I have thousands of files like this, and I want to extract the values of columns 6,7,8 for the rows corresponding to atoms ['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'],
ATOM 1 CG TOLU 1 -0.437 -0.756 1.802 1.00 1.99 PRO0
ATOM 2 HG TOLU 1 -0.689 -1.123 2.786 1.00 0.00 PRO0
ATOM 3 CD1 TOLU 1 0.041 -1.623 0.811 1.00 1.99 PRO0
ATOM 4 HD1 TOLU 1 0.331 -2.603 1.162 1.00 0.00 PRO0
ATOM 5 CD2 TOLU 1 -0.692 0.547 1.352 1.00 1.99 PRO0
ATOM 6 HD2 TOLU 1 -1.131 1.264 2.030 1.00 0.00 PRO0
ATOM 7 CE1 TOLU 1 0.246 -1.276 -0.504 1.00 1.99 PRO0
ATOM 8 HE1 TOLU 1 0.596 -2.073 -1.144 1.00 0.00 PRO0
ATOM 9 CE2 TOLU 1 -0.331 0.991 0.063 1.00 1.99 PRO0
ATOM 10 HE2 TOLU 1 -0.565 2.030 -0.117 1.00 0.00 PRO0
ATOM 11 CZ TOLU 1 0.136 0.076 -0.919 1.00 1.99 PRO0
ATOM 12 CT TOLU 1 0.561 0.474 -2.282 1.00 0.00 PRO0
ATOM 13 H11 TOLU 1 0.529 -0.410 -2.955 1.00 0.00 PRO0
ATOM 14 H12 TOLU 1 1.574 0.930 -2.294 1.00 0.00 PRO0
ATOM 15 H13 TOLU 1 -0.203 1.165 -2.699 1.00 0.00 PRO0
ATOM 16 CG TOLU 2 5.140 1.762 -1.390 1.00 1.99 PRO0
ATOM 17 HG TOLU 2 5.815 1.717 -2.231 1.00 0.00 PRO0
ATOM 18 CD1 TOLU 2 4.578 0.647 -0.862 1.00 1.99 PRO0
ATOM 19 HD1 TOLU 2 4.835 -0.329 -1.246 1.00 0.00 PRO0
ATOM 20 CD2 TOLU 2 4.786 3.044 -0.824 1.00 1.99 PRO0
ATOM 21 HD2 TOLU 2 5.184 3.982 -1.181 1.00 0.00 PRO0
ATOM 22 CE1 TOLU 2 3.734 0.667 0.248 1.00 1.99 PRO0
ATOM 23 HE1 TOLU 2 3.131 -0.167 0.574 1.00 0.00 PRO0
ATOM 24 CE2 TOLU 2 4.042 3.068 0.321 1.00 1.99 PRO0
ATOM 25 HE2 TOLU 2 3.753 3.969 0.841 1.00 0.00 PRO0
ATOM 26 CZ TOLU 2 3.465 1.886 0.893 1.00 1.99 PRO0
ATOM 27 CT TOLU 2 2.501 1.806 2.157 1.00 0.00 PRO0
ATOM 28 H11 TOLU 2 2.361 0.712 2.283 1.00 0.00 PRO0
ATOM 29 H12 TOLU 2 1.490 2.181 1.890 1.00 0.00 PRO0
ATOM 30 H13 TOLU 2 2.845 2.513 2.943 1.00 0.00 PRO0
TER
END
and notice that there exist two rows for each of the mentioned atoms. Therefore, I think two dictionaries with 12 keys would best fit my goal, like this
{1: {'CG':(0,0,0), 'CD1':(0,0,0), 'CD2':(0,0,0), 'CE1':(0,0,0), 'CE2':(0,0,0), 'CZ':(0,0,0)},
2: {'CG':(0,0,0), 'CD1':(0,0,0), 'CD2':(0,0,0), 'CE1':(0,0,0), 'CE2':(0,0,0), 'CZ':(0,0,0)}}
Where the first keys (1, 2) refer to the 5th column.
Can you tell me a robust way to read the file and assign each tuple of values to its correct place in the dictionary? I can do it with multiple if conditions, but I thought there must be a better way (maybe with numpy)
This will do the work:
atmlist = ['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ']
def Read_PDB(filename):
coord={r:{k:(0,0,0) for k in atmlist} for r in [0,1]}
try:
f = open(filename, 'r')
except IOError as err:
print ("I/O error({0}): {1}".format(err.errno, err.strerror))
quit()
for line in f:
for at in atmlist:
if (line.find(at) == 13):
line = line.strip()
temp = line.split()
crd = (float(temp[5]), float(temp[6]), float(temp[7]))
coord[int(temp[4])-1][at] = crd;
return coord`