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246e0a4c2d
Fixes #102 #351 Migrating support from Incentive for the following: - Nucleic Acid builder in the Builder panel (Jarrett Johnson @JarrettSJohnson) - `fnab` command to build nucleic acid chains by sequence (Jarrett Johnson @JarrettSJohnson) - Improvements to nucleic acid building from native structures (Thomas Stewart @TstewDev) - highlight attachment points for improved usability (Thomas Holder @speleo3) Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com> Co-authored-by: Thomas Stewart <thomas.stewart@schrodinger.com> Co-authored-by: Thomas Holder <thomas@thomas-holder.de>
62 lines
2.0 KiB
Python
62 lines
2.0 KiB
Python
"""
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Testing PyQt Fab & Builder
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"""
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from pymol import cmd, testing
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@testing.requires_version('2.3')
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class TestNucBuilder(testing.PyMOLTestCase):
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def testCanInit(self):
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self.assertEqual(cmd.fnab("A"), None)
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def testSingleDNAFASTA(self):
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dna = "ATGC"
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cmd.fnab(input=dna, mode="DNA", form="B", dbl_helix=-1)
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fasta_str = cmd.get_fastastr().splitlines()
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self.assertEqual(dna, fasta_str[1])
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def testSingleRNAFASTA(self):
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rna = "AUGC"
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cmd.fnab(input=rna, mode="RNA")
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fasta_str = cmd.get_fastastr().splitlines()
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self.assertEqual(rna, fasta_str[1])
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def testDoubleDNAFASTA(self):
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dna = "ATCCCCG"
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revcomp = "CGGGGAT"
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cmd.fnab(input=dna, dbl_helix=1)
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fasta_str = cmd.get_fastastr().splitlines()
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fasta_raw = (fasta_str[1], fasta_str[3])
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sense_strand = fasta_raw[0]
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antisense_strand = fasta_raw[1]
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self.assertEqual(dna, sense_strand)
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self.assertEqual(revcomp, antisense_strand)
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cmd.delete('all')
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cmd.fnab(input=dna)
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fasta_str = cmd.get_fastastr().splitlines()
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fasta_raw = (fasta_str[1], fasta_str[3])
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sense_strand = fasta_raw[0]
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antisense_strand = fasta_raw[1]
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self.assertEqual(dna, sense_strand)
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self.assertEqual(revcomp, antisense_strand)
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def testDoubleRNAFASTA(self):
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rna = "AUUUUUUUCG"
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cmd.fnab(input=rna, mode="RNA", form="B", dbl_helix=1)
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fasta_str = cmd.get_fastastr().splitlines()
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self.assertEqual(len(fasta_str), 2)
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sense_strand = fasta_str[1]
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self.assertEqual(rna, sense_strand)
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def testMixedCase(self):
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dna = "AtG"
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revcomp = "CAT"
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cmd.fnab(input=dna)
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fasta_str = cmd.get_fastastr().splitlines()
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fasta_raw = (fasta_str[1], fasta_str[3])
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sense_strand = fasta_raw[0]
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antisense_strand = fasta_raw[1]
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self.assertEqual(dna.upper(), sense_strand)
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self.assertEqual(revcomp, antisense_strand)
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