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import compiler
import compiler.ast
groups = ['ace_beginning_nt',
'adenine',
'ala_sidechain',
'alanine',
'alanine_ct',
'alanine_nt',
'arg_sidechain',
'arginine',
'arginine_ct',
'arginine_nt',
'asn_sidechain',
'asp_sidechain',
'asp_sidechain_neutral',
'asparagine',
'asparagine_ct',
'asparagine_nt',
'aspartic_acid',
'aspartic_acid_ct',
'aspartic_acid_neutral',
'aspartic_acid_nt',
'cym_sidechain',
'cys_sidechain',
'cysteine',
'cysteine_ct',
'cysteine_nt',
'cysteine_with_negative_charge',
'cystine_ss',
'cystine_ss_ct',
'cystine_ss_nt',
'cytosine',
'cyx_sidechain',
'd-adenosine',
'd-adenosine_3ter',
'd-adenosine_5ter',
'd-adenosine_5ter_3ter',
'd-cytosine',
'd-cytosine_3ter',
'd-cytosine_5ter',
'd-cytosine_5ter_3ter',
'd-guanosine',
'd-guanosine_3ter',
'd-guanosine_5ter',
'd-guanosine_5ter_3ter',
'd-thymine',
'd-thymine_3ter',
'd-thymine_5ter',
'd-thymine_5ter_3ter',
'desoxyribose',
'desoxyribose_3ter',
'desoxyribose_5ter',
'desoxyribose_5ter_3ter',
'gln_sidechain',
'glu_sidechain',
'glu_sidechain_neutral',
'glutamic_acid',
'glutamic_acid_ct',
'glutamic_acid_neutral',
'glutamic_acid_nt',
'glutamine',
'glutamine_ct',
'glutamine_nt',
'gly_nt_sidechain',
'gly_sidechain',
'glycine',
'glycine_ct',
'glycine_nt',
'guanine',
'hid_sidechain',
'hie_sidechain',
'hip_sidechain',
'histidine',
'histidine_ct',
'histidine_deltah',
'histidine_deltah_ct',
'histidine_deltah_nt',
'histidine_epsilonh',
'histidine_epsilonh_ct',
'histidine_epsilonh_nt',
'histidine_nt',
'histidine_plus',
'histidine_plus_ct',
'histidine_plus_nt',
'ile_sidechain',
'isoleucine',
'isoleucine_ct',
'isoleucine_nt',
'leu_sidechain',
'leucine',
'leucine_ct',
'leucine_nt',
'lys_sidechain',
'lys_sidechain_neutral',
'lysine',
'lysine_ct',
'lysine_neutral',
'lysine_neutral_ct',
'lysine_neutral_nt',
'lysine_nt',
'met_sidechain',
'methionine',
'methionine_ct',
'methionine_nt',
'na_phosphate',
'nmethyl_ct',
'peptide',
'peptide_ct',
'peptide_nt',
'peptide_nt_ct',
'peptide_proline',
'peptide_proline_ct',
'peptide_proline_nt',
'phe_sidechain',
'phenylalanine',
'phenylalanine_ct',
'phenylalanine_nt',
'pro_sidechain',
'pro_sidechain_nt',
'proline',
'proline_ct',
'proline_nt',
'r-adenosine',
'r-adenosine_3ter',
'r-adenosine_5ter',
'r-adenosine_5ter_3ter',
'r-cytosine',
'r-cytosine_3ter',
'r-cytosine_5ter',
'r-cytosine_5ter_3ter',
'r-guanosine',
'r-guanosine_3ter',
'r-guanosine_5ter',
'r-guanosine_5ter_3ter',
'r-uracil',
'r-uracil_3ter',
'r-uracil_5ter',
'r-uracil_5ter_3ter',
'ribose',
'ribose_3ter',
'ribose_5ter',
'ribose_5ter_3ter',
'ser_sidechain',
'serine',
'serine_ct',
'serine_nt',
'thr_sidechain',
'threonine',
'threonine_ct',
'threonine_nt',
'thymine',
'trp_sidechain',
'tryptophan',
'tryptophan_ct',
'tryptophan_nt',
'tyr_sidechain',
'tyrosine',
'tyrosine_ct',
'tyrosine_nt',
'uracil',
'val_sidechain',
'valine',
'valine_ct',
'valine_nt']
for filename in groups:
ast = compiler.parse(file(filename).read())
stmts = ast.getChildren()[1].getChildren()
vars = set()
for stmt in stmts:
if isinstance(stmt, compiler.ast.Assign):
var_name = stmt.getChildren()[0].getChildren()[0]
vars.add(var_name)
if 'amber_atom_type' in vars \
and 'amber12_atom_type' not in vars:
print filename
with file(filename, 'a') as f:
f.write("amber12_atom_type = amber_atom_type\n")
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