Module Expr Str Import alias Import alias Import alias identifier Import alias Import alias Import alias ImportFrom alias alias ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad Str Str attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad Str Str attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Str Expr Call AttributeLoad NameLoad attr NameLoad ListLoad ListLoad ListLoad Str Str Str ListLoad Str Str Str ListLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword Str ListLoad ListLoad ListLoad Str Str Str ListLoad Str Str Str ListLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword Str ListLoad ListLoad ListLoad Str Str Str ListLoad Str Str Str ListLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword Str ListLoad ListLoad ListLoad ListLoad ListLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword Str ListLoad ListLoad ListLoad ListLoad ListLoad Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad Str Str attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListLoad Num Num Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad AttributeLoad NameLoad attr NameLoad NameLoad Str Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListLoad Num Num Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad AttributeLoad NameLoad attr NameLoad NameLoad Str Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListLoad Num Num Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad AttributeLoad NameLoad attr NameLoad NameLoad Str Str keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad NameLoad Num Str Str NameLoad Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad NameLoad Num Str Str NameLoad Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad NameLoad Num Str Str NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Str Assign NameStore Call AttributeLoad Str attr Str For NameStore Call NameLoad Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index NameLoad Slice Num SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad Assign NameStore ListLoad ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListLoad ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num Expr Call NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad NameLoad Num Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr decorator_list decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr
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Created on 16/03/2012

@author: victor
 N/A unittest N/A pyproct.tools.pdbTools N/A pyproct.tools.test.data test_data N/A os N/A cStringIO N/A numpy pyproct.tools.pdbTools repair_MODEL_ENDMDL_tags grab_existing_frame_from_trajectory Test N/A N/A unittest TestCase N/A test_def_get_number_of_frames N/A N/A self N/A N/A N/A N/A N/A N/A open test_pdb_for_counting_1.pdb w write N/A test_data pdb_1_file_content N/A num_models N/A N/A N/A N/A pyproct tools pdbTools get_number_of_frames test_pdb_for_counting_1.pdb N/A N/A N/A os system rm test_pdb_for_counting_1.pdb N/A N/A N/A self assertEqual num_models N/A test_data pdb_1_num_of_models N/A test_get_remarks_and_filter N/A N/A self N/A N/A N/A N/A N/A N/A open test_pdb_for_remarks.pdb w write N/A test_data pdb_2_file_content N/A all_remarks N/A N/A N/A N/A pyproct tools pdbTools get_remarks test_pdb_for_remarks.pdb N/A N/A N/A self assertSequenceEqual all_remarks N/A N/A N/A REMARK 0 this
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 N/A N/A N/A self assertSequenceEqual N/A N/A N/A N/A pyproct tools pdbTools filter_remarks all_remarks subset ALL N/A N/A N/A REMARK 0 this
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 REMARKS 0 a remark
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 N/A N/A N/A self assertSequenceEqual N/A N/A N/A N/A pyproct tools pdbTools filter_remarks all_remarks subset NOT STANDARD N/A N/A N/A REMARK 0 this
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 REMARKS 0 a remark
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 N/A N/A N/A N/A self assertSequenceEqual N/A N/A N/A N/A pyproct tools pdbTools filter_remarks all_remarks subset STANDARD N/A N/A N/A N/A N/A REMARK 400 REGULAR REMARK
 N/A N/A N/A self assertSequenceEqual N/A N/A N/A N/A pyproct tools pdbTools filter_remarks all_remarks subset NONE N/A N/A N/A N/A N/A N/A N/A N/A os system rm test_pdb_for_remarks.pdb N/A test_get_number_of_atoms N/A N/A self N/A N/A N/A N/A N/A N/A open test_pdb_for_counting_2.pdb w write N/A test_data pdb_1_sub2_file_content N/A num_models N/A N/A N/A N/A pyproct tools pdbTools get_number_of_atoms test_pdb_for_counting_2.pdb N/A N/A N/A os system rm test_pdb_for_counting_2.pdb N/A N/A N/A self assertEqual num_models N/A test_data pdb1_num_of_atoms N/A test_extract_frames_from_trajectory_sequentially N/A N/A self N/A N/A N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_1_sub2_file_content N/A output N/A N/A cStringIO StringIO N/A frames N/A 2 5 N/A N/A N/A N/A N/A pyproct tools pdbTools extract_frames_from_trajectory_sequentially input_file N/A test_data pdb_1_num_of_models output frames MODEL TER N/A N/A N/A self assertEqual N/A N/A output getvalue N/A test_data extracted_pdbs_1 N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_2_file_content N/A output N/A N/A cStringIO StringIO N/A frames N/A 1 3 N/A N/A N/A N/A N/A pyproct tools pdbTools extract_frames_from_trajectory_sequentially input_file N/A test_data pdb_2_num_of_models output frames MODEL ENDMDL N/A N/A N/A self assertEqual N/A N/A output getvalue N/A test_data extracted_pdbs_3 N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_2_file_content N/A output N/A N/A cStringIO StringIO N/A frames N/A 1 3 N/A N/A N/A N/A N/A pyproct tools pdbTools extract_frames_from_trajectory_sequentially input_file N/A test_data pdb_2_num_of_models output frames MODEL ENDMDL keep_header True N/A N/A N/A self assertEqual N/A N/A output getvalue N/A test_data extracted_pdbs_4 N/A test_write_a_tfile_model_into_other_tfile N/A N/A self N/A N/A N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_1_sub2_file_content N/A output_file N/A N/A cStringIO StringIO N/A N/A N/A N/A N/A pyproct tools pdbTools write_a_tfile_model_into_other_tfile input_file output_file 0 MODEL TER False N/A N/A N/A N/A N/A pyproct tools pdbTools write_a_tfile_model_into_other_tfile input_file output_file 1 MODEL TER True N/A N/A N/A N/A N/A pyproct tools pdbTools write_a_tfile_model_into_other_tfile input_file output_file 2 MODEL TER False N/A N/A N/A self assertEqual N/A N/A output_file getvalue N/A test_data extracted_pdbs_2 N/A test_read_to_TAG N/A N/A self N/A N/A N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_1_sub2_file_content N/A lines N/A N/A N/A N/A pyproct tools pdbTools read_to_TAG input_file TER N/A expected_lines N/A N/A MODEL 0
ATOM      3  CA  ILE     3      -0.039   0.638   3.156  1.00  1.00
ATOM      4  CA  PHE     4      -8.605   2.189  -0.292  1.00  1.00
ATOM      5  CA  VAL     5      -5.540   2.776  -2.541  1.00  1.00
ATOM      6  CA  LYP     6      -5.228   5.331  -5.451  1.00  1.00
ATOM      7  CA  THR     7      -3.037   3.652  -8.112  1.00  1.00
 split N/A i N/A range N/A len lines N/A N/A N/A N/A self assertEqual N/A N/A lines N/A i N/A -1 N/A expected_lines N/A i N/A test_advance_to_TAG N/A N/A self N/A N/A N/A input_file N/A N/A cStringIO StringIO N/A test_data pdb_1_file_content N/A N/A N/A N/A N/A pyproct tools pdbTools advance_to_TAG input_file MODEL N/A N/A N/A N/A N/A pyproct tools pdbTools advance_to_TAG input_file MODEL N/A N/A N/A N/A N/A pyproct tools pdbTools advance_to_TAG input_file MODEL N/A line N/A N/A input_file readline N/A expected_line ATOM      3  CA  ILE     3      -2.039   0.638   3.156  1.00  3.00
 N/A N/A N/A self assertEqual line expected_line N/A test_create_CA_file N/A N/A self N/A N/A N/A input_file N/A N/A cStringIO StringIO N/A test_data amber_short_contents N/A output_file N/A N/A cStringIO StringIO N/A N/A N/A N/A N/A pyproct tools pdbTools create_CA_file input_file output_file N/A N/A N/A self assertEqual N/A N/A output_file getvalue N/A test_data amber_short_ca_contents N/A test_get_model_boundaries N/A N/A self N/A N/A N/A input_pdb_handler N/A N/A cStringIO StringIO N/A test_data pdb_1_sub2_file_content N/A boundaries N/A N/A N/A N/A pyproct tools pdbTools get_model_boundaries input_pdb_handler N/A expected_boundaries N/A N/A 1 5 N/A 8 12 N/A 15 19 N/A 22 26 N/A 29 33 N/A 36 40 N/A 43 45 N/A N/A N/A N/A numpy testing assert_equal boundaries expected_boundaries N/A test_repair_MODEL_ENDMDL_tags N/A N/A self N/A N/A N/A input_pdb_handler N/A N/A cStringIO StringIO N/A test_data pdb_1_sub2_file_content N/A output_file_handler N/A N/A cStringIO StringIO N/A boundaries N/A N/A 1 5 N/A 8 12 N/A 15 19 N/A 22 26 N/A 29 33 N/A 36 40 N/A 43 45 N/A N/A repair_MODEL_ENDMDL_tags input_pdb_handler output_file_handler boundaries N/A N/A N/A self assertEqual N/A N/A output_file_handler getvalue N/A test_data pdb_1_file_content N/A test_grab_existing_frames_from_trajectory N/A N/A self N/A N/A N/A input_pdb_handler N/A N/A cStringIO StringIO N/A test_data proto_pdb N/A output_file_handler N/A N/A cStringIO StringIO N/A N/A grab_existing_frame_from_trajectory input_pdb_handler output_file_handler 48 N/A N/A N/A self assertEqual N/A test_data proto_48_pdb N/A N/A output_file_handler getvalue N/A N/A N/A N/A __name__ __main__ N/A N/A N/A N/A unittest main