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24 """The Molmol macro methods of the specific API for model-free analysis."""
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26
27 from specific_analyses.model_free.macro_base import Macro
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29
31 """Class containing the Molmol specific functions for model-free analysis."""
32
34 """Colour the given peptide bond."""
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36
37 self.commands.append("SelectBond 'atom1.name = \"CA\" & atom2.name = \"C\" & res.num = " + repr(res_num-1) + "'")
38 self.commands.append("StyleBond neon")
39 self.commands.append("RadiusBond " + repr(width))
40 self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2]))
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42
43 self.commands.append("SelectBond 'atom1.name = \"C\" & atom2.name = \"N\" & res.num = " + repr(res_num-1) + "'")
44 self.commands.append("StyleBond neon")
45 self.commands.append("RadiusBond " + repr(width))
46 self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2]))
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48
49 self.commands.append("SelectBond 'atom1.name = \"N\" & atom2.name = \"CA\" & res.num = " + repr(res_num) + "'")
50 self.commands.append("StyleBond neon")
51 self.commands.append("RadiusBond " + repr(width))
52 self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + repr(rgb_array[1]) + " " + repr(rgb_array[2]))
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54
55 self.commands.append("")
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57
59 """Create the header for the molmol macro."""
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62 self.commands.append("SelectBond ''")
63 self.commands.append("StyleBond invisible")
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66 self.commands.append("SelectBond 'bb'")
67 self.commands.append("StyleBond line")
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70 self.commands.append("ColorBond 0 0 0")
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72
73 - def molmol_macro(self, data_type, style=None, colour_start=None, colour_end=None, colour_list=None, spin_id=None):
74 """Wrapper method for the create_macro method.
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76 @param data_type: The parameter name or data type.
77 @type data_type: str
78 @keyword style: The Molmol style.
79 @type style: None or str
80 @keyword colour_start: The starting colour (must be a MOLMOL or X11 name).
81 @type colour_start: str
82 @keyword colour_end: The ending colour (must be a MOLMOL or X11 name).
83 @type colour_end: str
84 @keyword colour_list: The colour list used, either 'molmol' or 'x11'.
85 @type colour_list: str
86 @keyword spin_id: The spin identification string.
87 @type spin_id: str
88 """
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90 self.create_macro(data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list, spin_id=spin_id)
91