def extra_fit(selection='(all)',
reference=None,
method='align',
zoom=1,
quiet=0,
_self=cmd,
**kwargs):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
alignto, cmd.util.mass_align, align_all.py from Robert Campbell
'''
zoom, quiet = int(zoom), int(quiet)
models = cmd.get_object_list('(%s)' % selection)
if reference is None:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
print('Unknown method ' + str(method))
raise CmdException
for model in models:
x = method(mobile='(%s) and model %s' % (selection, model),
target='(%s) and model %s' % (selection, reference),
**kwargs)
if not quiet:
if cmd.is_sequence(x):
print('%-20s RMS = %8.3f (%d atoms)' % (model, x[0], x[1]))
elif isinstance(x, float):
print('%-20s RMS = %8.3f' % (model, x))
elif _self.is_dict(x) and 'RMSD' in x:
natoms = x.get('alignment_length', 0)
suffix = (' (%s atoms)' % natoms) if natoms else ''
print('%-20s RMS = %8.3f' % (model, x['RMSD']) + suffix)
else:
print('%-20s' % (model, ))
if zoom:
cmd.zoom(selection)
def iterate_plot(selection, expr_y, expr_x=None, scatter=0, filename=None,
space=None, quiet=1):
'''
DESCRIPTION
Plot atomic properties.
ARGUMENTS
selection = string: atom selection
expr_y = string: python expression for y values
expr_x = string: python expression for x values {default: None}
scatter = 0/1: make line plot or scatter plot {default: 0, line plot}
EXAMPLE
# C-alpha b-factors
iterate_plot name CA, b, resv
'''
from . import matplotlib_fix
from matplotlib.pyplot import figure
scatter, quiet = int(scatter), int(quiet)
if space is None:
space = {'cmd': cmd, 'stored': cmd.pymol.stored}
if cmd.is_string(selection):
if selection.startswith('['):
sele_list = selection[1:-1].split(',')
else:
sele_list = ['(%s) and (%s)' % (model, selection) for model in
cmd.get_object_list('(' + selection + ')')]
else:
sele_list = selection
fig = figure()
plt = fig.add_subplot(111)
for selection in sele_list:
space['_values'] = y_values = []
cmd.iterate(selection, '_values.append(' + expr_y + ')', space=space)
if expr_x is None:
x_values = range(len(y_values))
else:
space['_values'] = x_values = []
cmd.iterate(selection, '_values.append(' + expr_x + ')', space=space)
color = get_model_color(selection)
if scatter:
plt.scatter(x_values, y_values, c=color)
else:
plt.plot(x_values, y_values, c=color)
_showfigure(fig, filename, quiet)
def iterate_plot(selection, expr_y, expr_x=None, scatter=0, filename=None,
space=None, quiet=1):
'''
DESCRIPTION
Plot atomic properties.
ARGUMENTS
selection = string: atom selection
expr_y = string: python expression for y values
expr_x = string: python expression for x values {default: None}
scatter = 0/1: make line plot or scatter plot {default: 0, line plot}
EXAMPLE
# C-alpha b-factors
iterate_plot name CA, b, resv
'''
from . import matplotlib_fix
from matplotlib.pyplot import figure
scatter, quiet = int(scatter), int(quiet)
if space is None:
space = {'cmd': cmd, 'stored': cmd.pymol.stored}
if cmd.is_string(selection):
if selection.startswith('['):
sele_list = selection[1:-1].split(',')
else:
sele_list = ['(%s) and (%s)' % (model, selection) for model in
cmd.get_object_list('(' + selection + ')')]
else:
sele_list = selection
fig = figure()
plt = fig.add_subplot(111)
for selection in sele_list:
space['_values'] = y_values = []
cmd.iterate(selection, '_values.append(' + expr_y + ')', space=space)
if expr_x is None:
x_values = list(range(len(y_values)))
else:
space['_values'] = x_values = []
cmd.iterate(selection, '_values.append(' + expr_x + ')', space=space)
color = get_model_color(selection)
if scatter:
plt.scatter(x_values, y_values, c=color)
else:
plt.plot(x_values, y_values, c=color)
_showfigure(fig, filename, quiet)
def extra_fit(selection='(all)', reference=None, method='align', zoom=1,
quiet=0, _self=cmd, **kwargs):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
alignto, cmd.util.mass_align, align_all.py from Robert Campbell
'''
zoom, quiet = int(zoom), int(quiet)
sele_name = cmd.get_unused_name('_')
cmd.select(sele_name, selection) # for speed
models = cmd.get_object_list(sele_name)
if reference is None:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
else:
cmd.select(sele_name, reference, merge=1)
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
print('Unknown method:', method)
raise CmdException
for model in models:
x = method(mobile='%s and model %s' % (sele_name, model),
target='%s and model %s' % (sele_name, reference), **kwargs)
if not quiet:
if cmd.is_sequence(x):
print('%-20s RMS = %8.3f (%d atoms)' % (model, x[0], x[1]))
elif isinstance(x, float):
print('%-20s RMS = %8.3f' % (model, x))
elif isinstance(x, dict) and 'RMSD' in x:
natoms = x.get('alignment_length', 0)
suffix = (' (%s atoms)' % natoms) if natoms else ''
print('%-20s RMS = %8.3f' % (model, x['RMSD']) + suffix)
else:
print('%-20s' % (model,))
if zoom:
cmd.zoom(sele_name)
cmd.delete(sele_name)
def write_html_ref(filename, prefix='psico', format='html'):
'''
DESCRIPTION
Write psico command reference to file.
SEE ALSO
cmd.write_html_ref
'''
if prefix == 'psico' and not __name__.startswith(prefix):
prefix = __name__.rsplit('.', 1)[0]
ref = []
for a in sorted(cmd.keyword):
if a.startswith('_'):
continue
func = cmd.keyword[a][0]
if (func.__module__, func.__name__) == ('pymol.helping',
'python_help'):
continue
if func.__module__.startswith(prefix) and hasattr(func, '__doc__'):
if cmd.is_string(func.__doc__):
ref.append([a, func])
f = open(filename, 'w')
if format == 'txt_short':
import re
pattern_header = re.compile(r'^[A-Z]+', flags=re.MULTILINE)
pattern_emptyline = re.compile(r'\s+$', flags=re.MULTILINE)
for (a, func) in ref:
doc = func.__doc__.partition('DESCRIPTION')[-1]
doc = pattern_header.split(doc, 1)[0]
doc = pattern_emptyline.sub('', doc)
f.write('%s\t%s\n\n' % (a, doc))
f.close
return
f.write("<html><head><style type='text/css'>")
f.write("body {font-family:sans-serif}")
f.write("p.api {font:small monospace;color:#999}")
f.write("</style></head><body><h1>pymol psico reference</h1><ul>")
for (a, _) in ref:
f.write("<li><a href='#%s'>%s</a>" % (a, a))
f.write("</ul>")
for (a, func) in ref:
doc = func.__doc__.strip().replace("<", "<")
f.write("<hr size=1><h2 id='%s'>%s</h2>" % (a, a))
f.write("<pre>%s</pre>" % (doc))
f.write("<p class='api'>api: %s.%s</p>" %
(func.__module__, func.__name__))
f.write("</body></html>")
f.close()
def write_html_ref(filename, prefix="psico", format="html"):
"""
DESCRIPTION
Write psico command reference to file.
SEE ALSO
cmd.write_html_ref
"""
if prefix == "psico" and not __name__.startswith(prefix):
prefix = __name__.rsplit(".", 1)[0]
ref = []
for a in sorted(cmd.keyword):
if a.startswith("_"):
continue
func = cmd.keyword[a][0]
if (func.__module__, func.__name__) == ("pymol.helping", "python_help"):
continue
if func.__module__.startswith(prefix) and hasattr(func, "__doc__"):
if cmd.is_string(func.__doc__):
ref.append([a, func])
f = open(filename, "w")
if format == "txt_short":
import re
pattern_header = re.compile(r"^[A-Z]+", flags=re.MULTILINE)
pattern_emptyline = re.compile(r"\s+$", flags=re.MULTILINE)
for (a, func) in ref:
doc = func.__doc__.partition("DESCRIPTION")[-1]
doc = pattern_header.split(doc, 1)[0]
doc = pattern_emptyline.sub("", doc)
f.write("%s\t%s\n\n" % (a, doc))
f.close
return
f.write("<html><head><style type='text/css'>")
f.write("body {font-family:sans-serif}")
f.write("p.api {font:small monospace;color:#999}")
f.write("</style></head><body><h1>pymol psico reference</h1><ul>")
for (a, _) in ref:
f.write("<li><a href='#%s'>%s</a>" % (a, a))
f.write("</ul>")
for (a, func) in ref:
doc = func.__doc__.strip().replace("<", "<")
f.write("<hr size=1><h2 id='%s'>%s</h2>" % (a, a))
f.write("<pre>%s</pre>" % (doc))
f.write("<p class='api'>api: %s.%s</p>" % (func.__module__, func.__name__))
f.write("</body></html>")
f.close()
def checkParams(needle, haystack, selName, het, firstOnly):
"""
This is just a helper function for checking the user input
"""
# check Needle
if len(needle) == 0 or not cmd.is_string(needle):
print("Error: Please provide a string 'needle' to search for.")
print("Error: For help type 'help motifFinder'.")
return False
# check Haystack
if len(haystack) == 0 or not cmd.is_string(haystack):
print("Error: Please provide valid PyMOL object or selection name")
print("Error: in which to search.")
print("Error: For help type 'help motifFinder'.")
return False
# check het
try:
het = bool(int(het))
except ValueError:
print("Error: The 'het' parameter was not 0 or 1.")
return False
# check first Only
try:
firstOnly = bool(int(het))
except ValueError:
print("Error: The 'firstOnly' parameter was not 0 or 1.")
return False
# check selName
if not cmd.is_string(selName):
print("Error: selName was not a string.")
return False
return True
def get_data(handle):
if not cmd.is_string(handle):
return handle
try:
import h5py
except ImportError:
raise CmdException("h5py module not available, cannot load vis files")
try:
handle = h5py.File(handle, "r")
except IOError:
raise CmdException("Failed to open file " + str(handle))
return next(iter(next(iter(handle.values())).values()))
def get_docstring(self):
'''
Get docstring either from loaded module, or try to parse first python
statement from file, without executing any code.
'''
if self.loaded:
return self.module.__doc__
try:
c = compile(''.join(open(self.filename)), 'x', 'single')
s = c.co_consts[0]
if cmd.is_string(s):
return s
except:
pass
def checkParams(needle, haystack, selName, het, firstOnly):
"""
This is just a helper function for checking the user input
"""
# check Needle
if len(needle) == 0 or not cmd.is_string(needle):
print("Error: Please provide a string 'needle' to search for.")
print("Error: For help type 'help motifFinder'.")
return False
# check Haystack
if len(haystack) == 0 or not cmd.is_string(haystack):
print("Error: Please provide valid PyMOL object or selection name")
print("Error: in which to search.")
print("Error: For help type 'help motifFinder'.")
return False
# check het
try:
het = bool(int(het))
except ValueError:
print("Error: The 'het' parameter was not 0 or 1.")
return False
# check first Only
try:
firstOnly = bool(int(het))
except ValueError:
print("Error: The 'firstOnly' parameter was not 0 or 1.")
return False
# check selName
if not cmd.is_string(selName):
print("Error: selName was not a string.")
return False
return True
def write_html_ref(filename, prefix='psico', format='html'):
'''
DESCRIPTION
Write psico command reference to file.
SEE ALSO
cmd.write_html_ref
'''
if prefix == 'psico' and not __name__.startswith(prefix):
prefix = __name__.rsplit('.', 1)[0]
ref = []
for a in sorted(cmd.keyword):
if a.startswith('_'):
continue
func = cmd.keyword[a][0]
if func.__module__.startswith(prefix) and hasattr(func, '__doc__'):
if cmd.is_string(func.__doc__):
ref.append([a, func])
f = open(filename, 'w')
if format == 'txt_short':
import re
pattern_header = re.compile(r'^[A-Z]+', flags=re.MULTILINE)
pattern_emptyline = re.compile(r'\s+$', flags=re.MULTILINE)
for (a, func) in ref:
doc = func.__doc__.partition('DESCRIPTION')[-1]
doc = pattern_header.split(doc, 1)[0]
doc = pattern_emptyline.sub('', doc)
f.write('%s\t%s\n\n' % (a, doc))
f.close
return
f.write("<html><head><style type='text/css'>")
f.write("p.api {font:small monospace;color:#999}")
f.write("</style></head><body><h1>pymol psico reference</h1><ul>")
for (a,_) in ref:
f.write("<li><a href='#%s'>%s</a>" % (a, a))
f.write("</ul>")
for (a, func) in ref:
doc = func.__doc__.strip().replace("<", "<")
f.write("<hr size=1><h2 id='%s'>%s</h2>" % (a, a))
f.write("<pre>%s</pre>" % (doc))
f.write("<p class='api'>api: %s.%s</p>" % (func.__module__, func.__name__))
f.write("</body></html>")
f.close()
def get_docstring(self):
'''
Get docstring either from loaded module, or try to parse first python
statement from file, without executing any code.
'''
if self.loaded:
return self.module.__doc__
try:
c = compile(b''.join(open(self.filename, 'rb')), 'x', 'exec', dont_inherit=True)
s = c.co_consts[0]
if cmd.is_string(s):
return s
except SyntaxError as e:
return 'WARNING: Plugin not Python 3.x compatible: ' + str(e)
except:
pass
def get_docstring(self):
'''
Get docstring either from loaded module, or try to parse first python
statement from file, without executing any code.
'''
if self.loaded:
return self.module.__doc__
try:
c = compile(''.join(open(self.filename)), 'x', 'exec', dont_inherit=True)
s = c.co_consts[0]
if cmd.is_string(s):
return s
except SyntaxError as e:
if sys.version_info[0] > 2:
return 'WARNING: Plugin not Python 3.x compatible: ' + str(e)
except:
pass
def pdbremarks(filename):
'''
DESCRIPTION
API only. Read REMARK lines from PDB file. Return dictionary with
remarkNum as key and list of lines as value.
'''
remarks = dict()
if not cmd.is_string(filename):
f = filename
elif filename[-3:] == '.gz':
import gzip
f = gzip.open(filename)
else:
f = open(filename)
for line in f:
recname = line[0:6]
if recname == 'REMARK':
num = int(line[7:10])
lstring = line[11:]
remarks.setdefault(num, []).append(lstring)
return remarks
def pdbremarks(filename):
'''
DESCRIPTION
API only. Read REMARK lines from PDB file. Return dictionary with
remarkNum as key and list of lines as value.
'''
remarks = dict()
if not cmd.is_string(filename):
f = filename
elif filename[-3:] == '.gz':
import gzip
f = gzip.open(filename)
else:
f = open(filename)
for line in f:
recname = line[0:6]
if recname == 'REMARK':
num = int(line[7:10])
lstring = line[11:]
remarks.setdefault(num, []).append(lstring)
return remarks
def ramp_levels(name, levels, quiet=1):
'''
DESCRIPTION
Changes the slot levels of a ramp.
SEE ALSO
ramp_new, isolevel
'''
quiet = int(quiet)
if cmd.is_string(levels):
levels = cmd.safe_list_eval(levels)
try:
position = cmd.get_names('all').index(name)
odata = cmd.get_session(name, 1, 1, 0, 0)['names'][0]
if odata[4] != 8:
raise TypeError('not a ramp')
data = odata[5]
except:
print(' Error: Get session data for ramp "%s" failed' % (name))
raise CmdException
if len(levels) != len(data[3]):
print(' Error: number of levels must agree with existing object')
raise CmdException
map_name = data[6]
colors = [data[4][i:i + 3] for i in range(0, len(data[4]), 3)]
cmd.ramp_new(name, map_name, levels, colors, quiet=quiet)
# restore original position
if position == 0:
cmd.order(name, location='top')
else:
cmd.order(cmd.get_names('all')[position - 1] + ' ' + name)
def ramp_levels(name, levels, quiet=1):
'''
DESCRIPTION
Changes the slot levels of a ramp.
SEE ALSO
ramp_new, isolevel
'''
quiet = int(quiet)
if cmd.is_string(levels):
levels = cmd.safe_list_eval(levels)
try:
position = cmd.get_names('all').index(name)
odata = cmd.get_session(name, 1, 1, 0, 0)['names'][0]
if odata[4] != 8:
raise TypeError('not a ramp')
data = odata[5]
except:
print(' Error: Get session data for ramp "%s" failed' % (name))
raise CmdException
if len(levels) != len(data[3]):
print(' Error: number of levels must agree with existing object')
raise CmdException
map_name = data[6]
colors = [data[4][i:i+3] for i in range(0, len(data[4]), 3)]
cmd.ramp_new(name, map_name, levels, colors, quiet=quiet)
# restore original position
if position == 0:
cmd.order(name, location='top')
else:
cmd.order(cmd.get_names('all')[position-1] + ' ' + name)
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 pmf(key,
cutoff=7.0,
selection1='(name CB)',
selection2='',
state=1,
quiet=1):
'''
DESCRIPTION
Potential of Mean Force
ARGUMENTS
key = string: aaindex key
cutoff = float: distance cutoff {default: 7.0}
cutoff = (float, float): distance shell
selection1 = string: atom selection {default: (name CB)}
selection2 = string: atom selection {default: selection1}
NOTES
Does also support a list of keys and a list of cutoffs to deal with
multiple distance shells.
EXAMPLES
# distance dependent c-beta contact potentials
pmf SIMK990101, 5, /2x19//A//CB
pmf SIMK990102, [5, 7.5], /2x19//A//CB
pmf [SIMK990101, SIMK990102, SIMK990103], [0, 5, 7.5, 10], /2x19//A//CB
# interface potential
sidechaincenters 2x19_scc, 2x19
pmf KESO980102, 7.0, /2x19_scc//A, /2x19_scc//B
distance /2x19_scc//A, /2x19_scc//B, cutoff=7.0
'''
from pymol import cmd, stored
from chempy import cpv
if cmd.is_string(key):
if key.lstrip().startswith('['):
key = cmd.safe_alpha_list_eval(key)
else:
key = [key]
if cmd.is_string(cutoff):
cutoff = eval(cutoff)
if not cmd.is_sequence(cutoff):
cutoff = [cutoff]
if len(cutoff) == len(key):
cutoff = [0.0] + list(cutoff)
if len(cutoff) != len(key) + 1:
print 'Error: Number of keys and number of cutoffs inconsistent'
return
state = int(state)
quiet = int(quiet)
if len(selection2) == 0:
selection2 = selection1
if not quiet and len(key) > 1:
print 'Distance shells:'
for i in range(len(key)):
print '%s %.1f-%.1f' % (key[i], cutoff[i], cutoff[i + 1])
idmap = dict()
cmd.iterate_state(state,
'(%s) or (%s)' % (selection1, selection2),
'idmap[model,index] = [(resn,name),(x,y,z)]',
space={'idmap': idmap})
twoN = cmd.count_atoms(selection1) + cmd.count_atoms(selection2)
pairs = cmd.find_pairs(selection1,
selection2,
cutoff=max(cutoff),
state1=state,
state2=state)
if len(pairs) == 0:
print 'Empty pair list'
return 0.0
matrix = map(get, key)
for i in matrix:
assert isinstance(i, MatrixRecord)
i_list = range(len(key))
u_sum = 0
count = 0
for id1, id2 in pairs:
a1 = idmap[id1]
a2 = idmap[id2]
r = cpv.distance(a1[1], a2[1])
for i in i_list:
if cutoff[i] <= r and r < cutoff[i + 1]:
try:
aa1 = to_one_letter_code[a1[0][0]]
aa2 = to_one_letter_code[a2[0][0]]
u_sum += matrix[i].get(aa1, aa2)
count += 1
except:
print 'Failed for', a1[0], a2[0]
value = float(u_sum) / twoN
if not quiet:
print 'PMF: %.4f (%d contacts, %d residues)' % (value, count, twoN)
return value
def load_consurf(filename, selection, palette='red_white_blue', quiet=1):
'''
DESCRIPTION
Color by evolutionary conservation. Writes scores to b-factor.
You need a "r4s.res" or "consurf.grades" input file.
USAGE
load_consurf filename, selection [, palette ]
SEE ALSO
consurfdb
'''
import re
from .seqalign import needle_alignment, alignment_mapping
from . import one_letter
# reduced pattern that matches both r4s.res and consurf.grades
pattern = re.compile(r'\s*(\d+)\s+([A-Y])\s+([-.0-9]+)\s')
scores = []
seqlist = []
if cmd.is_string(filename):
handle = open(filename)
else:
handle = filename
if len(cmd.get_chains(selection)) > 1:
print(' Warning: selection spans multiple chains')
for line in handle:
if line.startswith('#') or line.strip() == '':
continue
m = pattern.match(line)
if m is None:
continue
scores.append(float(m.group(3)))
seqlist.append(m.group(2))
selection = '(%s) and polymer' % selection
model_ca = cmd.get_model(selection + ' and guide')
model_seq = ''.join(one_letter.get(a.resn, 'X') for a in model_ca.atom)
sequence = ''.join(seqlist)
aln = needle_alignment(model_seq, sequence)
scores_resi = dict((model_ca.atom[i].resi, scores[j])
for (i, j) in alignment_mapping(*aln))
cmd.alter(selection, 'b=scores.get(resi, -10)',
space={'scores': scores_resi}, quiet=quiet)
if palette:
cmd.color('yellow', selection + ' and b<-9')
if ' ' in palette:
from .viewing import spectrumany as spectrum
else:
spectrum = cmd.spectrum
spectrum('b', palette, selection + ' and b>-9.5')
def save_movie_mpeg1(filename,
mode='',
first=0,
last=0,
preserve=0,
fps=25,
twopass=1,
vbitrate=16000,
quiet=1,
exe='mencoder'):
'''
DESCRIPTION
Save movie as MPEG1
This will not be the best quality possible for the file size, but
we were successfull to play those movies in PowerPoint.
Requires mencoder executable from http://mplayerhq.hu
ARGUMENTS
filename = string: Filename, should end on '.mpeg'
mode = normal | draw | ray
first, last = integer: first and last frame number
preserve = 0 or 1: delete temporary images if 0 {default: 0}
fps = integer: frames per second {default: 25}
twopass = 0 or 1: two pass mode encoding (improves quality) {default: 1}
vbitrate = integer: average video bitrate {default: 16000}
WARNING: 4-16000 (in kbit), 16001-24000000 (in bit)
SEE ALSO
cmd.movie.produce, http://www.freemol.org
'''
import os, subprocess, tempfile
first, last, quiet = int(first), int(last), int(quiet)
fps, twopass, vbitrate = int(fps), int(twopass), int(vbitrate)
if cmd.is_string(mode):
if mode == '':
if cmd.pymol.invocation.options.no_gui \
or cmd.get_setting_boolean('ray_trace_frames'):
mode = 'ray'
else:
mode = 'draw'
mode = produce_mode_sc.auto_err(mode, 'mode')
mode = produce_mode_dict[mode]
mode = int(mode)
try:
subprocess.call([exe])
except OSError:
print(' Error: Cannot execute "%s"' % (exe))
raise CmdException
if not quiet:
print(' save_movie: Rendering frames...')
tmp_path = tempfile.mkdtemp()
prefix = os.path.join(tmp_path, 'frame')
cmd.mpng(prefix, first, last, preserve, mode=mode)
mpeg1line = '-mf type=png:fps=%d -ovc lavc -forceidx -noskip -of rawvideo' \
+ ' -mpegopts format=mpeg1 -lavcopts vcodec=mpeg1video:vbitrate=%d' \
+ ':vhq:trell:keyint=25'
mpeg1line = mpeg1line % (fps, vbitrate)
cmdline = exe + ' -quiet mf://' + prefix + '* ' + mpeg1line
if not quiet:
print(' save_movie: Running mencoder...')
if twopass:
if not quiet:
print(' save_movie: First pass...')
cmdline1 = cmdline + ':vpass=1'
subprocess.call(cmdline1.split() + ['-o', os.devnull])
if not quiet:
print(' save_movie: Second pass...')
cmdline = cmdline + ':vpass=2'
subprocess.call(cmdline.split() + ['-o', filename])
if not preserve:
import shutil
shutil.rmtree(tmp_path)
elif not quiet:
print(' save_movie: Not deleting temporary directory: ' + tmp_path)
if not quiet:
print(' save_movie: Done')
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, bsync=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 pca_plot(aln_object, ref='all', state=0, maxlabels=20, size=20, invert='',
which=(0,1), alpha=0.75, filename=None, quiet=1, load_b=0):
'''
DESCRIPTION
Principal Component Analysis on a set of superposed conformations, given
by an alignment object. By default all states in all objects are
considered. Generates a 2d-plot of the first two principal components.
USAGE
pca_plot aln_object [, ref [, state [, maxlabels ]]]
ARGUMENTS
aln_object = string: name of alignment object, defines the selection
and the atom mapping between objects
ref = string: object names for which to calculate PCA for {default: all}
state = integer: if state=0 use all states {default: 0}
maxlabels = integer: label dots in plot if maxlabels<0 or number of models
not more than maxlabels {default: 20}
size = float: size of plot points in px^2 {default: 20}
invert = string: invert plotting axes x, y or xy {default: ''}
which = (int,int): indices of principal components to plot {default: (0,1)}
alpha = float: opacity of plotting points
filename = string: if given, plot to file {default: None}
EXAMPLE
fetch 1ake 4ake 1dvr 1ak2, async=0
split_chains
extra_fit (*_*) and name CA, reference=1ake_A, cycles=0, object=aln
pca_plot aln, 1ake_* 4ake_*
fetch 1ubq 2k39, async=0
align 2k39, 1ubq and guide, cycles=0, object=aln2
color blue, 1ubq
color orange, 2k39
pca_plot aln2, filename=pca-ubq.pdf
'''
from numpy import array, dot
from numpy.linalg import svd, LinAlgError
from . import matplotlib_fix
from matplotlib.pyplot import figure
state, quiet = int(state), int(quiet)
maxlabels = int(maxlabels)
if cmd.is_string(which):
which = cmd.safe_list_eval(which)
if aln_object not in cmd.get_names_of_type('object:alignment'):
print(' Warning: first argument should be an alignment object')
from .fitting import extra_fit
selection = aln_object
aln_object = cmd.get_unused_name('aln')
extra_fit(selection, cycles=0, transform=0, object=aln_object)
if state == 0:
states = list(range(1, cmd.count_states()+1))
elif state < 0:
states = [cmd.get_state()]
else:
states = [state]
models = cmd.get_object_list(aln_object)
references = set(cmd.get_object_list('(' + ref + ')')).intersection(models)
others = set(models).difference(references)
aln = cmd.get_raw_alignment(aln_object)
if not quiet:
print(' PCA References:', ', '.join(references))
print(' PCA Others:', ', '.join(others))
if len(references) == 0:
print(' PCA Error: No reference objects')
raise CmdException
model_count = len(models)
coords = dict((model, []) for model in models)
aln = [pos for pos in aln if len(pos) == model_count]
for state in states:
idx2xyz = dict()
cmd.iterate_state(state, aln_object, 'idx2xyz[model,index] = (x,y,z)',
space={'idx2xyz': idx2xyz})
for pos in aln:
for idx in pos:
if idx not in idx2xyz:
continue
c = coords[idx[0]]
if len(c) < state:
c.append([])
c[-1].extend(idx2xyz[idx])
c_iter = lambda models: ((c,model,i+1) for model in models
for (i,c) in enumerate(coords[model]))
X = array([i[0] for i in c_iter(references)])
Y = array([i[0] for i in c_iter(others)])
center = X.mean(0)
X = X - center
try:
U, L, V = svd(X)
except LinAlgError as e:
print(' PCA Error: ', e)
raise CmdException
if int(load_b):
cmd.alter('byobj ' + aln_object, 'b=-0.01')
b_dict = {}
i = which[0]
b_array = (V[i].reshape((-1, 3))**2).sum(1)**0.5
for pos, b in zip(aln, b_array):
for idx in pos:
b_dict[idx] = b
cmd.alter(aln_object, 'b=b_dict.get((model,index), -0.01)', space=locals())
cmd.color('yellow', 'byobj ' + aln_object)
cmd.spectrum('b', 'blue_red', aln_object + ' and b > -0.01')
X_labels = [i[1:3] for i in c_iter(references)]
Y_labels = [i[1:3] for i in c_iter(others)]
x_list = []
y_list = []
colors = []
text_list = []
def plot_pc_2d(X, labels):
pca_12 = dot(X, V.T)[:,which]
for (x,y), (model,state) in zip(pca_12, labels):
x_list.append(x)
y_list.append(y)
colors.append(get_model_color(model))
if maxlabels < 0 or len(pca_12) <= maxlabels:
text_list.append('%s(%d)' % (model, state))
else:
text_list.append(None)
plot_pc_2d(X, X_labels)
if len(Y) > 0:
Y = Y - center
plot_pc_2d(Y, Y_labels)
if 'x' in invert:
x_list = [-x for x in x_list]
if 'y' in invert:
y_list = [-y for y in y_list]
fig = figure()
plt = fig.add_subplot(111, xlabel='PC %d' % (which[0]+1), ylabel='PC %d' % (which[1]+1))
plt.scatter(x_list, y_list, float(size), colors, linewidths=0, alpha=float(alpha))
for (x, y, text) in zip(x_list, y_list, text_list):
if text is not None:
plt.text(x, y, text, horizontalalignment='left')
_showfigure(fig, filename, quiet)
def pca_plot(
aln_object,
ref="all",
state=0,
maxlabels=20,
size=20,
invert="",
which=(0, 1),
alpha=0.75,
filename=None,
quiet=1,
load_b=0,
):
"""
DESCRIPTION
Principal Component Analysis on a set of superposed conformations, given
by an alignment object. By default all states in all objects are
considered. Generates a 2d-plot of the first two principal components.
USAGE
pca_plot aln_object [, ref [, state [, maxlabels ]]]
ARGUMENTS
aln_object = string: name of alignment object, defines the selection
and the atom mapping between objects
ref = string: object names for which to calculate PCA for {default: all}
state = integer: if state=0 use all states {default: 0}
maxlabels = integer: label dots in plot if maxlabels<0 or number of models
not more than maxlabels {default: 20}
size = float: size of plot points in px^2 {default: 20}
invert = string: invert plotting axes x, y or xy {default: ''}
which = (int,int): indices of principal components to plot {default: (0,1)}
alpha = float: opacity of plotting points
filename = string: if given, plot to file {default: None}
EXAMPLE
fetch 1ake 4ake 1dvr 1ak2, async=0
split_chains
extra_fit (*_*) and name CA, reference=1ake_A, cycles=0, object=aln
pca_plot aln, 1ake_* 4ake_*
fetch 1ubq 2k39, async=0
align 2k39, 1ubq and guide, cycles=0, object=aln2
color blue, 1ubq
color orange, 2k39
pca_plot aln2, filename=pca-ubq.pdf
"""
from numpy import array, dot
from numpy.linalg import svd, LinAlgError
from . import matplotlib_fix
from matplotlib.pyplot import figure
state, quiet = int(state), int(quiet)
maxlabels = int(maxlabels)
if cmd.is_string(which):
which = cmd.safe_list_eval(which)
if aln_object not in cmd.get_names_of_type("object:"):
print(" Warning: first argument should be an alignment object")
from .fitting import extra_fit
selection = aln_object
aln_object = cmd.get_unused_name("aln")
extra_fit(selection, cycles=0, transform=0, object=aln_object)
if state == 0:
states = list(range(1, cmd.count_states() + 1))
elif state < 0:
states = [cmd.get_state()]
else:
states = [state]
models = cmd.get_object_list(aln_object)
references = set(cmd.get_object_list("(" + ref + ")")).intersection(models)
others = set(models).difference(references)
aln = cmd.get_raw_alignment(aln_object)
if not quiet:
print(" PCA References:", ", ".join(references))
print(" PCA Others:", ", ".join(others))
if len(references) == 0:
print(" PCA Error: No reference objects")
raise CmdException
model_count = len(models)
coords = dict((model, []) for model in models)
aln = [pos for pos in aln if len(pos) == model_count]
for state in states:
idx2xyz = dict()
cmd.iterate_state(state, aln_object, "idx2xyz[model,index] = (x,y,z)", space={"idx2xyz": idx2xyz})
for pos in aln:
for idx in pos:
if idx not in idx2xyz:
continue
c = coords[idx[0]]
if len(c) < state:
c.append([])
c[-1].extend(idx2xyz[idx])
c_iter = lambda models: ((c, model, i + 1) for model in models for (i, c) in enumerate(coords[model]))
X = array([i[0] for i in c_iter(references)])
Y = array([i[0] for i in c_iter(others)])
center = X.mean(0)
X = X - center
try:
U, L, V = svd(X)
except LinAlgError as e:
print(" PCA Error: ", e)
raise CmdException
if int(load_b):
cmd.alter("byobj " + aln_object, "b=-0.01")
b_dict = {}
i = which[0]
b_array = (V[i].reshape((-1, 3)) ** 2).sum(1) ** 0.5
for pos, b in zip(aln, b_array):
for idx in pos:
b_dict[idx] = b
cmd.alter(aln_object, "b=b_dict.get((model,index), -0.01)", space=locals())
cmd.color("yellow", "byobj " + aln_object)
cmd.spectrum("b", "blue_red", aln_object + " and b > -0.01")
X_labels = [i[1:3] for i in c_iter(references)]
Y_labels = [i[1:3] for i in c_iter(others)]
x_list = []
y_list = []
colors = []
text_list = []
def plot_pc_2d(X, labels):
pca_12 = dot(X, V.T)[:, which]
for (x, y), (model, state) in zip(pca_12, labels):
x_list.append(x)
y_list.append(y)
colors.append(get_model_color(model))
if maxlabels < 0 or len(pca_12) <= maxlabels:
text_list.append("%s(%d)" % (model, state))
else:
text_list.append(None)
plot_pc_2d(X, X_labels)
if len(Y) > 0:
Y = Y - center
plot_pc_2d(Y, Y_labels)
if "x" in invert:
x_list = [-x for x in x_list]
if "y" in invert:
y_list = [-y for y in y_list]
fig = figure()
plt = fig.add_subplot(111, xlabel="PC %d" % (which[0] + 1), ylabel="PC %d" % (which[1] + 1))
plt.scatter(x_list, y_list, float(size), colors, linewidths=0, alpha=float(alpha))
for (x, y, text) in zip(x_list, y_list, text_list):
if text is not None:
plt.text(x, y, text, horizontalalignment="left")
_showfigure(fig, filename, quiet)
def pdb2pqr_cli(name,
selection,
options,
state=-1,
preserve=0,
exe='pdb2pqr',
quiet=1,
fixrna=0,
_proclist=None):
import os, tempfile, subprocess, shutil
state, preserve, quiet = int(state), int(preserve), int(quiet)
if cmd.is_string(options):
import shlex
options = shlex.split(options)
args = [cmd.exp_path(exe)] + list(options)
tmpdir = tempfile.mkdtemp()
infile = os.path.join(tmpdir, 'in.pdb')
outfile = os.path.join(tmpdir, 'out.pqr')
args.extend([infile, outfile])
# For some reason, catching stdout/stderr with PIPE and communicate()
# blocks terminate() calls from terminating early. Using a file
# redirect doesn't show this problem.
f_stdout = open(os.path.join(tmpdir, 'stdout.txt'), 'w+')
# RNA resdiue names must be RA, RC, RG, and RU
tmpmodel = ''
if int(fixrna) and cmd.count_atoms('(%s) & resn A+C+G+U' % (selection)):
tmpmodel = cmd.get_unused_name('_tmp')
cmd.create(tmpmodel, selection, zoom=0)
cmd.alter(tmpmodel + ' & polymer.nucleic & resn A+C+G+U',
'resn = "R" + resn')
selection = tmpmodel
try:
cmd.save(infile, selection, state)
p = subprocess.Popen(
args,
cwd=tmpdir,
stdin=subprocess.PIPE, # Windows pythonw fix
stdout=f_stdout,
stderr=f_stdout)
p.stdin.close() # Windows pythonw fix
if _proclist is not None:
_proclist.append(p)
p.wait()
# This allows PyMOL to capture it and display the output in the GUI.
f_stdout.seek(0)
print(f_stdout.read().rstrip())
if p.returncode == -15: # SIGTERM
raise CmdException('pdb2pqr terminated')
if p.returncode != 0:
raise CmdException('%s failed with exit status %d' %
(args[0], p.returncode))
warnings = [
L[10:] for L in open(outfile) if L.startswith('REMARK 5')
]
warnings = ''.join(warnings).strip()
cmd.load(outfile, name)
return warnings
except OSError as e:
print(e)
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if tmpmodel:
cmd.delete(tmpmodel)
f_stdout.close()
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
def prepwizard(name,
selection='all',
options='',
state=-1,
preserve=0,
exe='$SCHRODINGER/utilities/prepwizard',
quiet=1,
_proclist=None):
'''
DESCRIPTION
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side
chains and converts MSE to MET. Other non-default options need to be
passed with the "options=" argument.
USAGE
prepwizard name [, selection [, options [, state ]]]
ARGUMENTS
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
'''
import os, tempfile, subprocess, shutil, shlex
state, preserve, quiet = int(state), int(preserve), int(quiet)
exe = cmd.exp_path(exe)
if not _is_exe(exe):
if 'SCHRODINGER' not in os.environ:
print(' Warning: SCHRODINGER environment variable not set')
raise CmdException('no such script: ' + exe)
args = [exe, '-mse', '-fillsidechains', '-WAIT']
if options:
if cmd.is_string(options):
options = shlex.split(options)
args.extend(options)
tmpdir = tempfile.mkdtemp()
infile = 'in.pdb'
outfile = 'out.mae'
args.extend([infile, outfile])
try:
cmd.save(os.path.join(tmpdir, infile), selection, state)
env = dict(os.environ)
env.pop('PYTHONEXECUTABLE', '') # messes up Python on Mac
p = subprocess.Popen(
args,
cwd=tmpdir,
env=env,
stdin=subprocess.PIPE, # Windows pythonw fix
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
if _proclist is not None:
_proclist.append(p)
print(p.communicate()[0].rstrip())
if p.wait() == -15: # SIGTERM
raise CmdException('prepwizard terminated')
if p.returncode != 0:
logfile = os.path.join(tmpdir, 'in.log')
if os.path.exists(logfile):
with open(logfile) as handle:
print(handle.read())
raise CmdException('%s failed with exit status %d' %
(args[0], p.returncode))
cmd.load(os.path.join(tmpdir, outfile), name)
except OSError as e:
print(e)
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(' Notice: not deleting', tmpdir)
if not quiet:
print(' prepwizard: done')
def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1):
'''
DESCRIPTION
Potential of Mean Force
ARGUMENTS
key = string: aaindex key
cutoff = float: distance cutoff {default: 7.0}
cutoff = (float, float): distance shell
selection1 = string: atom selection {default: (name CB)}
selection2 = string: atom selection {default: selection1}
NOTES
Does also support a list of keys and a list of cutoffs to deal with
multiple distance shells.
EXAMPLES
# distance dependent c-beta contact potentials
pmf SIMK990101, 5, /2x19//A//CB
pmf SIMK990102, [5, 7.5], /2x19//A//CB
pmf [SIMK990101, SIMK990102, SIMK990103], [0, 5, 7.5, 10], /2x19//A//CB
# interface potential
sidechaincenters 2x19_scc, 2x19
pmf KESO980102, 7.0, /2x19_scc//A, /2x19_scc//B
distance /2x19_scc//A, /2x19_scc//B, cutoff=7.0
'''
from pymol import cmd, stored
from chempy import cpv
if cmd.is_string(key):
if key.lstrip().startswith('['):
key = cmd.safe_alpha_list_eval(key)
else:
key = [key]
if cmd.is_string(cutoff):
cutoff = eval(cutoff)
if not cmd.is_sequence(cutoff):
cutoff = [cutoff]
if len(cutoff) == len(key):
cutoff = [0.0] + list(cutoff)
if len(cutoff) != len(key) + 1:
print('Error: Number of keys and number of cutoffs inconsistent')
return
state = int(state)
quiet = int(quiet)
if len(selection2) == 0:
selection2 = selection1
if not quiet and len(key) > 1:
print('Distance shells:')
for i in range(len(key)):
print('%s %.1f-%.1f' % (key[i], cutoff[i], cutoff[i + 1]))
idmap = dict()
cmd.iterate_state(state, '(%s) or (%s)' % (selection1, selection2),
'idmap[model,index] = [(resn,name),(x,y,z)]', space={'idmap': idmap})
twoN = cmd.count_atoms(selection1) + cmd.count_atoms(selection2)
pairs = cmd.find_pairs(selection1, selection2, cutoff=max(cutoff),
state1=state, state2=state)
if len(pairs) == 0:
print('Empty pair list')
return 0.0
matrix = list(map(get, key))
for i in matrix:
assert isinstance(i, MatrixRecord)
i_list = list(range(len(key)))
u_sum = 0
count = 0
for id1, id2 in pairs:
a1 = idmap[id1]
a2 = idmap[id2]
r = cpv.distance(a1[1], a2[1])
for i in i_list:
if cutoff[i] <= r and r < cutoff[i + 1]:
try:
aa1 = to_one_letter_code[a1[0][0]]
aa2 = to_one_letter_code[a2[0][0]]
u_sum += matrix[i].get(aa1, aa2)
count += 1
except:
print('Failed for', a1[0], a2[0])
value = float(u_sum) / twoN
if not quiet:
print('PMF: %.4f (%d contacts, %d residues)' % (value, count, twoN))
return value
def load_consurf(filename, selection, palette='red_white_blue', quiet=1):
'''
DESCRIPTION
Color by evolutionary conservation. Writes scores to b-factor.
You need a "r4s.res" or "consurf.grades" input file.
USAGE
load_consurf filename, selection [, palette ]
SEE ALSO
consurfdb
'''
import re
from .seqalign import needle_alignment, alignment_mapping
from . import one_letter
# reduced pattern that matches both r4s.res and consurf.grades
pattern = re.compile(r'\s*(\d+)\s+([A-Y])\s+([-.0-9]+)\s')
scores = []
seqlist = []
if cmd.is_string(filename):
handle = open(filename)
else:
handle = filename
if len(cmd.get_chains(selection)) > 1:
print(' Warning: selection spans multiple chains')
for line in handle:
if line.startswith('#') or line.strip() == '':
continue
m = pattern.match(line)
if m is None:
continue
scores.append(float(m.group(3)))
seqlist.append(m.group(2))
selection = '(%s) and polymer' % selection
model_ca = cmd.get_model(selection + ' and guide')
model_seq = ''.join(one_letter.get(a.resn, 'X') for a in model_ca.atom)
sequence = ''.join(seqlist)
aln = needle_alignment(model_seq, sequence)
scores_resi = dict((model_ca.atom[i].resi, scores[j])
for (i, j) in alignment_mapping(*aln))
cmd.alter(selection,
'b=scores.get(resi, -10)',
space={'scores': scores_resi},
quiet=quiet)
if palette:
cmd.color('yellow', selection + ' and b<-9')
if ' ' in palette:
from .viewing import spectrumany as spectrum
else:
spectrum = cmd.spectrum
spectrum('b', palette, selection + ' and b>-9.5')
def save_movie_mpeg1(filename, mode='', first=0, last=0, preserve=0,
fps=25, twopass=1, vbitrate=16000, quiet=1, exe='mencoder'):
'''
DESCRIPTION
Save movie as MPEG1
This will not be the best quality possible for the file size, but
we were successfull to play those movies in PowerPoint.
Requires mencoder executable from http://mplayerhq.hu
ARGUMENTS
filename = string: Filename, should end on '.mpeg'
mode = normal | draw | ray
first, last = integer: first and last frame number
preserve = 0 or 1: delete temporary images if 0 {default: 0}
fps = integer: frames per second {default: 25}
twopass = 0 or 1: two pass mode encoding (improves quality) {default: 1}
vbitrate = integer: average video bitrate {default: 16000}
WARNING: 4-16000 (in kbit), 16001-24000000 (in bit)
SEE ALSO
cmd.movie.produce, http://www.freemol.org
'''
import os, subprocess, tempfile
first, last, quiet = int(first), int(last), int(quiet)
fps, twopass, vbitrate = int(fps), int(twopass), int(vbitrate)
if cmd.is_string(mode):
if mode == '':
if cmd.pymol.invocation.options.no_gui \
or cmd.get_setting_boolean('ray_trace_frames'):
mode = 'ray'
else:
mode = 'draw'
mode = produce_mode_sc.auto_err(mode, 'mode')
mode = produce_mode_dict[mode]
mode = int(mode)
try:
subprocess.call([exe])
except OSError:
print ' Error: Cannot execute "%s"' % (exe)
raise CmdException
if not quiet:
print ' save_movie: Rendering frames...'
tmp_path = tempfile.mkdtemp()
prefix = os.path.join(tmp_path, 'frame')
cmd.mpng(prefix, first, last, preserve, mode=mode)
mpeg1line = '-mf type=png:fps=%d -ovc lavc -forceidx -noskip -of rawvideo' \
+ ' -mpegopts format=mpeg1 -lavcopts vcodec=mpeg1video:vbitrate=%d' \
+ ':vhq:trell:keyint=25'
mpeg1line = mpeg1line % (fps, vbitrate)
cmdline = exe + ' -quiet mf://' + prefix + '* ' + mpeg1line
if not quiet:
print ' save_movie: Running mencoder...'
if twopass:
if not quiet:
print ' save_movie: First pass...'
cmdline1 = cmdline + ':vpass=1'
subprocess.call(cmdline1.split() + ['-o', os.devnull])
if not quiet:
print ' save_movie: Second pass...'
cmdline = cmdline + ':vpass=2'
subprocess.call(cmdline.split() + ['-o', filename])
if not preserve:
import shutil
shutil.rmtree(tmp_path)
elif not quiet:
print ' save_movie: Not deleting temporary directory:', tmp_path
if not quiet:
print ' save_movie: Done'
def prepwizard(
name, selection="all", options="", state=-1, preserve=0, exe="$SCHRODINGER/utilities/prepwizard", quiet=1
):
"""
DESCRIPTION
Run the SCHRODINGER Protein Preparation Wizard. Builds missing side
chains and converts MSE to MET. Other non-default options need to be
passed with the "options=" argument.
USAGE
prepwizard name [, selection [, options [, state ]]]
ARGUMENTS
name = str: name of object to create
selection = str: atoms to send to the wizard {default: all}
options = str: additional command line options for prepwizard
state = int: object state {default: -1 (current)}
"""
import os, tempfile, subprocess, shutil, shlex
state, preserve, quiet = int(state), int(preserve), int(quiet)
exe = cmd.exp_path(exe)
if not os.path.exists(exe):
if "SCHRODINGER" not in os.environ:
print(" Warning: SCHRODINGER environment variable not set")
raise CmdException("no such script: " + exe)
args = [exe, "-mse", "-fillsidechains", "-WAIT"]
if options:
if cmd.is_string(options):
options = shlex.split(options)
args.extend(options)
tmpdir = tempfile.mkdtemp()
infile = "in.pdb"
outfile = "out.mae"
args.extend([infile, outfile])
try:
cmd.save(os.path.join(tmpdir, infile), selection, state)
p = subprocess.Popen(args, cwd=tmpdir, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
print(p.communicate()[0].rstrip())
if p.returncode != 0:
logfile = os.path.join(tmpdir, "in.log")
if os.path.exists(logfile):
with open(logfile) as handle:
print(handle.read())
raise CmdException("%s failed with exit status %d" % (args[0], p.returncode))
cmd.load(os.path.join(tmpdir, outfile), name)
except OSError:
raise CmdException('Cannot execute "%s"' % (exe))
finally:
if not preserve:
shutil.rmtree(tmpdir)
elif not quiet:
print(" Notice: not deleting", tmpdir)
if not quiet:
print(" prepwizard: done")
