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 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")