combine_score_files (*args, **kwargs) |
Reads a number of score files and combines them by merging rows of the same tag |
create_sequence (residues) |
Creates an amino acid sequence from a list of Residue objects. |
detect_bonds (a_chain) |
Detects bonds between atoms of this chain |
filter_score_file (scorefile, filter, column_name) |
Filters given column in scorefile with a given filtr |
parse_mol_data (mol_as_txt) |
Reads a text in mol2 format and creates a Molecule object |
parse_pdb_atom (atom_line) |
Parses an ATOM line of a PDB file and creates a new atom. |
parse_pdb_data (pdb_as_text, **kwargs) |
Parses PDB data |
read_clustal (input_text[, max_fields]) |
Reads a ClustalW file with Multiple Sequence Alignment |
read_clustering_tree (fname_or_data[, …]) |
Read a clustering tree produced by BioShell package. |
read_fasta (input_text) |
Reads a FASTA file that contains nucleic / amino acid sequences |
read_msf (input_text) |
Reads a MSF file |
read_newick_dictionary (newick[, if_read_file]) |
Reads a tree in the Newick format :param newick: (string ) - a file name or the data itself :param if_read_file: (boolean ) - if true, it’s assumed the input is a file name and the data must be loaded from a file. |
secondary_structure_residues (pdb_as_text, …) |
Reads PDB header and extracts residues that belong to secondary structure elements (SSEs) |
secondary_structure_string (pdb_as_text, residues) |
Reads PDB header and creates a secondary structure in FASTA format |
tree_from_dictionary (dict_root[, node_class]) |
Transforms a tree from a dictionary representation into a “true” tree of DendrogramNode nodes :param node_dict: (string ) - dictionary of nodes, e.g. |
write_pdb_atom (atom[, res_name, chain_id]) |
Returns a string in PDB format that holds data for a given atom |