def png(self, filename, *args, **kwargs):
'''
Save image to filename, with antialias=0.
'''
cmd.unset('antialias')
cmd.png(filename, *args, **kwargs)
cmd.draw()
def sculpt_relax(selection,
backbone=1,
neighbors=0,
model=None,
cycles=100,
state=0,
quiet=1):
'''
DESCRIPTION
Relax the given selection.
SO FAR ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
Do 100 iterations, 75 of them with all terms but low VDW weights,
and 25 with only local geometry terms. With default VDW weights and
atom clashes, the structure gets distorted very easily!
USAGE
sculpt_relax selection [, backbone [, neighbors [, model [, cycles ]]]]
'''
from pymol import selector
backbone, neighbors = int(backbone), int(neighbors)
cycles, state, quiet = int(cycles), int(state), int(quiet)
sele = selector.process(selection)
org = cmd.get_object_list(sele)[0]
if model is None:
model = org
elif model != org:
sele = sele.replace('(%s)' % org, '(%s)' % model)
cmd.protect()
cmd.deprotect(sele)
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_activate(model, state)
cmd.set('sculpt_vdw_weight', 0.25, model) # Low VDW forces
cmd.set('sculpt_field_mask', 0x1FF, model) # Default
if neighbors:
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.deprotect('byres (%s within 6.0 of (%s))' % (model, sele))
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_iterate(model, state, cycles=int(cycles * 0.50))
else:
cmd.sculpt_iterate(model, state, int(cycles * 0.75))
cmd.set('sculpt_field_mask', 0x01F, model) # Local Geometry Only
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.unset('sculpt_vdw_weight', model)
cmd.unset('sculpt_field_mask', model)
cmd.sculpt_deactivate(model)
cmd.deprotect()
def wait_for(name, state=0, quiet=1):
'''
DESCRIPTION
Wait for "name" to be available as selectable object.
'''
if cmd.count_atoms('?' + name, 1, state) == 0:
s = cmd.get_setting_boolean('suspend_updates')
if s: cmd.unset('suspend_updates')
cmd.refresh()
if s: cmd.set('suspend_updates')
def sculpt_relax(selection, backbone=1, neighbors=0, model=None, cycles=100,
state=0, quiet=1):
'''
DESCRIPTION
Relax the given selection.
SO FAR ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
Do 100 iterations, 75 of them with all terms but low VDW weights,
and 25 with only local geometry terms. With default VDW weights and
atom clashes, the structure gets distorted very easily!
USAGE
sculpt_relax selection [, backbone [, neighbors [, model [, cycles ]]]]
'''
from pymol import selector
backbone, neighbors = int(backbone), int(neighbors)
cycles, state, quiet = int(cycles), int(state), int(quiet)
sele = selector.process(selection)
org = cmd.get_object_list(sele)[0]
if model is None:
model = org
elif model != org:
sele = sele.replace('(%s)' % org, '(%s)' % model)
cmd.protect()
cmd.deprotect(sele)
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_activate(model, state)
cmd.set('sculpt_vdw_weight', 0.25, model) # Low VDW forces
cmd.set('sculpt_field_mask', 0x1FF, model) # Default
if neighbors:
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.deprotect('byres (%s within 6.0 of (%s))' % (model, sele))
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_iterate(model, state, cycles=int(cycles * 0.50))
else:
cmd.sculpt_iterate(model, state, int(cycles * 0.75))
cmd.set('sculpt_field_mask', 0x01F, model) # Local Geometry Only
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.unset('sculpt_vdw_weight', model)
cmd.unset('sculpt_field_mask', model)
cmd.sculpt_deactivate(model)
cmd.deprotect()
def testSet(self, sele, name, value, defaultvalue):
cmd.fragment('ala')
cmd.set(name, value, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'), 'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertAlmostEqual(stored.v, value)
if sele:
cmd.unset(name, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'), 'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertEqual(stored.v, defaultvalue)
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 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 testSet(self, sele, name, value, defaultvalue):
cmd.fragment('ala')
cmd.set(name, value, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'), 'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertAlmostEqual(stored.v, value)
if sele:
cmd.unset(name, sele)
n = cmd.iterate('first (%s)' % (sele or 'all'),
'stored.v = s.' + name)
self.assertEqual(n, 1)
self.assertEqual(stored.v, defaultvalue)
def unset_label_settings(selection):
# skipped: label_screen_point, label_position
names = ["label_anchor", "label_angle_digits", "label_bg_color",
"label_bg_outline", "label_bg_transparency", "label_color",
"label_connector", "label_connector_color",
"label_connector_ext_length", "label_connector_mode",
"label_connector_width", "label_digits", "label_dihedral_digits",
"label_distance_digits", "label_font_id",
"label_multiline_justification", "label_multiline_spacing",
"label_outline_color", "label_padding", "label_placement_offset",
"label_relative_mode", "label_shadow_mode", "label_size"]
for name in names:
cmd.unset(name, selection)
def testGet(self):
name_bool = 'cartoon_fancy_helices'
name_obj = 'ala'
cmd.fragment('ala', name_obj)
cmd.set(name_bool, 1, name_obj)
self.assertEqual('off', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.unset(name_bool, '*')
cmd.set(name_bool)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.set(name_bool, 0, name_obj)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('off', cmd.get(name_bool, name_obj))
def testGet(self):
name_bool = 'cartoon_fancy_helices'
name_obj = 'ala'
cmd.fragment('ala', name_obj)
cmd.set(name_bool, 1, name_obj)
self.assertEqual('off', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.unset(name_bool, '*')
cmd.set(name_bool)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('on', cmd.get(name_bool, name_obj))
cmd.set(name_bool, 0, name_obj)
self.assertEqual('on', cmd.get(name_bool))
self.assertEqual('off', cmd.get(name_bool, name_obj))
def unset_label_settings(selection):
# skipped: label_screen_point, label_position
names = [
"label_anchor", "label_angle_digits", "label_bg_color",
"label_bg_outline", "label_bg_transparency", "label_color",
"label_connector", "label_connector_color",
"label_connector_ext_length", "label_connector_mode",
"label_connector_width", "label_digits", "label_dihedral_digits",
"label_distance_digits", "label_font_id",
"label_multiline_justification", "label_multiline_spacing",
"label_outline_color", "label_padding", "label_placement_offset",
"label_relative_mode", "label_shadow_mode", "label_size"
]
for name in names:
cmd.unset(name, selection)
def load():
cmd.set("valence")
cmd.unset("auto_zoom")
cmd.zoom("center",100)
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.set_title('pdb',1,os.path.split(file)[-1])
cmd.refresh()
except:
traceback.print_exc()
map(lambda x:(random()-0.5)*box_size/2,[0]*3) + # x,y,z
[random()+0.5] + # r
map(lambda x:(random()-0.5),[0]*3) # vx,vy,vz
)
# create cloud object
for part in particle:
cmd.pseudoatom("cloud",
resi = part[0],
pos = part[1:4],
vdw = part[4])
# draw spheres efficiently
cmd.show_as("spheres")
cmd.unset("cull_spheres")
# defer geometry generation until needed
cmd.set("defer_builds",1)
# position the camera
cmd.zoom()
cmd.zoom("center",box_size)
# let there be color
cmd.spectrum()
# this is the main loop
"""
A script for stylizing PyMOL structures similarly to QuteMol.
"""
from pymol import cmd, util
cmd.set_color('oxygen', [1.0,0.4,0.4])
cmd.set_color('nitrogen', [0.5,0.5,1.0])
cmd.set_color('carbon', [0.2,0.2,0.2])
cmd.set_color('hydrogen', [0.7,0.7,0.7])
cmd.hide('everything')
cmd.show('spheres')
cmd.hide('everything', 'solvent')
util.cbaw
cmd.bg_color(color='white')
cmd.set('light_count', '10')
cmd.set('spec_count', '1')
cmd.set('shininess', '10')
cmd.set('specular', '0.25')
cmd.set('ambient', '0')
cmd.set('direct', '0')
cmd.set('reflect', '1.5')
cmd.set('ray_shadow_decay_factor', '0.1')
cmd.set('ray_shadow_decay_range', '2')
cmd.unset('depth_cue')
def make_figure(output='', mode='',size=900,opaque='transparent'):
"""
AUTHOR
Martin Christen
DESCRIPTION
"make_figure" creates publication-quality figures of the current scene.
It understands several predefined "modes" and sizes.
USAGE
make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]
ARGUMENTS
mode = string: type of desired figure (single, fb, sides, stereo or -nothing-)
size = integer: size of the figure in pixels OR # panels (if <= 12)
opaque = specify an opaque background.
By default, the script makes the background transparent.
EXAMPLES
make_figure output
make_figure output, single, 975, opaque
make_figure output, fb, 2
make_figure output, sides,4
make_figure output, stereo
NOTES
"single" mode makes a single 300 dpi figure
"fb" mode makes TWO 300 dpi figure
("front" and "back", rotating by 180 degrees about y)
"sides" mode makes FOUR 300 dpi figures
("front" "left" "right" and back, rotating by 90 degrees clockwise about y)
"stereo" generates two 300 dpi, 750 px figures
("L" and "R", to be combined as a stereo image)
If you specify the stereo mode, the size argument is IGNORED.
If no mode argument is given, the script generates quick figures
for general use: TWO figures (front and back) at 300 x 300 px, 72 dpi.
Size is interpreted as pixels, except if the number is ridiculously small
(<=12), in which case the script as "number of panels" to make.
Edit the script manually to define corresponding values.
"""
#define sizes here (in pixels)
panel1 = 1800
panel2 = 1350
panel3 = 900
panel4 = 900
panel5 = 750
panel6 = 750
panel7 = 675
panel8 = 675
panel9 = 600
panel10 = 585
panel11 = 585
panel12 = 585
#verify size is an integer number and convert to pixels
size = int(size)
if size > 12:
pixels = size
elif size == 1:
pixels = panel1
elif size == 2:
pixels = panel2
elif size == 3:
pixels = panel3
elif size == 4:
pixels = panel4
elif size == 5:
pixels = panel5
elif size == 6:
pixels = panel6
elif size == 7:
pixels = panel7
elif size == 8:
pixels = panel8
elif size == 9:
pixels = panel9
elif size == 10:
pixels = panel10
elif size == 11:
pixels = panel11
elif size == 3:
pixels = panel12
#change background
cmd.unset('opaque_background')
if opaque == 'opaque':
cmd.set('opaque_background')
#apply mode
if output == '':
print 'no output filename defined\n'
print 'try: \'make_figure filename\''
return -1
# abort if no output file name given
if mode =='':
cmd.set('surface_quality',1)
cmd.set('opaque_background')
cmd.png(output+"_back_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.png(output+"_front_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for quick mode
elif mode == 'single':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output, dpi=300)
cmd.set('surface_quality',0)
# make a figure for single mode
elif mode == 'fb':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_front", dpi=300)
cmd.turn('y',180)
cmd.ray(pixels, pixels)
cmd.png(output+"_back", dpi=300)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for single mode
elif mode == 'sides':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_1", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_2", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_3", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_4", dpi=300)
cmd.turn('y',90)
cmd.set('surface_quality',0)
# make front and back figures for single mode
elif mode == 'stereo':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(750, 750, angle=-3)
cmd.png(output+"_R", dpi=300)
cmd.ray(750, 750, angle=3)
cmd.png(output+"_L", dpi=300)
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue:', resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
for resi in range(0, particle_count):
particle.append([resi] +
map(lambda x: (random() - 0.5) * box_size / 2, [0] *
3) + # x,y,z
[random() + 0.5] + # r
map(lambda x: (random() - 0.5), [0] * 3) # vx,vy,vz
)
# create cloud object
for part in particle:
cmd.pseudoatom("cloud", resi=part[0], pos=part[1:4], vdw=part[4])
# draw spheres efficiently
cmd.show_as("spheres")
cmd.unset("cull_spheres")
# position the camera
cmd.zoom()
cmd.zoom("center", box_size)
# let there be color
cmd.spectrum()
# this is the main loop
def simulation():
import traceback
def make_figure(output='', mode='', size=900, opaque='transparent'):
"""
AUTHOR
Martin Christen
DESCRIPTION
"make_figure" creates publication-quality figures of the current scene.
It understands several predefined "modes" and sizes.
USAGE
make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]
ARGUMENTS
mode = string: type of desired figure (single, fb, sides, stereo or -nothing-)
size = integer: size of the figure in pixels OR # panels (if <= 12)
opaque = specify an opaque background.
By default, the script makes the background transparent.
EXAMPLES
make_figure output
make_figure output, single, 975, opaque
make_figure output, fb, 2
make_figure output, sides,4
make_figure output, stereo
NOTES
"single" mode makes a single 300 dpi figure
"fb" mode makes TWO 300 dpi figure
("front" and "back", rotating by 180 degrees about y)
"sides" mode makes FOUR 300 dpi figures
("front" "left" "right" and back, rotating by 90 degrees clockwise about y)
"stereo" generates two 300 dpi, 750 px figures
("L" and "R", to be combined as a stereo image)
If you specify the stereo mode, the size argument is IGNORED.
If no mode argument is given, the script generates quick figures
for general use: TWO figures (front and back) at 300 x 300 px, 72 dpi.
Size is interpreted as pixels, except if the number is ridiculously small
(<=12), in which case the script as "number of panels" to make.
Edit the script manually to define corresponding values.
"""
#define sizes here (in pixels)
panel1 = 1800
panel2 = 1350
panel3 = 900
panel4 = 900
panel5 = 750
panel6 = 750
panel7 = 675
panel8 = 675
panel9 = 600
panel10 = 585
panel11 = 585
panel12 = 585
#verify size is an integer number and convert to pixels
size = int(size)
if size > 12:
pixels = size
elif size == 1:
pixels = panel1
elif size == 2:
pixels = panel2
elif size == 3:
pixels = panel3
elif size == 4:
pixels = panel4
elif size == 5:
pixels = panel5
elif size == 6:
pixels = panel6
elif size == 7:
pixels = panel7
elif size == 8:
pixels = panel8
elif size == 9:
pixels = panel9
elif size == 10:
pixels = panel10
elif size == 11:
pixels = panel11
elif size == 3:
pixels = panel12
#change background
cmd.unset('opaque_background')
if opaque == 'opaque':
cmd.set('opaque_background')
#apply mode
if output == '':
print 'no output filename defined\n'
print 'try: \'make_figure filename\''
return -1
# abort if no output file name given
if mode == '':
cmd.set('surface_quality', 1)
cmd.set('opaque_background')
cmd.png(output + "_back_quick", 300, 300, dpi=72)
cmd.turn('y', 180)
cmd.png(output + "_front_quick", 300, 300, dpi=72)
cmd.turn('y', 180)
cmd.set('surface_quality', 0)
# make front and back figures for quick mode
elif mode == 'single':
cmd.set('surface_quality', 1)
cmd.set('ray_shadow', 0)
cmd.ray(pixels, pixels)
cmd.png(output, dpi=300)
cmd.set('surface_quality', 0)
# make a figure for single mode
elif mode == 'fb':
cmd.set('surface_quality', 1)
cmd.set('ray_shadow', 0)
cmd.ray(pixels, pixels)
cmd.png(output + "_front", dpi=300)
cmd.turn('y', 180)
cmd.ray(pixels, pixels)
cmd.png(output + "_back", dpi=300)
cmd.turn('y', 180)
cmd.set('surface_quality', 0)
# make front and back figures for single mode
elif mode == 'sides':
cmd.set('surface_quality', 1)
cmd.set('ray_shadow', 0)
cmd.ray(pixels, pixels)
cmd.png(output + "_1", dpi=300)
cmd.turn('y', 90)
cmd.ray(pixels, pixels)
cmd.png(output + "_2", dpi=300)
cmd.turn('y', 90)
cmd.ray(pixels, pixels)
cmd.png(output + "_3", dpi=300)
cmd.turn('y', 90)
cmd.ray(pixels, pixels)
cmd.png(output + "_4", dpi=300)
cmd.turn('y', 90)
cmd.set('surface_quality', 0)
# make front and back figures for single mode
elif mode == 'stereo':
cmd.set('surface_quality', 1)
cmd.set('ray_shadow', 0)
cmd.ray(750, 750, angle=-3)
cmd.png(output + "_R", dpi=300)
cmd.ray(750, 750, angle=3)
cmd.png(output + "_L", dpi=300)
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue: ' + resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
