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test-fei-vs-mine.py
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# lidia-core/test-fei-vs-mine.py
#
# Copyright 2013 by Medical Research Council
# Author: Paul Emsley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
#
import os
import subprocess
import glob
def get_fei_types(comp_id):
file_name = "../src/cod/AtomTypeTests2/"
file_name += comp_id
file_name += "_CodAtomType.txt"
try:
f = file(file_name)
lines = f.readlines()
atom_lines = lines[1:]
types = []
for atom_line in atom_lines:
part = atom_line.split('\t')
type = part[2][:-1]
types.append(type)
return types
except:
print 'problem with file', file_name
def get_pe_types(comp_id):
something = subprocess.check_output(['./test-cod-atom-types', comp_id])
lines = something.split('\n')
hit_types = False
types = []
for line in lines:
if hit_types == True:
parts = line.split()
if len(parts) == 2:
types.append(parts[1])
if line[:10] == 'PE-TYPES::':
hit_types = True
return types
# return success stats:
def diff_for_comp_id(comp_id):
fei_types = get_fei_types(comp_id)
# print 'fei_types:\n', fei_types
pe_types = get_pe_types(comp_id)
# print 'pe_types:\n', pe_types
if len(fei_types) != len(pe_types):
print 'Problem with mismatched type lengths for', comp_id, ' pe had', len(pe_types), 'types'
for i in range(len(pe_types)):
print ' ',i,' ',pe_types[i]
return [10, 0] # fake all failures
else:
# happy path
n_match = 0
fail_match = []
for i in range(len(fei_types)):
if pe_types[i] == fei_types[i]:
n_match += 1
else:
fail_match.append([i, pe_types[i], fei_types[i]])
print '::: comp-id:',comp_id,'matched', n_match, 'of', len(fei_types)
for failure in fail_match:
print ' ', failure[0], " ", failure[1], '\t', failure[2]
# return success stats:
return [len(fei_types), len(fei_types)-len(fail_match)]
def test_0s():
test_set = ["0AD", "024", "090", "099", "008", "074", "00A", "023", "057", "039", "0CP",
"0PJ", "032", "002", "059", "0E4", "047", "055", "064", "033", "01G", "0G6",
"094", "0PQ", "066", "098", "003", "061", "0Z6", "096", "088", "0UN",
"062", "0PN", "071", "0BD", "0JZ", "084", "0LI", "0CE", "000", "073", "017",
"012", "065", "0CO", "0EZ", "0E3", "031", "0BI", "0E2", "0MA", "072", "009",
"001", "006", "0AS", "01A", "0CL", "01K", "075", "0A5", "0PY", "0D5", "00C",
"0CS", "0NC", "0A0", "0AH", "0AJ", "069", "0A6", "0AK", "0AZ", "004", "0CR",
"0AB", "0A7", "0A8", "0PA", "00B", "0FA", "005", "0A9", "0AG", "0A1", "0BN",
"0YG", "028", "0AF", "01W", "0AO", "0AI", "0AY", "018", "007", "020", "0A2",
"0DC", "041", "00G", "0IN", "0DT", "01I", "0A4", "077", "0AP",
"0DG", "093", "068", "0MO", "097", "0A3", "0HG", "06C",
"042"]
# test_set = ['06C']
# test_set = ['024']
# test_set = ['039']
# test_set = ['0CP'] # bridged cyclohexane
# test_set = ['03R'] # coords of ideal are 0, hence null molecule
# test_set = ['017'] # bridge atom problem (I think ref types are wrong :)
# test_set = ['0CE'] # same as 017
# test_set = ['0JZ'] # macrocycle including Se, problem with Se order
# test_set = ['093'] #
sum_trials = 0
sum_success = 0
for test_id in test_set:
stats = diff_for_comp_id(test_id)
sum_trials += stats[0]
sum_success += stats[1]
print ' overall: {0}/{1} = {2:.2f}%'.format(sum_success, sum_trials,
float(sum_success*100)/float(sum_trials))
def gen_all():
output_dir = 'pe-types'
dict_dir = os.path.expandvars('$HOME/ccp4/ccp4-6.3.0/lib/data/monomers')
dirs = glob.glob(dict_dir + '/*')
dirs = [ os.path.join(dict_dir, "8"),
os.path.join(dict_dir, "9") ]
for dir in dirs:
if (os.path.isdir(dir)):
dir_basename = os.path.basename(dir)
# print dir
results_dir = os.path.join(output_dir, dir_basename)
if (not (os.path.isdir(results_dir))):
os.makedirs(results_dir)
print dir_basename, results_dir
files = glob.glob(dir + "/*.cif")
for file in files:
# print file
# get the comp-id from the file name
p = os.path.splitext(os.path.basename(file))
comp_id = p[0]
# A8D is a genuine library error.
# Note to self: what are the SMILES strings for these things!?
# B1M now passes
exclude = [ 'BVA', 'B51', 'B13', 'BCB', 'BF4', 'BCL', 'B12', 'BEF', 'BFD',
'7HE', 'ITM', 'ICA', 'JM1', 'AG1', 'A8D', 'AC9', 'APW', 'ALB', 'CN1',
'CHL', 'DVT', 'DW1', 'DWC', 'DAQ', 'DAE', 'DW2', 'CO3', 'CLZ', 'CL7',
'E52', 'C2C', 'CL1', 'FCI', 'FEM', 'FDC', 'FLL', 'FS2', 'FNE', 'CLA',
'HB1', 'HC0', 'HEG', 'HF5', 'HC1', 'HCN', 'CFC', 'CMO', 'CNF', 'KEG',
'KYT', 'KYS', 'LCO', 'MGF', 'NFV', 'NMQ', 'NFC', 'MAP', 'ONP', 'OXX',
'OEC', 'MO7', 'PFC', 'PTE', 'PEJ', 'PNQ', 'PMR', 'PCD', 'PHF', 'ME3',
'MNQ', 'MF4', 'RU7', 'REO', 'REP', 'RUC', 'RTC', 'TBR', 'TL2', 'V7O',
'VEA', 'WO3', 'WO2', 'YBT', 'ZRC', '202', '34B', '39B', '39E' ]
do_it = True
for c in exclude:
if (comp_id == c):
do_it = False
if (do_it):
out_file = os.path.join(results_dir, comp_id + '.types')
print " ", out_file
atom_types = get_pe_types(comp_id)
f = open(out_file, 'w')
for type in atom_types:
f.write(type)
f.write('\n')
f.close()
def types_hist():
atom_types = {}
output_dir = 'pe-types'
dirs = glob.glob(output_dir + '/*')
for dir in dirs:
files = glob.glob(dir + "/*.types")
for file in files:
f = open(file)
for line in f:
type = line.rstrip()
try:
atom_types[type] += 1
except:
atom_types[type] = 1
f.close()
sum = 0
if True:
for key in atom_types.keys():
sum += atom_types[key]
print atom_types[key], " ", key
if False:
l = []
for value in atom_types:
t = [atom_types[value], value]
l.append(t)
for i in l:
print i
if __name__ == "__main__":
# test_0s()
# gen_all()
types_hist()