def selections_group(self):
"""Group all selections"""
cmd.group('Structures', '%s %s %sCartoon' % (self.protname, self.ligname, self.protname))
cmd.group('Interactions', 'Hydrophobic HBonds HalogenBonds WaterBridges PiCation PiStackingP PiStackingT '
'Saltbridges MetalComplexes')
cmd.group('Atoms', '')
cmd.group('Atoms.Protein', 'Hydrophobic-P HBondAccept-P HBondDonor-P HalogenAccept Centroids-P PiCatRing-P '
'StackRings-P PosCharge-P NegCharge-P AllBSRes Chargecenter-P Metal-P')
cmd.group('Atoms.Ligand', 'Hydrophobic-L HBondAccept-L HBondDonor-L HalogenDonor Centroids-L NegCharge-L '
'PosCharge-L NegCharge-L ChargeCenter-L StackRings-L PiCatRing-L Metal-L Metal-M '
'Unpaired-HBA Unpaired-HBD Unpaired-HAL Unpaired-RINGS')
cmd.group('Atoms.Other', 'Water Metal-W')
cmd.order('*', 'y')
def test(self):
names_ungrouped = ['a0', 'a1', 'b0', 'b1', 'c0', 'c1', 'g1']
names_grouped = ['a0', 'a1', 'c0', 'c1', 'b0', 'g1', 'b1']
for name in names_ungrouped[:-1]:
cmd.pseudoatom(name)
cmd.group(names_ungrouped[-1])
self.assertEqual(cmd.get_names(), names_ungrouped)
cmd.group('g1', 'b*')
cmd.order('b0 g1', location="upper")
self.assertEqual(cmd.get_names(), names_grouped)
def testOrder(self):
# proper group ordering only in incentive, see jira/PYMOL-1382.py
for i in range(3):
cmd.pseudoatom('m%i' % i)
self.assertEqual(cmd.get_names(), ['m0', 'm1', 'm2'])
cmd.order('m2 m1')
self.assertEqual(cmd.get_names(), ['m0', 'm2', 'm1'])
cmd.order('m2 m1', location="top")
self.assertEqual(cmd.get_names(), ['m2', 'm1', 'm0'])
cmd.order('m2', location="bottom")
self.assertEqual(cmd.get_names(), ['m1', 'm0', 'm2'])
cmd.order('m2 m0', location="upper")
self.assertEqual(cmd.get_names(), ['m1', 'm2', 'm0'])
cmd.order('*', 'yes')
self.assertEqual(cmd.get_names(), ['m0', 'm1', 'm2'])
def testOrder(self):
# proper group ordering only in incentive, see jira/PYMOL-1382.py
for i in range(3):
cmd.pseudoatom('m%i' % i)
self.assertEqual(cmd.get_names(), ['m0', 'm1', 'm2'])
cmd.order('m2 m1')
self.assertEqual(cmd.get_names(), ['m0', 'm2', 'm1'])
cmd.order('m2 m1', location="top")
self.assertEqual(cmd.get_names(), ['m2', 'm1', 'm0'])
cmd.order('m2', location="bottom")
self.assertEqual(cmd.get_names(), ['m1', 'm0', 'm2'])
cmd.order('m2 m0', location="upper")
self.assertEqual(cmd.get_names(), ['m1', 'm2', 'm0'])
cmd.order('*', 'yes')
self.assertEqual(cmd.get_names(), ['m0', 'm1', 'm2'])
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 plot_noe(filename, line_color=None, line_width='1.0', advanced_coloring=0, single=0, quiet=1, aria=0, per_atom=0,
per_residue=1):
"""
DESCRIPTION
A function for plotting XPLOR NOE restraints on a structure
ARGUMENTS
filename = string: The filename of the NOE retraint file in XPLOR NIH format.
line_color = string: The color for the NOE lines. {default: yellow}
line_width = float: The thickness of the NOE lines. {default: 1.0}
advanced_coloring = color restraints by distance.
single = string: create a single object for all restraints.
aria = integer: Name NOEs after Aria IDs.
per_atom: Group NOEs on atom basis
per_residue: Group NOEs on residue basis (default)
NOE Restraint Format Example
assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7
EXAMPLE
PyMOL> plot_noe noe_short.tbl
"""
single, quiet, aria, per_residue, per_atom, advanced_coloring = \
int(single), int(quiet), int(aria), int(per_residue), int(per_atom), int(advanced_coloring)
count = 0
if advanced_coloring == 1:
cmd.set("group_auto_mode", 2)
rgx_assi = re.compile("\s*[asignASIGN]+\s+.*")
rgx_or = re.compile("\s*[orOR]+\s+.*")
rgx_bracket = re.compile("(\(|\))")
rgx_tick = re.compile("(\w)\'")
restraint_line = None
restraint_block = []
restraints_blocks = []
for line in open(filename):
if rgx_assi.match(line):
if restraint_line:
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraints_blocks.append(restraint_block)
restraint_block = []
restraint_line = line
elif rgx_or.match(line):
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraint_line = line
else:
restraint_line += line
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraints_blocks.append(restraint_block)
for restraint_block in restraints_blocks:
restraints = {"connections": []}
try:
shlex_split = shlex.split(restraint_block[0])
except ValueError:
print('Cannot process "%s"' % restraint_block[0])
try:
restraints["distance"] = float(shlex_split[11].strip())
except IndexError:
print('Cannot process "%s"' % "".join(restraint_block))
continue
except ValueError:
try:
restraints["distance"] = float(shlex_split[17].strip())
except ValueError:
print("Failed to extract distance, setting to 1A")
restraints["distance"] = 1
if len(shlex_split) > 20:
restraints["ID"] = shlex_split[26][3:-1].strip()
else:
restraints["ID"] = str(count + 1)
for restraint_line in restraint_block:
distance = {}
try:
shlex_split = shlex.split(restraint_line)
if len(shlex_split) > 6:
if shlex_split[1].strip().lower() == shlex_split[9].strip().lower() == "segid":
distance["src_segid"] = shlex_split[2].strip()
distance["src_resid"] = shlex_split[5].strip()
distance["src_atom"] = shlex_split[8].strip().replace("^", "'")
distance["dst_segid"] = shlex_split[10].strip()
distance["dst_resid"] = shlex_split[13].strip()
distance["dst_atom"] = shlex_split[16].strip().replace("^", "'")
else:
distance["src_segid"] = "A"
distance["src_resid"] = shlex_split[2].strip()
distance["src_atom"] = shlex_split[5].strip().replace("^", "'")
distance["dst_segid"] = "A"
distance["dst_resid"] = shlex_split[10].strip()
distance["dst_atom"] = shlex_split[13].strip().replace("^", "'")
else:
print('Cannot process "%s"' % restraint_line)
continue
except IndexError:
print('Cannot process "%s"' % restraint_line)
continue
except ValueError:
print('Cannot process "%s"' % restraint_line)
continue
restraints["connections"].append(distance)
count += _draw_restraint(
restraints,
line_color,
line_width,
single,
quiet,
per_residue,
per_atom,
advanced_coloring
)
if not quiet:
print(' Info: Created distance objects for %d restraints' % count)
cmd.order("NOE*", "yes")
def plot_noe(filename, selection='', line_color='gray20', line_width='1.0', single=0, quiet=1, aria=0, per_atom=0, per_residue=1):
"""
DESCRIPTION
A function for plotting XPLOR NOE restraints on a structure
ARGUMENTS
filename = string: The filename of the NOE retraint file in XPLOR NIH format.
selection = string: atom selection {default: all}
line_color = string: The color for the NOE lines. {default: black}
line_width = float: The thickness of the NOE lines. {default: 1.0}
aria = integer: Name NOEs after Aria IDs.
per_atom: Group NOEs on atom basis
per_residue: Group NOEs on residue basis (default)
NOE Restraint Format Example
assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7
EXAMPLE
PyMOL> plot_noe noe_short.tbl
"""
from pymol.parsing import split
single, quiet, aria, per_residue, per_atom = int(single), int(quiet), int(aria), int(per_residue), int(per_atom)
count = 0
parent_id = None
rgx_restraint = re.compile(
r"""
\s*(?P<parent>\w*)\s+\(
(segid\s+\"\s*(?P<src_segid>[\w\d]+)\"\s+and\s+)?
resid\s+(?P<src_resid>\d+)\s+and\s+
name\s+(?P<src_atom>[\w\d]+)
\)\s+\(
(segid\s+\"\s+(?P<dst_segid>[\w\d]+)\"\s+and\s+)?
resid\s*(?P<dst_resid>\d+)\s+and\s+
name\s*(?P<dst_atom>[\w\d]+)
\)
(\s+(?P<dist>[\d\.]+))?
(.*id=(?P<ID>\d+))?
.*
""", re.X)
for line in open(filename):
restraint = rgx_restraint.match(line)
count += 1
if restraint:
restraint = restraint.groupdict()
if restraint["src_segid"] == None:
restraint["src_segid"] = "A"
if restraint["dst_segid"] == None:
restraint["dst_segid"] = "A"
if restraint["parent"][:4].upper() == "ASSI":
parent = restraint
sele1 = 'segid %s and resi %s and name %s' % (restraint["src_segid"], restraint["src_resid"], restraint["src_atom"])
sele2 = 'segid %s and resi %s and name %s' % (restraint["dst_segid"], restraint["dst_resid"], restraint["dst_atom"])
if single:
label = "NOE"
elif aria and restraint["ID"]:
label = "NOE_" + restraint["ID"]
elif aria and parent and parent["ID"]:
label = "NOE_" + parent["ID"]
elif per_atom:
label = "NOE_%s_%s_%s" % (restraint["dst_segid"], restraint["dst_resid"], restraint["dst_atom"])
elif per_residue:
label = "NOE_%s_%s" % (restraint["dst_segid"], restraint["dst_resid"])
elif restraint["parent"][:4].upper() == "ASSI":
label = parent_id
else:
parent_id = "NOE_%d" % count
label = parent_id
try:
cmd.distance(label, sele1, sele2, quiet=quiet,
width=line_width, gap=0, label=0)
except CmdException:
print 'FAILED: %s - %s' % (sele1, sele2)
continue
cmd.set("dash_color", line_color, label)
else:
print line
cmd.order("NOE*", "yes")
if not quiet:
print ' Info: Created distance objects for %d restraints' % (count)
def read_moestr(contents,
object,
state=0,
finish=1,
discrete=1,
quiet=1,
zoom=-1,
_self=cmd):
moestr = contents
name = object
import sys
if sys.version_info[0] > 2 and isinstance(moestr, bytes):
moestr = moestr.decode()
cmd = _self
mr = MOEReader()
mr.appendFromStr(moestr)
split_chains = cmd.get_setting_int("moe_separate_chains")
cmd.group(name)
if hasattr(mr, 'system'):
have_valences = 0
chain_count = 0
cmd.set_color("_aseg0", [1.0, 1.0, 1.0])
aseg_color = cmd.get_color_index("_aseg0")
aseg_flag = 0
aseg_rep = {}
model = Indexed()
molecule = mr.system['molecule']
if 'atoms' in molecule:
n_atom = molecule['atoms']
model.atom = [Atom() for x in range(n_atom)]
residues = {}
chains = {}
for columns, data in molecule['attr']:
for row in data:
cur_atom = None
for key, value in zip(columns, row):
key = key[0]
if key == 'ID':
ID = value
else:
aProp = _atom_prop_map.get(key, None)
if aProp != None:
setattr(model.atom[ID - 1], aProp, value)
else:
xyz = _atom_coord_map.get(key, None)
if xyz != None:
coord = list(model.atom[ID - 1].coord)
coord[xyz] = value
model.atom[ID - 1].coord = coord
elif key in _atom_vis_map:
atom = model.atom[ID - 1]
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
if key == 'aBondLook':
if value == 'cylinder':
atom.visible = 0x00000001 | visible
elif value == 'line':
atom.visible = 0x00000080 | visible
elif value == 'none':
atom.visible = -129 & Visible # 0xFFFFFF7F
elif key == 'aNucleusLook':
if value == 'sphere':
atom.visible = 0x00000002 | visible
elif value == 'small-sphere': # need to set sphere_scale=0.2 for these atoms
atom.visible = 0x00000002 | visible
atom.sphere_scale = 0.2
elif value == 'point': # nonbonded
atom.visible = 0x00000800 | visible
elif value == 'none':
atom.visible = -2067 & visible # 0xFFFFF7ED
elif key == 'aHidden':
atom.visible = 0
atom.hidden = 1
if hasattr(
atom, 'hidden'
): # be sure that hidden atoms aren't shown
atom.visible = 0
elif key in _atom_color_map:
if key == 'aRGB':
model.atom[ID - 1].trgb = value
elif key == 'aColorBy':
model.atom[ID - 1].aColorBy = value
elif key in _atom_label_map:
atom = model.atom[ID - 1]
if hasattr(atom, 'label_dict'):
atom.label_dict[key] = None
else:
atom.label_dict = {key: None}
elif key in _residue_prop_map:
resi_dict = residues.get(ID, {})
resi_dict[key] = value
residues[ID] = resi_dict
elif key in _chain_prop_map:
chain_dict = chains.get(ID, {})
if ID not in chains:
chain_count = chain_count + 1
chain_dict['count'] = chain_count
chain_dict[key] = value
chains[ID] = chain_dict
chn_keys = list(chains.keys())
chn_keys.sort()
res_keys = list(residues.keys())
res_keys.sort()
# map chain properties onto residues
chn_resi = 0
ch_colors = copy.deepcopy(_ch_colors)
unique_chain_names = {}
for chn_idx in chn_keys:
chain_dict = chains[chn_idx]
cName = make_valid_name(chain_dict.get('cName', ''))
segi = cName[0:4]
chain = cName[-1:]
if not len(cName):
if 'count' in chain_dict:
cName = "chain_" + str(chain_dict['count'])
else:
cName = str(chn_idx)
if cName not in unique_chain_names:
unique_chain_names[cName] = cName
else:
cnt = 2
while (cName + "_" + str(cnt)) in unique_chain_names:
cnt = cnt + 1
newCName = cName + "_" + str(cnt)
unique_chain_names[newCName] = cName
cName = newCName
chain_dict['chain_color'] = ch_colors[0]
ch_colors = ch_colors[1:] + [ch_colors[0]]
cResCount = chain_dict.get('cResidueCount', 0)
for res_idx in range(chn_resi, chn_resi + cResCount):
resi_dict = residues[res_keys[res_idx]]
resi_dict['chain'] = chain
resi_dict['segi'] = segi
resi_dict['cName'] = cName
resi_dict['chain_dict'] = chain_dict
chn_resi = chn_resi + cResCount
# map residue properties onto atoms
res_atom = 0
for res_idx in res_keys:
resi_dict = residues[res_idx]
rRibbonMode = resi_dict.get('rRibbonMode', 'none')
rAtomCount = resi_dict['rAtomCount']
rType = resi_dict.get('rType', '')
if rAtomCount > 0:
for at_idx in range(res_atom, res_atom + rAtomCount):
atom = model.atom[at_idx]
setattr(
atom, 'resi',
string.strip(
str(resi_dict.get('rUID', '')) +
resi_dict.get('rINS', '')))
setattr(atom, 'resn', resi_dict.get('rName', ''))
setattr(atom, 'chain', resi_dict.get('chain', ''))
setattr(atom, 'segi', resi_dict.get('segi', ''))
setattr(atom, 'custom', resi_dict.get('cName', ''))
# add labels
if hasattr(atom, 'label_dict'):
label = ''
label_dict = atom.label_dict
if 'aLabelElement' in label_dict:
label = atom.symbol
if 'aLabelRes' in label_dict:
if len(label):
label = label + ","
label = label + atom.resn + "_" + atom.resi
if 'aLabelName' in label_dict:
if len(label):
label = label + "."
label = label + atom.name
atom.label = label
if rType not in ['none', 'heme']:
atom.hetatm = 0 # all normal atoms
else:
atom.flags = 0x02000000 # hetatom or ligand -- ignore when surfacing
if rRibbonMode != 'none':
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
rRibbonColorBy = resi_dict['rRibbonColorBy']
repeat = 1
while repeat:
repeat = 0
if rRibbonColorBy in ['rgb', 'r:rgb'
]: # handled automatically
pass
elif rRibbonColorBy == 'chain':
chain_dict = resi_dict['chain_dict']
cColorBy = chain_dict['cColorBy']
if cColorBy == 'rgb':
cColorBy = 'c:rgb'
rRibbonColorBy = cColorBy
repeat = 1
rRibbon_color = 0
rRibbon_trgb = 0xFFFFFF # default -- white
# now color ribbon
if rRibbonColorBy == 'r:rgb':
rRibbon_trgb = resi_dict.get('rRGB', 0xFFFFFF)
elif rRibbonColorBy == 'rgb':
rRibbon_trgb = resi_dict.get(
'rRibbonRGB', 0xFFFFFF)
elif rRibbonColorBy == 'c:rgb':
chain_dict = resi_dict['chain_dict']
rRibbon_trgb = chain_dict.get('cRGB', 0xFFFFFF)
elif rRibbonColorBy == 'r:aseg':
rRibbon_trgb = None
rRibbon_color = aseg_color
aseg_flag = 1
elif rRibbonColorBy == 'tempfactor':
pass # TO DO
elif rRibbonColorBy == 'c:number': # per chain colors
rRibbon_trgb = chain_dict['chain_color']
if rRibbonMode in ['line', 'trace']:
atom.visible = 0x00000040 | visible # PyMOL ribbon
if rRibbon_trgb != None:
atom.ribbon_trgb = rRibbon_trgb
else:
atom.ribbon_color = rRibbon_color
aseg_rep['ribbon'] = 1
else:
atom.visible = 0x00000020 | visible # PyMOL cartoon
if rRibbon_trgb != None:
atom.cartoon_trgb = rRibbon_trgb
else:
atom.cartoon_color = rRibbon_color
aseg_rep['cartoon'] = 1
if hasattr(atom, 'label'):
if hasattr(atom, 'visible'):
visible = atom.visible
else:
visible = _default_visible
atom.visible = 0x00000028 | visible # labels
if not hasattr(atom, 'aColorBy'):
atom.aColorBy = 'element'
if hasattr(atom, 'aColorBy'):
aColorBy = atom.aColorBy
repeat = 1
while repeat:
repeat = 0
if aColorBy == 'ribbon':
aColorBy = resi_dict.get('rRibbonColorBy')
if aColorBy == 'rgb':
aColorBy = 'rib:rgb'
else:
repeat = 1
# TO DO still need to handle "cartoon_color", "ribbon_color"
elif aColorBy == 'element':
if hasattr(atom, 'trgb'):
del atom.trgb
elif aColorBy in ['rgb', 'a:rgb'
]: # handled automatically
pass
elif aColorBy == 'residue':
rColorBy = resi_dict.get('rColorBy')
if rColorBy == 'rgb':
rColorBy = 'r:rgb'
aColorBy = rColorBy
repeat = 1
elif aColorBy == 'chain':
chain_dict = resi_dict['chain_dict']
cColorBy = chain_dict['cColorBy']
if cColorBy == 'rgb':
cColorBy = 'c:rgb'
aColorBy = cColorBy
repeat = 1
# now color atom...
if aColorBy == 'r:rgb':
atom.trgb = resi_dict.get('rRGB', 0xFFFFFF)
elif aColorBy == 'rib:rgb':
atom.trgb = resi_dict.get('rRibbonRGB', 0xFFFFFF)
elif aColorBy == 'c:rgb':
chain_dict = resi_dict['chain_dict']
atom.trgb = chain_dict.get('cRGB', 0xFFFFFF)
elif aColorBy == 'r:aseg':
pass # TO DO
elif aColorBy == 'tempfactor':
pass # TO DO
elif aColorBy == 'c:number': # per chain colors
atom.trgb = chain_dict['chain_color']
res_atom = res_atom + rAtomCount
bond_list = molecule.get('bond', [])
for bond in bond_list:
new_bond = Bond()
new_bond.index = [bond[0] - 1, bond[1] - 1]
if len(bond) > 2:
new_bond.order = bond[2]
if bond[2] == 2: # work around .MOE bug with triple bonds
if model.atom[new_bond.index[0]].hybridization == 'sp':
if model.atom[new_bond.index[1]].hybridization == 'sp':
new_bond.order = 3
have_valences = 1
model.bond.append(new_bond)
if 'ViewOrientationY' in mr.system:
vy = mr.system['ViewOrientationY']
vz = mr.system['ViewOrientationZ']
pos = mr.system['ViewLookAt']
scale = mr.system['ViewScale']
vx = cpv.cross_product(vy, vz)
m = [cpv.normalize(vx), cpv.normalize(vy), cpv.normalize(vz)]
m = cpv.transpose(m)
asp_rat = 0.8 # MOE default (versus 0.75 for PyMOL)
cmd.set("field_of_view", 25.0)
fov = float(cmd.get("field_of_view"))
window_height = scale * asp_rat
dist = (0.5 * window_height) / math.atan(3.1415 *
(0.5 * fov) / 180.0)
new_view = tuple(m[0] + m[1] + m[2] + [0.0, 0.0, -dist] + pos +
[dist * 0.5, dist * 1.5, 0.0])
cmd.set_view(new_view)
zoom = 0
cmd.set("auto_color", 0)
cmd.set_color("carbon", [0.5, 0.5, 0.5]) # default MOE grey
obj_name = name + ".system"
if split_chains < 0: # by default, don't split chains if over 50 objects would be created
if len(unique_chain_names) > 50:
split_chains = 0
if not split_chains:
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=quiet,
zoom=zoom)
obj_name_list = [obj_name]
else:
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=1,
zoom=zoom)
obj_name_list = []
system_name = obj_name
for chain in unique_chain_names.keys():
obj_name = name + "." + chain
obj_name_list.append(obj_name)
cmd.select("_moe_ext_tmp",
"custom %s" % chain,
domain=system_name)
cmd.extract(obj_name, "_moe_ext_tmp", quiet=quiet, zoom=0)
# cmd.extract(obj_name,system_name+" and text_type %s"%chain,quiet=quiet)
cmd.delete("_moe_ext_tmp")
if not cmd.count_atoms(system_name):
cmd.delete(system_name)
else:
obj_name_list.append(system_name)
cmd.order(name + ".*", sort=1)
for obj_name in obj_name_list:
cmd.set("stick_radius", 0.1, obj_name)
cmd.set("line_width", 2.0, obj_name)
cmd.set("label_color", "white", obj_name)
cmd.set("nonbonded_size", 0.05,
obj_name) # temporary workaround...
if have_valences: # if this MOE file has valences, then show em!
cmd.set("valence", 1, obj_name)
cmd.set("stick_valence_scale", 1.25, obj_name)
if aseg_flag:
cmd.dss(obj_name)
if 'cartoon' in aseg_rep:
cmd.set("cartoon_color", "red",
obj_name + " and cartoon_color _aseg0 and ss h")
cmd.set("cartoon_color", "yellow",
obj_name + " and cartoon_color _aseg0 and ss s")
cmd.set(
"cartoon_color", "cyan",
obj_name + " and cartoon_color _aseg0 and not ss h+s")
if 'ribbon' in aseg_rep:
cmd.set("ribbon_color", "red",
obj_name + " and ribbon_color _aseg0 and ss h"
) # need selection op ribbon_color
cmd.set("ribbon_color", "yellow",
obj_name + " and ribbon_color _aseg0 and ss s")
cmd.set(
"ribbon_color", "cyan",
obj_name + " and ribbon_color _aseg0 and not ss h+s")
if 'ViewZFront' in mr.system:
moe_front = mr.system['ViewZFront']
moe_width = mr.system['ViewZWidth']
extent = cmd.get_extent(
name) # will this work with groups? TO DO: check!
dx = (extent[0][0] - extent[1][0])
dy = (extent[0][1] - extent[1][1])
dz = (extent[0][2] - extent[1][2])
half_width = 0.5 * math.sqrt(dx * dx + dy * dy + dz * dz)
cmd.clip("atoms", 0.0, name)
cur_view = cmd.get_view()
center = (cur_view[-3] +
cur_view[-2]) * 0.5 # center of clipping slab
front = center - half_width
back = center + half_width
width = half_width * 2
new_view = tuple(
list(cur_view[0:15]) + [
front + width * moe_front, front + width *
(moe_front + moe_width), 0.0
])
cmd.set_view(new_view)
if 'graphics' in mr.system:
cgo_cnt = 1
lab_cnt = 1
unique_cgo_names = {}
for graphics in mr.system['graphics']:
cgo = []
for gvertex in graphics.get('gvertex', []):
vrt = gvertex[0]
seg_list = gvertex[1]['seg']
idx = gvertex[1]['idx']
len_idx = len(idx)
if not cmd.is_list(seg_list):
seg_list = [seg_list] * (len_idx / seg_list)
last_seg = None
ix_start = 0
for seg in seg_list:
if seg != last_seg:
if last_seg != None:
cgo.append(END)
if seg == 3:
cgo.extend([BEGIN, TRIANGLES])
elif seg == 2:
cgo.extend([BEGIN, LINES])
elif seg == 1:
cgo.extend([BEGIN, POINTS])
ix_stop = seg + ix_start
if seg == 3:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
elif seg == 2:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
elif seg == 1:
for s in idx[ix_start:ix_stop]:
v = vrt[s - 1]
cgo.extend([
COLOR, (0xFF & (v[0] >> 16)) / 255.0,
(0xFF & (v[0] >> 8)) / 255.0,
(0xFF & (v[0])) / 255.0
])
if len(v) > 4:
cgo.extend([NORMAL, v[4], v[5], v[6]])
cgo.extend([VERTEX, v[1], v[2], v[3]])
ix_start = ix_stop
last_seg = seg
if last_seg != None:
cgo.append(END)
for gtext in graphics.get('gtext', []):
lab_name = name + ".label_%02d" % lab_cnt
exists = 0
for entry in gtext:
exists = 1
cmd.pseudoatom(lab_name,
pos=[
float(entry[1]),
float(entry[2]),
float(entry[3])
],
color="0x%06x" % entry[0],
label=entry[4])
if exists:
cmd.set('label_color', -1, lab_name)
lab_cnt = lab_cnt + 1
# TO DO -- via CGO's?
if len(cgo):
cgo_name = name + "." + make_valid_name(
graphics.get('GTitle', 'graphics'))
if cgo_name not in unique_cgo_names:
unique_cgo_names[cgo_name] = cgo_name
else:
cnt = 2
while cgo_name + "_" + str(cnt) in unique_cgo_names:
cnt = cnt + 1
new_name = cgo_name + "_" + str(cnt)
unique_cgo_names[new_name] = new_name
cgo_name = new_name
cmd.load_cgo(cgo,
cgo_name,
state=state,
quiet=quiet,
zoom=0)
cgo_cnt = cgo_cnt + 1
cmd.set("two_sided_lighting", 1) # global setting...
cmd.set("cgo_line_width", 2, cgo_name)
if 'GTransparency' in graphics:
g_trans = graphics['GTransparency']
if len(g_trans) >= 2:
if g_trans[0] != 0:
cmd.set('cgo_transparency',
'%1.6f' % (g_trans[0] / 255.0),
cgo_name)
cmd.set('transparency_global_sort')
if 'meter' in mr.system:
meter_name = name + ".meter"
exists = 0
for meter_block in mr.system['meter']:
if meter_block[0][0:2] == ['type', 'atoms']:
for meter in meter_block[1]:
(type, atoms) = meter[0:2]
arg = tuple([meter_name] + list(
map(lambda x, o=name: o + " and id " + str(x - 1),
atoms)))
getattr(cmd, type)(*arg)
exists = 1
if exists:
cmd.color("green", meter_name)
# print mr.system['meter']
elif hasattr(mr, 'feature'):
model = Indexed()
cols = mr.feature[0]
rows = mr.feature[1]
col = {}
cnt = 0
for a in cols:
col[a] = cnt
cnt = cnt + 1
for row in rows:
atom = Atom()
atom.coord = [row[col['x']], row[col['y']], row[col['z']]]
atom.vdw = row[col['r']]
atom.custom = row[col['expr']]
model.atom.append(atom)
obj_name = name + ".feature"
cmd.load_model(model,
obj_name,
state=state,
finish=finish,
discrete=discrete,
quiet=quiet,
zoom=zoom)
rank = 1
for row in rows:
cmd.color("0x%06x" % row[col['color']],
obj_name + " & id %d" % (rank - 1))
rank = rank + 1
cmd.show("mesh", obj_name)
cmd.set("min_mesh_spacing", 0.55, obj_name)
cmd.label(obj_name, "' '+custom")
cmd.set("label_color", "yellow", obj_name)
else:
print(dir(mr))
def scanDamage(nucleosome, uvddb, cutoff=2, clashKeep=1, writeModels=False):
"""
USAGE
scanDamage nucleosome object (DNA in chains I and J),
UVDDB probe object (containing appropriately positioned 2 bp ssDNA in chain Z as residues 1-2 for superpositioning),
distance in Ångstrom closer than which atoms are considered clashing,
keep models with fewer than the specified number of clashes,
write all models (for scoring externally for instance)
"""
chains = ['I', 'J']
results = []
if writeModels:
dirName = None
dirName = ("%s_%s_models" % (nucleosome, uvddb))
if not os.path.exists(dirName):
os.mkdir("%s" % (dirName))
for chain in chains:
chainLength = (len(
cmd.get_model("polymer and %s and chain %s" %
(nucleosome, chain)).get_residues()))
for i in range(0, chainLength + 1):
# for i in range(130, 146):
j = (i + 1)
if chain == 'I':
comnplementaryChain = 'J'
elif chain == 'J':
matchedChain = 'I'
# Handle lack of 5' phosphate on first nucleotide
if i == 0:
cmd.select(
"moving",
"%s and chain Z and resi 2 and backbone and not (n. P or n. OP1 or n. OP2)"
% (uvddb))
cmd.select(
"target",
"%s and chain %s and resi %d and backbone and not (n. P or n. OP1 or n. OP2)"
% (nucleosome, chain, j))
elif i == 1:
cmd.select(
"moving",
"%s and chain Z and resi 1-2 and backbone and not (n. P or n. OP1 or n. OP2)"
% (uvddb))
cmd.select(
"target",
"%s and chain %s and resi %d-%d and backbone and not (n. P or n. OP1 or n. OP2)"
% (nucleosome, chain, i, j))
# Handle final base
elif i == chainLength:
cmd.select("moving",
"%s and chain Z and resi 1 and backbone" % (uvddb))
cmd.select(
"target", "%s and chain %s and resi %d and backbone" %
(nucleosome, chain, i))
else:
cmd.select(
"moving",
"%s and chain Z and resi 1-2 and backbone" % (uvddb))
cmd.select(
"target", "%s and chain %s and resi %d-%d and backbone" %
(nucleosome, chain, i, j))
#numAtomMoving=(cmd.count_atoms("moving"))
#print ("\nNumber of moving atoms: %d" % (numAtomMoving) )
#numAtomTarget=(cmd.count_atoms("target"))
#print ("Number of target atoms: %d" % (numAtomTarget) )
alignResult = []
alignResult = cmd.pair_fit("moving", "target")
# alignResult = cmd.super("moving", "target")
# print ("RMSD after refinement %.4f with %d atoms in alignhment after %d refinement cycles" % (alignResult[0],alignResult[1],alignResult[2]) )
# print(" ".join('%s' % x for x in alignResult))
clashes = ("clashes")
# Calculate clashes excluding DNA portion (chain Z resi 1-2) of UV-DDB probe
cmd.select(
"%s" % (clashes), "(%s and not chain Z) within %d of %s" %
(uvddb, float(cutoff), nucleosome))
scoreAtoms = (cmd.count_atoms("%s" % (clashes)))
cmd.select("%s" % (clashes), "clashes byres clashes")
scoreRes = (cmd.count_atoms("%s" % (clashes) + " and name CA"))
# Write out models (nucleosome + current superimposed UV-DDB probe) for Rosetta scoring
if writeModels:
modelName = None
modelName = ("%s_uvddb_%s_%d-%d" % (nucleosome, chain, i, j))
editing.copy_to("%s" % (modelName),
"(%s or %s)" % (nucleosome, uvddb))
cmd.save("%s/%s.pdb" % (dirName, modelName),
"(%s)" % (modelName))
cmd.delete("%s" % (modelName))
# Retain models with no. residue clashes less than or equal to 'clashKeep'
if scoreRes < (int(clashKeep) + 1):
editing.copy_to("uvddb_%s_%d-%d" % (chain, i, j),
"%s" % (uvddb))
cmd.group("ClashKeep %s)" % (clashKeep),
"nonclashing + uvddb_%s_%d-%d" % (chain, i, j))
cmd.order("uvddb_*", "yes")
print(
"DNA chain %s bases %d - %d : UV-DDB clashes atoms %d residues %d "
% (chain, i, j, scoreAtoms, scoreRes))
clashes = ("%s,%d,%d,%d,%d" % (chain, i, j, scoreAtoms, scoreRes))
results.append((clashes))
with open('%s_scanDamage.csv' % (nucleosome), 'w') as output:
output.write("DNAchain,start,end,atomClashes,residueClashes\n")
for i in results:
output.write("%s\n" % i)
print("\nOutput saved to %s_scanDamage.csv\n" % (nucleosome))
def plot_noe(filename, line_color=None, advanced_coloring=0, line_width='1.0', single=0, quiet=1, aria=0, per_atom=0,
per_residue=1):
"""
DESCRIPTION
A function for plotting XPLOR NOE restraints on a structure
ARGUMENTS
filename = string: The filename of the NOE retraint file in XPLOR NIH format.
single = string: create a single object for all restraints.
selection = string: atom selection {default: all}
line_color = string: The color for the NOE lines. {default: black}
line_width = float: The thickness of the NOE lines. {default: 1.0}
aria = integer: Name NOEs after Aria IDs.
per_atom: Group NOEs on atom basis
per_residue: Group NOEs on residue basis (default)
NOE Restraint Format Example
assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7
EXAMPLE
PyMOL> plot_noe noe_short.tbl
"""
single, quiet, aria, per_residue, per_atom, advanced_coloring = \
int(single), int(quiet), int(aria), int(per_residue), int(per_atom), int(advanced_coloring)
count = 0
if advanced_coloring == 1:
cmd.set("group_auto_mode", 2)
rgx_assi = re.compile("\s*[asignASIGN]+\s+.*")
rgx_or = re.compile("\s*[orOR]+\s+.*")
rgx_bracket = re.compile("(\(|\))")
rgx_tick = re.compile("(\w)\'")
restraint_line = None
restraint_block = []
restraints_blocks = []
for line in open(filename):
if rgx_assi.match(line):
if restraint_line:
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraints_blocks.append(restraint_block)
restraint_block = []
restraint_line = line
elif rgx_or.match(line):
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraint_line = line
else:
restraint_line += line
restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
restraints_blocks.append(restraint_block)
for restraint_block in restraints_blocks:
restraints = {"connections": []}
try:
shlex_split = shlex.split(restraint_block[0])
except ValueError:
print 'Cannot process "%s"' % restraint_block[0]
try:
restraints["distance"] = float(shlex_split[11].strip())
except IndexError:
print 'Cannot process "%s"' % "".join(restraint_block)
continue
except ValueError:
try:
restraints["distance"] = float(shlex_split[17].strip())
except ValueError:
print "Failed to extract distance, setting to 1A"
restraints["distance"] = 1
if len(shlex_split) > 20:
restraints["ID"] = shlex_split[26][3:-1].strip()
else:
restraints["ID"] = str(count + 1)
for restraint_line in restraint_block:
distance = {}
try:
shlex_split = shlex.split(restraint_line)
if len(shlex_split) > 6:
if shlex_split[1].strip().lower() == shlex_split[9].strip().lower() == "segid":
distance["src_segid"] = shlex_split[2].strip()
distance["src_resid"] = shlex_split[5].strip()
distance["src_atom"] = shlex_split[8].strip().replace("^", "'")
distance["dst_segid"] = shlex_split[10].strip()
distance["dst_resid"] = shlex_split[13].strip()
distance["dst_atom"] = shlex_split[16].strip().replace("^", "'")
else:
distance["src_segid"] = "A"
distance["src_resid"] = shlex_split[2].strip()
distance["src_atom"] = shlex_split[5].strip().replace("^", "'")
distance["dst_segid"] = "A"
distance["dst_resid"] = shlex_split[10].strip()
distance["dst_atom"] = shlex_split[13].strip().replace("^", "'")
else:
print 'Cannot process "%s"' % restraint_line
continue
except IndexError:
print 'Cannot process "%s"' % restraint_line
continue
except ValueError:
print 'Cannot process "%s"' % restraint_line
continue
restraints["connections"].append(distance)
count += _draw_restraint(
restraints,
line_color,
line_width,
single,
quiet,
per_residue,
per_atom,
advanced_coloring
)
if not quiet:
print ' Info: Created distance objects for %d restraints' % count
cmd.order("NOE*", "yes")
def scanFactor( nucleosome, probe, cutoff=2, clashKeep=1, writeModels=False ):
"""
USAGE
scanFactor nucleosome object,
probe object,
probe DNA chain ID,
distance in Ångstrom below which atoms are considered clashing,
keep models with fewer than the specified number of residue clashes
"""
results=[]
if writeModels:
dirName = None
dirName = ("%s_%s_models" % (nucleosome, probe) )
if not os.path.exists(dirName):
os.mkdir("%s" % (dirName) )
if not cmd.select("polymer.nucleic and %s" % (nucleosome) ) :
print("\nThe nucleosome object \'%s\' must contain contain DNA – are you sure this is a nucleosome model?\n" % (nucleosome) )
return
if not cmd.select("polymer.nucleic and %s" % (probe) ) :
print("\nThe probe object \'%s\' must contain at least two DNA bases for superposition, the first two of which should correspond\nto the position of the central two bases of the factor's recognition sequence when bound to DNA\n" % (probe) )
return
# Determine probe DNA chain ID
cmd.select("probeDNA","polymer.nucleic and %s" % (probe) )
probeDNAChain = cmd.get_model("probeDNA").atom[0].chain
# Renumber probe DNA chain to start from 1
firstBase = []
firstBase = int(cmd.get_model("%s and chain %s" % (probe, probeDNAChain)).atom[0].resi)
secondBase = firstBase+1
offset = firstBase-1
print ("Renumbering %s chain %s to start at residue 1\n" % (probe, probeDNAChain) )
cmd.alter("%s and chain %s" % (probe, probeDNAChain), "resi=str(int(resi)-%d)" % (offset) )
# Remove hydrogens
print ("\nRemoving hydrogens\n")
cmd.remove("hydrogens")
# Determine nucleosomal DNA chain IDs
chains = []
chains = cmd.get_chains("polymer.nucleic and %s" % (nucleosome) )
# Loop over nuclesomal DNA
for chain in chains:
firstBase = int(cmd.get_model("%s and chain %s" % (nucleosome, chain)).atom[0].resi)
chainLength = (len(cmd.get_model("polymer and %s and chain %s" % (nucleosome, chain)).get_residues()))
for i in range(firstBase, (firstBase + chainLength) ):
j=(i+1)
# Handle lack of 5' phosphates (such as on the first base)
if not cmd.select("%s and chain %s and resi %d and name P" % (nucleosome, chain, i) ) :
cmd.select("moving", "%s and chain %s and resi 2 and backbone and not (n. P or n. OP1 or n. OP2)" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d and backbone and not (n. P or n. OP1 or n. OP2)" % (nucleosome, chain, j) )
# Handle overhanging superposition for final base
elif i == (firstBase + chainLength - 1):
cmd.select("moving", "%s and chain %s and resi 1 and backbone" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d and backbone" % (nucleosome, chain, i) )
else:
cmd.select("moving", "%s and chain %s and resi 1-2 and backbone" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d-%d and backbone" % (nucleosome, chain, i, j) )
#numAtomMoving=(cmd.count_atoms("moving"))
#print ("Number of moving atoms: %d" % (numAtomMoving) )
#numAtomTarget=(cmd.count_atoms("target"))
#print ("Number of target atoms: %d" % (numAtomTarget) )
alignResult=[]
alignResult = cmd.pair_fit("moving", "target")
if alignResult:
# alignResult = cmd.super("moving", "target")
# print ("RMSD after refinement %.4f with %d atoms in alignhment after %d refinement cycles" % (alignResult[0],alignResult[1],alignResult[2]) )
# print(" ".join('%s' % x for x in alignResult))
clashes=("clashes")
# Calculate clashes excluding DNA portion of probe
cmd.select("%s" % (clashes), "(%s and not chain %s) within %f of %s" % (probe, probeDNAChain, float(cutoff), nucleosome) )
scoreAtoms = (cmd.count_atoms("%s" % (clashes) ))
cmd.select("%s" % (clashes), "clashes byres clashes")
scoreRes = (cmd.count_atoms("%s" % (clashes) + " and name CA"))
# Write out models (nuclesome + current superimposed probe) for Rosetta scoring
if writeModels :
modelName = None
modelName = ("%s_probe_%s_%d-%d" % (nucleosome, chain, i, j) )
editing.copy_to("%s" % (modelName), "(%s or %s)" % (nucleosome, probe) )
cmd.save("%s/%s.pdb" % (dirName,modelName), "(%s)" % (modelName) )
cmd.delete("%s" % (modelName) )
# Retain models with no. residue clashes less than or equal to 'clashKeep'
if scoreRes < (int(clashKeep)+1):
editing.copy_to("probe_%s_%d-%d" % (chain, i, j), "%s" % (probe) )
cmd.group("ClashKeep %s)" % (clashKeep),"nonclashing + probe_%s_%d-%d" % (chain, i, j) )
cmd.order("probe_*", "yes")
print ("DNA chain %s bases %d - %d : %s clashes with %d non-hydrogen atoms in %d residues" % (chain, i, j, probe, scoreAtoms, scoreRes) )
clashes=("%s,%d,%d,%d,%d" % (chain, i, j, scoreAtoms, scoreRes) )
results.append((clashes))
# Catch superpostion failures
else:
print ("DNA chain %s bases %d - %d : %s superpositon failed and clashes were not calculated – check for missing atoms, alternate conformations, or unsual bases at these positions" % (chain, i, j, probe) )
clashes=("%s,%d,%d,-,-" % (chain, i, j) )
results.append((clashes))
with open('%s_scanFactor.csv' % (nucleosome), 'w') as output:
output.write("DNAchain,start,end,atomClashes,residueClashes\n")
for i in results:
output.write("%s\n" % i)
print ("\nOutput saved to %s_scanFactor.csv\n" % (nucleosome) )