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update from laptop

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Daniel Bauer
2018-09-04 14:45:05 +02:00
parent a4643f9565
commit f8eac9c4ba
14 changed files with 357 additions and 848 deletions
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INCREMENT PYMOL_MAIN SCHROD 999 01-nov-2018 uncounted HOSTID=ANY \
ISSUED=01-Mar-2018 NOTICE="PyMOL for educational use only" \
START=01-Apr-2018 TS_OK SIGN="1105 4C2B 9FDB A342 EE69 01FA \
FD52 45EB A96D A598 C83A 6ABC 4814 2B73 5EFD 093F 4558 99F3 \
1F13 4414 EFBA 39B6 8749 13AA 46D6 8417 AF3D D869 02DF ADCC" \
SIGN2="04A4 3110 8811 34B4 D31E 093F F4CF 689F 8DAF 4090 F108 \
36D2 D171 7680 25AD 1055 506F 8D50 6616 18E3 EC15 22FD 87D1 \
FD92 0F1F D069 4EB3 D748 2CB7 5D4C"

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'''
(c) 2010 Thomas Holder
'''
from pymol import cmd, stored, CmdException
from chempy import cpv
import math
if cmd.get_version()[1] < 1.2:
def get_unused_name(name):
import random
return name + '%04d' % random.randint(0, 1000)
STATE = 1
else:
from pymol.cmd import get_unused_name
STATE = -1
def _vec_sum(vec_list):
# this is the same as
# return numpy.array(vec_list).sum(0).tolist()
vec = cpv.get_null()
for x in vec_list:
vec = cpv.add(vec, x)
return vec
def _mean_and_std(x):
# this is the same as
# return (numpy.mean(x), numpy.std(x, ddof=1))
N = len(x)
if N < 2:
return (x[0], 0.0)
mu = sum(x) / float(N)
var = sum([(i - mu) ** 2 for i in x]) / float(N - 1)
return (mu, var ** 0.5)
def _common_orientation(selection, vec, visualize=1, quiet=0):
'''
Common part of different helix orientation functions. Does calculate
the center of mass and does the visual feedback.
'''
stored.x = []
cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
'stored.x.append([x,y,z])')
if len(stored.x) < 2:
print('warning: count(CA) < 2')
raise CmdException
center = cpv.scale(_vec_sum(stored.x), 1. / len(stored.x))
if visualize:
scale = cpv.distance(stored.x[0], stored.x[-1])
visualize_orientation(vec, center, scale, True)
cmd.zoom(selection, buffer=2)
if not quiet:
print('Center: (%.2f, %.2f, %.2f) Direction: (%.2f, %.2f, %.2f)' % tuple(center + vec))
return center, vec
def visualize_orientation(direction, center=[0, 0, 0], scale=1.0, symmetric=False, color='green', color2='red'):
'''
Draw an arrow. Helper function for "helix_orientation" etc.
'''
from pymol import cgo
color_list = cmd.get_color_tuple(color)
color2_list = cmd.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([
radius,
0.8, 0.8, 0.8,
])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([
radius,
0.8, 0.8, 0.8,
])
obj.extend(color2_list)
coneend = cpv.add(end, cpv.scale(direction, 4.0 * radius))
if cmd.get_version()[1] >= 1.2:
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([
radius * 1.75,
0.0,
])
obj.extend(color_list * 2)
obj.extend([
1.0, 1.0, # Caps
])
cmd.load_cgo(obj, get_unused_name('oriVec'), zoom=0)
def cafit_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
import numpy
stored.x = list()
cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
'stored.x.append([x,y,z])')
x = numpy.array(stored.x)
U, s, Vh = numpy.linalg.svd(x - x.mean(0))
vec = cpv.normalize(Vh[0])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
return _common_orientation(selection, vec, visualize, quiet)
def loop_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize]
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name N+C' % (selection),
'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
vec = cpv.get_null()
count = 0
for x in stored.x.values():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
count += 1
if count == 0:
print('warning: count == 0')
raise CmdException
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
'''
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for helices and gives slightly different results than loop_orientation.
Averages direction of C(i)->O(i) bonds.
USAGE
helix_orientation selection [, visualize [, sigma_cutoff]]
ARGUMENTS
selection = string: atom selection of helix
visualize = 0 or 1: show fitted vector as arrow {default: 1}
sigma_cutoff = float: drop outliers outside
(standard_deviation * sigma_cutoff) {default: 1.5}
SEE ALSO
angle_between_helices, helix_orientation_hbond, loop_orientation, cafit_orientation
'''
visualize, quiet, sigma_cutoff = int(visualize), int(quiet), float(sigma_cutoff)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name C+O' % (selection),
'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
vec_list = []
count = 0
for x in stored.x.values():
if 'C' in x and 'O' in x:
vec_list.append(cpv.sub(x['O'], x['C']))
count += 1
if count == 0:
print('warning: count == 0')
raise CmdException
vec = _vec_sum(vec_list)
if count > 2 and sigma_cutoff > 0:
angle_list = [cpv.get_angle(vec, x) for x in vec_list]
angle_mu, angle_sigma = _mean_and_std(angle_list)
vec_list = [vec_list[i] for i in range(len(vec_list))
if abs(angle_list[i] - angle_mu) < angle_sigma * sigma_cutoff]
if not quiet:
print('Dropping %d outlier(s)' % (len(angle_list) - len(vec_list)))
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
'''
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for alpha helices and gives slightly different results than
helix_orientation. Averages direction of O(i)->N(i+4) hydrogen bonds.
USAGE
helix_orientation selection [, visualize [, cutoff]]
ARGUMENTS
cutoff = float: maximal hydrogen bond distance {default: 3.5}
SEE ALSO
helix_orientation
'''
visualize, quiet, cutoff = int(visualize), int(quiet), float(cutoff)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name N+O' % (selection),
'stored.x.setdefault(resv, dict())[name] = x,y,z')
vec_list = []
for resi in stored.x:
resi_other = resi + 4
if 'O' in stored.x[resi] and resi_other in stored.x:
if 'N' in stored.x[resi_other]:
vec = cpv.sub(stored.x[resi_other]['N'], stored.x[resi]['O'])
if cpv.length(vec) < cutoff:
vec_list.append(vec)
if len(vec_list) == 0:
print('warning: count == 0')
raise CmdException
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def angle_between_helices(selection1, selection2, method='helix_orientation', visualize=1, quiet=0):
'''
DESCRIPTION
Calculates the angle between two helices
USAGE
angle_between_helices selection1, selection2 [, method [, visualize]]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: function to calculate orientation {default: helix_orientation}
or int: 0: helix_orientation, 1: helix_orientation_hbond,
2: loop_orientation, 3: cafit_orientation
visualize = 0 or 1: show fitted vector as arrow {default: 1}
SEE ALSO
helix_orientation, helix_orientation_hbond, loop_orientation, cafit_orientation
'''
visualize, quiet = int(visualize), int(quiet)
methods = {
'0': helix_orientation,
'1': helix_orientation_hbond,
'2': loop_orientation,
'3': cafit_orientation,
}
methods.update([(x.__name__, x) for x in list(methods.values())])
try:
orientation = methods[str(method)]
except KeyError:
print('no such method: ' + str(method))
raise CmdException
if not quiet:
print('Using method: ' + orientation.__name__)
cen1, dir1 = orientation(selection1, visualize, quiet=1)
cen2, dir2 = orientation(selection2, visualize, quiet=1)
angle = cpv.get_angle(dir1, dir2)
angle_deg = math.degrees(angle)
if not quiet:
print('Angle: %.2f deg' % (angle_deg))
if visualize:
cmd.zoom('(%s) or (%s)' % (selection1, selection2), buffer=2)
return angle_deg
cmd.extend('helix_orientation', helix_orientation)
cmd.extend('helix_orientation_hbond', helix_orientation_hbond)
cmd.extend('loop_orientation', loop_orientation)
cmd.extend('cafit_orientation', cafit_orientation)
cmd.extend('angle_between_helices', angle_between_helices)

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.pymol/startup/axes.py
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@@ -37,8 +37,8 @@ class PutCenterCallback(object):
t = cpv.add(t, off_m)
z = -v[11] / 30.0
m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
cmd.set_object_ttt(self.name, m, homogenous=1)
m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
cmd.set_object_ttt(self.name, m)
def axes(name='axes'):
'''

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'''
(c) 2011-2012 Thomas Holder, MPI for Developmental Biology
'''
from __future__ import print_function
__author__ = 'Thomas Holder'
__version__ = '1.1'
__license__ = 'BSD-2-Clause'
from pymol import cmd, CmdException
def save_pdb_without_ter(filename, selection, **kwargs):
'''
DESCRIPTION
Save PDB file without TER records. External applications like TMalign and
DynDom stop reading PDB files at TER records, which might be undesired in
case of missing loops.
'''
v = cmd.get_setting_boolean('pdb_use_ter_records')
if v:
cmd.unset('pdb_use_ter_records')
cmd.save(filename, selection, **kwargs)
if v:
cmd.set('pdb_use_ter_records')
def alignwithanymethod(mobile, target, methods='align super cealign tmalign',
async=1, quiet=1):
'''
DESCRIPTION
Align copies of mobile to target with several alignment methods
ARGUMENTS
mobile = string: atom selection
target = string: atom selection
methods = string: space separated list of PyMOL commands which take
arguments "mobile" and "target" (in any order) {default: align super
cealign tmalign}
'''
import threading
import time
methods = methods.split()
async, quiet = int(async), int(quiet)
mobile_obj = cmd.get_object_list('first (' + mobile + ')')[0]
def myalign(method):
newmobile = cmd.get_unused_name(mobile_obj + '_' + method)
cmd.create(newmobile, mobile_obj)
start = time.time()
cmd.do('%s mobile=%s in %s, target=%s' % (method, newmobile, mobile, target))
if not quiet:
print('Finished: %s (%.2f sec)' % (method, time.time() - start))
for method in methods:
if async:
t = threading.Thread(target=myalign, args=(method,))
t.setDaemon(1)
t.start()
else:
myalign(method)
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
def tmscore(mobile, target, args='', exe='TMscore', quiet=0, **kwargs):
'''
DESCRIPTION
TMscore wrapper
Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
http://zhanglab.ccmb.med.umich.edu/TM-score/
ARGUMENTS
mobile, target = string: atom selections
args = string: Extra arguments like -d 5
exe = string: Path to TMscore executable {default: TMscore}
ter = 0/1: If ter=0, then ignore chain breaks because TMscore will stop
at first TER record {default: 0}
SEE ALSO
tmalign, mmalign
'''
kwargs.pop('_self', None)
return tmalign(mobile, target, args, exe, quiet=quiet, **kwargs)
def mmalign(mobile, target, args='', exe='MMalign', ter=0, transform=1, quiet=0):
'''
DESCRIPTION
MMalign wrapper
Reference: S. Mukherjee and Y. Zhang, Nucleic Acids Research 2009; 37: e83
http://zhanglab.ccmb.med.umich.edu/MM-align/
SEE ALSO
tmalign, tmscore
'''
return tmalign(mobile, target, args, exe, ter, transform, quiet=quiet)
# pymol commands
cmd.extend('alignwithanymethod', alignwithanymethod)
cmd.extend('tmalign', tmalign)
cmd.extend('tmscore', tmscore)
cmd.extend('mmalign', tmalign)
# autocompletion
cmd.auto_arg[0].update({
'tmalign': cmd.auto_arg[0]['align'],
'tmscore': cmd.auto_arg[0]['align'],
'mmalign': cmd.auto_arg[0]['align'],
})
cmd.auto_arg[1].update({
'tmalign': cmd.auto_arg[1]['align'],
'tmscore': cmd.auto_arg[1]['align'],
'mmalign': cmd.auto_arg[1]['align'],
})

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matplotlibrc
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#### CONFIGURATION BEGINS HERE
# The default backend; one of GTK GTKAgg GTKCairo GTK3Agg GTK3Cairo
# MacOSX Qt4Agg Qt5Agg TkAgg WX WXAgg Agg Cairo GDK PS PDF SVG
# Template.
# You can also deploy your own backend outside of matplotlib by
# referring to the module name (which must be in the PYTHONPATH) as
# 'module://my_backend'.
backend : Qt5Agg
# If you are using the Qt4Agg backend, you can choose here
# to use the PyQt4 bindings or the newer PySide bindings to
# the underlying Qt4 toolkit.
# backend.qt4 : PyQt4 # PyQt4 | PySide
# Note that this can be overridden by the environment variable
# QT_API used by Enthought Tool Suite (ETS); valid values are
# "pyqt" and "pyside". The "pyqt" setting has the side effect of
# forcing the use of Version 2 API for QString and QVariant.
# The port to use for the web server in the WebAgg backend.
# webagg.port : 8888
# If webagg.port is unavailable, a number of other random ports will
# be tried until one that is available is found.
# webagg.port_retries : 50
# When True, open the webbrowser to the plot that is shown
# webagg.open_in_browser : True
# When True, the figures rendered in the nbagg backend are created with
# a transparent background.
# nbagg.transparent : False
# if you are running pyplot inside a GUI and your backend choice
# conflicts, we will automatically try to find a compatible one for
# you if backend_fallback is True
#backend_fallback: True
#interactive : False
#toolbar : toolbar2 # None | toolbar2 ("classic" is deprecated)
#timezone : UTC # a pytz timezone string, e.g., US/Central or Europe/Paris
# Where your matplotlib data lives if you installed to a non-default
# location. This is where the matplotlib fonts, bitmaps, etc reside
#datapath : /home/jdhunter/mpldata
### LINES
# See http://matplotlib.org/api/artist_api.html#module-matplotlib.lines for more
# information on line properties.
lines.linewidth : 1 # line width in points
#lines.linestyle : - # solid line
#lines.color : C0 # has no affect on plot(); see axes.prop_cycle
#lines.marker : None # the default marker
#lines.markeredgewidth : 1.0 # the line width around the marker symbol
#lines.markersize : 6 # markersize, in points
#lines.dash_joinstyle : miter # miter|round|bevel
#lines.dash_capstyle : butt # butt|round|projecting
#lines.solid_joinstyle : miter # miter|round|bevel
#lines.solid_capstyle : projecting # butt|round|projecting
#lines.antialiased : True # render lines in antialiased (no jaggies)
# The three standard dash patterns. These are scaled by the linewidth.
#lines.dashed_pattern : 2.8, 1.2
#lines.dashdot_pattern : 4.8, 1.2, 0.8, 1.2
#lines.dotted_pattern : 1.1, 1.1
#lines.scale_dashes : True
#markers.fillstyle: full # full|left|right|bottom|top|none
### PATCHES
# Patches are graphical objects that fill 2D space, like polygons or
# circles. See
# http://matplotlib.org/api/artist_api.html#module-matplotlib.patches
# information on patch properties
#patch.linewidth : 1 # edge width in points.
#patch.facecolor : C0
#patch.edgecolor : black # if forced, or patch is not filled
#patch.force_edgecolor : False # True to always use edgecolor
#patch.antialiased : True # render patches in antialiased (no jaggies)
### HATCHES
#hatch.color : k
#hatch.linewidth : 1.0
### Boxplot
#boxplot.notch : False
#boxplot.vertical : True
#boxplot.whiskers : 1.5
#boxplot.bootstrap : None
#boxplot.patchartist : False
#boxplot.showmeans : False
#boxplot.showcaps : True
#boxplot.showbox : True
#boxplot.showfliers : True
#boxplot.meanline : False
#boxplot.flierprops.color : 'k'
#boxplot.flierprops.marker : 'o'
#boxplot.flierprops.markerfacecolor : 'none'
#boxplot.flierprops.markeredgecolor : 'k'
#boxplot.flierprops.markersize : 6
#boxplot.flierprops.linestyle : 'none'
#boxplot.flierprops.linewidth : 1.0
#boxplot.boxprops.color : 'k'
#boxplot.boxprops.linewidth : 1.0
#boxplot.boxprops.linestyle : '-'
#boxplot.whiskerprops.color : 'k'
#boxplot.whiskerprops.linewidth : 1.0
#boxplot.whiskerprops.linestyle : '-'
#boxplot.capprops.color : 'k'
#boxplot.capprops.linewidth : 1.0
#boxplot.capprops.linestyle : '-'
#boxplot.medianprops.color : 'C1'
#boxplot.medianprops.linewidth : 1.0
#boxplot.medianprops.linestyle : '-'
#boxplot.meanprops.color : 'C2'
#boxplot.meanprops.marker : '^'
#boxplot.meanprops.markerfacecolor : 'C2'
#boxplot.meanprops.markeredgecolor : 'C2'
#boxplot.meanprops.markersize : 6
#boxplot.meanprops.linestyle : 'none'
#boxplot.meanprops.linewidth : 1.0
### FONT
#
# font properties used by text.Text. See
# http://matplotlib.org/api/font_manager_api.html for more
# information on font properties. The 6 font properties used for font
# matching are given below with their default values.
#
# The font.family property has five values: 'serif' (e.g., Times),
# 'sans-serif' (e.g., Helvetica), 'cursive' (e.g., Zapf-Chancery),
# 'fantasy' (e.g., Western), and 'monospace' (e.g., Courier). Each of
# these font families has a default list of font names in decreasing
# order of priority associated with them. When text.usetex is False,
# font.family may also be one or more concrete font names.
#
# The font.style property has three values: normal (or roman), italic
# or oblique. The oblique style will be used for italic, if it is not
# present.
#
# The font.variant property has two values: normal or small-caps. For
# TrueType fonts, which are scalable fonts, small-caps is equivalent
# to using a font size of 'smaller', or about 83%% of the current font
# size.
#
# The font.weight property has effectively 13 values: normal, bold,
# bolder, lighter, 100, 200, 300, ..., 900. Normal is the same as
# 400, and bold is 700. bolder and lighter are relative values with
# respect to the current weight.
#
# The font.stretch property has 11 values: ultra-condensed,
# extra-condensed, condensed, semi-condensed, normal, semi-expanded,
# expanded, extra-expanded, ultra-expanded, wider, and narrower. This
# property is not currently implemented.
#
# The font.size property is the default font size for text, given in pts.
# 10 pt is the standard value.
#
#font.family : sans-serif
#font.style : normal
#font.variant : normal
#font.weight : medium
#font.stretch : normal
# note that font.size controls default text sizes. To configure
# special text sizes tick labels, axes, labels, title, etc, see the rc
# settings for axes and ticks. Special text sizes can be defined
# relative to font.size, using the following values: xx-small, x-small,
# small, medium, large, x-large, xx-large, larger, or smaller
#font.size : 10.0
#font.serif : DejaVu Serif, Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif
#font.sans-serif : DejaVu Sans, Bitstream Vera Sans, Lucida Grande, Verdana, Geneva, Lucid, Arial, Helvetica, Avant Garde, sans-serif
#font.cursive : Apple Chancery, Textile, Zapf Chancery, Sand, Script MT, Felipa, cursive
#font.fantasy : Comic Sans MS, Chicago, Charcoal, Impact, Western, Humor Sans, xkcd, fantasy
#font.monospace : DejaVu Sans Mono, Bitstream Vera Sans Mono, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace
### TEXT
# text properties used by text.Text. See
# http://matplotlib.org/api/artist_api.html#module-matplotlib.text for more
# information on text properties
#text.color : black
### LaTeX customizations. See http://wiki.scipy.org/Cookbook/Matplotlib/UsingTex
#text.usetex : False # use latex for all text handling. The following fonts
# are supported through the usual rc parameter settings:
# new century schoolbook, bookman, times, palatino,
# zapf chancery, charter, serif, sans-serif, helvetica,
# avant garde, courier, monospace, computer modern roman,
# computer modern sans serif, computer modern typewriter
# If another font is desired which can loaded using the
# LaTeX \usepackage command, please inquire at the
# matplotlib mailing list
#text.latex.unicode : False # use "ucs" and "inputenc" LaTeX packages for handling
# unicode strings.
#text.latex.preamble : # IMPROPER USE OF THIS FEATURE WILL LEAD TO LATEX FAILURES
# AND IS THEREFORE UNSUPPORTED. PLEASE DO NOT ASK FOR HELP
# IF THIS FEATURE DOES NOT DO WHAT YOU EXPECT IT TO.
# preamble is a comma separated list of LaTeX statements
# that are included in the LaTeX document preamble.
# An example:
# text.latex.preamble : \usepackage{bm},\usepackage{euler}
# The following packages are always loaded with usetex, so
# beware of package collisions: color, geometry, graphicx,
# type1cm, textcomp. Adobe Postscript (PSSNFS) font packages
# may also be loaded, depending on your font settings
#text.dvipnghack : None # some versions of dvipng don't handle alpha
# channel properly. Use True to correct
# and flush ~/.matplotlib/tex.cache
# before testing and False to force
# correction off. None will try and
# guess based on your dvipng version
#text.hinting : auto # May be one of the following:
# 'none': Perform no hinting
# 'auto': Use FreeType's autohinter
# 'native': Use the hinting information in the
# font file, if available, and if your
# FreeType library supports it
# 'either': Use the native hinting information,
# or the autohinter if none is available.
# For backward compatibility, this value may also be
# True === 'auto' or False === 'none'.
#text.hinting_factor : 8 # Specifies the amount of softness for hinting in the
# horizontal direction. A value of 1 will hint to full
# pixels. A value of 2 will hint to half pixels etc.
#text.antialiased : True # If True (default), the text will be antialiased.
# This only affects the Agg backend.
# The following settings allow you to select the fonts in math mode.
# They map from a TeX font name to a fontconfig font pattern.
# These settings are only used if mathtext.fontset is 'custom'.
# Note that this "custom" mode is unsupported and may go away in the
# future.
#mathtext.cal : cursive
#mathtext.rm : serif
#mathtext.tt : monospace
#mathtext.it : serif:italic
#mathtext.bf : serif:bold
#mathtext.sf : sans
#mathtext.fontset : dejavusans # Should be 'dejavusans' (default),
# 'dejavuserif', 'cm' (Computer Modern), 'stix',
# 'stixsans' or 'custom'
#mathtext.fallback_to_cm : True # When True, use symbols from the Computer Modern
# fonts when a symbol can not be found in one of
# the custom math fonts.
#mathtext.default : it # The default font to use for math.
# Can be any of the LaTeX font names, including
# the special name "regular" for the same font
# used in regular text.
### AXES
# default face and edge color, default tick sizes,
# default fontsizes for ticklabels, and so on. See
# http://matplotlib.org/api/axes_api.html#module-matplotlib.axes
#axes.facecolor : white # axes background color
#axes.edgecolor : black # axes edge color
#axes.linewidth : 0.8 # edge linewidth
#axes.grid : False # display grid or not
#axes.titlesize : large # fontsize of the axes title
#axes.titlepad : 6.0 # pad between axes and title in points
#axes.labelsize : medium # fontsize of the x any y labels
#axes.labelpad : 4.0 # space between label and axis
#axes.labelweight : normal # weight of the x and y labels
#axes.labelcolor : black
#axes.axisbelow : 'line' # draw axis gridlines and ticks below
# patches (True); above patches but below
# lines ('line'); or above all (False)
#axes.formatter.limits : -7, 7 # use scientific notation if log10
# of the axis range is smaller than the
# first or larger than the second
#axes.formatter.use_locale : False # When True, format tick labels
# according to the user's locale.
# For example, use ',' as a decimal
# separator in the fr_FR locale.
#axes.formatter.use_mathtext : False # When True, use mathtext for scientific
# notation.
#axes.formatter.useoffset : True # If True, the tick label formatter
# will default to labeling ticks relative
# to an offset when the data range is
# small compared to the minimum absolute
# value of the data.
#axes.formatter.offset_threshold : 4 # When useoffset is True, the offset
# will be used when it can remove
# at least this number of significant
# digits from tick labels.
# axes.spines.left : True # display axis spines
# axes.spines.bottom : True
# axes.spines.top : True
# axes.spines.right : True
#axes.unicode_minus : True # use unicode for the minus symbol
# rather than hyphen. See
# http://en.wikipedia.org/wiki/Plus_and_minus_signs#Character_codes
#axes.prop_cycle: cycler('color', ['0072B2', '009E73', 'D55E00', 'CC79A7', 'F0E442', '56B4E9'])
lines.linewidth : 1 # line width in points
font.size : 12
text.usetex : False # use latex for all text handling. The following fonts
axes.edgecolor : black # axes edge color
axes.grid : True # display grid or not
axes.titlesize : 12 # fontsize of the axes title
axes.labelsize : 12 # fontsize of the x any y labels
axes.spines.top : False
axes.spines.right : False
axes.prop_cycle: cycler('color', ['348ABD', 'A60628', '7A68A6', '467821', 'D55E00', 'CC79A7', '56B4E9', '009E73', 'F0E442', '0072B2'])
patch.facecolor: 0072B2
#axes.autolimit_mode : data # How to scale axes limits to the data.
# Use "data" to use data limits, plus some margin
# Use "round_number" move to the nearest "round" number
#axes.xmargin : .05 # x margin. See `axes.Axes.margins`
#axes.ymargin : .05 # y margin See `axes.Axes.margins`
#polaraxes.grid : True # display grid on polar axes
#axes3d.grid : True # display grid on 3d axes
### DATES
# These control the default format strings used in AutoDateFormatter.
# Any valid format datetime format string can be used (see the python
# `datetime` for details). For example using '%%x' will use the locale date representation
# '%%X' will use the locale time representation and '%%c' will use the full locale datetime
# representation.
# These values map to the scales:
# {'year': 365, 'month': 30, 'day': 1, 'hour': 1/24, 'minute': 1 / (24 * 60)}
# date.autoformatter.year : %Y
# date.autoformatter.month : %Y-%m
# date.autoformatter.day : %Y-%m-%d
# date.autoformatter.hour : %m-%d %H
# date.autoformatter.minute : %d %H:%M
# date.autoformatter.second : %H:%M:%S
# date.autoformatter.microsecond : %M:%S.%f
### TICKS
# see http://matplotlib.org/api/axis_api.html#matplotlib.axis.Tick
#xtick.top : False # draw ticks on the top side
#xtick.bottom : True # draw ticks on the bottom side
#xtick.major.size : 3.5 # major tick size in points
#xtick.minor.size : 2 # minor tick size in points
#xtick.major.width : 0.8 # major tick width in points
#xtick.minor.width : 0.6 # minor tick width in points
#xtick.major.pad : 3.5 # distance to major tick label in points
#xtick.minor.pad : 3.4 # distance to the minor tick label in points
#xtick.color : k # color of the tick labels
#xtick.labelsize : medium # fontsize of the tick labels
#xtick.direction : out # direction: in, out, or inout
#xtick.minor.visible : False # visibility of minor ticks on x-axis
#xtick.major.top : True # draw x axis top major ticks
#xtick.major.bottom : True # draw x axis bottom major ticks
#xtick.minor.top : True # draw x axis top minor ticks
#xtick.minor.bottom : True # draw x axis bottom minor ticks
#ytick.left : True # draw ticks on the left side
#ytick.right : False # draw ticks on the right side
#ytick.major.size : 3.5 # major tick size in points
#ytick.minor.size : 2 # minor tick size in points
#ytick.major.width : 0.8 # major tick width in points
#ytick.minor.width : 0.6 # minor tick width in points
#ytick.major.pad : 3.5 # distance to major tick label in points
#ytick.minor.pad : 3.4 # distance to the minor tick label in points
#ytick.color : k # color of the tick labels
#ytick.labelsize : medium # fontsize of the tick labels
#ytick.direction : out # direction: in, out, or inout
#ytick.minor.visible : False # visibility of minor ticks on y-axis
#ytick.major.left : True # draw y axis left major ticks
#ytick.major.right : True # draw y axis right major ticks
#ytick.minor.left : True # draw y axis left minor ticks
#ytick.minor.right : True # draw y axis right minor ticks
### GRIDS
#grid.color : b0b0b0 # grid color
#grid.linestyle : - # solid
#grid.linewidth : 0.8 # in points
#grid.alpha : 1.0 # transparency, between 0.0 and 1.0
### Legend
#legend.loc : best
#legend.frameon : True # if True, draw the legend on a background patch
#legend.framealpha : 0.8 # legend patch transparency
#legend.facecolor : inherit # inherit from axes.facecolor; or color spec
#legend.edgecolor : 0.8 # background patch boundary color
#legend.fancybox : True # if True, use a rounded box for the
# legend background, else a rectangle
#legend.shadow : False # if True, give background a shadow effect
#legend.numpoints : 1 # the number of marker points in the legend line
#legend.scatterpoints : 1 # number of scatter points
#legend.markerscale : 1.0 # the relative size of legend markers vs. original
#legend.fontsize : medium
# Dimensions as fraction of fontsize:
#legend.borderpad : 0.4 # border whitespace
#legend.labelspacing : 0.5 # the vertical space between the legend entries
#legend.handlelength : 2.0 # the length of the legend lines
#legend.handleheight : 0.7 # the height of the legend handle
#legend.handletextpad : 0.8 # the space between the legend line and legend text
#legend.borderaxespad : 0.5 # the border between the axes and legend edge
#legend.columnspacing : 2.0 # column separation
### FIGURE
# See http://matplotlib.org/api/figure_api.html#matplotlib.figure.Figure
#figure.titlesize : large # size of the figure title (Figure.suptitle())
#figure.titleweight : normal # weight of the figure title
figure.figsize : 11.69,8.27 # figure size in inches
axes.autolimit_mode : data # How to scale axes limits to the data.
axes.xmargin : .00 # x margin. See `axes.Axes.margins`
axes.ymargin : .00 # y margin See `axes.Axes.margins`
xtick.top : False # draw ticks on the top side
xtick.bottom : False # draw ticks on the bottom side
xtick.labelsize : 12 # fontsize of the tick labels
ytick.left : True # draw ticks on the left side
ytick.right : True # draw ticks on the right side
ytick.labelsize : 12 # fontsize of the tick labels
grid.linestyle : : # solid
grid.linewidth : 0.8 # in points
grid.alpha : 0.7 # transparency, between 0.0 and 1.0
legend.loc : best
legend.frameon : True # if True, draw the legend on a background patch
legend.framealpha : 1 # legend patch transparency
legend.edgecolor : 1 # background patch boundary color
legend.fontsize : 10
figure.figsize : 4.5,4.5 # figure size in inches
figure.dpi : 100 # figure dots per inch
#figure.facecolor : white # figure facecolor; 0.75 is scalar gray
#figure.edgecolor : white # figure edgecolor
figure.autolayout : True # When True, automatically adjust subplot
# parameters to make the plot fit the figure
#figure.max_open_warning : 20 # The maximum number of figures to open through
# the pyplot interface before emitting a warning.
# If less than one this feature is disabled.
# The figure subplot parameters. All dimensions are a fraction of the
#figure.subplot.left : 0.125 # the left side of the subplots of the figure
#figure.subplot.right : 0.9 # the right side of the subplots of the figure
#figure.subplot.bottom : 0.11 # the bottom of the subplots of the figure
#figure.subplot.top : 0.88 # the top of the subplots of the figure
#figure.subplot.wspace : 0.2 # the amount of width reserved for blank space between subplots,
# expressed as a fraction of the average axis width
#figure.subplot.hspace : 0.2 # the amount of height reserved for white space between subplots,
# expressed as a fraction of the average axis height
### IMAGES
#image.aspect : equal # equal | auto | a number
#image.interpolation : nearest # see help(imshow) for options
#image.cmap : viridis # A colormap name, gray etc...
#image.lut : 256 # the size of the colormap lookup table
#image.origin : upper # lower | upper
#image.resample : True
#image.composite_image : True # When True, all the images on a set of axes are
# combined into a single composite image before
# saving a figure as a vector graphics file,
# such as a PDF.
### CONTOUR PLOTS
#contour.negative_linestyle : dashed # dashed | solid
#contour.corner_mask : True # True | False | legacy
### ERRORBAR PLOTS
#errorbar.capsize : 0 # length of end cap on error bars in pixels
### HISTOGRAM PLOTS
#hist.bins : 10 # The default number of histogram bins.
# If Numpy 1.11 or later is
# installed, may also be `auto`
### SCATTER PLOTS
#scatter.marker : o # The default marker type for scatter plots.
### Agg rendering
### Warning: experimental, 2008/10/10
#agg.path.chunksize : 0 # 0 to disable; values in the range
# 10000 to 100000 can improve speed slightly
# and prevent an Agg rendering failure
# when plotting very large data sets,
# especially if they are very gappy.
# It may cause minor artifacts, though.
# A value of 20000 is probably a good
# starting point.
### SAVING FIGURES
#path.simplify : True # When True, simplify paths by removing "invisible"
# points to reduce file size and increase rendering
# speed
#path.simplify_threshold : 0.1 # The threshold of similarity below which
# vertices will be removed in the simplification
# process
#path.snap : True # When True, rectilinear axis-aligned paths will be snapped to
# the nearest pixel when certain criteria are met. When False,
# paths will never be snapped.
#path.sketch : None # May be none, or a 3-tuple of the form (scale, length,
# randomness).
# *scale* is the amplitude of the wiggle
# perpendicular to the line (in pixels). *length*
# is the length of the wiggle along the line (in
# pixels). *randomness* is the factor by which
# the length is randomly scaled.
# the default savefig params can be different from the display params
# e.g., you may want a higher resolution, or to make the figure
# background white
#savefig.dpi : figure # figure dots per inch or 'figure'
#savefig.facecolor : white # figure facecolor when saving
#savefig.edgecolor : white # figure edgecolor when saving
#savefig.format : png # png, ps, pdf, svg
#savefig.bbox : standard # 'tight' or 'standard'.
# 'tight' is incompatible with pipe-based animation
# backends but will workd with temporary file based ones:
# e.g. setting animation.writer to ffmpeg will not work,
# use ffmpeg_file instead
#savefig.pad_inches : 0.1 # Padding to be used when bbox is set to 'tight'
#savefig.jpeg_quality: 95 # when a jpeg is saved, the default quality parameter.
#savefig.directory : ~ # default directory in savefig dialog box,
# leave empty to always use current working directory
#savefig.transparent : False # setting that controls whether figures are saved with a
# transparent background by default
# tk backend params
#tk.window_focus : False # Maintain shell focus for TkAgg
# ps backend params
#ps.papersize : letter # auto, letter, legal, ledger, A0-A10, B0-B10
#ps.useafm : False # use of afm fonts, results in small files
#ps.usedistiller : False # can be: None, ghostscript or xpdf
# Experimental: may produce smaller files.
# xpdf intended for production of publication quality files,
# but requires ghostscript, xpdf and ps2eps
#ps.distiller.res : 6000 # dpi
#ps.fonttype : 3 # Output Type 3 (Type3) or Type 42 (TrueType)
# pdf backend params
#pdf.compression : 6 # integer from 0 to 9
# 0 disables compression (good for debugging)
#pdf.fonttype : 3 # Output Type 3 (Type3) or Type 42 (TrueType)
# svg backend params
#svg.image_inline : True # write raster image data directly into the svg file
#svg.fonttype : 'path' # How to handle SVG fonts:
# 'none': Assume fonts are installed on the machine where the SVG will be viewed.
# 'path': Embed characters as paths -- supported by most SVG renderers
# 'svgfont': Embed characters as SVG fonts -- supported only by Chrome,
# Opera and Safari
#svg.hashsalt : None # if not None, use this string as hash salt
# instead of uuid4
# docstring params
#docstring.hardcopy = False # set this when you want to generate hardcopy docstring
# Set the verbose flags. This controls how much information
# matplotlib gives you at runtime and where it goes. The verbosity
# levels are: silent, helpful, debug, debug-annoying. Any level is
# inclusive of all the levels below it. If your setting is "debug",
# you'll get all the debug and helpful messages. When submitting
# problems to the mailing-list, please set verbose to "helpful" or "debug"
# and paste the output into your report.
#
# The "fileo" gives the destination for any calls to verbose.report.
# These objects can a filename, or a filehandle like sys.stdout.
#
# You can override the rc default verbosity from the command line by
# giving the flags --verbose-LEVEL where LEVEL is one of the legal
# levels, e.g., --verbose-helpful.
#
# You can access the verbose instance in your code
# from matplotlib import verbose.
#verbose.level : silent # one of silent, helpful, debug, debug-annoying
#verbose.fileo : sys.stdout # a log filename, sys.stdout or sys.stderr
# Event keys to interact with figures/plots via keyboard.
# Customize these settings according to your needs.
# Leave the field(s) empty if you don't need a key-map. (i.e., fullscreen : '')
#keymap.fullscreen : f, ctrl+f # toggling
#keymap.home : h, r, home # home or reset mnemonic
#keymap.back : left, c, backspace # forward / backward keys to enable
#keymap.forward : right, v # left handed quick navigation
#keymap.pan : p # pan mnemonic
#keymap.zoom : o # zoom mnemonic
#keymap.save : s # saving current figure
#keymap.quit : ctrl+w, cmd+w # close the current figure
#keymap.grid : g # switching on/off a grid in current axes
#keymap.yscale : l # toggle scaling of y-axes ('log'/'linear')
#keymap.xscale : L, k # toggle scaling of x-axes ('log'/'linear')
#keymap.all_axes : a # enable all axes
# Control location of examples data files
#examples.directory : '' # directory to look in for custom installation
###ANIMATION settings
#animation.html : 'none' # How to display the animation as HTML in
# the IPython notebook. 'html5' uses
# HTML5 video tag.
#animation.writer : ffmpeg # MovieWriter 'backend' to use
#animation.codec : h264 # Codec to use for writing movie
#animation.bitrate: -1 # Controls size/quality tradeoff for movie.
# -1 implies let utility auto-determine
#animation.frame_format: 'png' # Controls frame format used by temp files
#animation.ffmpeg_path: 'ffmpeg' # Path to ffmpeg binary. Without full path
# $PATH is searched
#animation.ffmpeg_args: '' # Additional arguments to pass to ffmpeg
#animation.avconv_path: 'avconv' # Path to avconv binary. Without full path
# $PATH is searched
#animation.avconv_args: '' # Additional arguments to pass to avconv
#animation.mencoder_path: 'mencoder'
# Path to mencoder binary. Without full path
# $PATH is searched
#animation.mencoder_args: '' # Additional arguments to pass to mencoder
#animation.convert_path: 'convert' # Path to ImageMagick's convert binary.
# On Windows use the full path since convert
# is also the name of a system tool.