I have a file with very specific column spacing formatting,
I wish to do the following:
awk '{print $1, $2, $3, $4, $5, $6, $19-$7, $20-$8, $21-$9, $10, $11, $12}' merge.pdb > vector.pdb
but the format gets ruined.
I have tried with print -f but to no avail....
Please post sample before and after data, making it clear whether this is a fixed-length record and whether fields are left or right justified.
ATOM 1 N ALA B 1 -9.995 -6.835 2.255 0.00 0.00 BH ATOM 1 N ALA B 1 -13.079 -16.435 0.105 0.00 0.00 BH
ATOM 2 HT2 ALA B 1 -10.828 -7.444 2.585 0.00 0.00 BH ATOM 2 HT2 ALA B 1 -12.045 -16.716 -0.054 0.00 0.00 BH
ATOM 3 HT3 ALA B 1 -10.119 -6.623 1.230 0.00 0.00 BH ATOM 3 HT3 ALA B 1 -13.318 -16.970 0.909 0.00 0.00 BH
ATOM 4 CA ALA B 1 -10.201 -5.652 3.107 0.00 0.00 BH ATOM 4 CA ALA B 1 -12.997 -14.938 0.408 0.00 0.00 BH
ATOM 5 HA ALA B 1 -10.804 -4.989 2.587 0.00 0.00 BH ATOM 5 HA ALA B 1 -13.464 -14.356 -0.413 0.00 0.00 BH
ATOM 6 CB ALA B 1 -10.761 -6.301 4.361 0.00 0.00 BH ATOM 6 CB ALA B 1 -13.865 -14.850 1.756 0.00 0.00 BH
ATOM 7 HB1 ALA B 1 -11.677 -6.864 4.178 0.00 0.00 BH ATOM 7 HB1 ALA B 1 -14.845 -15.340 1.646 0.00 0.00 BH
ATOM 8 HB2 ALA B 1 -10.016 -7.019 4.786 0.00 0.00 BH ATOM 8 HB2 ALA B 1 -13.341 -15.381 2.572 0.00 0.00 BH
ATOM 9 HB3 ALA B 1 -11.114 -5.604 5.113 0.00 0.00 BH ATOM 9 HB3 ALA B 1 -14.123 -13.823 2.072 0.00 0.00 BH
ATOM 10 C ALA B 1 -8.943 -4.890 3.362 0.00 0.00 BH ATOM 10 C ALA B 1 -11.715 -14.231 0.505 0.00 0.00 BH
ATOM 11 O ALA B 1 -8.904 -3.716 3.057 0.00 0.00 BH ATOM 11 O ALA B 1 -10.624 -14.820 0.363 0.00 0.00 BH
ATOM 12 N ALA B 2 -7.940 -5.583 3.917 0.00 0.00 BH ATOM 12 N ALA B 2 -11.810 -12.904 0.758 0.00 0.00 BH
ATOM 13 HN ALA B 2 -8.114 -6.501 4.241 0.00 0.00 BH ATOM 13 HN ALA B 2 -12.700 -12.511 0.709 0.00 0.00 BH
ATOM 14 CA ALA B 2 -6.616 -5.044 4.344 0.00 0.00 BH ATOM 14 CA ALA B 2 -10.704 -12.044 0.971 0.00 0.00 BH
ATOM 15 HA ALA B 2 -6.828 -4.512 5.228 0.00 0.00 BH ATOM 15 HA ALA B 2 -10.083 -12.526 1.731 0.00 0.00 BH
Yes, fields are left-justified.
---------- Post updated at 09:51 AM ---------- Previous update was at 09:50 AM ----------
My output loses the format:
ATOM 1 N ALA B 1 -3.084 -9.6 -2.15 0.00 0.00 BH
ATOM 2 HT2 ALA B 1 -1.217 -9.272 -2.639 0.00 0.00 BH
ATOM 3 HT3 ALA B 1 -3.199 -10.347 -0.321 0.00 0.00 BH
ATOM 4 CA ALA B 1 -2.796 -9.286 -2.699 0.00 0.00 BH
ATOM 5 HA ALA B 1 -2.66 -9.367 -3 0.00 0.00 BH
ATOM 6 CB ALA B 1 -3.104 -8.549 -2.605 0.00 0.00 BH
ATOM 7 HB1 ALA B 1 -3.168 -8.476 -2.532 0.00 0.00 BH
ATOM 8 HB2 ALA B 1 -3.325 -8.362 -2.214 0.00 0.00 BH
ATOM 9 HB3 ALA B 1 -3.009 -8.219 -3.041 0.00 0.00 BH
ATOM 10 C ALA B 1 -2.772 -9.341 -2.857 0.00 0.00 BH
ATOM 11 O ALA B 1 -1.72 -11.104 -2.694 0.00 0.00 BH
ATOM 12 N ALA B 2 -3.87 -7.321 -3.159 0.00 0.00 BH
ATOM 13 HN ALA B 2 -4.586 -6.01 -3.532 0.00 0.00 BH
ATOM 14 CA ALA B 2 -4.088 -7 -3.373 0.00 0.00 BH
ATOM 15 HA ALA B 2 -3.255 -8.014 -3.497 0.00 0.00 BH
ATOM 16 CB ALA B 2 -4.279 -5.691 -5.06 0.00 0.00 BH
ATOM 17 HB1 ALA B 2 -3.994 -5.943 -4.604 0.00 0.00 BH
ATOM 18 HB2 ALA B 2 -5.97 -5.762 -6.094 0.00 0.00 BH
---------- Post updated 03-29-12 at 02:02 AM ---------- Previous update was 03-28-12 at 09:51 AM ----------
Here is an example of a script that deals with this kind of format:
# This file is fixpdb.awk.
# Useage awk -f fixpdb.awk [segid=wxyz] [chainID=X] <pdbfile.in >file.out
# [resname=abc]
# Extracts segments from pdb files and converts to a format acceptable by charmm.
# In command line can specify up to a four character segid with wxyz, e.g. prot. This
# field is ignored by current CHARMM versions, but needed for older versions.
# Can specify a one character chainID. If is specified on command line, extracts
# only lines whose character in column 22 matches chainID X. Use to extract specific
# subunit from pdb file.
# Instead, can specify a three character resname to select HOH or ligands like ARA.
# If resname is specified, extracts only lines whose resname in columns 18-20
# matches resname abc value.
# Writes header line as a remark.
# Ignores all other lines not beginning with ATOM or HETATM.
# If a single coordinate value for an atom is present, takes that.
# If multiple coordinates are present, signified by A, B, .. in column 17, takes only A.
# If protein and HOH lines are present and protein lacks a chainID, takes the
# protein lines only.
# Converts HOH to TIP and adds a 3, making TIP3, HIS to HSD, CD1 to CD_ for ILE,
# adds the segid in columns 73-76. Converts OXT or OCT1 to OT1 and OCT2 to OT2.
# Renumbers atoms starting from 1.
# Fields: Atom, Atom No, Space, Atom name, Alt Conf indic, Resname, Space,
# Chain Ident, Res Seq No, Spaces, x, y, z, Occup, Temp fact, Spaces, Segment ID
BEGIN {FIELDWIDTHS=" 6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6 4"}
{
if ($1 == "HEADER")
print "REMARK" substr($0, 7, 69)
if ($1 != "ATOM " && $1 != "HETATM")
endif
else if ($5 != " " && $5 != "A")
endif
else if ($6 == resname || $8 == chainID || ($8 == " " && $1 != "HETATM"))
{
atomno++
if ($6 == "HOH")
{ $4 = " OH2"
$6 = "TIP"
$7 = "3"
}
if ($1 == "HETATM")
$1 = "ATOM "
if ($6 == "HIS")
$6 = "HSD"
if ($6 == "ILE" && $4 == " CD1")
$4 = " CD "
if ($4 == " OXT" || $4 == "OCT1")
$4 = " OT2"
if ($4 == "OCT2")
$4 = " OT1"
printf "%6s",$1
printf "%5d", atomno
printf "%1s", " "
printf "%4s", $4
printf "%1s", " "
printf "%3s", $6
printf "%1s", $7
printf "%1s", " "
printf "%4s", $9
printf "%4s", " "
printf "%8s", $12
printf "%8s", $13
printf "%8s", $14
printf "%6s", $15
printf "%6s", $16
printf "%6s", " "
printf "%4s\n", segid
}
}
END {printf "%3s\n", "END"}
Why not use printf, as in your example script?
why dont you try another program...
---------- Post updated at 02:57 AM ---------- Previous update was at 02:56 AM ----------
or ask other people that has specialty in IT.
---------- Post updated at 02:57 AM ---------- Previous update was at 02:57 AM ----------
I'm sure they can help you..:)
Ok I tried writing the script:
BEGIN {FIELDWIDTHS=" 6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6 13 6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6 4"}
{ printf "%6s",$1
printf "%6d", $1
printf "%5d", $2
printf "%1s", $3
printf "%4s", $4
printf "%1s", $5
printf "%3s", $6
printf "%1s", $7
printf "%1s", $8
printf "%4s", $9
printf "%1s", $10
printf "%3s", $11
printf "%8s", $12-$30
printf "%8s", $13-$31
printf "%8s", $14-$32
printf "%6s", $15
printf "%6s", $16
printf "%6s", $17
printf "%13s\n", $18
}
END {printf "%3s\n", "END"}
But the output is still poor:
ATOM 0 1N ALAB 1-9.995-6.8352.2550.000.00 0 0 1 N ALA B 1
ATOM 0 2HT2 ALAB 1-10.828-7.4442.5850.000.00 0 0 2 HT2 ALA B 1
ATOM 0 3HT3 ALAB 1-10.119-6.6231.2300.000.00 0 0 3 HT3 ALA B 1
ATOM 0 4CA ALAB 1-10.201-5.6523.1070.000.00 0 0 4 CA ALA B 1
ATOM 0 5HA ALAB 1-10.804-4.9892.5870.000.00 0 0 5 HA ALA B 1
ATOM 0 6CB ALAB 1-10.761-6.3014.3610.000.00 0 0 6 CB ALA B 1
ATOM 0 7HB1 ALAB 1-11.677-6.8644.1780.000.00 0 0 7 HB1 ALA B 1
ATOM 0 8HB2 ALAB 1-10.016-7.0194.7860.000.00 0 0 8 HB2 ALA B 1
ATOM 0 9HB3 ALAB 1-11.114-5.6045.1130.000.00 0 0 9 HB3 ALA B 1
ATOM 0 10C ALAB 1-8.943-4.8903.3620.000.00 0 0 10 C ALA B 1
ATOM 0 11O ALAB 1-8.904-3.7163.0570.000.00 0 0 11 O ALA B 1
ATOM 0 12N ALAB 2-7.940-5.5833.9170.000.00 0 0 12 N ALA B 2
ATOM 0 13HN ALAB 2-8.114-6.5014.2410.000.00 0 0 13 HN ALA B 2
ATOM 0 14CA ALAB 2-6.616-5.0444.3440.000.00 0 0 14 CA ALA B 2
ATOM 0 15HA ALAB 2-6.828-4.5125.2280.000.00 0 0 15 HA ALA B 2
END
Alternatively, try this:
awk 'sub(" *"$7" *"$8" *"$9,sprintf("%12.3f%8.3f%8.3f",$19-$7, $20-$8, $21-$9))' infile | cut -c-74
That's because your field widths don't match the data - e.g. $3 is being written with a width of 1, but some rows are 3 characters (plus a space, if you want to pad it).