def testIdAtom(self):
cmd.fragment('gly', 'm1')
self.assertEqual(cmd.id_atom('ID 3'), 3)
self.assertEqual(cmd.id_atom('ID 3', 1), ('m1', 3))
cmd.feedback("disable", "cmd", "errors")
self.assertRaises(CmdException, cmd.id_atom, 'ID 3+4')
self.assertRaises(CmdException, cmd.id_atom, 'ID 100')
def start_pymol(quiet=False, options='-p', run=False):
"""Starts up PyMOL and sets general options. Quiet mode suppresses all PyMOL output.
Command line options can be passed as the second argument."""
import pymol
pymol.pymol_argv = ['pymol', '%s' % options] + sys.argv[1:]
if run:
initialize_pymol(options)
if quiet:
cmd.feedback('disable', 'all', 'everything')
def start_pymol(quiet=False, options='-p', run=False):
"""Starts up PyMOL and sets general options. Quiet mode suppresses all PyMOL output.
Command line options can be passed as the second argument."""
import pymol
pymol.pymol_argv = ['pymol', '%s' % options] + sys.argv[1:]
if run:
initialize_pymol(options)
if quiet:
cmd.feedback('disable', 'all', 'everything')
def png_workaround(filepath, width=1200, height=800):
"""Workaround for (a) severe bug(s) in PyMOL preventing ray-traced images to be produced in command-line mode.
Use this function in case neither cmd.ray() or cmd.png() work.
"""
sys.stdout = sys.__stdout__
cmd.feedback('disable', 'movie', 'everything')
cmd.viewport(width, height)
cmd.zoom('visible', 1.5) # Adapt the zoom to the viewport
cmd.set('ray_trace_frames',
1) # Frames are raytraced before saving an image.
cmd.mpng(filepath, config.MODEL,
config.MODEL) # Use batch png mode with 1 frame only
cmd.mplay() # cmd.mpng needs the animation to 'run'
cmd.refresh()
originalfile = "".join([
filepath,
(4 - len(str(config.MODEL))) * '0' + str(config.MODEL) + '.png'
])
newfile = "".join([filepath, '.png'])
#################################################
# Wait for file for max. 1 second and rename it #
#################################################
attempts = 0
while not os.path.isfile(originalfile) and attempts <= 10:
sleep(0.1)
attempts += 1
if os.name == 'nt': # In Windows, make sure there is no file of the same name, cannot be overwritten as in Unix
if os.path.isfile(newfile):
os.remove(newfile)
os.rename(originalfile, newfile) # Remove frame number in filename
# Check if imagemagick is available and crop + resize the images
if subprocess.call("type convert",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE) == 0:
attempts, ecode = 0, 1
# Check if file is truncated and wait if that's the case
while ecode != 0 and attempts <= 10:
ecode = subprocess.call(['convert', newfile, '/dev/null'],
stdout=open('/dev/null', 'w'),
stderr=subprocess.STDOUT)
sleep(0.1)
attempts += 1
trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';' # Trim the image
os.system(trim)
getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;' # Get the width of the new image
getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;' # Get the hight of the new image
newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;' # Set quadratic ratio
quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile # Fill with whitespace
os.system(getwidth + getheight + newres + quadratic)
else:
sys.stderr.write(
'Imagemagick not available. Images will not be resized or cropped.'
)
def electomo(self,cleanup=0):
if not cleanup:
cmd.feedback("disable","objectsurface","actions")
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/flagellar.pse"))
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",3)
cmd.rock()
cmd.do("replace_wizard toggle, Electron Tomography")
else:
cmd.mstop()
cmd.rock(0)
def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name,
i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][
4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name C%s)' % (sel, resi_j, atom_j),
mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name O%s)' % (sel, resi_j, atom_j),
mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
def setUp(self):
self.oldcwd = os.getcwd()
cmd.reinitialize()
cmd.viewport(640, 480)
cwd = self.moddirs[type(self).__module__]
os.chdir(cwd)
cmd.feedback('push')
cmd.feedback('disable', 'all', 'details actions')
self.timings = []
def electomo(self,cleanup=0):
if not cleanup:
cmd.feedback("disable","objectsurface","actions")
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/flagellar.pse"))
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",3)
cmd.rock()
cmd.do("replace_wizard toggle, Electron Tomography")
else:
cmd.mstop()
cmd.rock(0)
def setUp(self):
self.oldcwd = os.getcwd()
cmd.reinitialize()
cmd.viewport(640, 480)
cwd = self.moddirs[type(self).__module__]
os.chdir(cwd)
cmd.feedback('push')
cmd.feedback('disable', 'all', 'details actions')
self.timings = []
def movie(self, configurations):
n = 1
cmd.feedback("disable","executive","actions")
auto_zoom = cmd.get("auto_zoom")
cmd.set("auto_zoom", 0)
for conf in configurations:
self._setCoordinates(conf)
cmd.load_model(self.model, self.name, n)
n = n + 1
cmd.set("auto_zoom", auto_zoom)
cmd.feedback("enable","executive","actions")
cmd.mplay()
def movie(self, configurations):
n = 1
cmd.feedback("disable", "executive", "actions")
auto_zoom = cmd.get("auto_zoom")
cmd.set("auto_zoom", 0)
for conf in configurations:
self._setCoordinates(conf)
cmd.load_model(self.model, self.name, n)
n = n + 1
cmd.set("auto_zoom", auto_zoom)
cmd.feedback("enable", "executive", "actions")
cmd.mplay()
def setUp(self):
self.oldcwd = os.getcwd()
cmd.reinitialize()
cmd.viewport(640, 480)
if cliargs.no_undo:
cmd.set('suspend_undo', updates=0)
cwd = self.moddirs[type(self).__module__]
os.chdir(cwd)
cmd.feedback('push')
cmd.feedback('disable', 'all', 'details actions')
self.timings = []
def testCdLsPwd(self):
with testing.mkdtemp() as path:
cmd.cd(path)
self.assertEqual(os.getcwd(),
os.path.realpath(path))
touch('foo1.txt')
touch('foo2.txt')
touch('foo3.bin')
cmd.feedback("disable", "python", "output")
cmd.pwd()
# no test of output possible
cmd.ls('*.txt')
def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name, i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i), '%s (resi %s and name C%s)' % (sel, resi_j, atom_j), mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i), '%s (resi %s and name O%s)' % (sel, resi_j, atom_j), mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
def roving_density(self,cleanup=0):
if not cleanup:
try:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.map_new("map","gaussian","0.75","il2")
cmd.feedback("disable","objectmesh","actions")
cmd.set("ribbon_color","purple","il2")
cmd.set("roving_detail",1)
cmd.set("roving_origin",1)
cmd.set("stick_radius",0.12,"il2")
cmd.set("roving_sticks",0)
cmd.set("roving_polar_contacts",0)
cmd.set("line_width","3")
cmd.set("roving_map1_name","map")
cmd.isomesh("rov_m1","map",9999.0,"il2")
cmd.color("density","rov_m1")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
else:
cmd.set("roving_detail",0)
cmd.set("roving_map1_name","")
cmd.set("roving_polar_contacts",7)
cmd.set("roving_sticks",6)
cmd.delete("il2")
cmd.delete("map")
cmd.set("line_width",1.5)
cmd.refresh()
cmd.set("roving_detail",0)
cmd.delete("rov_*")
cmd.sync()
def roving_density(self, cleanup=0):
if not cleanup:
try:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.set("suspend_updates", 1, quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.map_new("map", "gaussian", "0.75", "il2")
cmd.feedback("disable", "objectmesh", "actions")
cmd.set("ribbon_color", "purple", "il2")
cmd.set("roving_detail", 1)
cmd.set("roving_origin", 1)
cmd.set("stick_radius", 0.12, "il2")
cmd.set("roving_sticks", 0)
cmd.set("roving_polar_contacts", 0)
cmd.set("line_width", "3")
cmd.set("roving_map1_name", "map")
cmd.isomesh("rov_m1", "map", 9999.0, "il2")
cmd.color("density", "rov_m1")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
finally:
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
else:
cmd.set("roving_detail", 0)
cmd.set("roving_map1_name", "")
cmd.set("roving_polar_contacts", 7)
cmd.set("roving_sticks", 6)
cmd.delete("il2")
cmd.delete("map")
cmd.set("line_width", 1.5)
cmd.refresh()
cmd.set("roving_detail", 0)
cmd.delete("rov_*")
cmd.sync()
def disable_feedback(what, level):
"""Disable feedback."""
pm.feedback("disable", what, level)
yield
pm.feedback("enable", what, level)
if not int(quiet):
print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
if int(center):
cmd.alter_state(1,
selection,
"(x,y,z)=sub((x,y,z), centroid)",
space={
'centroid': centroid,
'sub': cpv.sub
})
return centroid
cmd.feedback("disable", "all", "actions")
cmd.feedback("disable", "all", "results")
cmd.feedback("disable", "all", "warnings actions")
protName = path.basename(sys.argv[1])
ligName = path.basename(sys.argv[2])
cmd.load(sys.argv[1], protName)
cmd.load(sys.argv[2], ligName)
#if needed to center the search space on the ligand use this line instead
#(comX, comY, comZ) = centroid(ligName)
(comX, comY, comZ) = centroid(protName)
((maxX, maxY, maxZ), (minX, minY, minZ)) = cmd.get_extent(protName)
print(
'center_x = %8.4f\ncenter_y = %8.4f\ncenter_z = %8.4f\nsize_x = %8.4f\nsize_y = %8.4f\nsize_z = %8.4f\n'
cmd.iterate("(%s and id %d)"%(res_sele,b),"stored.names.append(name)")
name_list.append(tuple(pymol.stored.names))
res_dict = {}
for a in name_list:
dihe = cmd.get_dihedral("(%s and name %s)"%(res_sele,a[0]),
"(%s and name %s)"%(res_sele,a[1]),
"(%s and name %s)"%(res_sele,a[2]),
"(%s and name %s)"%(res_sele,a[3]))
res_dict[a]=dihe
if not prot_dict.has_key(resn):
prot_dict[resn]=[]
prot_dict[resn].append(res_dict)
sc_dict = {}
cmd.feedback('disable','selector','result')
cmd.feedback('disable','executive','action')
for fyle in glob("source/*"):
cmd.load(fyle)
cmd.remove("(het)")
cmd.remove("(hydro or not alt '')")
cmd.remove("(byres b>25)") # only use well-defined residues
cmd.remove("(not (byres name ca))")
cmd.remove("(not (byres name n))")
cmd.remove("(not (byres name c))")
cmd.refresh()
measure_all_torsions("all",sc_dict)
cmd.delete("all")
#for a in sc_dict.keys():
# 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.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.show_as("ribbon")
cmd.refresh()
cmd.show_as("sticks")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n>1:
cmd.rewind()
sys.__stderr__.write(file+"\n")
sys.__stderr__.flush()
for a in range(1,n+1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
cmd.feedback('disable','symmetry objectmolecule executive','everything')
load()
def tearDown(self):
cmd.feedback('pop')
os.chdir(self.oldcwd)
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib!= None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
f=open(dif_file)
l=f.readlines()
f.close()
if len(l):
print
for a in l:
print a,
# save it so we have something to look at...
os.system("/bin/cp -f %s %s_s"%(cmp_file,cmp_file))
os.system("/bin/cp -f %s %s_s"%(ref_file,ref_file))
os.system("/bin/cp -f %s %s_src"%(out_file,cmp_file))
os.system("/bin/cp -f %s %s_src"%(file,ref_file))
print file
else:
sys.__stdout__.write(".")
sys.__stdout__.flush()
except:
traceback.print_exc()
# allow the Tcl/Tk GUI time to get out of the way...
time.sleep(3)
cmd.set("retain_order",1)
cmd.feedback('disable','symmetry objectmolecule executive','everything')
# now start
load()
def testSplash(self):
cmd.feedback('disable', 'all', 'output')
cmd.splash()
da = 0.9 * 2 * np.pi / 3
loncirc.append(circle(p, r, v1, v2, amin=da, amax=2 * np.pi - da))
return loncirc
if __name__ == '__main__':
import pdbsurf
from pymol import cmd
import matplotlib.pyplot as plt
import misc.recutils as recutils
import misc.Clustering
from termcolor import colored
import glob
import argparse
import sys
cmd.feedback('disable', 'all', 'everything')
# argparse.ArgumentParser(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=argparse.HelpFormatter, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True, exit_on_error=True)
parser = argparse.ArgumentParser(description='')
# parser.add_argument(name or flags...[, action][, nargs][, const][, default][, type][, choices][, required][, help][, metavar][, dest])
parser.add_argument('-p', '--pdb')
parser.add_argument('-s', '--sel')
parser.add_argument('-c', '--caption')
parser.add_argument(
'--size',
type=float,
help='Size of the dots for the scatter plot (default=1.)',
default=1.)
parser.add_argument(
'--levels',
type=int,
help='Number of levels in the contour plot (default=10)',
# first we need a model
cmd.load("$PYMOL_PATH/test/dat/pept.pdb","demo")
# let's dress it up a little bit
cmd.show("sticks","demo")
cmd.show("spheres","resi 10")
cmd.color("yellow","resi 5 and element c")
# turn off some of the chatter about reloading the object...
cmd.feedback("disable","executive","actions")
# now loop, updating the coordinates and reloading the model into
# state 1 of the "demo" object
m = cmd.get_model()
while 1:
time.sleep(0.05)
try:
cmd.set("suspend_updates","1") # only necessary if multithreading...
for a in m.atom:
a.coord[0]+=(random()-0.5)*0.1
a.coord[1]+=(random()-0.5)*0.1
a.coord[2]+=(random()-0.5)*0.1
cmd.load_model(m,"demo",1)
except:
def print_dihedrals(selection='sele',
state=1,
quiet=1,
ss='',
fc=10.0,
chi=0,
label='ID'):
'''
DESCRIPTION
"print_dihedrals" return the phi, psi, and chi1 angles for a protein atom
selection.
ARGUMENTS
state = integer: object state {default: 1}
selection = string: atom selection {default: all}
amber = integer: generate AMBER rst file {default: 1;ON}
label = string: label type ('ID' or 'index') {default: ID}
fc = float: force constant for the dihedral angles {default: 10.0}
chi = 0: Do not print chi angles (default)
chi = 1: print chi1 dihedral angle (if exists)
chi = 2: print chi1 and chi2 dihedral angles (if exists) (not implemented yet)
SEE ALSO
phipsi
'''
# selectionからCalpha原子のIDリストを取得
chi = int(chi)
caindex = []
cmd.iterate('bycalpha (%s)' % selection,
'caindex.append(ID)',
space=locals())
# Calpha原子が属する残基ごとに処理を行う
for ca in caindex:
# resinameに残基名のみ取得
n_sele = "((byres ID %s) & name N)" % ca
c_sele = "((byres ID %s) & name C)" % ca
ca_sele = "((byres ID %s) & name CA)" % ca
cb_sele = "((byres ID %s) & name CB)" % ca
resiname_sele = []
cmd.iterate(ca_sele, "resiname_sele.append(resn)", space=locals())
resiname = str(resiname_sele[0])
if resiname == 'ILE' or resiname == 'VAL':
cg_sele = "((byres ID %s) & name CG1)" % ca
elif resiname == 'THR':
cg_sele = "((byres ID %s) & name OG1)" % ca
elif resiname == 'CYS' or resiname == 'CYX':
cg_sele = "((byres ID %s) & name SG)" % ca
else:
cg_sele = "((byres ID %s) & name CG)" % ca
cm_sele = "((neighbor (%s)) and not (byres (%s)))" % (n_sele, n_sele
) #前の残基のC
np_sele = "((neighbor (%s)) and not (byres (%s)))" % (c_sele, c_sele
) #次の残基のN
cmd.feedback("push")
cmd.feedback("disable", "selector", "everything")
cm_cnt = cmd.select("_pp_cm", cm_sele)
n_cnt = cmd.select("_pp_n", n_sele)
c_cnt = cmd.select("_pp_c", c_sele)
ca_cnt = cmd.select("_pp_ca", ca_sele)
cb_cnt = cmd.select("_pp_cb", cb_sele)
cg_cnt = cmd.select("_pp_cg", cg_sele)
np_cnt = cmd.select("_pp_np", np_sele)
# 残基名＋残基番号取得(ASP704みたいな)
rname = []
cmd.iterate(ca_sele, "rname.append(resn+resi)", space=locals())
if (cm_cnt and n_cnt and ca_cnt and c_cnt):
phi = cmd.get_dihedral("_pp_c", "_pp_ca", "_pp_n", "_pp_cm")
else:
phi = None
if (n_cnt and ca_cnt and c_cnt and np_cnt):
psi = cmd.get_dihedral("_pp_np", "_pp_c", "_pp_ca", "_pp_n")
else:
psi = None
if (n_cnt and ca_cnt and cb_cnt and cg_cnt):
chi1 = cmd.get_dihedral("_pp_cg", "_pp_cb", "_pp_ca", "_pp_n")
else:
chi1 = None
atomdict = {}
strings = [
"_pp_cm", "_pp_n", "_pp_c", "_pp_ca", "_pp_cb", "_pp_np", "_pp_cg"
]
for i in strings:
temp = cmd.identify(i)
# tempが空リストでなければatomdictに追加
if temp:
atomdict[i] = temp[0]
# phi, psi用に制限を設ける
# 引数でssが指定されている場合、その範囲になるよう設定
def phir2limit(x, sigma, ss):
if ss == '':
val = x - sigma
if val <= -180.0:
val = -180.0
return val
elif ss == 'alpha':
val = -80.0
return val
elif ss == 'beta':
val = -155.0
return val
def phir3limit(x, sigma, ss):
if ss == '':
val = x + sigma
if val >= 180.0:
val = 180.0
return val
elif ss == 'alpha':
val = -50.0
return val
elif ss == 'beta':
val = -125.0
return val
def psir2limit(x, sigma, ss):
if ss == '':
val = x - sigma
if val <= -180.0:
val = -180.0
return val
elif ss == 'alpha':
val = -55.0
return val
elif ss == 'beta':
val = 115.0
return val
def psir3limit(x, sigma, ss):
if ss == '':
val = x + sigma
if val >= 180.0:
val = 180.0
return val
elif ss == 'alpha':
val = -25.0
return val
elif ss == 'beta':
val = 145.0
return val
def r2limit(x, sigma):
val = x - sigma
if val <= -180.0:
val = -180.0
return val
def r3limit(x, sigma):
val = x + sigma
if val >= 180.0:
val = 180.0
return val
if phi is not None:
print('''# {6} phi
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_c']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']),
int(atomdict['_pp_cm']),
phir2limit(phi, 10.0, ss),
phir3limit(phi, 10.0, ss), str(rname[0]),
float(fc)))
if psi is not None:
print('''# {6} psi
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_np']),
int(atomdict['_pp_c']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']),
psir2limit(psi, 10.0, ss),
psir3limit(psi, 10.0, ss), str(rname[0]),
float(fc)))
if (chi > 0) and (chi1 is not None):
print('''# {6} chi1
&rst iat= {0}, {1}, {2}, {3},
r1=-180.0, r2={4:.2f}, r3={5:.2f}, r4= 180.0,
rk2= {7}, rk3= {7},\n/'''.format(int(atomdict['_pp_cg']),
int(atomdict['_pp_cb']),
int(atomdict['_pp_ca']),
int(atomdict['_pp_n']), r2limit(chi1, 10.0),
r3limit(chi1,
10.0), str(rname[0]), float(fc)))
def tearDown(self):
cmd.feedback('pop')
os.chdir(self.oldcwd)
def testSplash(self):
cmd.feedback('disable', 'all', 'output')
cmd.splash()
def do_library(self):
cmd = self.cmd
pymol = cmd._pymol
if not (
(cmd.count_atoms("(%s) and name n" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name c" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name o" % src_sele) == 1)
):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable", "selector", "everythin")
cmd.feedback("disable", "editor", "actions")
self.prompt = ["Loading rotamers..."]
pymol.stored.name = "residue"
cmd.iterate("first (%s)" % src_sele, 'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight", src_sele)
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele, animate=-1)
self.lib_mode = self.mode
if self.lib_mode == "current":
pymol.stored.resn = ""
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn, pymol.stored.resn)
if (self.c_cap != "none") or (self.n_cap != "none") or (self.hyd != "auto"):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name, src_sele, 1, 1)
if self.c_cap == "open":
cmd.remove("%s and name OXT" % frag_name)
if self.lib_mode != "current":
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == "posi") and (frag_type[0:3] != "NT_"):
if not (cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) &! r. ace" % (src_sele, src_sele))):
# use N-terminal fragment
frag_type = "NT_" + frag_type
if (self.c_cap == "nega") and (frag_type[0:3] != "CT_"):
if not (cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele))):
# use C-terminal fragment
frag_type = "CT_" + frag_type
if rot_type[0:3] in ["NT_", "CT_"]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(string.lower(frag_type), frag_name)
# trim off hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# copy identifying information
cmd.iterate("(%s and n;ca)" % src_sele, "stored.chain=chain")
cmd.alter("(%s)" % frag_name, "chain=stored.chain")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resi=resi")
cmd.alter("(%s)" % frag_name, "resi=stored.resi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.segi=segi")
cmd.alter("(%s)" % frag_name, "segi=stored.segi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.ss=ss")
cmd.alter("(%s)" % frag_name, "ss=stored.ss")
# move the fragment
if (cmd.count_atoms("(%s and n;cb)" % frag_name) == 1) and (
cmd.count_atoms("(%s and n;cb)" % src_sele) == 1
):
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;cb)" % frag_name,
"(%s and n;cb)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
else:
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
# fix the carbonyl position...
cmd.iterate_state(1, "(%s and n;o)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;o)" % frag_name, "(x,y,z)=stored.list")
if cmd.count_atoms("(%s and n;oxt)" % src_sele):
cmd.iterate_state(1, "(%s and n;oxt)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;oxt)" % frag_name, "(x,y,z)=stored.list")
elif cmd.count_atoms("(%s and n;oxt)" % frag_name): # place OXT if no template exists
angle = cmd.get_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;o)" % frag_name,
)
cmd.protect("(%s and n;o)" % frag_name)
cmd.set_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;oxt)" % frag_name,
180.0 + angle,
)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % frag_name) == 1:
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % src_sele) == 1:
cmd.iterate_state(1, "(elem h and bound_to (n;n and (%s)))" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(elem h and bound_to (n;n and (%s)))" % frag_name, "(x,y,z)=stored.list")
elif cmd.select(tmp_sele1, "(n;c and bound_to (%s and e;n))" % src_sele) == 1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral(
"(%s and n;c)" % frag_name, "(%s and n;ca)" % frag_name, "(%s and n;n)" % frag_name, tmp_sele1
)
cmd.set_dihedral(
"(%s and n;c)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;n)" % frag_name,
"(%s and n;h)" % frag_name,
180.0 + angle,
)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in ["amin", "nmet"]:
if not cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele)):
if cmd.count_atoms("n;c & (%s)" % (frag_name)) == 1:
if self.c_cap == "amin":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nhh")
elif self.c_cap == "nmet":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nme")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & bound_to (n;c & (%s))" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# add n-cap (if appropriate)
if self.n_cap in ["acet"]:
if not cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) & !r. ace " % (src_sele, src_sele)):
if cmd.count_atoms("n;n & (%s)" % (frag_name)) == 1:
if self.n_cap == "acet":
editor.attach_amino_acid("n;n & (%s)" % (frag_name), "ace")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & (%s)" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
cartoon = cmd.count_atoms("(%s and n;ca and rep cartoon)" % src_sele) > 0
sticks = cmd.count_atoms("(%s and n;ca and rep sticks)" % src_sele) > 0
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == "dep":
try:
result = cmd.phi_psi("%s" % src_sele)
if len(result) == 1:
(phi, psi) = result[result.keys()[0]]
(phi, psi) = (int(10 * round(phi / 10)), int(10 * (round(psi / 10))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(20 * round(phi / 20)), int(20 * (round(psi / 20))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(60 * round(phi / 60)), int(60 * (round(psi / 60))))
key = (rot_type, phi, psi)
lib = self.dep_library.get(key, None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key, None)
if (lib != None) and self.dep == "dep":
print " Mutagenesis: no phi/psi, using backbone-independent rotamers."
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name, frag_name, 1, state)
if state == 1:
cmd.select(mut_sele, "(byres (%s like %s))" % (obj_name, src_sele))
if rot_type == "PRO":
cmd.unbond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
for b in a.keys():
if b != "FREQ":
cmd.set_dihedral(
"(%s & n;%s)" % (mut_sele, b[0]),
"(%s & n;%s)" % (mut_sele, b[1]),
"(%s & n;%s)" % (mut_sele, b[2]),
"(%s & n;%s)" % (mut_sele, b[3]),
a[b],
state=state,
)
else:
cmd.set_title(obj_name, state, "%1.1f%%" % (a[b] * 100))
if rot_type == "PRO":
cmd.bond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
state = state + 1
cmd.delete(frag_name)
print " Mutagenesis: %d rotamers loaded." % len(lib)
if self.bump_check:
cmd.delete(bump_name)
cmd.create(
bump_name,
"(((byobj %s) within 6 of (%s and not name n+c+ca+o+h+ha)) and (not (%s)))|(%s)"
% (src_sele, mut_sele, src_sele, mut_sele),
singletons=1,
)
cmd.color("gray50", bump_name + " and elem c")
cmd.set("seq_view", 0, bump_name, quiet=1)
cmd.hide("everything", bump_name)
if (cmd.select(tmp_sele1, "(n;N and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;C and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
if (cmd.select(tmp_sele1, "(n;C and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;N and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name n+c+ca+o+h+ha))" % (bump_name, bump_name, mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo", bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode", 1, bump_name)
state = 1
for a in lib:
cmd.sculpt_iterate(bump_name, state=state)
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name, frag_name, 1, 1)
print " Mutagenesis: no rotamers found in library."
cmd.set("seq_view", 0, obj_name, quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("(" + obj_name + ")")
cmd.show(self.rep, obj_name)
cmd.show("lines", obj_name) # neighbor always show lines
if cartoon:
cmd.show("cartoon", obj_name)
if sticks:
cmd.show("sticks", obj_name)
cmd.set("auto_zoom", auto_zoom, quiet=1)
cmd.delete(frag_name)
cmd.frame(0)
cmd.unpick()
cmd.feedback("pop")
cmd.iterate("(%s and id %d)"%(res_sele,b),"stored.names.append(name)")
name_list.append(tuple(pymol.stored.names))
res_dict = {}
for a in name_list:
dihe = cmd.get_dihedral("(%s and name %s)"%(res_sele,a[0]),
"(%s and name %s)"%(res_sele,a[1]),
"(%s and name %s)"%(res_sele,a[2]),
"(%s and name %s)"%(res_sele,a[3]))
res_dict[a]=dihe
if resn not in prot_dict:
prot_dict[resn]=[]
prot_dict[resn].append(res_dict)
sc_dict = {}
cmd.feedback('disable','selector','result')
cmd.feedback('disable','executive','action')
for fyle in glob("source/*"):
cmd.load(fyle)
cmd.remove("(het)")
cmd.remove("(hydro or not alt '')")
cmd.remove("(byres b>25)") # only use well-defined residues
cmd.remove("(not (byres name ca))")
cmd.remove("(not (byres name n))")
cmd.remove("(not (byres name c))")
cmd.refresh()
measure_all_torsions("all",sc_dict)
cmd.delete("all")
#for a in sc_dict.keys():
cont = True
# first we need a model
cmd.load("$PYMOL_PATH/test/dat/pept.pdb", "demo")
# let's dress it up a little bit
cmd.show("sticks", "demo")
cmd.show("spheres", "resi 10")
cmd.color("yellow", "resi 5 and element C")
# turn off some of the chatter about reloading the object...
cmd.feedback("disable", "executive", "actions")
# now loop, updating the coordinates and reloading the model into
# state 1 of the "demo" object
m = cmd.get_model()
while cont:
time.sleep(0.05)
try:
cmd.set("suspend_updates", "1") # only necessary if multithreading...
for a in m.atom:
a.coord[0] += (random() - 0.5) * 0.1
a.coord[1] += (random() - 0.5) * 0.1
a.coord[2] += (random() - 0.5) * 0.1
cmd.load_model(m, "demo", 1)
cmd.set("suspend_updates", "0") # only necessary if multithreading...
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib is None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib is not None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib is not None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
def mcm(pose, mc_steps, SASA, randomize):
################################# MCM Parameters ##########################
T = 300. # Temperature
k = 0.0019872041 # Boltzmann constant
angles_prob = [1/3, 1/3, 1/3] # probability to sample phi, psi or chi
accepted = 0
############################################################################
#
first, last = pose_from_pdb(pose)
if first or last:
print('Starting MCM')
from energy import minimize, set_sasa, get_sasa
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'everything') ##uncomment for debugging
cmd.set('pdb_conect_all', 1)
glyco_bonds = get_glyco_bonds(first, last)
con_matrix = writer(glyco_bonds)
# Remove previous pdb files
prev_files = glob.glob('mcm_*.pdb')
for prev_file in prev_files:
os.remove(prev_file)
# set all paramenters for sasa-energy computation
if SASA:
params, points, const = set_sasa(n=1000)
## randomize initial conformation
if randomize:
for i in range(len(con_matrix)-1):
bond = con_matrix[i]
angle_values = np.random.uniform(-180, 180, size=2)
set_psi(pose, bond, angle_values[0])
set_phi(pose, bond, angle_values[1])
for i in range(6):
set_chi(pose, bond)
# minimize energy of starting conformation and save it
NRG_old = minimize(pose, nsteps=5000, rigid_geometry=False)
NRG_min = NRG_old
cmd.save('mcm_%08d.pdb' % accepted)
## start MCM routine
fd = open("mcm_log.txt", "w")
print('# iterations remaining = %s' % (mc_steps))
for i in range(1, mc_steps+1):
if i % (mc_steps//10) == 0:
print('#remaining iterations = %s' % (mc_steps-i))
if True:
sample_uniform(pose, con_matrix, angles_prob)
NRG_new = minimize('tmp', nsteps=100, rigid_geometry=False)
if SASA:
solvatation_nrg = get_sasa(params, points, const, selection='all',
probe=0)[0]
NRG_new = NRG_new + solvatation_nrg
if NRG_new < NRG_old:
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
else:
delta = np.exp(-(NRG_new-NRG_old)/(T*k))
if delta > np.random.uniform(0, 1):
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
cmd.delete('tmp')
if NRG_new < NRG_min:
NRG_min = NRG_new
cmd.save('mcm_min.pdb')
fd.close()
cmd.delete('all')
print('Savings all accepted conformations on a single file')
cmd.set('defer_builds_mode', 5)
for i in range(0, accepted):
cmd.load('mcm_%08d.pdb' % i, 'mcm_trace')
cmd.save('mcm_trace.pdb', 'all', state=0)
cmd.delete('all')
cmd.load('mcm_trace.pdb')
cmd.intra_fit('mcm_trace')
print(' MCM completed')
cmd.set('suspend_updates', 'off')
def mcm(pose, mc_steps, SASA, randomize):
################################# MCM Parameters ##########################
T = 300. # Temperature
k = 0.0019872041 # Boltzmann constant
kT = k * T
# probability to sample phi, psi or chi
angles_prob = [1 / 3, 1 / 3, 1 / 3]
accepted = 0
##########################################################################
#
first, last = pose_from_pdb(pose)
if first or last:
print('Starting MCM')
from energy import minimize, set_sasa, get_sasa
sus_updates = cmd.get('suspend_updates')
cmd.set('suspend_updates', 'on')
# uncomment for debugging
cmd.feedback('disable', 'executive', 'everything')
pdb_conect = cmd.get('pdb_conect_all')
cmd.set('pdb_conect_all', 1)
glyco_bonds = get_glyco_bonds(first, last)
con_matrix = writer(glyco_bonds)
# Remove previous pdb files
prev_files = glob.glob('mcm_*.pdb')
for prev_file in prev_files:
os.remove(prev_file)
# set all paramenters for sasa-energy computation
if SASA:
params, points, const = set_sasa(n=1000)
# randomize initial conformation
if randomize:
for i in range(len(con_matrix) - 1):
bond = con_matrix[i]
angle_values = np.random.uniform(-180, 180, size=2)
set_psi(pose, bond, angle_values[0])
set_phi(pose, bond, angle_values[1])
for i in range(6):
set_chi(pose, bond)
# minimize energy of starting conformation and save it
NRG_old = minimize(pose, nsteps=5000, rigid_geometry=False)
NRG_min = NRG_old
cmd.save('mcm_%08d.pdb' % accepted)
# start MCM routine
fd = open("mcm_log.txt", "w")
print('# iterations remaining = %s' % (mc_steps))
for i in range(1, mc_steps + 1):
if i % (mc_steps // 10) == 0:
print('#remaining iterations = %s' % (mc_steps - i))
if True:
sample_uniform(pose, con_matrix, angles_prob)
NRG_new = minimize('tmp', nsteps=100, rigid_geometry=False)
if SASA:
solvatation_nrg = get_sasa(params,
points,
const,
selection='all',
probe=0)[0]
NRG_new = NRG_new + solvatation_nrg
if NRG_new < NRG_old:
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
else:
delta = np.exp(-(NRG_new - NRG_old) / (kT))
if delta > np.random.uniform(0, 1):
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
cmd.delete('tmp')
if NRG_new < NRG_min:
NRG_min = NRG_new
cmd.save('mcm_min.pdb')
fd.close()
cmd.delete('all')
print('Savings all accepted conformations on a single file')
de_builds = cmd.get('defer_builds_mode')
cmd.set('defer_builds_mode', 5)
for i in range(0, accepted):
cmd.load('mcm_%08d.pdb' % i, 'mcm_trace')
cmd.save('mcm_trace.pdb', 'all', state=0)
cmd.delete('all')
cmd.load('mcm_trace.pdb')
cmd.intra_fit('mcm_trace')
print('MCM completed')
# restore settings
cmd.set('suspend_updates', sus_updates)
cmd.set('pdb_conect_all', pdb_conect)
cmd.set('defer_builds_mode', de_builds)
