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#!/usr/bin/env python3
# This script checks if 3x3 matrices from the MTRIX record (or _struct_ncs_oper
# in mmCIF) are rotation matrices (i.e. orthogonal with det=1).
import sys
import gemmi
def check_mtrix_rot(path):
st = gemmi.read_structure(path)
for ncs in st.ncs:
mat = ncs.tr.mat
m_mt = mat.multiply(mat.transpose()).tolist()
eps = max(abs(m_mt[i][j] - (i == j))
for i in [0, 1, 2] for j in [0, 1, 2])
det = mat.determinant()
if eps < 0.5e-4 and abs(det - 1) < 0.5e-4:
status = ' ok'
else:
status = '%3s orthogonal +/- %.4f, det=%+.4f' % (
'' if eps < 0.01 else 'NOT', eps, det)
print('%s %3s %c %s' % (st.name, ncs.id, 'NY'[ncs.given], status))
def main():
if len(sys.argv) < 2:
sys.exit('Specify files, directories or PDB codes.')
for arg in sys.argv[1:]:
for path in gemmi.CoorFileWalk(arg, try_pdbid='M'):
check_mtrix_rot(path)
if __name__ == '__main__':
main()
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