gro_lib package¶
Submodules¶
gro_lib.gro module¶
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class
gro_lib.gro.
Gro
(system_name=None, num_of_atoms=None, residue_id=None, residue_name=None, atom_name=None, atom_id=None, x=None, y=None, z=None, v_x=None, v_y=None, v_z=None, box=None)[source]¶ Bases:
object
the central class in gropy
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copy_atom_entry
(another_gro_object, i_atom)[source]¶ copy the i-th atom entry from another gro object and append to the end of current gro object
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copy_atoms
(another_gro_object, atom_name_list)[source]¶ copy atoms with the provided atom names from another gro object and append to the end of current gro object
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copy_residue_entry
(another_gro_object, residue_id, residue_name)[source]¶ copy atoms of the specified residue from another gro object and append to the end of current gro object
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copy_residues
(another_gro_object, residue_name_list)[source]¶ copy atoms with the provided residue names from another gro object and append to the end of current gro object
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rename_atoms
(old_atom_names, new_atom_names)[source]¶ rename atoms from the old_atom_names to the new_atom_names
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rename_residues
(old_residue_names, new_residue_names)[source]¶ rename residues with an old_residue_name to a new_residue_name
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renumber_atoms
(renumber_residues=True, renumber_residues_per_chain=True)[source]¶ renumber residue_id and atom_id starting from 1; the original composition of each resdiue is maintained
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replace_atom_entry
(i_atom, another_gro_object, j_atom)[source]¶ replace the i-th atom of the current gro object with the j-th atom of another gro object
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sort_residues
(residue_name_list)[source]¶ sort residues in the provided order, attaching other unspecified residues to the end
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