def Btn_ExtractLigand_Clicked(self):
state = cmd.get_state()
# Get the Drop Down List Selection Name
ddlSelection = self.defaultOption.get()
if ddlSelection == '' or self.Validate_ObjectSelection(
ddlSelection, 'Ligand', state):
return
LigandPath = tkFileDialog.asksaveasfilename(
filetypes=[('PDB File', '*.pdb')],
initialdir=self.top.FlexAIDLigandProject_Dir,
title='Save the PDB File',
initialfile=ddlSelection,
defaultextension='.pdb')
if len(LigandPath) > 0:
LigandPath = os.path.normpath(LigandPath)
if General.validate_String(LigandPath, '.pdb', True, False, True):
self.DisplayMessage(
" ERROR: Could not save the file because you entered an invalid name.",
2)
return
if self.top.ValidateSaveProject(LigandPath, 'Ligand'):
self.DisplayMessage(
" ERROR: The file can only be saved at its default location",
2)
return
try:
cmd.save(LigandPath, ddlSelection, state)
LigandName = os.path.basename(os.path.splitext(LigandPath)[0])
cmd.extract(self.ExtractObject, ddlSelection)
cmd.set_name(self.ExtractObject, LigandName)
if ddlSelection != LigandName:
# as if the object was renamed, delete the object
cmd.delete(ddlSelection)
except:
self.DisplayMessage(
" ERROR: An error occured while extracting the ligand object.",
1)
return
self.LigandPath.set(os.path.normpath(LigandPath))
self.LigandName.set(LigandName)
#self.LigandMD5.set(General.hashfile(self.LigandPath.get()))
self.Reset_Ligand()
self.DisplayMessage(
' Successfully extracted the ligand: ' +
self.LigandName.get() + "'", 0)
def Btn_ExtractLigand_Clicked(self):
state = cmd.get_state()
# Get the Drop Down List Selection Name
ddlSelection = self.defaultOption.get()
if ddlSelection == '' or self.Validate_ObjectSelection(ddlSelection, 'Ligand', state):
return
LigandPath = tkFileDialog.asksaveasfilename(filetypes=[('PDB File','*.pdb')],
initialdir=self.top.FlexAIDLigandProject_Dir, title='Save the PDB File',
initialfile=ddlSelection, defaultextension='.pdb')
if len(LigandPath) > 0:
LigandPath = os.path.normpath(LigandPath)
if General.validate_String(LigandPath, '.pdb', True, False, True):
self.DisplayMessage(" ERROR: Could not save the file because you entered an invalid name.", 2)
return
if self.top.ValidateSaveProject(LigandPath, 'Ligand'):
self.DisplayMessage(" ERROR: The file can only be saved at its default location", 2)
return
try:
cmd.save(LigandPath, ddlSelection, state)
LigandName = os.path.basename(os.path.splitext(LigandPath)[0])
cmd.extract(self.ExtractObject, ddlSelection)
cmd.set_name(self.ExtractObject, LigandName)
if ddlSelection != LigandName:
# as if the object was renamed, delete the object
cmd.delete(ddlSelection)
except:
self.DisplayMessage(" ERROR: An error occured while extracting the ligand object.", 1)
return
self.LigandPath.set(os.path.normpath(LigandPath))
self.LigandName.set(LigandName)
#self.LigandMD5.set(General.hashfile(self.LigandPath.get()))
self.Reset_Ligand()
self.DisplayMessage(' Successfully extracted the ligand: ' + self.LigandName.get() + "'", 0)
def split(operator, selection, prefix='entity'):
'''
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
'''
cmd.disable(' '.join(cmd.get_object_list('(' + selection + ')')))
tmp = cmd.get_unused_name('_')
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + ' first model ' + tmp)
r += 1
cmd.delete(tmp)
return r
def split(operator, selection, prefix='entity'):
'''
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
'''
cmd.disable(' '.join(cmd.get_object_list('(' + selection + ')')))
tmp = cmd.get_unused_name('_')
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + ' first model ' + tmp)
r += 1
cmd.delete(tmp)
return r
def split(operator, selection, prefix="entity"):
"""
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
"""
cmd.disable(" ".join(cmd.get_object_list("(" + selection + ")")))
tmp = cmd.get_unused_name("_")
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + " first model " + tmp)
r += 1
cmd.delete(tmp)
return r
def clean(self, selection_name=None, small_molecule=None):
if selection_name is None:
selection_name = self.selection
if small_molecule is None:
extract_string = '{}'.format(self.sele_macro)
if small_molecule is not None:
if small_molecule == self.small_molecule:
small_molecule = self.small_molecule
extract_string = '{} or (resn {} w. 10 of {})'.format(
self.sele_macro, small_molecule, self.sele_macro)
self.get
cmd.remove('solvent')
cmd.extract('{}'.format(selection_name), extract_string)
print('{}'.format(selection_name), extract_string)
def split_protein_ligand(complex_pdb,
protein_pdb,
ligand_pdb,
ligand_sdf=None,
ligand_smiles=None,
ligand_resname=None):
import pymol
from pymol import cmd as pymol_cmd
# load complex in pymol session
pymol_cmd.load(complex_pdb, 'complex')
pymol_cmd.remove('hydrogens')
# extract ligand
if ligand_resname is not None:
pymol_cmd.extract('ligand', f'resn {ligand_resname}')
else:
pymol_cmd.extract('ligand', 'not polymer')
# extract protein
pymol_cmd.extract('receptor', 'polymer')
# save protein
pymol_cmd.save(protein_pdb, 'receptor')
# save ligand
pymol_cmd.save(ligand_pdb, 'ligand')
# delete session
pymol_cmd.delete('all')
# pdb to sdf
if ligand_sdf is not None:
if ligand_smiles:
try:
m_smiles = Chem.RemoveHs(Chem.MolFromSmiles(ligand_smiles))
m_pdb = Chem.RemoveHs(Chem.MolFromPDBFile(ligand_pdb))
m = AllChem.AssignBondOrdersFromTemplate(m_smiles, m_pdb)
w = Chem.SDWriter(ligand_sdf)
w.write(m)
w.close()
except Exception as e:
print(f"{ligand_sdf} failed: {e}")
os.system(f'obabel {ligand_pdb} -O {ligand_sdf}')
else:
os.system(f'obabel {ligand_pdb} -O {ligand_sdf}')
return
def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0, selName="interface"):
"""
interfaceResidues -- finds 'interface' residues between two chains in a complex.
PARAMS
cmpx
The complex containing cA and cB
cA
The first chain in which we search for residues at an interface
with cB
cB
The second chain in which we search for residues at an interface
with cA
cutoff
The difference in area OVER which residues are considered
interface residues. Residues whose dASA from the complex to
a single chain is greater than this cutoff are kept. Zero
keeps all residues.
selName
The name of the selection to return.
RETURNS
* A selection of interface residues is created and named
depending on what you passed into selName
* An array of values is returned where each value is:
( modelName, residueNumber, dASA )
NOTES
If you have two chains that are not from the same PDB that you want
to complex together, use the create command like:
create myComplex, pdb1WithChainA or pdb2withChainX
then pass myComplex to this script like:
interfaceResidues myComlpex, c. A, c. X
This script calculates the area of the complex as a whole. Then,
it separates the two chains that you pass in through the arguments
cA and cB, alone. Once it has this, it calculates the difference
and any residues ABOVE the cutoff are called interface residues.
AUTHOR:
Jason Vertrees, 2009.
"""
# Save user's settings, before setting dot_solvent
oldDS = cmd.get("dot_solvent")
cmd.set("dot_solvent", 1)
# set some string names for temporary objects/selections
tempC, selName1 = "tempComplex", selName+"1"
chA, chB = "chA", "chB"
# operate on a new object & turn off the original
cmd.create(tempC, cmpx)
cmd.disable(cmpx)
# remove cruft and inrrelevant chains
cmd.remove(tempC + " and not (polymer and (%s or %s))" % (cA, cB))
# get the area of the complete complex
cmd.get_area(tempC, load_b=1)
# copy the areas from the loaded b to the q, field.
cmd.alter(tempC, 'q=b')
# extract the two chains and calc. the new area
# note: the q fields are copied to the new objects
# chA and chB
cmd.extract(chA, tempC + " and (" + cA + ")")
cmd.extract(chB, tempC + " and (" + cB + ")")
cmd.get_area(chA, load_b=1)
cmd.get_area(chB, load_b=1)
# update the chain-only objects w/the difference
cmd.alter( "%s or %s" % (chA,chB), "b=b-q" )
# The calculations are done. Now, all we need to
# do is to determine which residues are over the cutoff
# and save them.
stored.r, rVal, seen = [], [], []
cmd.iterate('%s or %s' % (chA, chB), 'stored.r.append((model,resi,b))')
cmd.enable(cmpx)
cmd.select(selName1, 'none')
for (model,resi,diff) in stored.r:
key=resi+"-"+model
if abs(diff)>=float(cutoff):
if key in seen: continue
else: seen.append(key)
rVal.append( (model,resi,diff) )
# expand the selection here; I chose to iterate over stored.r instead of
# creating one large selection b/c if there are too many residues PyMOL
# might crash on a very large selection. This is pretty much guaranteed
# not to kill PyMOL; but, it might take a little longer to run.
cmd.select( selName1, selName1 + " or (%s and i. %s)" % (model,resi))
# this is how you transfer a selection to another object.
cmd.select(selName, cmpx + " in " + selName1)
# clean up after ourselves
cmd.delete(selName1)
cmd.delete(chA)
cmd.delete(chB)
cmd.delete(tempC)
# show the selection
cmd.enable(selName)
# reset users settings
cmd.set("dot_solvent", oldDS)
return rVal
def testExtract(self):
cmd.fragment('ala', 'm1')
cmd.extract('m2', 'elem C')
self.assertEqual(cmd.count_atoms('m1'), 7)
self.assertEqual(cmd.count_atoms('m2'), 3)
def interfaceResidues(cmpx,
cA='c. A',
cB='c. B',
cutoff=1.0,
selName="interface"):
"""
interfaceResidues -- finds 'interface' residues between two chains in a complex.
PARAMS
cmpx
The complex containing cA and cB
cA
The first chain in which we search for residues at an interface
with cB
cB
The second chain in which we search for residues at an interface
with cA
cutoff
The difference in area OVER which residues are considered
interface residues. Residues whose dASA from the complex to
a single chain is greater than this cutoff are kept. Zero
keeps all residues.
selName
The name of the selection to return.
RETURNS
* A selection of interface residues is created and named
depending on what you passed into selName
* An array of values is returned where each value is:
( modelName, residueNumber, dASA )
NOTES
If you have two chains that are not from the same PDB that you want
to complex together, use the create command like:
create myComplex, pdb1WithChainA or pdb2withChainX
then pass myComplex to this script like:
interfaceResidues myComlpex, c. A, c. X
This script calculates the area of the complex as a whole. Then,
it separates the two chains that you pass in through the arguments
cA and cB, alone. Once it has this, it calculates the difference
and any residues ABOVE the cutoff are called interface residues.
AUTHOR:
Jason Vertrees, 2009.
"""
# Save user's settings, before setting dot_solvent
oldDS = cmd.get("dot_solvent")
cmd.set("dot_solvent", 1)
# set some string names for temporary objects/selections
tempC, selName1 = "tempComplex", selName + "1"
chA, chB = "chA", "chB"
# operate on a new object & turn off the original
cmd.create(tempC, cmpx)
cmd.disable(cmpx)
# remove cruft and inrrelevant chains
cmd.remove(tempC + " and not (polymer and (%s or %s))" % (cA, cB))
# get the area of the complete complex
cmd.get_area(tempC, load_b=1)
# copy the areas from the loaded b to the q, field.
cmd.alter(tempC, 'q=b')
# extract the two chains and calc. the new area
# note: the q fields are copied to the new objects
# chA and chB
cmd.extract(chA, tempC + " and (" + cA + ")")
cmd.extract(chB, tempC + " and (" + cB + ")")
cmd.get_area(chA, load_b=1)
cmd.get_area(chB, load_b=1)
# update the chain-only objects w/the difference
cmd.alter("%s or %s" % (chA, chB), "b=b-q")
# The calculations are done. Now, all we need to
# do is to determine which residues are over the cutoff
# and save them.
stored.r, rVal, seen = [], [], []
cmd.iterate('%s or %s' % (chA, chB), 'stored.r.append((model,resi,b))')
cmd.enable(cmpx)
cmd.select(selName1, None)
for (model, resi, diff) in stored.r:
key = resi + "-" + model
if abs(diff) >= float(cutoff):
if key in seen: continue
else: seen.append(key)
rVal.append((model, resi, diff))
# expand the selection here; I chose to iterate over stored.r instead of
# creating one large selection b/c if there are too many residues PyMOL
# might crash on a very large selection. This is pretty much guaranteed
# not to kill PyMOL; but, it might take a little longer to run.
cmd.select(selName1,
selName1 + " or (%s and i. %s)" % (model, resi))
# this is how you transfer a selection to another object.
cmd.select(selName, cmpx + " in " + selName1)
# clean up after ourselves
cmd.delete(selName1)
cmd.delete(chA)
cmd.delete(chB)
cmd.delete(tempC)
# show the selection
cmd.enable(selName)
# reset users settings
cmd.set("dot_solvent", oldDS)
return rVal
def spl_extract():
for name in cmd.get_names("all"):
print(" \ Extracting mode for %s" % name)
if 'h3_6QW6'.lower() in name.lower():
cmd.extract("PRP8_h3_6QW6", "chain 5A and h3_6QW6")
cmd.extract("BRR2_h3_6QW6", "chain 5B and h3_6QW6")
cmd.extract("SNU114_h3_6QW6", "chain 5C and h3_6QW6")
cmd.extract("U5_h3_6QW6", "chain 5 and h3_6QW6")
cmd.extract("U6_h3_6QW6", "chain 6 and h3_6QW6")
cmd.extract("U4_h3_6QW6", "chain 4 and h3_6QW6")
cmd.extract("PRP4_h3_6QW6", "chain 4B and h3_6QW6")
cmd.extract("PRP31_h3_6QW6", "chain 4C and h3_6QW6")
cmd.extract("PRP6_h3_6QW6", "chain 5J and h3_6QW6")
cmd.extract("PRP3_h3_6QW6", "chain 4A and h3_6QW6")
cmd.extract("SNU13_h3_6QW6", "chain 4D and h3_6QW6")
cmd.extract("SNU66_h3_6QW6", "chain S and h3_6QW6")
cmd.extract("U5-40K_h3_6QW6", "chain 5O and h3_6QW6")
cmd.extract("DIM1_h3_6QW6", "chain 5D and h3_6QW6")
cmd.extract("PRP28_h3_6QW6", "chain 5X and h3_6QW6")
cmd.extract("SAD1_h3_6QW6", "chain U and h3_6QW6")
cmd.extract("RBM42_h3_6QW6", "chain R and h3_6QW6")
cmd.extract("SNRNP27_27K_h3_6QW6", "chain X and h3_6QW6")
cmd.extract("U5_Sm_ring_h3_6QW6", "(chain 51 or chain 52 or chain 53 or chain 5b or chain 5e or chain 5f or chain 5g ) and h3_6QW6")
cmd.extract("U4_Sm_ring_h3_6QW6", "(chain 41 or chain 42 or chain 43 or chain 4b or chain 4e or chain 4f or chain 4g ) and h3_6QW6")
cmd.extract("Lsm_ring_h3_6QW6", "(chain 62 or chain 63 or chain 64 or chain 65 or chain 66 or chain 67 or chain 68 ) and h3_6QW6")
cmd.set_name("h3_6QW6", "unknown_other_h3_6QW6")
cmd.group("h3_6QW6", "*_h3_6QW6")
cmd.do("order *, yes")
if 'hBpre_6QX9'.lower() in name.lower():
cmd.extract("PRP8_hBpre_6QX9", "chain 5A and hBpre_6QX9")
cmd.extract("SNU114_hBpre_6QX9", "chain 5C and hBpre_6QX9")
cmd.extract("U2_hBpre_6QX9", "chain 2 and hBpre_6QX9")
cmd.extract("U5_hBpre_6QX9", "chain 5 and hBpre_6QX9")
cmd.extract("U6_hBpre_6QX9", "chain 6 and hBpre_6QX9")
cmd.extract("U4_hBpre_6QX9", "chain 4 and hBpre_6QX9")
cmd.extract("Intron_hBpre_6QX9", "chain I and hBpre_6QX9")
cmd.extract("U1_hBpre_6QX9", "chain 1 and hBpre_6QX9")
cmd.extract("PRP4_hBpre_6QX9", "chain 4B and hBpre_6QX9")
cmd.extract("PRP31_hBpre_6QX9", "chain 4C and hBpre_6QX9")
cmd.extract("PRP6_hBpre_6QX9", "chain 5J and hBpre_6QX9")
cmd.extract("PRP3_hBpre_6QX9", "chain 4A and hBpre_6QX9")
cmd.extract("SNU66_hBpre_6QX9", "chain S and hBpre_6QX9")
cmd.extract("U5-40K_hBpre_6QX9", "chain 5O and hBpre_6QX9")
cmd.extract("DIM1_hBpre_6QX9", "chain 5D and hBpre_6QX9")
cmd.extract("PRP28_hBpre_6QX9", "chain 5X and hBpre_6QX9")
cmd.extract("SAD1_hBpre_6QX9", "chain U and hBpre_6QX9")
cmd.extract("RBM42_hBpre_6QX9", "chain R and hBpre_6QX9")
cmd.extract("SNRNP27_27K_hBpre_6QX9", "chain X and hBpre_6QX9")
cmd.extract("U5_Sm_ring_hBpre_6QX9", "(chain 51 or chain 52 or chain 53 or chain 5b or chain 5e or chain 5f or chain 5g ) and hBpre_6QX9")
cmd.extract("U4_Sm_ring_hBpre_6QX9", "(chain 41 or chain 42 or chain 43 or chain 4b or chain 4e or chain 4f or chain 4g ) and hBpre_6QX9")
cmd.extract("Lsm_ring_hBpre_6QX9", "(chain 62 or chain 63 or chain 64 or chain 65 or chain 66 or chain 67 or chain 68 ) and hBpre_6QX9")
cmd.extract("U1_Sm_ring_hBpre_6QX9", "(chain 11 or chain 12 or chain 13 or chain 1b or chain 1e or chain 1f or chain 1g ) and hBpre_6QX9")
cmd.extract("U1A_hBpre_6QX9", "chain 1A and hBpre_6QX9")
cmd.extract("U170k_hBpre_6QX9", "chain 1K and hBpre_6QX9")
cmd.extract("U1C_hBpre_6QX9", "chain 1C and hBpre_6QX9")
cmd.extract("SF3B1_hBpre_6QX9", "chain B1 and hBpre_6QX9")
cmd.extract("SF3B3_hBpre_6QX9", "chain B3 and hBpre_6QX9")
cmd.extract("SF3B2_hBpre_6QX9", "chain B2 and hBpre_6QX9")
cmd.extract("SF3B4_hBpre_6QX9", "chain B4 and hBpre_6QX9")
cmd.extract("PHF5A_hBpre_6QX9", "chain BP and hBpre_6QX9")
cmd.extract("SF3A3_hBpre_6QX9", "chain A3 and hBpre_6QX9")
cmd.extract("SF3A2_hBpre_6QX9", "chain A2 and hBpre_6QX9")
cmd.extract("SF3A1_hBpre_6QX9", "chain A1 and hBpre_6QX9")
cmd.extract("U2A_hBpre_6QX9", "chain 2A and hBpre_6QX9")
cmd.extract("U2B_hBpre_6QX9", "chain 2B and hBpre_6QX9")
cmd.extract("SF3B5_hBpre_6QX9", "chain B5 and hBpre_6QX9")
cmd.extract("U2_Sm_ring_hBpre_6QX9", "(chain 21 or chain 22 or chain 23 or chain 2b or chain 2e or chain 2f or chain 2g ) and hBpre_6QX9")
cmd.extract("Prp4Kinase_hBpre_6QX9", "chain K and hBpre_6QX9")
cmd.set_name("hBpre_6QX9", "unknown_other_hBpre_6QX9")
cmd.group("hBpre_6QX9", "*_hBpre_6QX9")
cmd.do("order *, yes")
if 'hB_6AHD'.lower() in name.lower():
cmd.extract("PRP8_hB_6AHD", "chain A and hB_6AHD")
cmd.extract("BRR2_hB_6AHD", "chain D and hB_6AHD")
cmd.extract("SNU114_hB_6AHD", "chain C and hB_6AHD")
cmd.extract("U2_hB_6AHD", "chain H and hB_6AHD")
cmd.extract("U5_hB_6AHD", "chain B and hB_6AHD")
cmd.extract("U6_hB_6AHD", "chain F and hB_6AHD")
cmd.extract("U4_hB_6AHD", "chain I and hB_6AHD")
cmd.extract("Intron_hB_6AHD", "chain G and hB_6AHD")
cmd.extract("PRP4_hB_6AHD", "chain K and hB_6AHD")
cmd.extract("PRP31_hB_6AHD", "chain L and hB_6AHD")
cmd.extract("PRP6_hB_6AHD", "chain N and hB_6AHD")
cmd.extract("PRP3_hB_6AHD", "chain J and hB_6AHD")
cmd.extract("DIB1_hB_6AHD", "chain O and hB_6AHD")
cmd.extract("SNU13_hB_6AHD", "chain M and hB_6AHD")
cmd.extract("SNU66_hB_6AHD", "chain 9 and hB_6AHD")
cmd.extract("U5-40K_hB_6AHD", "chain E and hB_6AHD")
cmd.extract("U5_Sm_ring_hB_6AHD", "(chain a or chain b or chain c or chain d or chain e or chain f or chain g ) and hB_6AHD")
cmd.extract("U4_Sm_ring_hB_6AHD", "(chain U or chain V or chain P or chain Q or chain R or chain S or chain T ) and hB_6AHD")
cmd.extract("Lsm_ring_hB_6AHD", "(chain q or chain r or chain s or chain t or chain x or chain y or chain z ) and hB_6AHD")
cmd.extract("SF3B1_hB_6AHD", "chain 1 and hB_6AHD")
cmd.extract("SF3B3_hB_6AHD", "chain 3 and hB_6AHD")
cmd.extract("SF3B2_hB_6AHD", "chain 2 and hB_6AHD")
cmd.extract("SF3B4_hB_6AHD", "chain 4 and hB_6AHD")
cmd.extract("PHF5A_hB_6AHD", "chain 6 and hB_6AHD")
cmd.extract("SF3A3_hB_6AHD", "chain w and hB_6AHD")
cmd.extract("SF3A2_hB_6AHD", "chain v and hB_6AHD")
cmd.extract("SF3A1_hB_6AHD", "chain u and hB_6AHD")
cmd.extract("U2A_hB_6AHD", "chain o and hB_6AHD")
cmd.extract("U2B_hB_6AHD", "chain p and hB_6AHD")
cmd.extract("SF3B5_hB_6AHD", "chain 7 and hB_6AHD")
cmd.extract("U2_Sm_ring_hB_6AHD", "(chain i or chain j or chain k or chain l or chain m or chain n or chain h ) and hB_6AHD")
cmd.extract("FBP21_hB_6AHD", "chain X and hB_6AHD")
cmd.extract("PPIH_hB_6AHD", "chain W and hB_6AHD")
cmd.extract("UBL5_hB_6AHD", "chain A0 and hB_6AHD")
cmd.extract("MFAP1_hB_6AHD", "chain 0 and hB_6AHD")
cmd.extract("PRPF38A_hB_6AHD", "chain Z and hB_6AHD")
cmd.extract("ZMAT2_hB_6AHD", "chain 8 and hB_6AHD")
cmd.extract("SMU1_hB_6AHD", "chain Y and hB_6AHD")
cmd.extract("SF3B6_hB_6AHD", "chain 5 and hB_6AHD")
cmd.set_name("hB_6AHD", "unknown_other_hB_6AHD")
cmd.group("hB_6AHD", "*_hB_6AHD")
cmd.do("order *, yes")
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 setup_fragment_view(selection_name = "(all)", context_object_name = "context"):
colorInterface(selection_name)
cmd.extract(context_object_name, "%s and chain A" % selection_name)
cmd.zoom(selection_name)
cmd.show("surface", context_object_name)
cmd.set("transparency", .5)
def setup_fragment_match(selection_name = "(all)", stub_object_name = "stubs"):
colorInterface(selection_name)
cmd.extract(stub_object_name, "%s and chain C:E" % selection_name)
cmd.zoom(selection_name)
def spl_extract():
for name in cmd.get_names("all"):
#if name in ['5zwo', '5gm6', '5lj3', '5mps', '6exn', '5ylz', '5y88', '3jb9', '6icz', '6ff7', '5yzg', '5xjc', '5gan', '6qw6', '3jcr', '6qx9', '6ah0']: # this should be auto
print(" \ Extracting mode for %s" % name)
for n in cmd.get_names("all"):
if '5zwo' in n:
object_name = n
print(object_name)
if '5zwo' in name.lower():
cmd.extract("PRP8_B5zwo", "chain A and " + object_name)
cmd.extract("BRR2_B5zwo", "chain D and " + object_name)
cmd.extract("LEA1_B5zwo", "chain o and " + object_name)
cmd.extract("Msl1_B5zwo", "chain p and " + object_name)
cmd.extract("SNU114_B5zwo", "chain C and " + object_name)
cmd.extract("U2_B5zwo", "chain H and " + object_name)
cmd.extract("U5_B5zwo", "chain B and " + object_name)
cmd.extract("U6_B5zwo", "chain F and " + object_name)
cmd.extract("U4_B5zwo", "chain I and " + object_name)
cmd.extract("Intron_B5zwo", "chain G and " + object_name)
cmd.extract("PRP4_B5zwo", "chain K and " + object_name)
cmd.extract("PRP31_B5zwo", "chain L and " + object_name)
cmd.extract("PRP6_B5zwo", "chain N and " + object_name)
cmd.extract("PRP3_B5zwo", "chain J and " + object_name)
cmd.extract("DIB1_B5zwo", "chain E and " + object_name)
cmd.extract("SNU13_B5zwo", "chain M and " + object_name)
cmd.extract("LSM8_B5zwo", "chain z and " + object_name)
cmd.extract("LSM2_B5zwo", "chain q and " + object_name)
cmd.extract("LSM3_B5zwo", "chain r and " + object_name)
cmd.extract("LSM6_B5zwo", "chain x and " + object_name)
cmd.extract("LSM5_B5zwo", "chain t and " + object_name)
cmd.extract("LSM7_B5zwo", "chain y and " + object_name)
cmd.extract("LSM4_B5zwo", "chain s and " + object_name)
cmd.extract("SNU66_B5zwo", "chain O and " + object_name)
cmd.extract("BUD13_B5zwo", "chain Y and " + object_name)
cmd.extract("Cus1_B5zwo", "chain 2 and " + object_name)
cmd.extract("HSH155_B5zwo", "chain 1 and " + object_name)
cmd.extract("HSH49_B5zwo", "chain 4 and " + object_name)
cmd.extract("PML1_B5zwo", "chain Z and " + object_name)
cmd.extract("PRP11_B5zwo", "chain v and " + object_name)
cmd.extract("RDS3_B5zwo", "chain 5 and " + object_name)
cmd.extract("RSE1_B5zwo", "chain 3 and " + object_name)
cmd.extract("SNU17_B5zwo", "chain X and " + object_name)
cmd.extract("Ysf3_B5zwo", "chain 6 and " + object_name)
cmd.extract("SMB1_1_B5zwo", "chain a and " + object_name)
cmd.extract("SMB1_2_B5zwo", "chain P and " + object_name)
cmd.extract("SMB1_3_B5zwo", "chain h and " + object_name)
cmd.extract("SME1_1_B5zwo", "chain e and " + object_name)
cmd.extract("SME1_2_B5zwo", "chain T and " + object_name)
cmd.extract("SME1_3_B5zwo", "chain i and " + object_name)
cmd.extract("SMX3_1_B5zwo", "chain f and " + object_name)
cmd.extract("SMX3_2_B5zwo", "chain U and " + object_name)
cmd.extract("SMX3_3_B5zwo", "chain j and " + object_name)
cmd.extract("SMX2_1_B5zwo", "chain g and " + object_name)
cmd.extract("SMX2_2_B5zwo", "chain V and " + object_name)
cmd.extract("SMX2_3_B5zwo", "chain k and " + object_name)
cmd.extract("SMD3_1_B5zwo", "chain d and " + object_name)
cmd.extract("SMD3_2_B5zwo", "chain S and " + object_name)
cmd.extract("SMD3_3_B5zwo", "chain l and " + object_name)
cmd.extract("SMD1_1_B5zwo", "chain b and " + object_name)
cmd.extract("SMD1_2_B5zwo", "chain Q and " + object_name)
cmd.extract("SMD1_3_B5zwo", "chain m and " + object_name)
cmd.extract("SMD2_1_B5zwo", "chain c and " + object_name)
cmd.extract("SMD2_2_B5zwo", "chain R and " + object_name)
cmd.extract("SMD2_3_B5zwo", "chain n and " + object_name)
cmd.extract("PRP9_B5zwo", "chain u and " + object_name)
cmd.extract("PRP21_B5zwo", "chain w and " + object_name)
cmd.extract("SNU23_B5zwo", "chain W and " + object_name)
cmd.extract("PRP38_B5zwo", "chain 0 and " + object_name)
cmd.extract("SPP381_B5zwo", "chain 9 and " + object_name)
cmd.set_name(object_name, "unknown_other_B5zwo")
cmd.group("B5zwo", "*_B5zwo")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5gm6' in n:
object_name = n
print(object_name)
if '5gm6' in name.lower():
cmd.extract("PRP8_Ba5gm6", "chain A and " + object_name)
cmd.extract("BRR2_Ba5gm6", "chain B and " + object_name)
cmd.extract("BUD31_Ba5gm6", "chain T and " + object_name)
cmd.extract("CEF1_Ba5gm6", "chain c and " + object_name)
cmd.extract("CWC15_Ba5gm6", "chain S and " + object_name)
cmd.extract("CWC2_hRBM22_Ba5gm6", "chain R and " + object_name)
cmd.extract("CWC21_Ba5gm6", "chain X and " + object_name)
cmd.extract("CWC22_Ba5gm6", "chain Z and " + object_name)
cmd.extract("PRP45_Ba5gm6", "chain P and " + object_name)
cmd.extract("CDC40_Ba5gm6", "chain n and " + object_name)
cmd.extract("PRP19_Ba5gm6", "chain f and " + object_name)
cmd.extract("PRP46_Ba5gm6", "chain O and " + object_name)
cmd.extract("SLT11/ECM2_Ba5gm6", "chain Q and " + object_name)
cmd.extract("SNT309_Ba5gm6", "chain t and " + object_name)
cmd.extract("SNU114_Ba5gm6", "chain C and " + object_name)
cmd.extract("SYF2_Ba5gm6", "chain f and " + object_name)
cmd.extract("SYF1_Ba5gm6", "chain v and " + object_name)
cmd.extract("U2_Ba5gm6", "chain 2 and " + object_name)
cmd.extract("U5_Ba5gm6", "chain 5 and " + object_name)
cmd.extract("U6_Ba5gm6", "chain 6 and " + object_name)
cmd.extract("Intron_Ba5gm6", "chain M and " + object_name)
cmd.extract("Exon_Ba5gm6", "chain N and " + object_name)
cmd.extract("BUD13_Ba5gm6", "chain W and " + object_name)
cmd.extract("CLF2_Ba5gm6", "chain d and " + object_name)
cmd.extract("Cus1_Ba5gm6", "chain H and " + object_name)
cmd.extract("CWC24_Ba5gm6", "chain a and " + object_name)
cmd.extract("CWC27_Ba5gm6", "chain b and " + object_name)
cmd.extract("HSH155_Ba5gm6", "chain G and " + object_name)
cmd.extract("HSH49_Ba5gm6", "chain e and " + object_name)
cmd.extract("PML1_Ba5gm6", "chain U and " + object_name)
cmd.extract("PRP11_Ba5gm6", "chain I and " + object_name)
cmd.extract("PRP2_Ba5gm6", "chain Y and " + object_name)
cmd.extract("RDS3_Ba5gm6", "chain J and " + object_name)
cmd.extract("RSE1_Ba5gm6", "chain F and " + object_name)
cmd.extract("SNU17_Ba5gm6", "chain V and " + object_name)
cmd.extract("Ysf3_Ba5gm6", "chain K and " + object_name)
cmd.set_name(object_name, "unknown_other_Ba5gm6")
cmd.group("Ba5gm6", "*_Ba5gm6")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5lj3' in n:
object_name = n
print(object_name)
if '5lj3' in name.lower():
cmd.extract("PRP8_C5lj3", "chain A and " + object_name)
cmd.extract("BUD31_C5lj3", "chain L and " + object_name)
cmd.extract("CEF1_C5lj3", "chain O and " + object_name)
cmd.extract("CLF1_C5lj3", "chain S and " + object_name)
cmd.extract("CWC15_C5lj3", "chain P and " + object_name)
cmd.extract("CWC16/YJU2_C5lj3", "chain D and " + object_name)
cmd.extract("CWC2_hRBM22_C5lj3", "chain M and " + object_name)
cmd.extract("CWC21_C5lj3", "chain R and " + object_name)
cmd.extract("CWC22_C5lj3", "chain H and " + object_name)
cmd.extract("CWC25_C5lj3", "chain F and " + object_name)
cmd.extract("ISY1_C5lj3", "chain G and " + object_name)
cmd.extract("LEA1_C5lj3", "chain W and " + object_name)
cmd.extract("Msl1_C5lj3", "chain Y and " + object_name)
cmd.extract("PRP45_C5lj3", "chain K and " + object_name)
cmd.extract("PRP46_C5lj3", "chain J and " + object_name)
cmd.extract("SLT11/ECM2_C5lj3", "chain N and " + object_name)
cmd.extract("SNU114_C5lj3", "chain C and " + object_name)
cmd.extract("SYF1_C5lj3", "chain T and " + object_name)
cmd.extract("U2_C5lj3", "chain Z and " + object_name)
cmd.extract("U5_C5lj3", "chain U and " + object_name)
cmd.extract("U6_C5lj3", "chain V and " + object_name)
cmd.extract("Intron_C5lj3", "chain I and " + object_name)
cmd.extract("Exon_C5lj3", "chain E and " + object_name)
cmd.extract("SMB1_1_C5lj3", "chain b and " + object_name)
cmd.extract("SMB1_2_C5lj3", "chain k and " + object_name)
cmd.extract("SME1_1_C5lj3", "chain e and " + object_name)
cmd.extract("SME1_2_C5lj3", "chain p and " + object_name)
cmd.extract("SMX3_1_C5lj3", "chain f and " + object_name)
cmd.extract("SMX3_2_C5lj3", "chain q and " + object_name)
cmd.extract("SMX2_1_C5lj3", "chain g and " + object_name)
cmd.extract("SMX2_2_C5lj3", "chain r and " + object_name)
cmd.extract("SMD3_1_C5lj3", "chain d and " + object_name)
cmd.extract("SMD3_2_C5lj3", "chain n and " + object_name)
cmd.extract("SMD1_1_C5lj3", "chain h and " + object_name)
cmd.extract("SMD1_2_C5lj3", "chain l and " + object_name)
cmd.extract("SMD2_1_C5lj3", "chain j and " + object_name)
cmd.extract("SMD2_2_C5lj3", "chain m and " + object_name)
cmd.set_name(object_name, "unknown_other_C5lj3")
cmd.group("C5lj3", "*_C5lj3")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5mps' in n:
object_name = n
print(object_name)
if '5mps' in name.lower():
cmd.extract("PRP8_Cs5mps", "chain A and " + object_name)
cmd.extract("BUD31_Cs5mps", "chain L and " + object_name)
cmd.extract("CEF1_Cs5mps", "chain O and " + object_name)
cmd.extract("CLF1_Cs5mps", "chain S and " + object_name)
cmd.extract("CWC15_Cs5mps", "chain P and " + object_name)
cmd.extract("CWC2_hRBM22_Cs5mps", "chain M and " + object_name)
cmd.extract("CWC21_Cs5mps", "chain R and " + object_name)
cmd.extract("CWC22_Cs5mps", "chain H and " + object_name)
cmd.extract("PRP45_Cs5mps", "chain K and " + object_name)
cmd.extract("CDC40_Cs5mps", "chain o and " + object_name)
cmd.extract("PRP46_Cs5mps", "chain J and " + object_name)
cmd.extract("SLT11/ECM2_Cs5mps", "chain N and " + object_name)
cmd.extract("SNU114_Cs5mps", "chain C and " + object_name)
cmd.extract("SYF2_Cs5mps", "chain y and " + object_name)
cmd.extract("SYF1_Cs5mps", "chain T and " + object_name)
cmd.extract("U2_Cs5mps", "chain 2 and " + object_name)
cmd.extract("U5_Cs5mps", "chain 5 and " + object_name)
cmd.extract("U6_Cs5mps", "chain 6 and " + object_name)
cmd.extract("5EXON_Cs5mps", "chain E and " + object_name)
cmd.extract("Intron_Cs5mps", "chain I and " + object_name)
cmd.extract("Exon_Cs5mps", "chain E and " + object_name)
cmd.extract("SMB1_Cs5mps", "chain b and " + object_name)
cmd.extract("SME1_Cs5mps", "chain e and " + object_name)
cmd.extract("SMX3_Cs5mps", "chain f and " + object_name)
cmd.extract("SMX2_Cs5mps", "chain g and " + object_name)
cmd.extract("SMD3_Cs5mps", "chain d and " + object_name)
cmd.extract("SMD1_Cs5mps", "chain h and " + object_name)
cmd.extract("SMD2_Cs5mps", "chain j and " + object_name)
cmd.extract("PRP18_Cs5mps", "chain a and " + object_name)
cmd.extract("SLU7_Cs5mps", "chain c and " + object_name)
cmd.set_name(object_name, "unknown_other_Cs5mps")
cmd.group("Cs5mps", "*_Cs5mps")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6exn' in n:
object_name = n
print(object_name)
if '6exn' in name.lower():
cmd.extract("PRP8_P6exn", "chain A and " + object_name)
cmd.extract("BUD31_P6exn", "chain L and " + object_name)
cmd.extract("CEF1_P6exn", "chain O and " + object_name)
cmd.extract("CLF1_P6exn", "chain S and " + object_name)
cmd.extract("CWC15_P6exn", "chain P and " + object_name)
cmd.extract("CWC16/YJU2_P6exn", "chain D and " + object_name)
cmd.extract("CWC2_hRBM22_P6exn", "chain M and " + object_name)
cmd.extract("CWC21_P6exn", "chain R and " + object_name)
cmd.extract("CWC22_P6exn", "chain H and " + object_name)
cmd.extract("LEA1_P6exn", "chain W and " + object_name)
cmd.extract("Msl1_P6exn", "chain Y and " + object_name)
cmd.extract("PRP45_P6exn", "chain K and " + object_name)
cmd.extract("CDC40_P6exn", "chain o and " + object_name)
cmd.extract("PRP19_1_P6exn", "chain t and " + object_name)
cmd.extract("PRP19_2_P6exn", "chain u and " + object_name)
cmd.extract("PRP19_3_P6exn", "chain v and " + object_name)
cmd.extract("PRP19_4_P6exn", "chain w and " + object_name)
cmd.extract("PRP46_P6exn", "chain J and " + object_name)
cmd.extract("SLT11/ECM2_P6exn", "chain N and " + object_name)
cmd.extract("SNU114_P6exn", "chain C and " + object_name)
cmd.extract("SYF1_P6exn", "chain T and " + object_name)
cmd.extract("U2_P6exn", "chain 2 and " + object_name)
cmd.extract("U5_P6exn", "chain 5 and " + object_name)
cmd.extract("U6_P6exn", "chain 6 and " + object_name)
cmd.extract("Intron_P6exn", "chain I and " + object_name)
cmd.extract("Exon_P6exn", "chain E and " + object_name)
cmd.extract("SMB1_1_P6exn", "chain b and " + object_name)
cmd.extract("SMB1_2_P6exn", "chain k and " + object_name)
cmd.extract("SME1_1_P6exn", "chain e and " + object_name)
cmd.extract("SME1_2_P6exn", "chain p and " + object_name)
cmd.extract("SMX3_1_P6exn", "chain f and " + object_name)
cmd.extract("SMX3_2_P6exn", "chain q and " + object_name)
cmd.extract("SMX2_1_P6exn", "chain g and " + object_name)
cmd.extract("SMX2_2_P6exn", "chain r and " + object_name)
cmd.extract("SMD3_1_P6exn", "chain d and " + object_name)
cmd.extract("SMD3_2_P6exn", "chain n and " + object_name)
cmd.extract("SMD1_1_P6exn", "chain h and " + object_name)
cmd.extract("SMD1_2_P6exn", "chain l and " + object_name)
cmd.extract("SMD2_1_P6exn", "chain j and " + object_name)
cmd.extract("SMD2_2_P6exn", "chain m and " + object_name)
cmd.extract("PRP22_P6exn", "chain V and " + object_name)
cmd.extract("PRP18_P6exn", "chain a and " + object_name)
cmd.extract("SLU7_P6exn", "chain c and " + object_name)
cmd.extract("unassigned_P6exn", "chain X and " + object_name)
cmd.set_name(object_name, "unknown_other_P6exn")
cmd.group("P6exn", "*_P6exn")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5ylz' in n:
object_name = n
print(object_name)
if '5ylz' in name.lower():
cmd.extract("PRP8_P5ylz", "chain A and " + object_name)
cmd.extract("BUD31_P5ylz", "chain L and " + object_name)
cmd.extract("CEF1_P5ylz", "chain J and " + object_name)
cmd.extract("CLF1_P5ylz", "chain I and " + object_name)
cmd.extract("CWC15_P5ylz", "chain P and " + object_name)
cmd.extract("CWC2_hRBM22_P5ylz", "chain N and " + object_name)
cmd.extract("CWC21_P5ylz", "chain R and " + object_name)
cmd.extract("CWC22_P5ylz", "chain S and " + object_name)
cmd.extract("LEA1_P5ylz", "chain o and " + object_name)
cmd.extract("Msl1_P5ylz", "chain p and " + object_name)
cmd.extract("PRP45_P5ylz", "chain Q and " + object_name)
cmd.extract("CDC40_P5ylz", "chain T and " + object_name)
cmd.extract("PRP19_1_P5ylz", "chain q and " + object_name)
cmd.extract("PRP19_2_P5ylz", "chain r and " + object_name)
cmd.extract("PRP19_3_P5ylz", "chain s and " + object_name)
cmd.extract("PRP19_4_P5ylz", "chain t and " + object_name)
cmd.extract("PRP46_P5ylz", "chain O and " + object_name)
cmd.extract("SLT11/ECM2_P5ylz", "chain M and " + object_name)
cmd.extract("SNT309_P5ylz", "chain G and " + object_name)
cmd.extract("SNU114_P5ylz", "chain C and " + object_name)
cmd.extract("SYF2_P5ylz", "chain K and " + object_name)
cmd.extract("SYF1_P5ylz", "chain H and " + object_name)
cmd.extract("U2_P5ylz", "chain F and " + object_name)
cmd.extract("U5_P5ylz", "chain B and " + object_name)
cmd.extract("U6_P5ylz", "chain D and " + object_name)
cmd.extract("Intron_P5ylz", "chain E and " + object_name)
cmd.extract("SMB1_1_P5ylz", "chain a and " + object_name)
cmd.extract("SMB1_2_P5ylz", "chain h and " + object_name)
cmd.extract("SME1_1_P5ylz", "chain b and " + object_name)
cmd.extract("SME1_2_P5ylz", "chain i and " + object_name)
cmd.extract("SMX3_1_P5ylz", "chain c and " + object_name)
cmd.extract("SMX3_2_P5ylz", "chain j and " + object_name)
cmd.extract("SMX2_1_P5ylz", "chain d and " + object_name)
cmd.extract("SMX2_2_P5ylz", "chain k and " + object_name)
cmd.extract("SMD3_1_P5ylz", "chain e and " + object_name)
cmd.extract("SMD3_2_P5ylz", "chain l and " + object_name)
cmd.extract("SMD1_1_P5ylz", "chain f and " + object_name)
cmd.extract("SMD1_2_P5ylz", "chain m and " + object_name)
cmd.extract("SMD2_1_P5ylz", "chain g and " + object_name)
cmd.extract("SMD2_2_P5ylz", "chain n and " + object_name)
cmd.extract("PRP22_P5ylz", "chain W and " + object_name)
cmd.extract("PRP18_P5ylz", "chain U and " + object_name)
cmd.extract("SLU7_P5ylz", "chain V and " + object_name)
cmd.set_name(object_name, "unknown_other_P5ylz")
cmd.group("P5ylz", "*_P5ylz")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5y88' in n:
object_name = n
print(object_name)
if '5y88' in name.lower():
cmd.extract("PRP8_I5y88", "chain A and " + object_name)
cmd.extract("BUD31_I5y88", "chain L and " + object_name)
cmd.extract("CLF1_I5y88", "chain I and " + object_name)
cmd.extract("CWC15_I5y88", "chain P and " + object_name)
cmd.extract("CWC16/YJU2_I5y88", "chain R and " + object_name)
cmd.extract("CWC2_hRBM22_I5y88", "chain N and " + object_name)
cmd.extract("CWC25_I5y88", "chain G and " + object_name)
cmd.extract("Intron_2_I5y88", "chain E and " + object_name)
cmd.extract("LEA1_I5y88", "chain o and " + object_name)
cmd.extract("Msl1_I5y88", "chain p and " + object_name)
cmd.extract("PRP45_I5y88", "chain Q and " + object_name)
cmd.extract("CDC40_I5y88", "chain S and " + object_name)
cmd.extract("PRP19_1_I5y88", "chain q and " + object_name)
cmd.extract("PRP19_2_I5y88", "chain r and " + object_name)
cmd.extract("PRP19_3_I5y88", "chain s and " + object_name)
cmd.extract("PRP19_4_I5y88", "chain t and " + object_name)
cmd.extract("PRP46_I5y88", "chain O and " + object_name)
cmd.extract("SLT11/ECM2_I5y88", "chain M and " + object_name)
cmd.extract("SNT309_I5y88", "chain G and " + object_name)
cmd.extract("SNU114_I5y88", "chain C and " + object_name)
cmd.extract("SYF2_I5y88", "chain K and " + object_name)
cmd.extract("SYF1_I5y88", "chain H and " + object_name)
cmd.extract("U2_I5y88", "chain F and " + object_name)
cmd.extract("U5_I5y88", "chain B and " + object_name)
cmd.extract("U6_I5y88", "chain D and " + object_name)
cmd.extract("Intron_I5y88", "chain x and " + object_name)
cmd.extract("RNA_I5y88", "chain x and " + object_name)
cmd.extract("cwc23_I5y88", "chain T and " + object_name)
cmd.extract("SPP382_I5y88", "chain U and " + object_name)
cmd.extract("NTR2_I5y88", "chain V and " + object_name)
cmd.extract("PRP43_I5y88", "chain W and " + object_name)
cmd.extract("SMB1_1_I5y88", "chain a and " + object_name)
cmd.extract("SMB1_2_I5y88", "chain h and " + object_name)
cmd.extract("SME1_1_I5y88", "chain b and " + object_name)
cmd.extract("SME1_2_I5y88", "chain i and " + object_name)
cmd.extract("SMX3_1_I5y88", "chain c and " + object_name)
cmd.extract("SMX3_2_I5y88", "chain j and " + object_name)
cmd.extract("SMX2_1_I5y88", "chain d and " + object_name)
cmd.extract("SMX2_2_I5y88", "chain k and " + object_name)
cmd.extract("SMD3_1_I5y88", "chain e and " + object_name)
cmd.extract("SMD3_2_I5y88", "chain l and " + object_name)
cmd.extract("SMD1_1_I5y88", "chain f and " + object_name)
cmd.extract("SMD1_2_I5y88", "chain m and " + object_name)
cmd.extract("SMD2_1_I5y88", "chain g and " + object_name)
cmd.extract("SMD2_2_I5y88", "chain n and " + object_name)
cmd.set_name(object_name, "unknown_other_I5y88")
cmd.group("I5y88", "*_I5y88")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '3jb9' in n:
object_name = n
print(object_name)
if '3jb9' in name.lower():
cmd.extract("U2_3jb9", "chain P and " + object_name)
cmd.extract("U5_3jb9", "chain C and " + object_name)
cmd.extract("U6_3jb9", "chain N and " + object_name)
cmd.extract("Intron_1_3jb9", "chain O and " + object_name)
cmd.extract("Intron_2_3jb9", "chain Q and " + object_name)
cmd.extract("Spp42_yPrp8_3jb9", "chain A and " + object_name)
cmd.extract("CWF15_yCWC15_3jb9", "chain h and " + object_name)
cmd.set_name(object_name, "unknown_other_3jb9")
cmd.group("3jb9", "*_3jb9")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6icz' in n:
object_name = n
print(object_name)
if '6icz' in name.lower():
cmd.extract("CWC15_hP_6icz", "chain P and " + object_name)
cmd.extract("U2_hP_6icz", "chain H and " + object_name)
cmd.extract("U5_hP_6icz", "chain B and " + object_name)
cmd.extract("U6_hP_6icz", "chain F and " + object_name)
cmd.extract("Intron_hP_6icz", "chain G and " + object_name)
cmd.extract("cwc23_hP_6icz", "chain 6ICZ and " + object_name)
cmd.set_name(object_name, "unknown_other_hP_6icz")
cmd.group("hP_6icz", "*_hP_6icz")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6ff7' in n:
object_name = n
print(object_name)
if '6ff7' in name.lower():
cmd.extract("CWC15_hBa_6ff7", "chain R and " + object_name)
cmd.extract("CWC2_hRBM22_hBa_6ff7", "chain P and " + object_name)
cmd.extract("U2_hBa_6ff7", "chain 2 and " + object_name)
cmd.extract("U5_hBa_6ff7", "chain 5 and " + object_name)
cmd.extract("U6_hBa_6ff7", "chain 6 and " + object_name)
cmd.extract("Intron_hBa_6ff7", "chain Z and " + object_name)
cmd.set_name(object_name, "unknown_other_hBa_6ff7")
cmd.group("hBa_6ff7", "*_hBa_6ff7")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5yzg' in n:
object_name = n
print(object_name)
if '5yzg' in name.lower():
cmd.extract("CWC15_hC_5yzg", "chain P and " + object_name)
cmd.extract("CWC2_hRBM22_hC_5yzg", "chain O and " + object_name)
cmd.extract("CWC25_hC_5yzg", "chain X and " + object_name)
cmd.extract("PRP16_hDHX38_hC_5yzg", "chain Z and " + object_name)
cmd.extract("U2_hC_5yzg", "chain H and " + object_name)
cmd.extract("U5_hC_5yzg", "chain B and " + object_name)
cmd.extract("U6_hC_5yzg", "chain F and " + object_name)
cmd.extract("Intron_hC_5yzg", "chain G and " + object_name)
cmd.set_name(object_name, "unknown_other_hC_5yzg")
cmd.group("hC_5yzg", "*_hC_5yzg")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5xjc' in n:
object_name = n
print(object_name)
if '5xjc' in name.lower():
cmd.extract("CWC15_hX_5xjc", "chain P and " + object_name)
cmd.extract("CWC25_hX_5xjc", "chain X and " + object_name)
cmd.extract("U2_hX_5xjc", "chain H and " + object_name)
cmd.extract("U5_hX_5xjc", "chain B and " + object_name)
cmd.extract("U6_hX_5xjc", "chain F and " + object_name)
cmd.extract("Intron_hX_5xjc", "chain G and " + object_name)
cmd.extract("PRKRIP1_hX_5xjc", "chain X and " + object_name)
cmd.set_name(object_name, "unknown_other_hX_5xjc")
cmd.group("hX_5xjc", "*_hX_5xjc")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '5gan' in n:
object_name = n
print(object_name)
if '5gan' in name.lower():
cmd.extract("PRP8_y3_5gan", "chain A and " + object_name)
cmd.extract("BRR2_y3_5gan", "chain B and " + object_name)
cmd.extract("PRP45_y3_5gan", "chain H and " + object_name)
cmd.extract("SNU114_y3_5gan", "chain C and " + object_name)
cmd.extract("U5_y3_5gan", "chain U and " + object_name)
cmd.extract("U6_y3_5gan", "chain W and " + object_name)
cmd.extract("U4_y3_5gan", "chain V and " + object_name)
cmd.extract("PRP31_y3_5gan", "chain F and " + object_name)
cmd.extract("PRP6_y3_5gan", "chain J and " + object_name)
cmd.extract("PRP3_y3_5gan", "chain G and " + object_name)
cmd.extract("DIB1_y3_5gan", "chain D and " + object_name)
cmd.extract("SNU13_y3_5gan", "chain K and " + object_name)
cmd.extract("LSM8_y3_5gan", "chain 8 and " + object_name)
cmd.extract("LSM2_y3_5gan", "chain 2 and " + object_name)
cmd.extract("LSM3_y3_5gan", "chain 3 and " + object_name)
cmd.extract("LSM6_y3_5gan", "chain 6 and " + object_name)
cmd.extract("LSM5_y3_5gan", "chain 5 and " + object_name)
cmd.extract("LSM7_y3_5gan", "chain 7 and " + object_name)
cmd.extract("LSM4_y3_5gan", "chain 4 and " + object_name)
cmd.extract("SNU66_y3_5gan", "chain E and " + object_name)
cmd.extract("SMB1_1_y3_5gan", "chain b and " + object_name)
cmd.extract("SMB1_2_y3_5gan", "chain k and " + object_name)
cmd.extract("SME1_1_y3_5gan", "chain e and " + object_name)
cmd.extract("SME1_2_y3_5gan", "chain p and " + object_name)
cmd.extract("SMX3_1_y3_5gan", "chain f and " + object_name)
cmd.extract("SMX3_2_y3_5gan", "chain q and " + object_name)
cmd.extract("SMX2_1_y3_5gan", "chain g and " + object_name)
cmd.extract("SMX2_2_y3_5gan", "chain r and " + object_name)
cmd.extract("SMD3_1_y3_5gan", "chain d and " + object_name)
cmd.extract("SMD3_2_y3_5gan", "chain n and " + object_name)
cmd.extract("SMD1_1_y3_5gan", "chain h and " + object_name)
cmd.extract("SMD1_2_y3_5gan", "chain l and " + object_name)
cmd.extract("SMD2_1_y3_5gan", "chain j and " + object_name)
cmd.extract("SMD2_2_y3_5gan", "chain m and " + object_name)
cmd.extract("unassigned_y3_5gan", "chain X and " + object_name)
cmd.set_name(object_name, "unknown_other_y3_5gan")
cmd.group("y3_5gan", "*_y3_5gan")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6qw6' in n:
object_name = n
print(object_name)
if '6qw6' in name.lower():
cmd.extract("PRP8_h3_6qw6", "chain 5A and " + object_name)
cmd.extract("U5_h3_6qw6", "chain 5 and " + object_name)
cmd.extract("U6_h3_6qw6", "chain 6 and " + object_name)
cmd.extract("U4_h3_6qw6", "chain 4 and " + object_name)
cmd.extract("Prp28_h3_6qw6", "chain 5X and " + object_name)
cmd.set_name(object_name, "unknown_other_h3_6qw6")
cmd.group("h3_6qw6", "*_h3_6qw6")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '3jcr' in n:
object_name = n
print(object_name)
if '3jcr' in name.lower():
cmd.extract("PRP8_h3_3jcr", "chain A and " + object_name)
cmd.extract("BRR2_h3_3jcr", "chain C and " + object_name)
cmd.extract("SNU114_h3_3jcr", "chain B and " + object_name)
cmd.extract("U5_h3_3jcr", "chain H and " + object_name)
cmd.extract("U6_h3_3jcr", "chain N and " + object_name)
cmd.extract("U4_h3_3jcr", "chain M and " + object_name)
cmd.extract("PRP4_h3_3jcr", "chain L and " + object_name)
cmd.extract("PRP31_h3_3jcr", "chain J and " + object_name)
cmd.extract("PRP6_h3_3jcr", "chain G and " + object_name)
cmd.extract("PRP3_h3_3jcr", "chain K and " + object_name)
cmd.extract("SNU13_h3_3jcr", "chain I and " + object_name)
cmd.extract("LSM8_h3_3jcr", "chain 8 and " + object_name)
cmd.extract("LSM2_h3_3jcr", "chain 2 and " + object_name)
cmd.extract("LSM3_h3_3jcr", "chain 3 and " + object_name)
cmd.extract("LSM5_h3_3jcr", "chain 5 and " + object_name)
cmd.extract("LSM7_h3_3jcr", "chain 7 and " + object_name)
cmd.extract("LSM4_h3_3jcr", "chain 4 and " + object_name)
cmd.extract("SMD3_1_h3_3jcr", "chain R and " + object_name)
cmd.extract("SMD3_2_h3_3jcr", "chain r and " + object_name)
cmd.extract("SMD1_1_h3_3jcr", "chain P and " + object_name)
cmd.extract("SMD1_2_h3_3jcr", "chain p and " + object_name)
cmd.extract("SMD2_1_h3_3jcr", "chain Q and " + object_name)
cmd.extract("SMD2_2_h3_3jcr", "chain q and " + object_name)
cmd.extract("U5-40K_h3_3jcr", "chain D and " + object_name)
cmd.extract("Dim1_h3_3jcr", "chain E and " + object_name)
cmd.extract("Prp28_h3_3jcr", "chain F and " + object_name)
cmd.extract("SmE_1_h3_3jcr", "chain S and " + object_name)
cmd.extract("SmE_2_h3_3jcr", "chain s and " + object_name)
cmd.extract("SmF_1_h3_3jcr", "chain T and " + object_name)
cmd.extract("SmF_2_h3_3jcr", "chain t and " + object_name)
cmd.extract("SmG_1_h3_3jcr", "chain U and " + object_name)
cmd.extract("SmG_2_h3_3jcr", "chain u and " + object_name)
cmd.extract("Sad1_h3_3jcr", "chain V and " + object_name)
cmd.extract("SmB_1_h3_3jcr", "chain O and " + object_name)
cmd.extract("SmB_2_h3_3jcr", "chain o and " + object_name)
cmd.set_name(object_name, "unknown_other_h3_3jcr")
cmd.group("h3_3jcr", "*_h3_3jcr")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6qx9' in n:
object_name = n
print(object_name)
if '6qx9' in name.lower():
cmd.extract("PRP8_h3_6qx9", "chain 5A and " + object_name)
cmd.extract("U2_h3_6qx9", "chain 2 and " + object_name)
cmd.extract("U5_h3_6qx9", "chain 5 and " + object_name)
cmd.extract("U6_h3_6qx9", "chain 6 and " + object_name)
cmd.extract("U4_h3_6qx9", "chain 4 and " + object_name)
cmd.extract("Intron_h3_6qx9", "chain I and " + object_name)
cmd.extract("U1_h3_6qx9", "chain 1 and " + object_name)
cmd.extract("Prp28_h3_6qx9", "chain 5X and " + object_name)
cmd.set_name(object_name, "unknown_other_h3_6qx9")
cmd.group("h3_6qx9", "*_h3_6qx9")
cmd.do("order *, yes")
for n in cmd.get_names("all"):
if '6ah0' in n:
object_name = n
print(object_name)
if '6ah0' in name.lower():
cmd.extract("PRP8_h_Bp_6ah0", "chain A and " + object_name)
cmd.extract("U2_h_Bp_6ah0", "chain H and " + object_name)
cmd.extract("U5_h_Bp_6ah0", "chain B and " + object_name)
cmd.extract("U6_h_Bp_6ah0", "chain F and " + object_name)
cmd.extract("U4_h_Bp_6ah0", "chain I and " + object_name)
cmd.extract("Intron_h_Bp_6ah0", "chain G and " + object_name)
cmd.extract("Prp28_h_Bp_6ah0", "chain X and " + object_name)
cmd.set_name(object_name, "unknown_other_h_Bp_6ah0")
cmd.group("h_Bp_6ah0", "*_h_Bp_6ah0")
cmd.do("order *, yes")
def spl_extract():
for name in cmd.get_names("all"):
#if name in ['5zwo', '5gm6', '5lj3', '5mps', '6exn', '5ylz', '5y88', '3jb9', '6icz', '6ff7', '5yzg', '5xjc', '5mq0', '5lj5', '6g90', '6n7r', '6n7p']: # this should be auto
print(" \ Extracting mode for %s" % name)
if '5zwo' in name.lower():
cmd.extract("PRP8_B5zwo", "chain A and 5zwo")
cmd.extract("BRR2_B5zwo", "chain D and 5zwo")
cmd.extract("LEA1_B5zwo", "chain o and 5zwo")
cmd.extract("Msl1_B5zwo", "chain p and 5zwo")
cmd.extract("SNU114_B5zwo", "chain C and 5zwo")
cmd.extract("U2_B5zwo", "chain H and 5zwo")
cmd.extract("U5_B5zwo", "chain B and 5zwo")
cmd.extract("U6_B5zwo", "chain F and 5zwo")
cmd.extract("U4_B5zwo", "chain I and 5zwo")
cmd.extract("Intron_B5zwo", "chain G and 5zwo")
cmd.extract("PRP4_B5zwo", "chain K and 5zwo")
cmd.extract("PRP31_B5zwo", "chain L and 5zwo")
cmd.extract("PRP6_B5zwo", "chain N and 5zwo")
cmd.extract("PRP3_B5zwo", "chain J and 5zwo")
cmd.extract("DIB1_B5zwo", "chain E and 5zwo")
cmd.extract("SNU13_B5zwo", "chain M and 5zwo")
cmd.extract("LSM8_B5zwo", "chain z and 5zwo")
cmd.extract("LSM2_B5zwo", "chain q and 5zwo")
cmd.extract("LSM3_B5zwo", "chain r and 5zwo")
cmd.extract("LSM6_B5zwo", "chain x and 5zwo")
cmd.extract("LSM5_B5zwo", "chain t and 5zwo")
cmd.extract("LSM7_B5zwo", "chain y and 5zwo")
cmd.extract("LSM4_B5zwo", "chain s and 5zwo")
cmd.extract("SNU66_B5zwo", "chain O and 5zwo")
cmd.extract("BUD13_B5zwo", "chain Y and 5zwo")
cmd.extract("Cus1_B5zwo", "chain 2 and 5zwo")
cmd.extract("HSH155_B5zwo", "chain 1 and 5zwo")
cmd.extract("HSH49_B5zwo", "chain 4 and 5zwo")
cmd.extract("PML1_B5zwo", "chain Z and 5zwo")
cmd.extract("PRP11_B5zwo", "chain v and 5zwo")
cmd.extract("RDS3_B5zwo", "chain 5 and 5zwo")
cmd.extract("RSE1_B5zwo", "chain 3 and 5zwo")
cmd.extract("SNU17_B5zwo", "chain X and 5zwo")
cmd.extract("Ysf3_B5zwo", "chain 6 and 5zwo")
cmd.extract("SMB1_1_B5zwo", "chain a and 5zwo")
cmd.extract("SMB1_2_B5zwo", "chain P and 5zwo")
cmd.extract("SMB1_3_B5zwo", "chain h and 5zwo")
cmd.extract("SME1_1_B5zwo", "chain e and 5zwo")
cmd.extract("SME1_2_B5zwo", "chain T and 5zwo")
cmd.extract("SME1_3_B5zwo", "chain i and 5zwo")
cmd.extract("SMX3_1_B5zwo", "chain f and 5zwo")
cmd.extract("SMX3_2_B5zwo", "chain U and 5zwo")
cmd.extract("SMX3_3_B5zwo", "chain j and 5zwo")
cmd.extract("SMX2_1_B5zwo", "chain g and 5zwo")
cmd.extract("SMX2_2_B5zwo", "chain V and 5zwo")
cmd.extract("SMX2_3_B5zwo", "chain k and 5zwo")
cmd.extract("SMD3_1_B5zwo", "chain d and 5zwo")
cmd.extract("SMD3_2_B5zwo", "chain S and 5zwo")
cmd.extract("SMD3_3_B5zwo", "chain l and 5zwo")
cmd.extract("SMD1_1_B5zwo", "chain b and 5zwo")
cmd.extract("SMD1_2_B5zwo", "chain Q and 5zwo")
cmd.extract("SMD1_3_B5zwo", "chain m and 5zwo")
cmd.extract("SMD2_1_B5zwo", "chain c and 5zwo")
cmd.extract("SMD2_2_B5zwo", "chain R and 5zwo")
cmd.extract("SMD2_3_B5zwo", "chain n and 5zwo")
cmd.extract("PRP9_B5zwo", "chain u and 5zwo")
cmd.extract("PRP21_B5zwo", "chain w and 5zwo")
cmd.extract("SNU23_B5zwo", "chain W and 5zwo")
cmd.extract("PRP38_B5zwo", "chain 0 and 5zwo")
cmd.extract("SPP381_B5zwo", "chain 9 and 5zwo")
cmd.set_name("5zwo", "unknown_other_B5zwo")
cmd.group("B5zwo", "*_B5zwo")
cmd.do("order *, yes")
if '5gm6' in name.lower():
cmd.extract("PRP8_Ba5gm6", "chain A and 5gm6")
cmd.extract("BRR2_Ba5gm6", "chain B and 5gm6")
cmd.extract("BUD31_Ba5gm6", "chain T and 5gm6")
cmd.extract("CEF1_Ba5gm6", "chain c and 5gm6")
cmd.extract("CWC15_Ba5gm6", "chain S and 5gm6")
cmd.extract("CWC2_hRBM22_Ba5gm6", "chain R and 5gm6")
cmd.extract("CWC21_Ba5gm6", "chain X and 5gm6")
cmd.extract("CWC22_Ba5gm6", "chain Z and 5gm6")
cmd.extract("PRP45_Ba5gm6", "chain P and 5gm6")
cmd.extract("CDC40_Ba5gm6", "chain n and 5gm6")
cmd.extract("PRP19_Ba5gm6", "chain f and 5gm6")
cmd.extract("PRP46_Ba5gm6", "chain O and 5gm6")
cmd.extract("SLT11/ECM2_Ba5gm6", "chain Q and 5gm6")
cmd.extract("SNT309_Ba5gm6", "chain t and 5gm6")
cmd.extract("SNU114_Ba5gm6", "chain C and 5gm6")
cmd.extract("SYF2_Ba5gm6", "chain f and 5gm6")
cmd.extract("SYF1_Ba5gm6", "chain v and 5gm6")
cmd.extract("U2_Ba5gm6", "chain 2 and 5gm6")
cmd.extract("U5_Ba5gm6", "chain 5 and 5gm6")
cmd.extract("U6_Ba5gm6", "chain 6 and 5gm6")
cmd.extract("Intron_Ba5gm6", "chain M and 5gm6")
cmd.extract("Exon_Ba5gm6", "chain N and 5gm6")
cmd.extract("BUD13_Ba5gm6", "chain W and 5gm6")
cmd.extract("CLF2_Ba5gm6", "chain d and 5gm6")
cmd.extract("Cus1_Ba5gm6", "chain H and 5gm6")
cmd.extract("CWC24_Ba5gm6", "chain a and 5gm6")
cmd.extract("CWC27_Ba5gm6", "chain b and 5gm6")
cmd.extract("HSH155_Ba5gm6", "chain G and 5gm6")
cmd.extract("HSH49_Ba5gm6", "chain e and 5gm6")
cmd.extract("PML1_Ba5gm6", "chain U and 5gm6")
cmd.extract("PRP11_Ba5gm6", "chain I and 5gm6")
cmd.extract("PRP2_Ba5gm6", "chain Y and 5gm6")
cmd.extract("RDS3_Ba5gm6", "chain J and 5gm6")
cmd.extract("RSE1_Ba5gm6", "chain F and 5gm6")
cmd.extract("SNU17_Ba5gm6", "chain V and 5gm6")
cmd.extract("Ysf3_Ba5gm6", "chain K and 5gm6")
cmd.set_name("5gm6", "unknown_other_Ba5gm6")
cmd.group("Ba5gm6", "*_Ba5gm6")
cmd.do("order *, yes")
if '5lj3' in name.lower():
cmd.extract("PRP8_C5lj3", "chain A and 5lj3")
cmd.extract("BUD31_C5lj3", "chain L and 5lj3")
cmd.extract("CEF1_C5lj3", "chain O and 5lj3")
cmd.extract("CLF1_C5lj3", "chain S and 5lj3")
cmd.extract("CWC15_C5lj3", "chain P and 5lj3")
cmd.extract("CWC16/YJU2_C5lj3", "chain D and 5lj3")
cmd.extract("CWC2_hRBM22_C5lj3", "chain M and 5lj3")
cmd.extract("CWC21_C5lj3", "chain R and 5lj3")
cmd.extract("CWC22_C5lj3", "chain H and 5lj3")
cmd.extract("CWC25_C5lj3", "chain F and 5lj3")
cmd.extract("ISY1_C5lj3", "chain G and 5lj3")
cmd.extract("LEA1_C5lj3", "chain W and 5lj3")
cmd.extract("Msl1_C5lj3", "chain Y and 5lj3")
cmd.extract("PRP45_C5lj3", "chain K and 5lj3")
cmd.extract("PRP46_C5lj3", "chain J and 5lj3")
cmd.extract("SLT11/ECM2_C5lj3", "chain N and 5lj3")
cmd.extract("SNU114_C5lj3", "chain C and 5lj3")
cmd.extract("SYF1_C5lj3", "chain T and 5lj3")
cmd.extract("U2_C5lj3", "chain Z and 5lj3")
cmd.extract("U5_C5lj3", "chain U and 5lj3")
cmd.extract("U6_C5lj3", "chain V and 5lj3")
cmd.extract("Intron_C5lj3", "chain I and 5lj3")
cmd.extract("Exon_C5lj3", "chain E and 5lj3")
cmd.extract("SMB1_1_C5lj3", "chain b and 5lj3")
cmd.extract("SMB1_2_C5lj3", "chain k and 5lj3")
cmd.extract("SME1_1_C5lj3", "chain e and 5lj3")
cmd.extract("SME1_2_C5lj3", "chain p and 5lj3")
cmd.extract("SMX3_1_C5lj3", "chain f and 5lj3")
cmd.extract("SMX3_2_C5lj3", "chain q and 5lj3")
cmd.extract("SMX2_1_C5lj3", "chain g and 5lj3")
cmd.extract("SMX2_2_C5lj3", "chain r and 5lj3")
cmd.extract("SMD3_1_C5lj3", "chain d and 5lj3")
cmd.extract("SMD3_2_C5lj3", "chain n and 5lj3")
cmd.extract("SMD1_1_C5lj3", "chain h and 5lj3")
cmd.extract("SMD1_2_C5lj3", "chain l and 5lj3")
cmd.extract("SMD2_1_C5lj3", "chain j and 5lj3")
cmd.extract("SMD2_2_C5lj3", "chain m and 5lj3")
cmd.set_name("5lj3", "unknown_other_C5lj3")
cmd.group("C5lj3", "*_C5lj3")
cmd.do("order *, yes")
if '5mps' in name.lower():
cmd.extract("PRP8_Cs5mps", "chain A and 5mps")
cmd.extract("BUD31_Cs5mps", "chain L and 5mps")
cmd.extract("CEF1_Cs5mps", "chain O and 5mps")
cmd.extract("CLF1_Cs5mps", "chain S and 5mps")
cmd.extract("CWC15_Cs5mps", "chain P and 5mps")
cmd.extract("CWC2_hRBM22_Cs5mps", "chain M and 5mps")
cmd.extract("CWC21_Cs5mps", "chain R and 5mps")
cmd.extract("CWC22_Cs5mps", "chain H and 5mps")
cmd.extract("PRP45_Cs5mps", "chain K and 5mps")
cmd.extract("CDC40_Cs5mps", "chain o and 5mps")
cmd.extract("PRP46_Cs5mps", "chain J and 5mps")
cmd.extract("SLT11/ECM2_Cs5mps", "chain N and 5mps")
cmd.extract("SNU114_Cs5mps", "chain C and 5mps")
cmd.extract("SYF2_Cs5mps", "chain y and 5mps")
cmd.extract("SYF1_Cs5mps", "chain T and 5mps")
cmd.extract("U2_Cs5mps", "chain 2 and 5mps")
cmd.extract("U5_Cs5mps", "chain 5 and 5mps")
cmd.extract("U6_Cs5mps", "chain 6 and 5mps")
cmd.extract("5EXON_Cs5mps", "chain E and 5mps")
cmd.extract("Intron_Cs5mps", "chain I and 5mps")
cmd.extract("Exon_Cs5mps", "chain E and 5mps")
cmd.extract("SMB1_Cs5mps", "chain b and 5mps")
cmd.extract("SME1_Cs5mps", "chain e and 5mps")
cmd.extract("SMX3_Cs5mps", "chain f and 5mps")
cmd.extract("SMX2_Cs5mps", "chain g and 5mps")
cmd.extract("SMD3_Cs5mps", "chain d and 5mps")
cmd.extract("SMD1_Cs5mps", "chain h and 5mps")
cmd.extract("SMD2_Cs5mps", "chain j and 5mps")
cmd.extract("PRP18_Cs5mps", "chain a and 5mps")
cmd.extract("SLU7_Cs5mps", "chain c and 5mps")
cmd.set_name("5mps", "unknown_other_Cs5mps")
cmd.group("Cs5mps", "*_Cs5mps")
cmd.do("order *, yes")
if '6exn' in name.lower():
cmd.extract("PRP8_P6exn", "chain A and 6exn")
cmd.extract("BUD31_P6exn", "chain L and 6exn")
cmd.extract("CEF1_P6exn", "chain O and 6exn")
cmd.extract("CLF1_P6exn", "chain S and 6exn")
cmd.extract("CWC15_P6exn", "chain P and 6exn")
cmd.extract("CWC16/YJU2_P6exn", "chain D and 6exn")
cmd.extract("CWC2_hRBM22_P6exn", "chain M and 6exn")
cmd.extract("CWC21_P6exn", "chain R and 6exn")
cmd.extract("CWC22_P6exn", "chain H and 6exn")
cmd.extract("LEA1_P6exn", "chain W and 6exn")
cmd.extract("Msl1_P6exn", "chain Y and 6exn")
cmd.extract("PRP45_P6exn", "chain K and 6exn")
cmd.extract("CDC40_P6exn", "chain o and 6exn")
cmd.extract("PRP19_1_P6exn", "chain t and 6exn")
cmd.extract("PRP19_2_P6exn", "chain u and 6exn")
cmd.extract("PRP19_3_P6exn", "chain v and 6exn")
cmd.extract("PRP19_4_P6exn", "chain w and 6exn")
cmd.extract("PRP46_P6exn", "chain J and 6exn")
cmd.extract("SLT11/ECM2_P6exn", "chain N and 6exn")
cmd.extract("SNU114_P6exn", "chain C and 6exn")
cmd.extract("SYF1_P6exn", "chain T and 6exn")
cmd.extract("U2_P6exn", "chain 2 and 6exn")
cmd.extract("U5_P6exn", "chain 5 and 6exn")
cmd.extract("U6_P6exn", "chain 6 and 6exn")
cmd.extract("Intron_P6exn", "chain I and 6exn")
cmd.extract("Exon_P6exn", "chain E and 6exn")
cmd.extract("SMB1_1_P6exn", "chain b and 6exn")
cmd.extract("SMB1_2_P6exn", "chain k and 6exn")
cmd.extract("SME1_1_P6exn", "chain e and 6exn")
cmd.extract("SME1_2_P6exn", "chain p and 6exn")
cmd.extract("SMX3_1_P6exn", "chain f and 6exn")
cmd.extract("SMX3_2_P6exn", "chain q and 6exn")
cmd.extract("SMX2_1_P6exn", "chain g and 6exn")
cmd.extract("SMX2_2_P6exn", "chain r and 6exn")
cmd.extract("SMD3_1_P6exn", "chain d and 6exn")
cmd.extract("SMD3_2_P6exn", "chain n and 6exn")
cmd.extract("SMD1_1_P6exn", "chain h and 6exn")
cmd.extract("SMD1_2_P6exn", "chain l and 6exn")
cmd.extract("SMD2_1_P6exn", "chain j and 6exn")
cmd.extract("SMD2_2_P6exn", "chain m and 6exn")
cmd.extract("PRP22_P6exn", "chain V and 6exn")
cmd.extract("PRP18_P6exn", "chain a and 6exn")
cmd.extract("SLU7_P6exn", "chain c and 6exn")
cmd.extract("unassigned_P6exn", "chain X and 6exn")
cmd.set_name("6exn", "unknown_other_P6exn")
cmd.group("P6exn", "*_P6exn")
cmd.do("order *, yes")
if '5ylz' in name.lower():
cmd.extract("PRP8_P5ylz", "chain A and 5ylz")
cmd.extract("BUD31_P5ylz", "chain L and 5ylz")
cmd.extract("CEF1_P5ylz", "chain J and 5ylz")
cmd.extract("CLF1_P5ylz", "chain I and 5ylz")
cmd.extract("CWC15_P5ylz", "chain P and 5ylz")
cmd.extract("CWC2_hRBM22_P5ylz", "chain N and 5ylz")
cmd.extract("CWC21_P5ylz", "chain R and 5ylz")
cmd.extract("CWC22_P5ylz", "chain S and 5ylz")
cmd.extract("LEA1_P5ylz", "chain o and 5ylz")
cmd.extract("Msl1_P5ylz", "chain p and 5ylz")
cmd.extract("PRP45_P5ylz", "chain Q and 5ylz")
cmd.extract("CDC40_P5ylz", "chain T and 5ylz")
cmd.extract("PRP19_1_P5ylz", "chain q and 5ylz")
cmd.extract("PRP19_2_P5ylz", "chain r and 5ylz")
cmd.extract("PRP19_3_P5ylz", "chain s and 5ylz")
cmd.extract("PRP19_4_P5ylz", "chain t and 5ylz")
cmd.extract("PRP46_P5ylz", "chain O and 5ylz")
cmd.extract("SLT11/ECM2_P5ylz", "chain M and 5ylz")
cmd.extract("SNT309_P5ylz", "chain G and 5ylz")
cmd.extract("SNU114_P5ylz", "chain C and 5ylz")
cmd.extract("SYF2_P5ylz", "chain K and 5ylz")
cmd.extract("SYF1_P5ylz", "chain H and 5ylz")
cmd.extract("U2_P5ylz", "chain F and 5ylz")
cmd.extract("U5_P5ylz", "chain B and 5ylz")
cmd.extract("U6_P5ylz", "chain D and 5ylz")
cmd.extract("Intron_P5ylz", "chain E and 5ylz")
cmd.extract("SMB1_1_P5ylz", "chain a and 5ylz")
cmd.extract("SMB1_2_P5ylz", "chain h and 5ylz")
cmd.extract("SME1_1_P5ylz", "chain b and 5ylz")
cmd.extract("SME1_2_P5ylz", "chain i and 5ylz")
cmd.extract("SMX3_1_P5ylz", "chain c and 5ylz")
cmd.extract("SMX3_2_P5ylz", "chain j and 5ylz")
cmd.extract("SMX2_1_P5ylz", "chain d and 5ylz")
cmd.extract("SMX2_2_P5ylz", "chain k and 5ylz")
cmd.extract("SMD3_1_P5ylz", "chain e and 5ylz")
cmd.extract("SMD3_2_P5ylz", "chain l and 5ylz")
cmd.extract("SMD1_1_P5ylz", "chain f and 5ylz")
cmd.extract("SMD1_2_P5ylz", "chain m and 5ylz")
cmd.extract("SMD2_1_P5ylz", "chain g and 5ylz")
cmd.extract("SMD2_2_P5ylz", "chain n and 5ylz")
cmd.extract("PRP22_P5ylz", "chain W and 5ylz")
cmd.extract("PRP18_P5ylz", "chain U and 5ylz")
cmd.extract("SLU7_P5ylz", "chain V and 5ylz")
cmd.set_name("5ylz", "unknown_other_P5ylz")
cmd.group("P5ylz", "*_P5ylz")
cmd.do("order *, yes")
if '5y88' in name.lower():
cmd.extract("PRP8_I5y88", "chain A and 5y88")
cmd.extract("BUD31_I5y88", "chain L and 5y88")
cmd.extract("CLF1_I5y88", "chain I and 5y88")
cmd.extract("CWC15_I5y88", "chain P and 5y88")
cmd.extract("CWC16/YJU2_I5y88", "chain R and 5y88")
cmd.extract("CWC2_hRBM22_I5y88", "chain N and 5y88")
cmd.extract("CWC25_I5y88", "chain G and 5y88")
cmd.extract("Intron_2_I5y88", "chain E and 5y88")
cmd.extract("LEA1_I5y88", "chain o and 5y88")
cmd.extract("Msl1_I5y88", "chain p and 5y88")
cmd.extract("PRP45_I5y88", "chain Q and 5y88")
cmd.extract("CDC40_I5y88", "chain S and 5y88")
cmd.extract("PRP19_1_I5y88", "chain q and 5y88")
cmd.extract("PRP19_2_I5y88", "chain r and 5y88")
cmd.extract("PRP19_3_I5y88", "chain s and 5y88")
cmd.extract("PRP19_4_I5y88", "chain t and 5y88")
cmd.extract("PRP46_I5y88", "chain O and 5y88")
cmd.extract("SLT11/ECM2_I5y88", "chain M and 5y88")
cmd.extract("SNT309_I5y88", "chain G and 5y88")
cmd.extract("SNU114_I5y88", "chain C and 5y88")
cmd.extract("SYF2_I5y88", "chain K and 5y88")
cmd.extract("SYF1_I5y88", "chain H and 5y88")
cmd.extract("U2_I5y88", "chain F and 5y88")
cmd.extract("U5_I5y88", "chain B and 5y88")
cmd.extract("U6_I5y88", "chain D and 5y88")
cmd.extract("Intron_I5y88", "chain x and 5y88")
cmd.extract("RNA_I5y88", "chain x and 5y88")
cmd.extract("cwc23_I5y88", "chain T and 5y88")
cmd.extract("SPP382_I5y88", "chain U and 5y88")
cmd.extract("NTR2_I5y88", "chain V and 5y88")
cmd.extract("PRP43_I5y88", "chain W and 5y88")
cmd.extract("SMB1_1_I5y88", "chain a and 5y88")
cmd.extract("SMB1_2_I5y88", "chain h and 5y88")
cmd.extract("SME1_1_I5y88", "chain b and 5y88")
cmd.extract("SME1_2_I5y88", "chain i and 5y88")
cmd.extract("SMX3_1_I5y88", "chain c and 5y88")
cmd.extract("SMX3_2_I5y88", "chain j and 5y88")
cmd.extract("SMX2_1_I5y88", "chain d and 5y88")
cmd.extract("SMX2_2_I5y88", "chain k and 5y88")
cmd.extract("SMD3_1_I5y88", "chain e and 5y88")
cmd.extract("SMD3_2_I5y88", "chain l and 5y88")
cmd.extract("SMD1_1_I5y88", "chain f and 5y88")
cmd.extract("SMD1_2_I5y88", "chain m and 5y88")
cmd.extract("SMD2_1_I5y88", "chain g and 5y88")
cmd.extract("SMD2_2_I5y88", "chain n and 5y88")
cmd.set_name("5y88", "unknown_other_I5y88")
cmd.group("I5y88", "*_I5y88")
cmd.do("order *, yes")
if '3jb9' in name.lower():
cmd.extract("U2_3jb9", "chain P and 3jb9")
cmd.extract("U5_3jb9", "chain C and 3jb9")
cmd.extract("U6_3jb9", "chain N and 3jb9")
cmd.extract("Intron_1_3jb9", "chain O and 3jb9")
cmd.extract("Intron_2_3jb9", "chain Q and 3jb9")
cmd.extract("Spp42_yPrp8_3jb9", "chain A and 3jb9")
cmd.extract("CWF15_yCWC15_3jb9", "chain h and 3jb9")
cmd.set_name("3jb9", "unknown_other_3jb9")
cmd.group("3jb9", "*_3jb9")
cmd.do("order *, yes")
if '6icz' in name.lower():
cmd.extract("CWC15_hP_6icz", "chain P and 6icz")
cmd.extract("U2_hP_6icz", "chain H and 6icz")
cmd.extract("U5_hP_6icz", "chain B and 6icz")
cmd.extract("U6_hP_6icz", "chain F and 6icz")
cmd.extract("Intron_hP_6icz", "chain G and 6icz")
cmd.extract("cwc23_hP_6icz", "chain 6ICZ and 6icz")
cmd.set_name("6icz", "unknown_other_hP_6icz")
cmd.group("hP6icz", "*_hP_6icz")
cmd.do("order *, yes")
if '6ff7' in name.lower():
cmd.extract("CWC15_hBa_6ff7", "chain R and 6ff7")
cmd.extract("CWC2_hRBM22_hBa_6ff7", "chain P and 6ff7")
cmd.extract("U2_hBa_6ff7", "chain 2 and 6ff7")
cmd.extract("U5_hBa_6ff7", "chain 5 and 6ff7")
cmd.extract("U6_hBa_6ff7", "chain 6 and 6ff7")
cmd.extract("Intron_hBa_6ff7", "chain Z and 6ff7")
cmd.set_name("6ff7", "unknown_other_hBa_6ff7")
cmd.group("hBa6ff7", "*_hBa_6ff7")
cmd.do("order *, yes")
if '5yzg' in name.lower():
cmd.extract("CWC15_hC_5yzg", "chain P and 5yzg")
cmd.extract("CWC2_hRBM22_hC_5yzg", "chain O and 5yzg")
cmd.extract("CWC25_hC_5yzg", "chain X and 5yzg")
cmd.extract("PRP16_hDHX38_hC_5yzg", "chain Z and 5yzg")
cmd.extract("U2_hC_5yzg", "chain H and 5yzg")
cmd.extract("U5_hC_5yzg", "chain B and 5yzg")
cmd.extract("U6_hC_5yzg", "chain F and 5yzg")
cmd.extract("Intron_hC_5yzg", "chain G and 5yzg")
cmd.set_name("5yzg", "unknown_other_hC_5yzg")
cmd.group("hC5yzg", "*_hC_5yzg")
cmd.do("order *, yes")
if '5xjc' in name.lower():
cmd.extract("CWC15_hX_5xjc", "chain P and 5xjc")
cmd.extract("CWC25_hX_5xjc", "chain X and 5xjc")
cmd.extract("U2_hX_5xjc", "chain H and 5xjc")
cmd.extract("U5_hX_5xjc", "chain B and 5xjc")
cmd.extract("U6_hX_5xjc", "chain F and 5xjc")
cmd.extract("Intron_hX_5xjc", "chain G and 5xjc")
cmd.extract("PRKRIP1_hX_5xjc", "chain X and 5xjc")
cmd.set_name("5xjc", "unknown_other_hX_5xjc")
cmd.group("hX5xjc", "*_hX_5xjc")
cmd.do("order *, yes")
if '5mq0' in name.lower():
cmd.extract("CWC15_yCs_5mq0", "chain P and 5mq0")
cmd.extract("CWC2_hRBM22_yCs_5mq0", "chain M and 5mq0")
cmd.extract("U2_yCs_5mq0", "chain 2 and 5mq0")
cmd.extract("U5_yCs_5mq0", "chain 5 and 5mq0")
cmd.extract("U6_yCs_5mq0", "chain 6 and 5mq0")
cmd.extract("5EXON_yCs_5mq0", "chain E and 5mq0")
cmd.extract("Intron_yCs_5mq0", "chain I and 5mq0")
cmd.extract("exon-3_yCs_5mq0", "chain 3 and 5mq0")
cmd.set_name("5mq0", "unknown_other_yCs_5mq0")
cmd.group("yCs5mq0", "*_yCs_5mq0")
cmd.do("order *, yes")
if '5lj5' in name.lower():
cmd.extract("PRP8_yC_5lj5", "chain A and 5lj5")
cmd.extract("BRR2_yC_5lj5", "chain B and 5lj5")
cmd.extract("BUD31_yC_5lj5", "chain L and 5lj5")
cmd.extract("CEF1_yC_5lj5", "chain O and 5lj5")
cmd.extract("CLF1_yC_5lj5", "chain S and 5lj5")
cmd.extract("CWC15_yC_5lj5", "chain P and 5lj5")
cmd.extract("CWC16/YJU2_yC_5lj5", "chain D and 5lj5")
cmd.extract("CWC2_hRBM22_yC_5lj5", "chain M and 5lj5")
cmd.extract("CWC21_yC_5lj5", "chain R and 5lj5")
cmd.extract("CWC22_yC_5lj5", "chain H and 5lj5")
cmd.extract("CWC25_yC_5lj5", "chain F and 5lj5")
cmd.extract("ISY1_yC_5lj5", "chain G and 5lj5")
cmd.extract("Msl1_yC_5lj5", "chain Y and 5lj5")
cmd.extract("PRP45_yC_5lj5", "chain K and 5lj5")
cmd.extract("PRP16_hDHX38_yC_5lj5", "chain Q and 5lj5")
cmd.extract("PRP19_1_yC_5lj5", "chain t and 5lj5")
cmd.extract("PRP19_2_yC_5lj5", "chain u and 5lj5")
cmd.extract("PRP19_3_yC_5lj5", "chain v and 5lj5")
cmd.extract("PRP19_4_yC_5lj5", "chain w and 5lj5")
cmd.extract("PRP46_yC_5lj5", "chain J and 5lj5")
cmd.extract("SLT11/ECM2_yC_5lj5", "chain N and 5lj5")
cmd.extract("SNT309_yC_5lj5", "chain s and 5lj5")
cmd.extract("SNU114_yC_5lj5", "chain C and 5lj5")
cmd.extract("SYF1_yC_5lj5", "chain T and 5lj5")
cmd.extract("U2_yC_5lj5", "chain Z and 5lj5")
cmd.extract("U5_yC_5lj5", "chain U and 5lj5")
cmd.extract("U6_yC_5lj5", "chain V and 5lj5")
cmd.extract("5EXON_yC_5lj5", "chain E and 5lj5")
cmd.extract("Intron_yC_5lj5", "chain I and 5lj5")
cmd.extract("SMB1_1_yC_5lj5", "chain b and 5lj5")
cmd.extract("SMB1_2_yC_5lj5", "chain k and 5lj5")
cmd.extract("SME1_1_yC_5lj5", "chain e and 5lj5")
cmd.extract("SME1_2_yC_5lj5", "chain p and 5lj5")
cmd.extract("SMX3_1_yC_5lj5", "chain f and 5lj5")
cmd.extract("SMX3_2_yC_5lj5", "chain q and 5lj5")
cmd.extract("SMX2_1_yC_5lj5", "chain g and 5lj5")
cmd.extract("SMX2_2_yC_5lj5", "chain r and 5lj5")
cmd.extract("SMD3_1_yC_5lj5", "chain d and 5lj5")
cmd.extract("SMD3_2_yC_5lj5", "chain n and 5lj5")
cmd.extract("SMD1_1_yC_5lj5", "chain h and 5lj5")
cmd.extract("SMD1_2_yC_5lj5", "chain l and 5lj5")
cmd.extract("SMD2_1_yC_5lj5", "chain j and 5lj5")
cmd.extract("SMD2_2_yC_5lj5", "chain m and 5lj5")
cmd.extract("unassigned_yC_5lj5", "chain x and 5lj5")
cmd.set_name("5lj5", "unknown_other_yC_5lj5")
cmd.group("yC5lj5", "*_yC_5lj5")
cmd.do("order *, yes")
if '6g90' in name.lower():
cmd.extract("LEA1_yPre_6g90", "chain W and 6g90")
cmd.extract("Msl1_yPre_6g90", "chain Y and 6g90")
cmd.extract("Ysf3_yPre_6g90", "chain Z and 6g90")
cmd.extract("SMB1_1_yPre_6g90", "chain b and 6g90")
cmd.extract("SMB1_2_yPre_6g90", "chain s and 6g90")
cmd.extract("SME1_1_yPre_6g90", "chain e and 6g90")
cmd.extract("SME1_2_yPre_6g90", "chain w and 6g90")
cmd.extract("SMX3_1_yPre_6g90", "chain f and 6g90")
cmd.extract("SMX3_2_yPre_6g90", "chain x and 6g90")
cmd.extract("SMX2_1_yPre_6g90", "chain g and 6g90")
cmd.extract("SMX2_2_yPre_6g90", "chain y and 6g90")
cmd.extract("SMD3_1_yPre_6g90", "chain d and 6g90")
cmd.extract("SMD3_2_yPre_6g90", "chain v and 6g90")
cmd.extract("SMD1_1_yPre_6g90", "chain h and 6g90")
cmd.extract("SMD1_2_yPre_6g90", "chain t and 6g90")
cmd.extract("SMD2_1_yPre_6g90", "chain i and 6g90")
cmd.extract("SMD2_2_yPre_6g90", "chain u and 6g90")
cmd.extract("unassigned_yPre_6g90", "chain X and 6g90")
cmd.extract("MUD1_yPre_6g90", "chain A and 6g90")
cmd.extract("SNP1_yPre_6g90", "chain B and 6g90")
cmd.extract("YHC1_yPre_6g90", "chain C and 6g90")
cmd.extract("PRP39_yPre_6g90", "chain D and 6g90")
cmd.extract("PRP42_yPre_6g90", "chain E and 6g90")
cmd.extract("NAM8_yPre_6g90", "chain F and 6g90")
cmd.extract("SNU56_yPre_6g90", "chain G and 6g90")
cmd.extract("LUC7_yPre_6g90", "chain H and 6g90")
cmd.extract("SNU71_yPre_6g90", "chain J and 6g90")
cmd.extract("HSH155_yPre_6g90", "chain O and 6g90")
cmd.extract("RSE1_yPre_6g90", "chain P and 6g90")
cmd.extract("CUS1_yPre_6g90", "chain Q and 6g90")
cmd.extract("HSH49_yPre_6g90", "chain R and 6g90")
cmd.extract("RDS3_yPre_6g90", "chain S and 6g90")
cmd.extract("PRP9_yPre_6g90", "chain T and 6g90")
cmd.extract("PRP11_yPre_6g90", "chain U and 6g90")
cmd.extract("PRP21_yPre_6g90", "chain V and 6g90")
cmd.set_name("6g90", "unknown_other_yPre_6g90")
cmd.group("yPre6g90", "*_yPre_6g90")
cmd.do("order *, yes")
if '6n7r' in name.lower():
cmd.extract("Intron_yE_6n7r", "chain r and 6n7r")
cmd.extract("SMB1_yE_6n7r", "chain K and 6n7r")
cmd.extract("SME1_yE_6n7r", "chain O and 6n7r")
cmd.extract("SMX3_yE_6n7r", "chain P and 6n7r")
cmd.extract("SMX2_yE_6n7r", "chain Q and 6n7r")
cmd.extract("SMD3_yE_6n7r", "chain N and 6n7r")
cmd.extract("SMD1_yE_6n7r", "chain L and 6n7r")
cmd.extract("SMD2_yE_6n7r", "chain M and 6n7r")
cmd.extract("MUD1_yE_6n7r", "chain C and 6n7r")
cmd.extract("SNP1_yE_6n7r", "chain A and 6n7r")
cmd.extract("YHC1_yE_6n7r", "chain B and 6n7r")
cmd.extract("PRP39_yE_6n7r", "chain E and 6n7r")
cmd.extract("PRP42_yE_6n7r", "chain D and 6n7r")
cmd.extract("NAM8_yE_6n7r", "chain F and 6n7r")
cmd.extract("SNU56_yE_6n7r", "chain G and 6n7r")
cmd.extract("LUC7_yE_6n7r", "chain I and 6n7r")
cmd.extract("SNU71_yE_6n7r", "chain H and 6n7r")
cmd.extract("U1_yE_6n7r", "chain R and 6n7r")
cmd.set_name("6n7r", "unknown_other_yE_6n7r")
cmd.group("yE6n7r", "*_yE_6n7r")
cmd.do("order *, yes")
if '6n7p' in name.lower():
cmd.extract("Intron_yE_6n7p", "chain r and 6n7p")
cmd.extract("SMB1_yE_6n7p", "chain K and 6n7p")
cmd.extract("SME1_yE_6n7p", "chain O and 6n7p")
cmd.extract("SMX3_yE_6n7p", "chain P and 6n7p")
cmd.extract("SMX2_yE_6n7p", "chain Q and 6n7p")
cmd.extract("SMD3_yE_6n7p", "chain N and 6n7p")
cmd.extract("SMD1_yE_6n7p", "chain L and 6n7p")
cmd.extract("SMD2_yE_6n7p", "chain M and 6n7p")
cmd.extract("MUD1_yE_6n7p", "chain C and 6n7p")
cmd.extract("SNP1_yE_6n7p", "chain A and 6n7p")
cmd.extract("YHC1_yE_6n7p", "chain B and 6n7p")
cmd.extract("PRP39_yE_6n7p", "chain E and 6n7p")
cmd.extract("PRP42_yE_6n7p", "chain D and 6n7p")
cmd.extract("NAM8_yE_6n7p", "chain F and 6n7p")
cmd.extract("SNU56_yE_6n7p", "chain G and 6n7p")
cmd.extract("LUC7_yE_6n7p", "chain I and 6n7p")
cmd.extract("SNU71_yE_6n7p", "chain H and 6n7p")
cmd.extract("U1_yE_6n7p", "chain R and 6n7p")
cmd.extract("PRP40_yE_6n7p", "chain J and 6n7p")
cmd.extract("STO1_yE_6n7p", "chain X and 6n7p")
cmd.extract("CBC2_yE_6n7p", "chain Y and 6n7p")
cmd.set_name("6n7p", "unknown_other_yE_6n7p")
cmd.group("yE6n7p", "*_yE_6n7p")
cmd.do("order *, yes")
def spl_extract(): # sp
for name in cmd.get_names("all"):
print(" \ Extracting mode for %s" % name)
if 'hpCs-II_7W5A'.lower() in name.lower():
cmd.extract("PRP8_hpCs-II_7W5A", "chain A and hpCs-II_7W5A")
cmd.extract("BUD31_hpCs-II_7W5A", "chain N and hpCs-II_7W5A")
cmd.extract("CWC15_hpCs-II_7W5A", "chain P and hpCs-II_7W5A")
cmd.extract("CWC2_RBM22_hpCs-II_7W5A", "chain O and hpCs-II_7W5A")
cmd.extract("CWC22_hpCs-II_7W5A", "chain V and hpCs-II_7W5A")
cmd.extract("PRP46_hpCs-II_7W5A", "chain T and hpCs-II_7W5A")
cmd.extract("SYF2_hpCs-II_7W5A", "chain M and hpCs-II_7W5A")
cmd.extract("SYF1_hpCs-II_7W5A", "chain I and hpCs-II_7W5A")
cmd.extract("U2_hpCs-II_7W5A", "chain H and hpCs-II_7W5A")
cmd.extract("U5_hpCs-II_7W5A", "chain B and hpCs-II_7W5A")
cmd.extract("U6_hpCs-II_7W5A", "chain F and hpCs-II_7W5A")
cmd.extract("5EXON_hpCs-II_7W5A", "chain 4 and hpCs-II_7W5A")
cmd.extract("Intron_hpCs-II_7W5A", "chain G and hpCs-II_7W5A")
cmd.extract("SLU7_hpCs-II_7W5A", "chain 1 and hpCs-II_7W5A")
cmd.extract("PRKRIP1_hpCs-II_7W5A", "chain 2 and hpCs-II_7W5A")
cmd.extract("AQR_hpCs-II_7W5A", "chain Q and hpCs-II_7W5A")
cmd.extract("SNRP116_hpCs-II_7W5A", "chain C and hpCs-II_7W5A")
cmd.extract("PPIL1_hpCs-II_7W5A", "chain S and hpCs-II_7W5A")
cmd.extract("SNRNP200_hpCs-II_7W5A", "chain D and hpCs-II_7W5A")
cmd.extract("PPIE_hpCs-II_7W5A", "chain y and hpCs-II_7W5A")
cmd.extract("SNRNP40_hpCs-II_7W5A", "chain E and hpCs-II_7W5A")
cmd.extract("SNRPD3_hpCs-II_7W5A",
"(chain a or chain h ) and hpCs-II_7W5A")
cmd.extract("SNRPB_hpCs-II_7W5A",
"(chain b or chain i ) and hpCs-II_7W5A")
cmd.extract("EIF4A3_hpCs-II_7W5A", "chain u and hpCs-II_7W5A")
cmd.extract("SNRPD1_hpCs-II_7W5A",
"(chain c or chain j ) and hpCs-II_7W5A")
cmd.extract("MAGOH_hpCs-II_7W5A", "chain v and hpCs-II_7W5A")
cmd.extract("SNRPD2_hpCs-II_7W5A",
"(chain d or chain k ) and hpCs-II_7W5A")
cmd.extract("RBM8A_hpCs-II_7W5A", "chain w and hpCs-II_7W5A")
cmd.extract("SNRPF_hpCs-II_7W5A",
"(chain f or chain m ) and hpCs-II_7W5A")
cmd.extract("CASC3_hpCs-II_7W5A", "chain x and hpCs-II_7W5A")
cmd.extract("SNRPE_hpCs-II_7W5A",
"(chain e or chain l ) and hpCs-II_7W5A")
cmd.extract("SNRPG_hpCs-II_7W5A",
"(chain g or chain n ) and hpCs-II_7W5A")
cmd.extract("SNRPA1_hpCs-II_7W5A", "chain o and hpCs-II_7W5A")
cmd.extract("SNRPB2_hpCs-II_7W5A", "chain p and hpCs-II_7W5A")
cmd.extract("CRNKL1_hpCs-II_7W5A", "chain J and hpCs-II_7W5A")
cmd.extract("CDC5L_hpCs-II_7W5A", "chain L and hpCs-II_7W5A")
cmd.extract(
"PRPF19_hpCs-II_7W5A",
"(chain q or chain r or chain s or chain t ) and hpCs-II_7W5A")
cmd.extract("BCAS2_hpCs-II_7W5A", "chain K and hpCs-II_7W5A")
cmd.extract("SKIP_hpCs-II_7W5A", "chain R and hpCs-II_7W5A")
cmd.extract("SRRM2_hpCs-II_7W5A", "chain U and hpCs-II_7W5A")
cmd.extract("CDC40_hpCs-II_7W5A", "chain W and hpCs-II_7W5A")
cmd.extract("DHX8_hpCs-II_7W5A", "chain Y and hpCs-II_7W5A")
cmd.extract("FAM32A_hpCs-II_7W5A", "chain z and hpCs-II_7W5A")
cmd.extract("NKAP_hpCs-II_7W5A", "chain 3 and hpCs-II_7W5A")
cmd.extract("Cactin_hpCs-II_7W5A", "chain Z and hpCs-II_7W5A")
cmd.set_name("hpCs-II_7W5A", "unknown_other_hpCs-II_7W5A")
cmd.group("hpCs-II_7W5A", "*_hpCs-II_7W5A")
cmd.do("order *, yes")
if 'hpCs-I_7W59'.lower() in name.lower():
cmd.extract("PRP8_hpCs-I_7W59", "chain A and hpCs-I_7W59")
cmd.extract("BUD31_hpCs-I_7W59", "chain N and hpCs-I_7W59")
cmd.extract("CWC15_hpCs-I_7W59", "chain P and hpCs-I_7W59")
cmd.extract("CWC2_RBM22_hpCs-I_7W59", "chain O and hpCs-I_7W59")
cmd.extract("CWC22_hpCs-I_7W59", "chain V and hpCs-I_7W59")
cmd.extract("PRP46_hpCs-I_7W59", "chain T and hpCs-I_7W59")
cmd.extract("SYF2_hpCs-I_7W59", "chain M and hpCs-I_7W59")
cmd.extract("SYF1_hpCs-I_7W59", "chain I and hpCs-I_7W59")
cmd.extract("U2_hpCs-I_7W59", "chain H and hpCs-I_7W59")
cmd.extract("U5_hpCs-I_7W59", "chain B and hpCs-I_7W59")
cmd.extract("U6_hpCs-I_7W59", "chain F and hpCs-I_7W59")
cmd.extract("5EXON_hpCs-I_7W59", "chain 4 and hpCs-I_7W59")
cmd.extract("Intron_hpCs-I_7W59", "chain G and hpCs-I_7W59")
cmd.extract("SLU7_hpCs-I_7W59", "chain 1 and hpCs-I_7W59")
cmd.extract("PRKRIP1_hpCs-I_7W59", "chain 2 and hpCs-I_7W59")
cmd.extract("AQR_hpCs-I_7W59", "chain Q and hpCs-I_7W59")
cmd.extract("SNRP116_hpCs-I_7W59", "chain C and hpCs-I_7W59")
cmd.extract("PPIL1_hpCs-I_7W59", "chain S and hpCs-I_7W59")
cmd.extract("SNRNP200_hpCs-I_7W59", "chain D and hpCs-I_7W59")
cmd.extract("PPIE_hpCs-I_7W59", "chain y and hpCs-I_7W59")
cmd.extract("SNRNP40_hpCs-I_7W59", "chain E and hpCs-I_7W59")
cmd.extract("SNRPD3_hpCs-I_7W59",
"(chain a or chain h ) and hpCs-I_7W59")
cmd.extract("SNRPB_hpCs-I_7W59",
"(chain b or chain i ) and hpCs-I_7W59")
cmd.extract("EIF4A3_hpCs-I_7W59", "chain u and hpCs-I_7W59")
cmd.extract("SNRPD1_hpCs-I_7W59",
"(chain c or chain j ) and hpCs-I_7W59")
cmd.extract("MAGOH_hpCs-I_7W59", "chain v and hpCs-I_7W59")
cmd.extract("SNRPD2_hpCs-I_7W59",
"(chain d or chain k ) and hpCs-I_7W59")
cmd.extract("RBM8A_hpCs-I_7W59", "chain w and hpCs-I_7W59")
cmd.extract("SNRPF_hpCs-I_7W59",
"(chain f or chain m ) and hpCs-I_7W59")
cmd.extract("CASC3_hpCs-I_7W59", "chain x and hpCs-I_7W59")
cmd.extract("SNRPE_hpCs-I_7W59",
"(chain e or chain l ) and hpCs-I_7W59")
cmd.extract("SNRPG_hpCs-I_7W59",
"(chain g or chain n ) and hpCs-I_7W59")
cmd.extract("SNRPA1_hpCs-I_7W59", "chain o and hpCs-I_7W59")
cmd.extract("SNRPB2_hpCs-I_7W59", "chain p and hpCs-I_7W59")
cmd.extract("CRNKL1_hpCs-I_7W59", "chain J and hpCs-I_7W59")
cmd.extract("CDC5L_hpCs-I_7W59", "chain L and hpCs-I_7W59")
cmd.extract(
"PRPF19_hpCs-I_7W59",
"(chain q or chain r or chain s or chain t ) and hpCs-I_7W59")
cmd.extract("BCAS2_hpCs-I_7W59", "chain K and hpCs-I_7W59")
cmd.extract("SKIP_hpCs-I_7W59", "chain R and hpCs-I_7W59")
cmd.extract("SRRM2_hpCs-I_7W59", "chain U and hpCs-I_7W59")
cmd.extract("CDC40_hpCs-I_7W59", "chain W and hpCs-I_7W59")
cmd.extract("DHX8_hpCs-I_7W59", "chain Y and hpCs-I_7W59")
cmd.extract("FAM32A_hpCs-I_7W59", "chain z and hpCs-I_7W59")
cmd.extract("NKAP_hpCs-I_7W59", "chain 3 and hpCs-I_7W59")
cmd.extract("Cactin_hpCs-I_7W59", "chain Z and hpCs-I_7W59")
cmd.set_name("hpCs-I_7W59", "unknown_other_hpCs-I_7W59")
cmd.group("hpCs-I_7W59", "*_hpCs-I_7W59")
cmd.do("order *, yes")
if 'hpCs_7W5B'.lower() in name.lower():
cmd.extract("PRP8_hpCs_7W5B", "chain A and hpCs_7W5B")
cmd.extract("BUD31_hpCs_7W5B", "chain N and hpCs_7W5B")
cmd.extract("CWC15_hpCs_7W5B", "chain P and hpCs_7W5B")
cmd.extract("CWC2_RBM22_hpCs_7W5B", "chain O and hpCs_7W5B")
cmd.extract("CWC22_hpCs_7W5B", "chain V and hpCs_7W5B")
cmd.extract("PRP46_hpCs_7W5B", "chain T and hpCs_7W5B")
cmd.extract("SYF2_hpCs_7W5B", "chain M and hpCs_7W5B")
cmd.extract("SYF1_hpCs_7W5B", "chain I and hpCs_7W5B")
cmd.extract("U2_hpCs_7W5B", "chain H and hpCs_7W5B")
cmd.extract("U5_hpCs_7W5B", "chain B and hpCs_7W5B")
cmd.extract("U6_hpCs_7W5B", "chain F and hpCs_7W5B")
cmd.extract("5EXON_hpCs_7W5B", "chain 4 and hpCs_7W5B")
cmd.extract("Intron_hpCs_7W5B", "chain G and hpCs_7W5B")
cmd.extract("SLU7_hpCs_7W5B", "chain 1 and hpCs_7W5B")
cmd.extract("PRKRIP1_hpCs_7W5B", "chain 2 and hpCs_7W5B")
cmd.extract("AQR_hpCs_7W5B", "chain Q and hpCs_7W5B")
cmd.extract("SNRP116_hpCs_7W5B", "chain C and hpCs_7W5B")
cmd.extract("PPIL1_hpCs_7W5B", "chain S and hpCs_7W5B")
cmd.extract("SNRNP200_hpCs_7W5B", "chain D and hpCs_7W5B")
cmd.extract("PPIE_hpCs_7W5B", "chain y and hpCs_7W5B")
cmd.extract("SNRNP40_hpCs_7W5B", "chain E and hpCs_7W5B")
cmd.extract("SNRPD3_hpCs_7W5B",
"(chain a or chain h ) and hpCs_7W5B")
cmd.extract("SNRPB_hpCs_7W5B",
"(chain b or chain i ) and hpCs_7W5B")
cmd.extract("EIF4A3_hpCs_7W5B", "chain u and hpCs_7W5B")
cmd.extract("SNRPD1_hpCs_7W5B",
"(chain c or chain j ) and hpCs_7W5B")
cmd.extract("MAGOH_hpCs_7W5B", "chain v and hpCs_7W5B")
cmd.extract("SNRPD2_hpCs_7W5B",
"(chain d or chain k ) and hpCs_7W5B")
cmd.extract("RBM8A_hpCs_7W5B", "chain w and hpCs_7W5B")
cmd.extract("SNRPF_hpCs_7W5B",
"(chain f or chain m ) and hpCs_7W5B")
cmd.extract("CASC3_hpCs_7W5B", "chain x and hpCs_7W5B")
cmd.extract("SNRPE_hpCs_7W5B",
"(chain e or chain l ) and hpCs_7W5B")
cmd.extract("SNRPG_hpCs_7W5B",
"(chain g or chain n ) and hpCs_7W5B")
cmd.extract("SNRPA1_hpCs_7W5B", "chain o and hpCs_7W5B")
cmd.extract("SNRPB2_hpCs_7W5B", "chain p and hpCs_7W5B")
cmd.extract("CRNKL1_hpCs_7W5B", "chain J and hpCs_7W5B")
cmd.extract("CDC5L_hpCs_7W5B", "chain L and hpCs_7W5B")
cmd.extract(
"PRPF19_hpCs_7W5B",
"(chain q or chain r or chain s or chain t ) and hpCs_7W5B")
cmd.extract("BCAS2_hpCs_7W5B", "chain K and hpCs_7W5B")
cmd.extract("SKIP_hpCs_7W5B", "chain R and hpCs_7W5B")
cmd.extract("SRRM2_hpCs_7W5B", "chain U and hpCs_7W5B")
cmd.extract("CDC40_hpCs_7W5B", "chain W and hpCs_7W5B")
cmd.extract("DHX8_hpCs_7W5B", "chain Y and hpCs_7W5B")
cmd.extract("FAM32A_hpCs_7W5B", "chain z and hpCs_7W5B")
cmd.extract("NKAP_hpCs_7W5B", "chain 3 and hpCs_7W5B")
cmd.extract("Cactin_hpCs_7W5B", "chain Z and hpCs_7W5B")
cmd.set_name("hpCs_7W5B", "unknown_other_hpCs_7W5B")
cmd.group("hpCs_7W5B", "*_hpCs_7W5B")
cmd.do("order *, yes")
