Module Expr Str Import alias Import alias Import alias Import alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias FunctionDef arguments args NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num Call NameLoad NameLoad Assign NameStore ListLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Print Str NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore BinOpAdd BinOpAdd BinOpAdd Str SubscriptLoad NameLoad Index Num Str SubscriptLoad NameLoad Index Num Expr Call NameLoad BinOpAdd Str SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad Call AttributeLoad NameLoad attr Index NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr For NameStore Call NameLoad Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str NameLoad Expr Call NameLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr NameLoad Return TupleLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call NameLoad keyword Str keyword NameLoad Expr Call NameLoad Call NameLoad Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str decorator_list If CompareEq NameLoad Str body Assign TupleStore NameStore NameStore NameStore NameStore Call NameLoad AttributeLoad NameLoad attr For NameStore Call NameLoad Call NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Assign NameStore Call NameLoad NameLoad For NameStore Call NameLoad Num body Assign NameStore ListLoad For NameStore Call NameLoad BinOpMult NameLoad Num body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad TupleLoad NameLoad Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr ListLoad BinOpAdd NameLoad NameLoad Expr Call NameLoad Call AttributeLoad Call AttributeLoad NameLoad attr Str attr BinOpAdd NameLoad Str Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str NameLoad
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Created on 16/08/2012

@author: victor
 N/A sys N/A prody N/A random N/A numpy pyproct.tools.scriptTools create_directory pyRMSD.RMSDCalculator RMSDCalculator pyRMSD.condensedMatrix CondensedMatrix pyproct.tools.plotTools matrixToImage get_frame_numbers N/A N/A args N/A N/A N/A cluster_frames_str N/A N/A sys argv N/A 3 N/A len args N/A cluster_frames N/A N/A c cluster_frames_str N/A N/A N/A N/A cluster_frames append N/A int c N/A cluster_frames N/A N/A numpy array cluster_frames N/A Using frames  cluster_frames N/A cluster_frames N/A preprocess_pdb N/A N/A args N/A N/A N/A pdb_file N/A args N/A 1 N/A output N/A N/A N/A ./ N/A args N/A 2 / N/A args N/A 2 N/A N/A create_directory N/A ./ N/A args N/A 2 N/A cluster_frames N/A get_frame_numbers args N/A pdb N/A N/A prody parsePDB pdb_file N/A input_coordsets N/A N/A numpy array N/A N/A N/A pdb getCoordsets N/A cluster_frames N/A N/A N/A pdb delCoordset N/A range N/A N/A pdb numCoordsets N/A input_pdb N/A N/A prody parsePDB pdb_file N/A N/A N/A input_pdb delCoordset N/A range N/A N/A input_pdb numCoordsets N/A i N/A range N/A len cluster_frames N/A N/A N/A N/A input_pdb addCoordset N/A input_coordsets N/A i N/A N/A N/A prody writePDB N/A output _ini.pdb input_pdb N/A N/A print_matrix N/A N/A N/A N/A input_pdb select name CA getCoordsets output N/A N/A pdb input_coordsets cluster_frames output N/A print_matrix N/A N/A input_coordsets output N/A N/A N/A calculator N/A RMSDCalculator calculatorType QCP_OMP_CALCULATOR fittingCoordsets input_coordsets N/A N/A matrixToImage N/A CondensedMatrix N/A N/A calculator pairwiseRMSDMatrix N/A output .png N/A N/A N/A __name__ __main__ N/A N/A N/A pdb input_coordsets cluster_frames output N/A preprocess_pdb N/A sys argv N/A f N/A range N/A len cluster_frames N/A N/A base_coordinates N/A input_coordsets N/A f N/A numatoms N/A len base_coordinates N/A i N/A range 100 N/A N/A rand_list N/A N/A r N/A range N/A numatoms 3 N/A N/A N/A N/A rand_list append N/A N/A random uniform -1 1 N/A rand_displacements N/A N/A numpy resize N/A N/A numpy array rand_list N/A numatoms 3 N/A N/A N/A pdb addCoordset N/A N/A numpy array N/A N/A rand_displacements base_coordinates N/A N/A print_matrix N/A N/A N/A N/A pdb select name CA getCoordsets N/A output _big N/A N/A N/A prody writePDB N/A output .pdb pdb