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substitute_atom

esta.general.substitute_atom

substitute_atom_by_atoms(atomid, atom_id_subs=1, xyzfile=None, xyz_subs_file=None)

Notes

substitute an atom (specified by the atomid) in xyzfile with ligand present in xyz_subs_file. atom_id_subs is the atom (in the ligand) approaching to atom indexed by the atomid (in main xyz str). generally atom_id_subs is 1

Parameters:

  • atomid –

    atom number which is to be substituted in the xyz file

  • atom_id_subs –

    atom with atom number (in the ligand) approaching to atom (specified by the atomid) in xyz; default is 1 IN other words, which atom in the ligand is to be placed at the atom (specified by the atomid)

  • xyzfile –

    name of input xyz file

  • xyz_subs_file –

    name of the xyz file with substituent/ligand in it

Returns:

  • a new xyz file with ligand or substituent is created –

substitute_atom_by_atoms_in_path(atomid, atom_id_subs=1, xyzfile_list=None, xyz_subs_file=None)

substitute an atom in a list of files with ligand present in xyz_subs_file atom_id_subs is the atom if for atom approaching to atomid in main xyz str generally atom_id_subs is 1

Parameters:

  • atomid –

    atom number which is to be substituted in the xyz file

  • atom_id_subs –

    atom with atom number (in the ligand) approaching to atom (specified by the atomid) in xyz; default is 1 IN other words, which atom in the ligand is to be placed at the atom (specified by the atomid)

  • xyzfile_list –

    list of many xyz file (this constitute the path or trajectory)

  • xyz_subs_file –

    name of the xyz file with substituent/ligand in it

Returns:

  • a new xyz file with ligand or substituent is created –

substitute_atom_by_atoms_in_path_(atomid, atom_id_subs=1, xyzfile_path=None, xyz_subs_file=None)

Note

similar to method substitute_atom_by_atoms_in_path, but instead of xyzfile_list; a new variable xyzfile_path for just one xyz path file is used; this make things easy

Parameters:

  • atomid –

    atom number which is to be substituted in the xyz file

  • atom_id_subs –

    atom with atom number (in the ligand) approaching to atom (specified by the atomid) in xyz; default is 1 IN other words, which atom in the ligand is to be placed at the atom (specified by the atomid)

  • xyzfile_path –

    path file in xyz format

  • xyz_subs_file –

    name of the xyz file with substituent/ligand in it

Returns:

  • a new xyz file with ligand or substituent is created –