def sele_exists(sele):
sess = cmd.get_session()
for i in sess["names"]:
if type(i) is ListType:
if sele==i[0]:
return 1
return 0
def testGetSession(self):
cmd.fragment('ala')
x = cmd.count_atoms()
s = cmd.get_session()
cmd.reinitialize()
cmd.set_session(s)
self.assertEqual(['ala'], cmd.get_names())
self.assertEqual(x, cmd.count_atoms())
def testGetSession(self):
cmd.fragment('ala')
x = cmd.count_atoms()
s = cmd.get_session()
cmd.reinitialize()
cmd.set_session(s)
self.assertEqual(['ala'], cmd.get_names())
self.assertEqual(x, cmd.count_atoms())
def dump_rep(name):
if 'PYMOL_GIT_MOD' in os.environ:
import shutil
try:
shutil.copytree(
os.path.join(os.environ['PYMOL_GIT_MOD'], 'pymol2glmol', 'js'),
os.path.join(os.getcwd(), 'js'))
except OSError:
pass
names = cmd.get_session()['names']
cmd.set('pdb_retain_ids', 1)
ret = ''
for obj in names:
if (obj == None):
continue
if (obj[2] == 0): # not visible
continue
if (obj[1] == 0 and obj[4] == 1 and obj[0] == name):
ret += parseObjMol(obj)
if (obj[1] == 0
and obj[4] == 4): # currently all dist objects are exported
ret += parseDistObj(obj)
cmd.turn('z', 180)
view = cmd.get_view()
cmd.turn('z', 180)
cx = -view[12]
cy = -view[13]
cz = -view[14]
cameraZ = -view[11] - 150
fov = float(cmd.get("field_of_view"))
fogStart = float(cmd.get("fog_start"))
slabNear = view[15] + view[11]
slabFar = view[16] + view[11]
ret += "\nview:%.3f,%.3f,%.3f,%.3f,%.3f,%.3f,%.3f,%.3f" % \
(cx, cy, cz, cameraZ, slabNear, slabFar, fogStart, fov)
for i in range(9):
ret += ",%.3f" % view[i]
bgcolor = cmd.get_setting_tuple('bg_rgb')[1]
ret += "\nbgcolor:%02x%02x%02x" % (int(255 * float(bgcolor[0])), \
int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
if 'PYMOL_GIT_MOD' in os.environ:
template = open(os.path.join(os.environ['PYMOL_GIT_MOD'], 'pymol2glmol', 'imported.html')).read().\
replace("###INCLUDE_PDB_FILE_HERE###", cmd.get_pdbstr(name)).\
replace('###INCLUDE_REPRESENTATION_HERE###', ret)
else:
template = open('imported.html').read().\
replace("###INCLUDE_PDB_FILE_HERE###", cmd.get_pdbstr(name)).\
replace('###INCLUDE_REPRESENTATION_HERE###', ret)
f = open(name + '.html', 'w')
f.write(template)
f.close()
def testGetMovieLocked(self):
self.assertEqual(cmd.get_movie_locked(), 0)
cmd.mset('1x1')
cmd.mdo(1, 'cmd.color("blue")')
s = cmd.get_session()
cmd.set_session(s)
self.assertEqual(cmd.get_movie_locked(), 1)
cmd.set('security', 0)
cmd.set_session(s)
self.assertEqual(cmd.get_movie_locked(), 0)
def sele2Color_deprecated(self):
globalShader = self.optionMenu_shader.getvalue()
# (color:shader) dictionary
# be used in shaderFactory.SCString()
#self.spColorShaderDict = {}
# get all the selection name
sess = cmd.get_session()['names']
for i in sess:
if type(i) is ListType:
# for each selection in the scene
# also should exist in seleShaderDict
if i[0] in self.seleShaderDict:
newShader = self.seleShaderDict[i[0]]
if newShader != globalShader: # should be different from global shader, otherwise do nothing
newColorInc = ShaderFactory.seleSlot[newShader]
# pymol api routine
# get the color for all the atoms in current selection
stored.idcolor_list = []
cmd.iterate(i[0], 'stored.idcolor_list.append((ID, int(color)))')
# for a set of atoms have the same new color
# apply color all at once for better performance
# cmd.color is slow
# example result: (color_index: [atom ids])
# {25: [2, 3, 6], 6: [1], 9: [4, 5]}
colorSetDict = {}
for (atom_id, color) in stored.idcolor_list:
colorSetDict.setdefault(color, []).append(str(atom_id))
#print repr(colorSetDict)
# for each color
#for (atom_id, color) in stored.idcolor_list:
for color in colorSetDict:
atom_set = colorSetDict[color]
rgb_color = cmd.get_color_tuple(color)
#newColorInc = 0.001
if rgb_color[2] >= 0.990:
color_id = '%s %s %s' % (str(rgb_color[0])[0:5].ljust(5, '0'), str(rgb_color[1])[0:5].ljust(5, '0'), str(rgb_color[2]-newColorInc)[0:5])
else:
color_id = '%s %s %s' % (str(rgb_color[0])[0:5].ljust(5, '0'), str(rgb_color[1])[0:5].ljust(5, '0'), str(rgb_color[2]+newColorInc)[0:5])
#print atom_id, color, color_id, repr(rgb_color)
# color_id from all the sele:shader dictionary
# determine color_id:shader pair
if color_id not in self.spColorShaderDict:
self.spColorShaderDict[color_id] = [newShader, i[0]]
# apply new color to atom set
newRGB = color_id.split(' ')
newColor = [float(newRGB[0]), float(newRGB[1]), float(newRGB[2])]
cmd.set_color(color_id, newColor)
cmd.color(color_id, ('ID %s' % '+'.join(atom_set)))
print 'apply shader [%s] to selection [%s].' % (newShader, i[0])
def setNative(self, base=""): # --- get last structure --- # if base == "": sess = cmd.get_session() for i in sess["names"]: if type(i) is ListType: base = i[0] cmd.set_name(base, "native") file = base + ".pdb" self.viewer.setNative(file) self.viewer.displayNative()
def stereo_ray(output='', width='', height=''):
if output == '':
print 'no output filename defined\n'
print 'try: \'stereo_ray filename\''
return -1
# abort if no output file name given
if width == '':
width,height = cmd.get_session()['main'][0:2]
# get dimensions from viewer if not given
elif height == '':
oldWidth,oldHeight = cmd.get_session()['main'][0:2]
height = int(width)*oldHeight/oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output+"_r")
cmd.ray(width, height, angle=3)
cmd.png(output+"_l")
def stereo_ray(output="", width="", height=""):
"""
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.
USAGE
stereo_ray filename [, width [, height]]
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
"""
if output == "":
print "no output filename defined\n"
print "try: 'stereo_ray filename'"
return -1
# abort if no output file name given
if width == "":
width, height = cmd.get_session()["main"][0:2]
# get dimensions from viewer if not given
elif height == "":
oldWidth, oldHeight = cmd.get_session()["main"][0:2]
height = int(width) * oldHeight / oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output + "_r")
cmd.ray(width, height, angle=3)
cmd.png(output + "_l")
def get_mdo_commands(quiet=1):
'''
DESCRIPTION
Get the list of mdo commands.
'''
s = cmd.get_session("none")
commands = s["movie"][5] or []
if not int(quiet):
for frame, command in enumerate(commands, 1):
if command:
print('mdo {}: {}'.format(frame, command.strip(';')))
return commands
def stereo_ray(output='', width='', height=''):
if output == '':
print 'no output filename defined\n'
print 'try: \'stereo_ray filename\''
return -1
# abort if no output file name given
if width == '':
width, height = cmd.get_session()['main'][0:2]
# get dimensions from viewer if not given
elif height == '':
oldWidth, oldHeight = cmd.get_session()['main'][0:2]
height = int(width) * oldHeight / oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output + "_r")
cmd.ray(width, height, angle=3)
cmd.png(output + "_l")
def get_keyframes(quiet=1):
'''
DESCRIPTION
Get the list of camera keyframes for the current movie.
'''
s = cmd.get_session("none")
viewelem_list = s["movie"][6]
if not viewelem_list:
return []
r = [i for (i,v) in enumerate(viewelem_list, 1) if v[12] == 2]
if not int(quiet):
print(r)
return r
def setDesigned(self, base=""): # --- get last structure --- # if base == "": sess = cmd.get_session() for i in sess["names"]: if type(i) is ListType: base = i[0] file = base + ".pdb" cmd.set_name(base, "designed") self.viewer.setDesign(file) self.viewer.selectCatalytic() self.viewer.displayDesigned()
def get_keyframes(quiet=1):
'''
DESCRIPTION
Get the list of camera keyframes for the current movie.
'''
s = cmd.get_session("none")
viewelem_list = s["movie"][6]
if not viewelem_list:
return []
r = [i for (i, v) in enumerate(viewelem_list, 1) if v[12] == 2]
if not int(quiet):
print(r)
return r
def __init__(self): Wizard.__init__(self) self.viewer = design_viewer() self.resfile = Resfile() sess = cmd.get_session() base = "" for i in sess["names"]: if type(i) is ListType: base = i[0] if base != "": self.setDesigned(base) self.wiz_ros = wizard_rosetta()
def applyShader_deprecated(self):
sele = self.varSelectionName.get()
shader = self.optionMenu_selectionShader.getvalue()
sess = cmd.get_session()['names']
match_flag = False
for i in sess:
if type(i) is ListType:
match = re.search(sele, i[0])
#print 'sele: %s, i[0]: %s, match: %s' % (sele, i[0], repr(match))
# exact word match
# pattern s1, string: 1t3r
# match == None
if match is None:
continue
# when using regular expression like 's*'
# match is always not None
# match.group(0) == '' if not matching
if match is not None:
#print repr(match.group(0))
if match.group(0) == '':
continue
match_flag = True
#if match.group(0):
#if sele == i[0]:
# user clicked apply for a selection more than once
if i[0] in self.seleShaderDict:
for key in self.spColorShaderDict:
sele_in_dict = self.spColorShaderDict[key][1]
if i[0] == sele_in_dict:
self.selectionConsole.set('Shader for [%s] is not empty. \n Click [Unset all] if scene has been changed.' % i[0])
return
#self.spColorShaderDict.pop(key, 0)
self.seleShaderDict[i[0]] = shader
self.selectionConsole.set('Set [%s] with [%s] shader' % (sele, self.seleShaderDict[i[0]]))
# add into dictionary
self.sele2Color()
if match_flag == False:
self.selectionConsole.set('Error: Selection [%s] does not exist.' % sele)
def test_pse(self):
self.ambientOnly()
viewport = (50, 50)
cmd.viewport(*viewport)
objname = 'simpletri'
obj = []
obj.extend([
cgo.BEGIN, cgo.TRIANGLES, cgo.COLOR, 1.0, 0., 0., cgo.VERTEX, 0.0,
0.0, 1.0, cgo.VERTEX, 1.0, 0.0, 0.0, cgo.VERTEX, 0.0, 1.0, 0.0,
cgo.END
])
cmd.load_cgo(obj, objname, 1)
s = cmd.get_session()
cmd.set_session(s)
self.assertEqual([objname], cmd.get_names())
self.assertImageHasColor('red')
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 testDistanceMode4(self):
# create two 2-state objects
cmd.fragment('gly', 'm1', origin=0)
cmd.create('m1', 'm1', 1, 2)
cmd.create('m2', 'm1', 1, 1)
cmd.create('m2', 'm1', 1, 2)
# shift one state by 5 and the other by 9 angstrom
cs = cmd.get_coordset('m1', state=1, copy=0)
cs += [5., 0., 0.]
cs = cmd.get_coordset('m2', state=2, copy=0)
cs += [9., 0., 0.]
# creates one distance measure per state
d = cmd.distance('d1', '?m1', '?m2', mode=4)
# expecting 7 = (5 + 9) / 2
self.assertAlmostEqual(d, 7.0, delta=1e-4)
# one distance measurement has 2 * 3 coordinates
d1states = cmd.get_session('d1', 1, 1, 0, 0)['names'][0][5][2]
self.assertEqual(len(d1states[0][1]), 6)
self.assertEqual(len(d1states[1][1]), 6)
def testDistanceMode4(self):
# create two 2-state objects
cmd.fragment('gly', 'm1', origin=0)
cmd.create('m1', 'm1', 1, 2)
cmd.create('m2', 'm1', 1, 1)
cmd.create('m2', 'm1', 1, 2)
# shift one state by 5 and the other by 9 angstrom
cs = cmd.get_coordset('m1', state=1, copy=0)
cs += [5., 0., 0.]
cs = cmd.get_coordset('m2', state=2, copy=0)
cs += [9., 0., 0.]
# creates one distance measure per state
d = cmd.distance('d1', '?m1', '?m2', mode=4)
# expecting 7 = (5 + 9) / 2
self.assertAlmostEqual(d, 7.0, delta=1e-4)
# one distance measurement has 2 * 3 coordinates
d1states = cmd.get_session('d1', 1, 1, 0, 0)['names'][0][5][2]
self.assertEqual(len(d1states[0][1]), 6)
self.assertEqual(len(d1states[1][1]), 6)
def test_pse(self):
self.ambientOnly()
viewport = (50, 50)
cmd.viewport(*viewport)
objname = 'simpletri'
obj = []
obj.extend([
cgo.BEGIN, cgo.TRIANGLES,
cgo.COLOR, 1.0, 0., 0.,
cgo.VERTEX, 0.0, 0.0, 1.0,
cgo.VERTEX, 1.0, 0.0, 0.0,
cgo.VERTEX, 0.0, 1.0, 0.0,
cgo.END
])
cmd.load_cgo(obj, objname, 1)
s = cmd.get_session()
cmd.set_session(s)
self.assertEqual([objname], cmd.get_names())
self.assertImageHasColor('red')
def get_raw_distances(names='', state=1, selection='all', quiet=1):
'''
DESCRIPTION
Get the list of pair items from distance objects. Each list item is a
tuple of (index1, index2, distance).
Based on a script from Takanori Nakane, posted on pymol-users mailing list.
http://www.mail-archive.com/[email protected]/msg10143.html
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
SEE ALSO
select_distances, cmd.find_pairs, cmd.get_raw_alignment
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 1:
state = cmd.get_state()
valid_names = cmd.get_names_of_type('object:measurement')
if names == '':
names = ' '.join(valid_names)
else:
for name in names.split():
if name not in valid_names:
print(' Error: no such distance object: ' + name)
raise CmdException
raw_objects = cmd.get_session(names, 1, 1, 0, 0)['names']
xyz2idx = {}
cmd.iterate_state(state, selection, 'xyz2idx[x,y,z] = (model,index)',
space=locals())
r = []
for obj in raw_objects:
try:
points = obj[5][2][state-1][1]
if points is None:
raise ValueError
except (KeyError, ValueError):
continue
for i in range(0, len(points), 6):
xyz1 = tuple(points[i:i+3])
xyz2 = tuple(points[i+3:i+6])
try:
r.append((xyz2idx[xyz1], xyz2idx[xyz2], cpv.distance(xyz1, xyz2)))
if not quiet:
print(' get_raw_distances: ' + str(r[-1]))
except KeyError:
if quiet < 0:
print(' Debug: no index for %s %s' % (xyz1, xyz2))
return r
def get_raw_distances(names='', state=1, selection='all', quiet=1):
'''
DESCRIPTION
Get the list of pair items from distance objects. Each list item is a
tuple of (index1, index2, distance).
Based on a script from Takanori Nakane, posted on pymol-users mailing list.
http://www.mail-archive.com/[email protected]/msg10143.html
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
SEE ALSO
select_distances, cmd.find_pairs, cmd.get_raw_alignment
'''
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 1:
state = cmd.get_state()
valid_names = cmd.get_names_of_type('object:measurement')
if names == '':
names = ' '.join(valid_names)
else:
for name in names.split():
if name not in valid_names:
print((' Error: no such distance object:', name))
raise CmdException
raw_objects = cmd.get_session(names, 1, 1, 0, 0)['names']
xyz2idx = {}
cmd.iterate_state(state,
selection,
'xyz2idx[x,y,z] = (model,index)',
space=locals())
r = []
for obj in raw_objects:
try:
points = obj[5][2][state - 1][1]
if points is None:
raise ValueError
except (KeyError, ValueError):
continue
for i in range(0, len(points), 6):
xyz1 = tuple(points[i:i + 3])
xyz2 = tuple(points[i + 3:i + 6])
try:
r.append(
(xyz2idx[xyz1], xyz2idx[xyz2], cpv.distance(xyz1, xyz2)))
if not quiet:
print((' get_raw_distances:', r[-1]))
except KeyError:
if quiet < 0:
print((' Debug: no index for', xyz1, xyz2))
return r
def get_raw_distances(names='',
state=1,
selection='all',
fc=2.0,
amber=0,
gro=0,
label='ID',
quiet=1):
'''
DESCRIPTION
Get the list of pair items from distance objects. Each list item is a
tuple of (ID1, ID2, distance).
Based on a script from Takanori Nakane, posted on pymol-users mailing list.
http://www.mail-archive.com/[email protected]/msg10143.html
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
amber = integer: generate AMBER rst file {default: 0}
gro = integer: generate GROMACS rst file {default: 0}
label = string: label type ('ID' or 'index') {default: ID}
SEE ALSO
select_distances, cmd.find_pairs, cmd.get_raw_alignment
'''
from chempy import cpv
state, quiet, fc = int(state), int(quiet), float(fc)
if state < 1:
state = cmd.get_state()
valid_names = cmd.get_names_of_type('object:measurement')
if names == '':
names = ' '.join(valid_names)
else:
for name in names.split():
if name not in valid_names:
print(' Error: no such distance object: ' + name)
raise CmdException
raw_objects = cmd.get_session(names, 1, 1, 0, 0)['names']
xyz2idx = {}
cmd.iterate_state(state,
selection,
'xyz2idx[x,y,z] = (model, resi, resn, name, ' + label +
')',
space=locals())
r = []
for obj in raw_objects:
try:
points = obj[5][2][state - 1][1]
if points is None:
raise ValueError
except (KeyError, ValueError):
continue
for i in range(0, len(points), 6):
xyz1 = tuple(points[i:i + 3])
xyz2 = tuple(points[i + 3:i + 6])
try:
r.append(
(xyz2idx[xyz1], xyz2idx[xyz2], cpv.distance(xyz1, xyz2)))
if not quiet:
print(' get_raw_distances: ' + str(r[-1]))
except KeyError:
if quiet < 0:
print(' Debug: no index for %s %s' % (xyz1, xyz2))
# print(r)
# for generate amber MD restraint file.
if (int(amber)):
for i in r:
print("""# {0}{1} {2} - {3}{4} {5}
&rst
iat={6}, {7},
r1=0, r2=0.5,
r3={8:.2f}, r4=8,
rk2={9}, rk3={9},
/""".format(str(i[0][1]), str(i[0][2]), str(i[0][3]), str(i[1][1]),
str(i[1][2]), str(i[1][3]), str(i[0][4]), str(i[1][4]),
float(i[2]), float(fc)))
# for generate GROMACS MD restraint file.
if (int(gro)):
for i in r:
print(
"{6} {7} 10 0.00 {8:.3f} 0.800 800 ; {0}{1} {2} - {3}{4} {5} 2kcal/mol/A2"
.format(str(i[0][1]), str(i[0][2]), str(i[0][3]), str(i[1][1]),
str(i[1][2]), str(i[1][3]), str(i[0][4]), str(i[1][4]),
float(i[2]) / 10))
return r
def get_raw_distances(names='',
state=1,
selection='all',
quiet=1,
filename='intrs.txt'):
'''
DESCRIPTION
Get the list of pair items from distance objects. Each list item is a
tuple of (index1, index2, distance).
Based on a script from Takanori Nakane, posted on pymol-users mailing list.
http://www.mail-archive.com/[email protected]/msg10143.html
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
quiet = boolen
filename
SEE ALSO
select_distances, cmd.find_pairs, cmd.get_raw_alignment
'''
foo = cmd.do('l = [];') ## ugly hack!
from chempy import cpv
state, quiet = int(state), int(quiet)
if state < 1:
state = cmd.get_state()
valid_names = cmd.get_names_of_type('object:measurement')
if names == '':
names = ' '.join(valid_names)
else:
for name in names.split():
if name not in valid_names:
print(' Error: no such distance object: ' + name)
raise CmdException
raw_objects = cmd.get_session(names, 1, 1, 0, 0)['names']
xyz2idx = {}
cmd.iterate_state(state,
selection,
'xyz2idx[x,y,z] = (model,index)',
space=locals())
r = []
rresi = []
for obj in raw_objects:
try:
points = obj[5][2][state - 1][1]
if not quiet:
print(points)
if points is None:
raise ValueError
except (KeyError, ValueError):
continue
for i in range(0, len(points), 6):
xyz1 = tuple(points[i:i + 3])
xyz2 = tuple(points[i + 3:i + 6])
try:
r.append(
(xyz2idx[xyz1], xyz2idx[xyz2], cpv.distance(xyz1, xyz2)))
# (('yC_5lj3_U6', 1183)
if not quiet:
print(' get_raw_distances: ' + str(r[-1]))
rresi.append([
unid(xyz2idx[xyz1][0], xyz2idx[xyz1][1]),
unid(xyz2idx[xyz2][0], xyz2idx[xyz2][1])
])
if not quiet:
print(' ', unid(xyz2idx[xyz1][0], xyz2idx[xyz1][1]),
'<->', unid(xyz2idx[xyz2][0], xyz2idx[xyz2][1]))
except KeyError:
if quiet < 0:
print(' Debug: no index for %s %s' % (xyz1, xyz2))
if rresi:
with open(filename, 'w') as f:
for r in rresi:
# not fully correct
# f.write('Prp8' +',' + r[0] + '\n')
f.write(r[0] + ',' + r[1] + '\n')
print('File saved:', filename)
return r, rresi
