Exemple #1
0
def builder(residues, bonds, mol_name):
    """Using the list generated by read_input connects monosacharides in 
    a single oligosaccharide"""
    cmd.set('suspend_updates', 'on')
    cmd.feedback('disable', 'executive', 'actions')
    every_object = cmd.get_object_list('all')
    if mol_name in every_object:
        cmd.delete(mol_name)
        every_object.remove(mol_name)
    if every_object:
        sel = 'not (' + ' or '.join(every_object) + ') and'
    else:
        sel = ''
    for i in range(0, len(residues)):
        res_name = residues[i]
        cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
        cmd.set_name(res_name,
                     i)  #rename object (necessary to avoid repeating names)
        cmd.alter(i, 'resi = %s' % i)  #name residues for further referencing
        cmd.sort(i)
    for i in range(0, len(bonds)):
        resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][
            4], bonds[i][5]
        if atom_i > atom_j:
            cmd.remove('%s (resi %s and name O%s+H%so)' %
                       (sel, resi_j, atom_j, atom_j))
            cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
            cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i),
                     '%s (resi %s and name C%s)' % (sel, resi_j, atom_j),
                     mode=2)
        else:
            cmd.remove('%s (resi %s and name O%s+H%so)' %
                       (sel, resi_i, atom_i, atom_i))
            cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
            cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i),
                     '%s (resi %s and name O%s)' % (sel, resi_j, atom_j),
                     mode=2)
        cmd.delete('%s' % i)
    cmd.copy(mol_name, '%s' % resi_j)
    cmd.delete('%s' % resi_j)
    for i in range(0, len(bonds)):
        set_phi(mol_name, bonds[i], -60)
        set_psi(mol_name, bonds[i], 120)
    cmd.delete('pk1')
    cmd.delete('pk2')
    cmd.delete('pkbond')
    cmd.delete('pkmol')
    if babel:
        fast_min(mol_name, 5000)
        minimize(mol_name)
    else:
        fast_min(mol_name, 5000)
    cmd.feedback('enable', 'executive', 'actions')
    cmd.set('suspend_updates', 'off')
    def apply(self):
        '''
        Permanently applies the mutation upon the selected residue
        Overrides method from Wizard class
        '''
        cmd = self.cmd
        if self._status == Status.NO_SELECTION:
            return

        #Remove all atoms that are not in the sugar/phosphate group
        #Needed for non-canonical bases
        cmd.select("_tmp_sele_invert", "(none)")
        for a in self._sugar_phos_atoms:
            cmd.select("_tmp_sele_invert",
                       "_tmp_sele_invert | (%s & name %s)" % (SRC_SELE, a))

        cmd.select("_tmp_sele_invert",
                   "%s and not _tmp_sele_invert" % SRC_SELE)

        cmd.remove("_tmp_sele_invert")

        try:
            new_name = cmd.get_object_list(SRC_SELE)[0]
        except IndexError:
            print(" Mutagenesis: object not found.")
            return

        frag_name_three = self._mode_labels[self.mode]
        frag_name_one = self._base3_to_1[frag_name_three.lower()]

        # FUSE
        cmd.fuse(
            "%s & name %s" % (FRAG_NAME, self._frag_N_atom_name),
            "/%s/%s/%s/%s & name %s" %
            (new_name, self._stored.identifiers[0],
             self._stored.identifiers[1], self._stored.identifiers[2],
             self._src_Cp_atom_name), 1)

        #Check to see if DNA
        dnaPrefix = ''
        if cmd.count_atoms("%s & name O2'" % SRC_SELE) == 0:
            dnaPrefix = 'D'

        cmd.alter(
            "/%s/%s/%s/%s" %
            (new_name, self._stored.identifiers[0],
             self._stored.identifiers[1], self._stored.identifiers[2]),
            "(resn) = '%s%s'" % (dnaPrefix, frag_name_one.upper()),
            space=self._space)

        cmd.unpick()
        self.clear()
    def apply(self):
        '''
        Permanently applies the mutation upon the selected residue
        Overrides method from Wizard class
        '''
        cmd = self.cmd
        if self._status == Status.NO_SELECTION:
            return

        #Remove all atoms that are not in the sugar/phosphate group
        #Needed for non-canonical bases
        cmd.select("_tmp_sele_invert", "(none)")
        for a in self._sugar_phos_atoms:
            cmd.select("_tmp_sele_invert",
                       "_tmp_sele_invert | (%s & name %s)" % (SRC_SELE, a))

        cmd.select("_tmp_sele_invert",
                   "%s and not _tmp_sele_invert" % SRC_SELE)

        cmd.remove("_tmp_sele_invert")

        try:
            new_name = cmd.get_object_list(SRC_SELE)[0]
        except IndexError:
            print(" Mutagenesis: object not found.")
            return

        frag_name_three = self._mode_labels[self.mode]
        frag_name_one = self._base3_to_1[frag_name_three.lower()]

        # FUSE
        cmd.fuse(
            "%s & name %s" % (FRAG_NAME, self._frag_N_atom_name),
            "/%s/%s/%s/%s & name %s" %
            (new_name, self._stored.identifiers[0],
             self._stored.identifiers[1], self._stored.identifiers[2],
             self._src_Cp_atom_name), 1)

        #Check to see if DNA
        dnaPrefix = ''
        if cmd.count_atoms("%s & name O2'" % SRC_SELE) == 0:
            dnaPrefix = 'D'

        cmd.alter(
            "/%s/%s/%s/%s" %
            (new_name, self._stored.identifiers[0],
             self._stored.identifiers[1], self._stored.identifiers[2]),
            "(resn) = '%s%s'" % (dnaPrefix, frag_name_one.upper()),
            space=self._space)

        cmd.unpick()
        self.clear()
Exemple #4
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def builder(residues, bonds, mol_name):
    """Using the list generated by read_input connects monosacharides in 
    a single oligosaccharide"""
    cmd.set('suspend_updates', 'on')
    cmd.feedback('disable', 'executive', 'actions')
    every_object = cmd.get_object_list('all')
    if mol_name in every_object:
        cmd.delete(mol_name)
        every_object.remove(mol_name)
    if every_object:
        sel = 'not (' + ' or '.join(every_object) + ') and'
    else:
        sel = ''
    for i in range(0, len(residues)):
        res_name = residues[i]
        cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
        cmd.set_name(res_name, i)  #rename object (necessary to avoid repeating names)
        cmd.alter(i, 'resi = %s' % i)  #name residues for further referencing
        cmd.sort(i)
    for i in range(0, len(bonds)):
        resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][4], bonds[i][5]
        if atom_i > atom_j:
            cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_j, atom_j, atom_j))
            cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
            cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i), '%s (resi %s and name C%s)' % (sel, resi_j, atom_j), mode=2)
        else:
            cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_i, atom_i, atom_i))
            cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
            cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i), '%s (resi %s and name O%s)' % (sel, resi_j, atom_j), mode=2)
        cmd.delete('%s' % i)
    cmd.copy(mol_name, '%s' % resi_j)
    cmd.delete('%s' % resi_j)          
    for i in range(0, len(bonds)):
        set_phi(mol_name, bonds[i], -60)
        set_psi(mol_name, bonds[i], 120) 
    cmd.delete('pk1')
    cmd.delete('pk2')
    cmd.delete('pkbond')
    cmd.delete('pkmol')
    if babel:
        fast_min(mol_name, 5000)
        minimize(mol_name)
    else:
        fast_min(mol_name, 5000)
    cmd.feedback('enable', 'executive', 'actions')
    cmd.set('suspend_updates', 'off')
Exemple #5
0
def attach_amino_acid(selection,amino_acid,phi,psi):
  if not selection in cmd.get_names("selections"):
    if amino_acid in cmd.get_names("objects"):
      print " Error: an object with than name already exists"
      raise QuietException
    cmd.fragment(amino_acid)
    if cmd.get_setting_legacy("auto_remove_hydrogens"):
      cmd.remove("(hydro and %s)"%amino_acid)
    if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
      cmd.edit("((%s) and name c)"%amino_acid)
  else:
    cmd.fragment(amino_acid,tmp_editor)
    if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
      cmd.select(tmp_ed_save,"(%s)"%selection)
      cmd.iterate("(%s)"%selection,"stored.resv=resv")
      stored.resi = str(stored.resv-1)
      cmd.alter(tmp_editor,"resi=stored.resi")
      cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
      if cmd.get_setting_legacy("auto_remove_hydrogens"):
        cmd.remove("(pkmol and hydro)")
      cmd.set_dihedral("(name ca and neighbor pk2)",
                            "(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
      cmd.set_geometry("pk2",3,3) # make nitrogen planer
      cmd.select(tpk1,"pk2")
      cmd.select(tpk2,"pk1")
      if amino_acid[0:3]!='pro':
        cmd.set_dihedral( # PHI
            "(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
            "(name ca and neighbor "+tpk1+")", # CA 
            tpk1, # N
            tpk2, # C
            phi)
      cmd.set_dihedral( # PSI (n-1)
          tpk1, # N
          tpk2, # C
          "(name ca and neighbor "+tpk2+")", # CA
          "(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
          psi)
      cmd.delete(tpk1)
      cmd.delete(tpk2)
      sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
                (tmp_ed_save,tmp_ed_save))
      if cmd.count_atoms(sele,quiet=1):
        cmd.edit(sele)
      cmd.delete(tmp_ed_save)
                
    elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
      cmd.select(tmp_ed_save,"(%s)"%selection)
      cmd.iterate("(%s)"%selection,"stored.resv=resv")
      stored.resi = str(stored.resv+1)
      cmd.alter(tmp_editor,"resi=stored.resi")
      cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
      if cmd.get_setting_legacy("auto_remove_hydrogens"):
        cmd.remove("(pkmol and hydro)")
      cmd.set_dihedral("(name ca and neighbor pk2)",
                            "(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
      cmd.set_geometry("pk1",3,3) # make nitrogen planar
      cmd.select(tpk1,"pk1")
      cmd.select(tpk2,"pk2")
      if amino_acid[0:3]!='pro':
        cmd.set_dihedral( # PHI
            tpk2, # C
            tpk1, # N
            "(name ca and neighbor "+tpk1+")", # CA 
            "(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
            phi)
      cmd.set_dihedral( # PSI (n-1)
          "(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
          "(name ca and neighbor "+tpk2+")", # CA
          tpk2, # C
          tpk1, # N
          psi)
      cmd.delete(tpk1)
      cmd.delete(tpk2)
      sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
                (tmp_ed_save,tmp_ed_save))
      if cmd.count_atoms(sele,quiet=1):
        cmd.edit(sele)
      cmd.delete(tmp_ed_save)
    elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
      print " Error: please pick a nitrogen or carbonyl carbon to grow from."
      cmd.delete(tmp_editor)
      raise QuietException
  
  cmd.delete(tmp_editor)
def add_missing_atoms(selection='all', cycles=200, quiet=1):
    '''
DESCRIPTION

    Mutate those residues to themselves which have missing atoms

SEE ALSO

    stub2ala
    '''
    from collections import defaultdict
    from chempy import fragments

    cycles, quiet = int(cycles), int(quiet)

    reference = {
        'ALA': set(['CB']),
        'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
        'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
        'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
        'CYS': set(['CB', 'SG']),
        'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
        'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
        'GLY': set([]),
        'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
        'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
        'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
        'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
        'MET': set(['CB', 'CG', 'CE', 'SD']),
        'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
        'PRO': set(['CB', 'CG', 'CD']),
        'SER': set(['OG', 'CB']),
        'THR': set(['CB', 'OG1', 'CG2']),
        'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
        'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
        'VAL': set(['CB', 'CG1', 'CG2']),
    }

    namedsele = cmd.get_unused_name('_')
    cmd.select(namedsele, selection, 0)

    namelists = defaultdict(list)
    cmd.iterate('(%s) and polymer' % namedsele,
            'namelists[model,segi,chain,resn,resi,resv].append(name)',
            space=locals())

    sele_dict = defaultdict(list)
    tmp_name = cmd.get_unused_name('_')

    for key, namelist in namelists.items():
        resn = key[3]
        if resn not in reference:
            if not quiet:
                print(' Unknown residue: + ' + resn)
            continue
        if not reference[resn].issubset(namelist):
            try:
                frag = fragments.get(resn.lower())
                for a in frag.atom:
                    a.segi = key[1]
                    a.chain = key[2]
                    a.resi = key[4]
                    a.resi_number = key[5]
                cmd.load_model(frag, tmp_name, 1, zoom=0)

                skey = '/%s/%s/%s/%s`%s' % key[:5]
                cmd.remove(skey + ' and not name N+C+O+OXT+CA')
                cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
                cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
                cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
                if resn == 'PRO':
                    cmd.bond(skey + '/N', skey + '/CD')
                cmd.unpick()
                cmd.delete(tmp_name)

                sele_dict[key[0]].append(skey)

                if not quiet:
                    print(' Mutated ' + skey)
            except:
                print(' Mutating ' + skey + ' failed')

    for model in sele_dict:
        cmd.sort(model)
        sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)

    cmd.delete(namedsele)
Exemple #7
0
def add_missing_atoms(selection='all', cycles=200, quiet=1):
    '''
DESCRIPTION

    Mutate those residues to themselves which have missing atoms

SEE ALSO

    stub2ala
    '''
    from collections import defaultdict
    from chempy import fragments

    cycles, quiet = int(cycles), int(quiet)

    reference = {
        'ALA': set(['CB']),
        'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
        'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
        'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
        'CYS': set(['CB', 'SG']),
        'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
        'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
        'GLY': set([]),
        'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
        'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
        'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
        'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
        'MET': set(['CB', 'CG', 'CE', 'SD']),
        'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
        'PRO': set(['CB', 'CG', 'CD']),
        'SER': set(['OG', 'CB']),
        'THR': set(['CB', 'OG1', 'CG2']),
        'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
        'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
        'VAL': set(['CB', 'CG1', 'CG2']),
    }

    namedsele = cmd.get_unused_name('_')
    cmd.select(namedsele, selection, 0)

    namelists = defaultdict(list)
    cmd.iterate('(%s) and polymer' % namedsele,
            'namelists[model,segi,chain,resn,resi,resv].append(name)',
            space=locals())

    sele_dict = defaultdict(list)
    tmp_name = cmd.get_unused_name('_')

    for key, namelist in namelists.items():
        resn = key[3]
        if resn not in reference:
            if not quiet:
                print(' Unknown residue:', resn)
            continue
        if not reference[resn].issubset(namelist):
            try:
                frag = fragments.get(resn.lower())
                for a in frag.atom:
                    a.segi = key[1]
                    a.chain = key[2]
                    a.resi = key[4]
                    a.resi_number = key[5]
                cmd.load_model(frag, tmp_name, 1, zoom=0)

                skey = '/%s/%s/%s/%s`%s' % key[:5]
                cmd.remove(skey + ' and not name N+C+O+OXT+CA')
                cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
                cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
                cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
                if resn == 'PRO':
                    cmd.bond(skey + '/N', skey + '/CD')
                cmd.unpick()
                cmd.delete(tmp_name)

                sele_dict[key[0]].append(skey)

                if not quiet:
                    print(' Mutated ', skey)
            except:
                print(' Mutating', skey, 'failed')

    for model in sele_dict:
        cmd.sort(model)
        sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)

    cmd.delete(namedsele)
Exemple #8
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 def test_fuse(self):
     cmd.fragment('ala')
     cmd.fragment('gly')
     cmd.fuse("gly and elem N", "ala and elem O")
     self.assertEqual(17, cmd.count_atoms('ala'))
Exemple #9
0
def attach_amino_acid(selection,amino_acid,phi,psi):
  if not selection in cmd.get_names("selections"):
    if amino_acid in cmd.get_names("objects"):
      print " Error: an object with than name already exists"
      raise QuietException
    cmd.fragment(amino_acid)
    if cmd.get_setting_legacy("auto_remove_hydrogens"):
      cmd.remove("(hydro and %s)"%amino_acid)
    if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
      cmd.edit("((%s) and name c)"%amino_acid)
  else:
    cmd.fragment(amino_acid,tmp_editor)
    if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
      cmd.select(tmp_ed_save,"(%s)"%selection)
      cmd.iterate("(%s)"%selection,"stored.resv=resv")
      stored.resi = str(stored.resv-1)
      cmd.alter(tmp_editor,"resi=stored.resi")
      cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
      if cmd.get_setting_legacy("auto_remove_hydrogens"):
        cmd.remove("(pkmol and hydro)")
      cmd.set_dihedral("(name ca and neighbor pk2)",
                            "(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
      cmd.set_geometry("pk2",3,3) # make nitrogen planer
#      if ss:
      cmd.select(tpk1,"pk2")
      cmd.select(tpk2,"pk1")
      if amino_acid[0:3]!='pro':
        cmd.set_dihedral( # PHI
            "(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
            "(name ca and neighbor "+tpk1+")", # CA 
            tpk1, # N
            tpk2, # C
            phi)
      cmd.set_dihedral( # PSI (n-1)
          tpk1, # N
          tpk2, # C
          "(name ca and neighbor "+tpk2+")", # CA
          "(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
          psi)
      cmd.delete(tpk1)
      cmd.delete(tpk2)
      sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
                (tmp_ed_save,tmp_ed_save))
      if cmd.count_atoms(sele,quiet=1):
        cmd.edit(sele)
      cmd.delete(tmp_ed_save)

    elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
      cmd.select(tmp_ed_save,"(%s)"%selection)
      cmd.iterate("(%s)"%selection,"stored.resv=resv")
      stored.resi = str(stored.resv+1)
      cmd.alter(tmp_editor,"resi=stored.resi")
      cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
      if cmd.get_setting_legacy("auto_remove_hydrogens"):
        cmd.remove("(pkmol and hydro)")
      cmd.set_dihedral("(name ca and neighbor pk2)",
                            "(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
      cmd.set_geometry("pk1",3,3) # make nitrogen planer
#      if ss:
      cmd.select(tpk1,"pk1")
      cmd.select(tpk2,"pk2")
      if amino_acid[0:3]!='pro':
        cmd.set_dihedral( # PHI
            tpk2, # C
            tpk1, # N
            "(name ca and neighbor "+tpk1+")", # CA 
            "(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
            phi)
      cmd.set_dihedral( # PSI (n-1)
          "(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
          "(name ca and neighbor "+tpk2+")", # CA
          tpk2, # C
          tpk1, # N
          psi)
      cmd.delete(tpk1)
      cmd.delete(tpk2)
      sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
                (tmp_ed_save,tmp_ed_save))
      if cmd.count_atoms(sele,quiet=1):
        cmd.edit(sele)
      cmd.delete(tmp_ed_save)
    elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
      print " Error: please pick a nitrogen or carbonyl carbon to grow from."
      cmd.delete(tmp_editor)
      raise QuietException

  cmd.delete(tmp_editor)
Exemple #10
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        ligand_name = file.split('_')[0]
        loaded_ligs.append(ligand_name)
        cmd.load('ligs/' + file, ligand_name)

#select the ligand atomes of the original ligand to align with
target_atom1 = 'RA95_target and name C3'
target_atom2 = 'RA95_target and name C4'
target_atom3 = 'RA95_target and name C5'

#select the ligand atomes of the new ligand to align with and align the selected atoms of old and new ligand
for ligand in loaded_ligs:
    mobile_atom1 = ligand + ' and name CL1'
    mobile_atom2 = ligand + ' and name CL'
    mobile_atom3 = ligand + ' and name CL2'
    cmd.pair_fit(mobile_atom1, target_atom1, mobile_atom2, target_atom2,
                 mobile_atom3, target_atom3)

#remove old ligand
cmd.remove('RA95_target and resn PEN')

#build bond between Lys83 and the new ligand and generate pdb file
for ligand in loaded_ligs:
    cmd.copy('RA95_' + ligand, 'RA95_target')
    cmd.fuse(ligand + ' and name CL',
             'RA95_' + ligand + ' and resn LYX and name NZ', '3')
    cmd.bond('RA95_' + ligand + ' and resn LYX and name NZ',
             'RA95_' + ligand + ' and name CL')
    cmd.alter('RA95_' + ligand + ' and resn ' + ligand, 'segi="B"')
    cmd.sort('RA95_' + ligand)
    cmd.save('RA95_' + ligand + '.pdb', 'RA95_' + ligand, '0')
Exemple #11
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 def test_fuse(self):
     cmd.fragment('ala')
     cmd.fragment('gly')
     cmd.fuse("gly and elem N", "ala and elem O")
     self.assertEqual(17, cmd.count_atoms('ala'))