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src/c/o/cogent-1.5.3/cogent/format/motif.py   cogent(Download)
 
from cogent.motif.util import MotifFormatter
from cogent.format.pdb_color import get_matching_chains,\
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
from cogent.format.rna_struct import color_on_structure, draw_structure
        #Get PDB chains
        pdb_matching, ungapped_to_pdb = \
            get_matching_chains(subject_seq,curr_pdb,sequence_type)
 
        pdb_aligned = align_subject_to_pdb(subject_seq,pdb_matching)

src/p/y/pycogent-HEAD/cogent/format/motif.py   pycogent(Download)
 
from cogent.motif.util import MotifFormatter
from cogent.format.pdb_color import get_matching_chains,\
    align_subject_to_pdb, PYMOL_FUNCTION_STRING, MAIN_FUNCTION_STRING
from cogent.format.rna_struct import color_on_structure, draw_structure
        #Get PDB chains
        pdb_matching, ungapped_to_pdb = \
            get_matching_chains(subject_seq,curr_pdb,sequence_type)
 
        pdb_aligned = align_subject_to_pdb(subject_seq,pdb_matching)

src/c/o/cogent-1.5.3/tests/test_format/test_pdb_color.py   cogent(Download)
#!/usr/bin/env python
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import app_path
from cogent.format.pdb_color import get_aligned_muscle, make_color_list, \
        res_100 = {}
        #Threshold of .3
        test_30, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        TEST_PDB_STRING_1.split('\n'),\
                                        subject_type='Nucleotide',\
                                        threshold=.3)
        #Threshold of .8
        test_80, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        threshold=.8)
        #Threshold of 1
        test_100, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        TEST_PDB_STRING_1.split('\n'),\
                                        subject_type='Nucleotide',\
                                        threshold=1)
        #Incorrect subject_type
        #Threshold of .3
        test_wrong_subject, ungapped_to_pdb = get_matching_chains(subject_seq, \

src/p/y/pycogent-HEAD/tests/test_format/test_pdb_color.py   pycogent(Download)
#!/usr/bin/env python
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import app_path
from cogent.format.pdb_color import get_aligned_muscle, make_color_list, \
        res_100 = {}
        #Threshold of .3
        test_30, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        TEST_PDB_STRING_1.split('\n'),\
                                        subject_type='Nucleotide',\
                                        threshold=.3)
        #Threshold of .8
        test_80, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        threshold=.8)
        #Threshold of 1
        test_100, ungapped_to_pdb = get_matching_chains(subject_seq, \
                                        TEST_PDB_STRING_1.split('\n'),\
                                        subject_type='Nucleotide',\
                                        threshold=1)
        #Incorrect subject_type
        #Threshold of .3
        test_wrong_subject, ungapped_to_pdb = get_matching_chains(subject_seq, \