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#!/usr/bin/env python3
# Show differences between two Refmac intermediate files.
# The intermediate files should have content of both crd and rst files.
# Usage: ./crd-diff.py first.crd second.crd
import argparse
from collections import namedtuple
from itertools import zip_longest
from gemmi import cif
COLUMNS = ['record', 'number', 'label', 'period',
'atom_id_1', 'atom_id_2', 'atom_id_3', 'atom_id_4',
'value', 'dev', 'val_obs']
Restraint = namedtuple('Restraint', COLUMNS)
Crd = namedtuple('Crd', ['atoms', 'real_serial'])
ignore_tors = False
def read_rst(doc):
result = []
for row in doc['restraints'].find('_restr.', COLUMNS):
if row[0] in ['MONO', 'LINK']:
result.append((row[0].lower(), row[2].lower(), []))
else:
data = Restraint(*[x.lower() if x != '.' else None for x in row])
if ignore_tors and data.record == 'tors':
continue
result[-1][2].append(data)
return [r for r in result if r[2]]
def read_crd(doc):
block = doc[0]
sites = block.find('_atom_site.', ['id', 'label_atom_id', 'label_alt_id',
'label_comp_id', 'occupancy',
'calc_flag'])
atoms = [a for a in sites if a[-1] != 'M']
len_diff = len(sites) - len(atoms)
if len_diff != 0:
print('Removed %d atoms with calc_flag=M' % len_diff)
real_serial = {None: None, '.': '.'}
for a in atoms:
real_serial[a[0]] = len(real_serial) - 1
return Crd(atoms, real_serial)
def get_crd_atom_row(crd, atom_id):
idx = crd.real_serial[atom_id] - 1
return crd.atoms[idx]
# hydrogen distances in Refmac may not be ideal
def can_have_wrong_val_obs(crd, rst1):
def is_hydrogen(atom_id):
atom = get_crd_atom_row(crd, atom_id)
return cif.as_string(atom[1]).startswith('H')
if rst1.record == 'bond':
return is_hydrogen(rst1.atom_id_2)
elif rst1.record == 'angl':
return is_hydrogen(rst1.atom_id_3)
elif rst1.record == 'tors':
return is_hydrogen(rst1.atom_id_4)
elif rst1.record == 'plan':
# we can't easily check here if there are H's in the plane
return True
#return is_hydrogen(rst1.atom_id_1)
return False
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-v', action='store_true', help='verbose output')
parser.add_argument('--no-tors', action='store_true',
help='ignore torsion angles')
parser.add_argument('file1_crd', metavar='file1.crd')
parser.add_argument('file2_crd', metavar='file2.crd')
args = parser.parse_args()
if args.no_tors:
global ignore_tors
ignore_tors = True
doc1 = cif.read(args.file1_crd)
doc2 = cif.read(args.file2_crd)
crd1 = read_crd(doc1)
crd2 = read_crd(doc2)
if len(crd1.atoms) != len(crd2.atoms):
print('_atom_site count differs: %d vs %d' %
(len(crd1.atoms), len(crd2.atoms)))
for a1, a2 in zip(crd1.atoms, crd2.atoms):
if any(a1.str(i) != a2.str(i) for i in [1, 2, 3, 5]):
print('First difference:')
print('ATOM %s %s %s %s' % (a1[0], a1.str(1), a1[2], a1[3]))
print('ATOM %s %s %s %s' % (a2[0], a2.str(1), a2[2], a2[3]))
return
if float(a1[4]) != float(a2[4]):
print('ATOM %s/%s %s %s %s occupancy %s vs %s' % (
a1[0], a2[0], a1.str(1), a1[2], a1[3], a1[4], a2[4]))
r1 = read_rst(doc1)
r2 = read_rst(doc2)
mono_count_1 = sum(t[0] == 'mono' for t in r1)
mono_count_2 = sum(t[0] == 'mono' for t in r2)
if mono_count_1 == mono_count_2:
print('MONO count same:', mono_count_1)
else:
print('MONO count differs:', mono_count_1, mono_count_2)
link_count_1 = sum(t[0] == 'link' for t in r1)
link_count_2 = sum(t[0] == 'link' for t in r2)
if link_count_1 == link_count_2:
print('LINK count same:', link_count_1)
else:
print('LINK count differs:', link_count_1, link_count_2)
def same_nums(a, b, eps=0.003, mod360=False):
if a == b:
return True
abs_diff = abs(float(a) - float(b))
return abs_diff < eps or (mod360 and abs(abs_diff - 360) < eps)
def fmt_atom_id(atom_id, crd):
if atom_id is None:
return '.'
atom = get_crd_atom_row(crd, atom_id)
alt = ''
if atom[2] != '.':
alt = '.' + atom[2]
return '%s(%s %s%s)' % (atom_id, atom[3], atom[1], alt)
def fmt(r, crd):
return '%s %s %s %s %s : %s : %s : %s %s ± %s (%s)' % (
r.record, r.number, r.label or '.', r.period or '.',
fmt_atom_id(r.atom_id_1, crd), fmt_atom_id(r.atom_id_2, crd),
fmt_atom_id(r.atom_id_3, crd), fmt_atom_id(r.atom_id_4, crd),
r.value, r.dev, r.val_obs)
def has_same_ids(rst1, rst2):
return (rst1.record == rst2.record
and all(crd1.real_serial[u] == crd2.real_serial[v]
for u, v in zip(rst1[4:8], rst2[4:8])))
for n, (a, b) in enumerate(zip_longest(r1, r2, fillvalue=[None, None, []])):
if a[:2] != b[:2]:
print('item', n, 'differs:', a[:2], 'vs', b[:2])
if a[0] != b[0]:
print('stop')
break
else:
if args.v:
print('---', n, a[0], a[1])
if len(a[2]) != len(b[2]):
print('Item %d (%s) has different restr count: %d vs %d' %
(n, a[0], len(a[2]), len(b[2])))
n_rst1 = 0
n_rst2 = 0
while n_rst1 < len(a[2]) or n_rst2 < len(b[2]):
r_str = '%s/%s restraint %d:%d/%d' % (b[0], b[1], n, n_rst1, n_rst2)
if n_rst1 >= len(a[2]):
rst2 = b[2][n_rst2]
print('ADDED record %s:\n%s\n' % (r_str, fmt(rst2, crd2)))
n_rst2 += 1
continue
if n_rst2 >= len(b[2]):
rst1 = a[2][n_rst1]
print('REMOVED record %s:\n%s\n' % (r_str, fmt(rst1, crd1)))
n_rst1 += 1
continue
rst1 = a[2][n_rst1]
rst2 = b[2][n_rst2]
same_ids = has_same_ids(rst1, rst2)
if not same_ids:
a2 = a[2]
b2 = b[2]
if any(n_rst2+k < len(b2) and has_same_ids(rst1, b2[n_rst2+k])
for k in range(1,10)):
print('ADDED record %s:\n%s\n' % (r_str, fmt(rst2, crd2)))
n_rst2 += 1
continue
if any(n_rst1+k < len(a2) and has_same_ids(a2[n_rst1+k], rst2)
for k in range(1,10)):
print('REMOVED record %s:\n%s\n' % (r_str, fmt(rst1, crd1)))
n_rst1 += 1
continue
if rst1.record != rst2.record:
print('Different records %s:\n%s\nvs\n%s\n' %
(r_str, fmt(rst1, crd1), fmt(rst2, crd2)))
elif (rst1.label != rst2.label if rst1.record != 'chir'
else rst1.label[0] != rst2.label[0]):
print('Different labels in %s:\n%s\nvs\n%s\n' %
(r_str, fmt(rst1, crd1), fmt(rst2, crd2)))
elif rst1.period != rst2.period:
print('Different period in %s:\n%s\nvs\n%s\n' %
(r_str, fmt(rst1, crd1), fmt(rst2, crd2)))
elif not same_ids:
print('Different atom id in %s:\n%s\nvs\n%s\n' %
(r_str, fmt(rst1, crd1), fmt(rst2, crd2)))
elif not same_nums(rst1.value, rst2.value):
print('Different value for %s (%s vs %s) in:\n%s\n' %
(r_str, rst1.value, rst2.value, fmt(rst1, crd1)))
elif not same_nums(rst1.dev, rst2.dev):
print('Different dev for %s (%s vs %s) in:\n%s\n' %
(r_str, rst1.dev, rst2.dev, fmt(rst1, crd1)))
elif not (same_nums(rst1.val_obs, rst2.val_obs,
eps=val_obs_eps(rst1.record),
mod360=(rst1.record == 'tors'))
or can_have_wrong_val_obs(crd1, rst1)):
print('val_obs differs for %s (%s vs %s) in:\n%s\n' %
(r_str, rst1.val_obs, rst2.val_obs, fmt(rst1, crd1)))
#elif rst1.number != rst2.number:
# print('Serial number differs in %s: %s -> %s' %
# (r_str, rst1[1], rst2[1]))
n_rst1 += 1
n_rst2 += 1
def val_obs_eps(record):
if record == 'tors':
return 0.15
elif record == 'plan':
return 0.015
else:
return 0.004
if __name__ == '__main__':
try:
main()
except BrokenPipeError:
pass
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