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object --+ | StructureBuilder
Builder class for the mmLib.Structure object hierarchy. StructureBuilder must be subclassed with a working parse_format() method to implement a working builder.
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Inherited from |
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Inherited from |
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x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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This methods needs to be reimplemented in a functional subclass. This function is called with the file object (or any other object passed in to build a Structure from) to begin the reading process. This is usually used to open the source file. |
Called after the read_start method. Does nothing currently, but may be used in the future. |
This method needs to be reimplemented in a functional subclass. The subclassed read_atoms method should call load_atom once for every atom in the structure, and should not call any other load_* methods. |
Called repeatedly by the implementation of read_atoms to load all the data for a single atom. The data is contained in the atm_map argument, and is not well documented at this point. Look at this function and you'll figure it out. |
Runs the name service on all atoms needing to be named. This is a complicated function which corrects most commonly found errors and omissions from PDB files. |
This method needs to be reimplemented in a functional subclass. The subclassed read_metadata method should call the various load_* methods to set non-atom coordinate data for the Structure. |
Call by the implementation of load_metadata to load bond information on the structure. The keys of the bond map are a 2-tuple of the bonded Atom instances, and the value is a dictionary containing information on the type of bond, which may also be a symmetry operator. [bond_map] keys: (atm1, atm2) values: bond_data_map(s) [bond_data_map] bond_type -> text description of bond type: covalent, salt bridge, hydrogen, cispeptide atm1_symop -> symmetry operation (if any) to be applied to atm1 atm2_symop -> same as above, for atom 2 The symmetry operations themselves are a 3x4 array of floating point values composed of the 3x3 rotation matrix and the 3x1 translation. |
The argument helix_list is a list of Python dictionaries with information to build build AlphaHelix objects into the Structure. The dictionary has attributes: helix_id: The ID of the helix chain_id: The chain_id where the helix is located frag_id1: The start fragment_id of the helix frag_id2: The end fragment_id of the helix helix_class: The PDB helix class number detaisl: Text commont about the helix |
The argument beta_sheet_list is a list of Python dictionaries with information to build build BetaSheet objects into the Structure. The dictionary has attributes: sheet_id: ID of the sheet num_strands: total number of strands in the beta sheet strand_list: list of dictionaries describing the strand with the following attributes: chain_id1/frag_id1: chain_id and fragment_id of inital residue in the strand chain_id2/frag_id2: chain_id and fragment_id of end residue in the strand sense: the sense of the strand with respect to the previous strand, either the string parallel or anti_parallel reg_chain_id, reg_frag_id, reg_atom: registration atom in current strand reg_prev_chain_id, reg_prev_frag_id, reg_prev_atom: registration atom in previous strand |
This method needs to be reimplemented in a functional subclass. The subclassed read_end method can be used for any clean up from the file loading process you need, or may be left unimplemented. |
Called for final cleanup after structure source reading is done. Currently, this method does nothing but may be used in future versions. |
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