PyMol Python API Only Functions

This section provides a quick introduction on PyMol Python API only functions. They are not available in the PyMol command line interface.

As mentioned previously, all PyMol commands are covered by the Python API. And there are additional functions supported only in the API, not in the command line interface. Here is a list of those API only functions:

cmd.exp_path
cmd.extend
cmd.extendaa
cmd.find_pairs
cmd.get_atom_coords
cmd.get_cifstr
cmd.get_color_index
cmd.get_color_indices
cmd.get_color_tuple
cmd.get_coords
cmd.get_coordset
cmd.get_fastastr
cmd.get_frame
cmd.get_legal_name
cmd.get_model
cmd.get_names
cmd.get_names_of_type
cmd.get_object_list
cmd.get_object_matrix
cmd.get_object_state
cmd.get_object_ttt
cmd.get_pdbstr
cmd.get_phipsi
cmd.get_raw_alignment
cmd.get_scene_list
cmd.get_session
cmd.get_setting_boolean
cmd.get_setting_float
cmd.get_setting_int
cmd.get_setting_text
cmd.get_setting_tuple
cmd.get_state
cmd.get_str
cmd.get_unused_name
cmd.get_volume_field
cmd.get_volume_histogram
cmd.get_wizard
cmd.get_wizard_stack
cmd.load_brick
cmd.load_callback
cmd.load_cgo
cmd.load_coords
cmd.load_coordset
cmd.load_map
cmd.load_model
cmd.load_object
cmd.read_mmodstr
cmd.read_molstr
cmd.read_pdbstr
cmd.read_sdfstr
cmd.read_xplorstr
cmd.select_list
cmd.set_frame
cmd.set_object_color
cmd.set_object_ttt
cmd.set_session
cmd.set_state_order
cmd.set_wizard
cmd.set_wizard_stack
cmd.transform_object
cmd.transform_selection
cmd.translate_atom

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

PyMol Python Integration

 Run Python Statements from PyMol

 PyMol Python API

 Launch PyMol from Python Interpreter

PyMol Python API Only Functions

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB