Prepares analyzes of model geometry. Checks whether all angles and bonds length values are in proper range. Writes the result of the analyze to string. arguments: model_str - string representation of Model object model_chain_name - model chain name; default value = None file_name - ;default value = None returned value: str(analyze_geometry(model,file_name)) - result of analysis in string format

Applies all operations on single bases that are in an alignment: Copying identical residues, exchanging mismatches, adding modifications, and removing modifications. arguments: template_str - string representation of Template object aln_str - string representation of Alignment object temp_chain_name - template chain name model_chain_name- model chain name returned value: model_str - string representation of Model object example >>> model_str = soap_apply_alignment(t,a,'A') >>> print model_str

Finds and inserts the best loop candidate for each gap region in the alignment. To receive more information look on moderna.py arguments: template_str - string representation of Template object aln_str - string representation of Alignment object temp_chain_name - template chain name model_chain_name- model chain name returned value: model_str - string representation of Model object example: >>> model_str = soap_apply_all_loops(a,t,m,'A') >>> print model_str

arguments: aln_str - string representation of Alignment object template_str - string representation of Template object model_str - string representation of Model object temp_chain_name - template chain name model_chain_name - model chain name; default value = None returned value: model_str - string representation of Model object example: >>> soap_apply_missing_ends(a,t,m,'A') >>> model_str = soap_apply_missing_ends(a,t,m,'A','B')

Creates a RNA structure model. Produces a string representation of RNAModel object that can be used in other soap functions. If no arguments are given, an empty RNAModel is created. If both a Template and an Alignment are given as arguments, the complete model is built automatically. The chain id that the model should have can be specified optionally. Examples:: m = soap_create_model() m = soap_create_model(model_chain_name='K' m = soap_create_model(t,a) m = soap_create_model(t,a,model_chain_name='K') Arguments: * template_str : string that represents Template object in pdb format (optional) * aln_str : string that represents Alignment object in fasta format (optional) * temp_chain_name : string that represents Alignment object in fasta format (optional) * chain id of the model to be built

Detects interatomic clashes (overlapping atom radii) between atoms from two distinct residues. As input, a model or a list of residues is taken. arguments: model_str - string representation of Model object returned value: str(List_Of_Clashes) - list of founded clashes in string format

Checks, if the sequence of a model structure is equal to the second sequence in the alignment. If not, it throws an exception. arguments: aln_str - string representation of Alignment object template_str - string representation of Template object model_str - string representation of Model object temp_chain_name - template chain name model_chain_name - model chain name; default value = None returned value: model_str - string representation of Model object example: >>> soap_match_alignment_with_model(a,t,m,'A') >>>