amino acids: chain {0}-{1}aa, chain {2}-{3}aa'
.format(ch1, num2, ch2, num1))
seleALL = sele1 + sele2
seleALL_ca = seleALL.select('protein and name CA')
from .gnm import GNM
model = GNM('prot analysis')
model.buildKirchhoff(seleALL_ca, cutoff)
model.calcModes()
ndf_matrix0 = model.getNormDistFluct(seleALL_ca)
ndf_c1 = np.delete(ndf_matrix0, np.s_[0:num1], axis=0) # rows
ndf_matrix = np.delete(ndf_c1, np.s_[num1:(num1+num2)], axis=1)
perc = (np.amax(ndf_matrix)-np.min(ndf_matrix))*percent*0.01
maxRange = np.amax(ndf_matrix)-perc
minRange = np.min(ndf_matrix)+perc
writePDB(filename, coords)
out_tcl = open(filename+'.tcl','w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./'+filename+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write('display depthcue off \ndisplay rendermode GLSL \naxes location Off \n')
out_tcl.write('color Display Background white \n')
out_tcl.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modselect 0 0 protein \nmol modcolor 0 0 Chain \n')
out_tcl.write('mol modmaterial 0 0 BrushedMetal\n')
out_tcl.write('m')
mmRange = {'minRange':minRange,'maxRange':maxRange}
ch = [ch2, ch1]
color = ['1','7'] # red-maxRange, red-minRange
out_pairs = open(filename+'_pairs.txt','w')
for nr_j,j in enumerate(mmRange):
if j == 'minRange':
x,y = np.where(ndf_matrix < mmRange[j])
out_pairs.write(j+' (< '+str(mmRange[j])+') \n')
elif j == 'maxRange':
x,y = np.where(ndf_matrix > mmRange[j])
out_pairs.write(j+' (> '+str(mmRange[j])+') \n')
vmd_ch_list = [[],[]]
for i in range(len(x)):
out_pairs.write("{}{} {}{} {}\n".format(sele1.select('protein and name \
CA').getResnames()[y[i]], sele1.select('protein and name CA').getResnums()[y[i]], \
sele2.select('protein and name CA').getResnames()[x[i]], sele2.select('protein and \
name CA').getResnums()[x[i]], ndf_matrix[x[i],y[i]]))
vmd_ch_list[0].append(sele1.select('protein and name CA').getResnums()[y[i]])
vmd_ch_list[1].append(sele2.select('protein and name CA').getResnums()[x[i]])
out_pairs.write('\n')
for k in range(len(vmd_ch_list)):
out_tcl.write('mol addrep 0\n')
out_tcl.write('mol modselect '+color[nr_j]+' 0 protein and name chain '+ch[k]+\
' and resid '+str(list(set(vmd_ch_list[k]))).replace(',','')[1:-1]+'\n')
out_tcl.write('mol modcolor '+color[nr_j]+' 0 ColorID '+color[nr_j]+'\n')
out_tcl.write('mol modstyle '+color[nr_j]+' 0 CPK 1.000000 0.300000 12.000000 12.000000\n')
out_tcl.write('mol color ColorID '+color[nr_j]+'\n')
out_tcl.write('mol representation CPK 1.000000 0.300000 12.000000 12.000000\n')
out_tcl.write('mol selection protein and chain '+ch[k]+' and resid '\
+str(list(set(vmd_ch_list[k]))).replace(',','')[1:-1]+'\n')
out_tcl.write('mol material Opaque \n')
#out_tcl.write('mol addrep 0\n')
LOGGER.info('Finded residues in {0}: {1}'.format(mmRange.keys()[nr_j],\
len(list(set(vmd_ch_list[1])))+len(list(set(vmd_ch_list[0])))))
LOGGER.info('chain {0} and resid {1}'.format(ch[0], \
str(list(set(vmd_ch_list[0]))).replace(',','')[1:-1]))
LOGGER.info('chain {0} and resid {1}'.format(ch[1], \
str(list(set(vmd_ch_list[1]))).replace(',','')[1:-1]))
out_tcl.write('mol addrep 0\n')
LOGGER.info('Created TCL file.')
out_tcl.close()
out_pairs.close()
if (loadToVMD == True):
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
return ndf_matrix
