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object --+ | _NotSortable --+ | _StructureAtom
Access of mmct atoms properties pythonically.
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str or NoneType |
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Inherited from Inherited from |
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_doc =
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_index The atom index. |
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index The atom index. |
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structure Return the parent Structure object for this atom. |
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bond_total Number of bonds to the atom. |
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bond List of bonds to the atom (_StructureBond objects). |
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bonded_atoms Iterator for atoms bonded to this atom (_StructureAtom objects). |
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atomic_weight Return the atomic weight of the atom. |
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growname Maestro grow name. |
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pdbname PDB atom name. |
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pdbres PDB residue name. |
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pdbcode One-letter PDB residue code. |
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resnum PDB residue number. |
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inscode PDB residue insertion code. |
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atom_type MacroModel atom type. |
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atom_type_name MacroModel atom type name. |
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color Atom color. |
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chain Atom chain. |
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atom_name Name of the atom. |
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name Name of the atom. |
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entry_id Maestro entry ID |
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element Element character of the atom. |
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partial_charge Partial charge of the atom. |
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solvation_charge | |||
formal_charge Formal charge of the atom. |
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isotope Mass number charge of the atom. |
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secondary_structure | |||
temperature_factor | |||
vdw_radius | |||
is_halogen | |||
molecule_number | |||
number_by_molecule | |||
number_by_entry | |||
atomic_number Atomic number of the atom's element. |
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x X-coordinate of the atom. |
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y Y-coordinate of the atom. |
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z Z-coordinate of the atom. |
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xyz XYZ-coordinates of the atom. |
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alt_xyz Alternative XYZ-coordinates of the atom, if available, otherwise returns None. |
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chirality Chirality of the atom. |
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atom_style | |||
style | |||
visible | |||
label_format | |||
label_color | |||
label_user_text | |||
property Dictionary-like container of Atom-level properties. |
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Create an instance from the Structure object and the atom index. Note that the index used starts at 1 as per the underlying mmct lib.
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The atom index. Read only. |
hash(x)
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str(x)
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Add a bond between the current atom and atom2. @param bond_order Takes an integer bond order or a BondType |
Reassign the MacroModel atom type based on the bond orders and formal charge. This function should be called after either of these have been changed. |
Return the RGB color of this atom as a tuple (R,G.B). The color values have a range between 0 and 255. |
Set the RGB color of this atom as a tuple (R,G.B). Each color value should be an integer between 0 and 255. |
Return the entry id from the structure's property dictionary
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_indexThe atom index. Read only.
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indexThe atom index. Read only.
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structureReturn the parent Structure object for this atom.
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bond_totalNumber of bonds to the atom.
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bondList of bonds to the atom (_StructureBond objects).
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bonded_atomsIterator for atoms bonded to this atom (_StructureAtom objects).
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atomic_weightReturn the atomic weight of the atom. If implicit hydrogens are present, these are included with the weight of the atom they are attached to.
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grownameMaestro grow name.
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pdbnamePDB atom name.
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pdbresPDB residue name.
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pdbcodeOne-letter PDB residue code.
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resnumPDB residue number.
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inscodePDB residue insertion code.
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atom_typeMacroModel atom type. Note that changing the atom type does not automatically update the charge. See schrodinger.structure.Structure.retype.
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atom_type_nameMacroModel atom type name.
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colorAtom color.
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chainAtom chain.
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atom_nameName of the atom.
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nameName of the atom.
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entry_idMaestro entry ID
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elementElement character of the atom.
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partial_chargePartial charge of the atom.
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solvation_charge
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formal_chargeFormal charge of the atom.
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isotopeMass number charge of the atom.
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secondary_structure
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temperature_factor
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vdw_radius
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is_halogen
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molecule_number
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number_by_molecule
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number_by_entry
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atomic_numberAtomic number of the atom's element.
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alt_xyzAlternative XYZ-coordinates of the atom, if available, otherwise returns None.
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chiralityChirality of the atom. R, S, ANR, ANS, undef, or None.
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atom_style
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visible
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label_format
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label_color
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label_user_text
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propertyDictionary-like container of Atom-level properties. Keys are strings
of the form
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