MobleyLab / chemper

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Showing 1 of 1 files from the diff.

@@ -87,11 +87,11 @@
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    a_out = 0
88 88
    while smirks.find('$(') != -1:
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        # Find first atom
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        atom, a_in, a_out = _find_embedded_brackets(smirks, '\[', '\]')
90 +
        atom, a_in, a_out = _find_embedded_brackets(smirks, r'\[', r'\]')
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        d = atom.find('$(')
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        # Find atom with the $ string embedded
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        while d == -1:
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            atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], '\[', '\]')
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            atom, temp_in, temp_out = _find_embedded_brackets(smirks[a_out+1:], r'\[', r'\]')
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            a_in = a_out + temp_in + 1
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            a_out += temp_out + 1
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            d = atom.find('$(')
@@ -109,11 +109,11 @@
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        else:
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            ring_out = ''
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        embedded, p_in, p_out = _find_embedded_brackets(atom, '\(', '\)')
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        embedded, p_in, p_out = _find_embedded_brackets(atom, r'\(', r'\)')
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        # two forms of embedded strings $(*~stuff) or $([..]~stuff)
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        # in the latter case the first atom refers the current atom
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        if embedded[1] == '[':
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            first, f_in, f_out = _find_embedded_brackets(embedded, '\[','\]')
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            first, f_in, f_out = _find_embedded_brackets(embedded, r'\[',r'\]')
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            first = _convert_embedded_SMIRKS(first)
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            new_atom = atom[:d]+first[1:-1]+atom[p_out+1:]
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            embedded = embedded[f_out+1:]
@@ -285,7 +285,7 @@
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            # Add label to the end of SMARTS
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            else:
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                sub_string, start, end = _find_embedded_brackets(smirks, '\[','\]')
288 +
                sub_string, start, end = _find_embedded_brackets(smirks, r'\[',r'\]')
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                if self.ring is not None:
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                    return sub_string[:-1] + ':' + str(self.index) + ']'+str(self.ring)
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                else:
@@ -470,7 +470,8 @@
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        # Generate RegEx string for decorators:
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        self.no_bracket_atom_reg = r'('+'|'.join([element_sym, aro_sym, replace_str])+')'
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        self.atom_reg = '|'.join([element_num, aro_ali, needs_int,
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            optional_int, chirality, replace_str, element_sym, aro_sym])
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                                  optional_int, chirality, replace_str,
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                                  element_sym, aro_sym])
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        self.atom_reg = r'('+self.atom_reg+')'
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        # Define bond regular expression options below in order:
@@ -573,7 +574,7 @@
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        store = list() # to store indices while branching
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        bondingTo = idx # which atom are we going to bond to
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        atom_string, start, end = _find_embedded_brackets(smirks, '\[', '\]')
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        atom_string, start, end = _find_embedded_brackets(smirks, r'\[', r'\]')
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        if start != 0: # first atom is not in square brackets
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            if start != -1:
@@ -625,7 +626,7 @@
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                continue
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            # find beginning and end of next [atom]
628 -
            atom_string, start, end = _find_embedded_brackets(leftover, '\[', '\]')
629 +
            atom_string, start, end = _find_embedded_brackets(leftover, r'\[', r'\]')
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            if start != -1: # no more square brackets
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                bond_string = leftover[:start]

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Files Coverage
chemper/__init__.py 100.00%
chemper/chemper_utils.py 62.07%
chemper/graphs/cluster_graph.py 93.06%
chemper/graphs/environment.py 92.76%
chemper/graphs/fragment_graph.py 95.38%
chemper/mol_toolkits/__init__.py 87.50%
chemper/mol_toolkits/adapters.py 53.03%
chemper/mol_toolkits/cp_openeye.py 96.50%
chemper/mol_toolkits/cp_rdk.py 96.05%
chemper/mol_toolkits/mol_toolkit.py 85.71%
chemper/smirksify.py 93.93%
Project Totals (11 files) 89.40%
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