MD-scripts/dcd_to_pdb.sh at master · g-rutter/MD-scripts · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
#!/bin/bash

if [ $# -lt 3 ]; then
    echo "Usage: $0 [DCD_file] [PSF_file] [stride] {start_percent} {end_percent}"
    exit
fi

################################
#  Settings from command-line  #
################################

DCD_file=$1
PSF_file=$2
stride=$3

###########################
#  Check DCD file exists  #
###########################

if [ -f $DCD_file ]; then
    DCD_frames=`catdcd -num $DCD_file | grep "Total frames:" | sed 's/Total frames: //'`
else
    echo "No such file $DCD_file. Exiting."
    exit
fi

############################################
#  Optional (start and finish %) settings  #
############################################

start_percent=$4
end_percent=$5

if [[ $start_percent == '' ]]; then
    start_percent=0
fi

if [[ $end_percent == '' ]]; then
    end_percent=100
fi

start_frame=$((DCD_frames*$start_percent/100))
end_frame=$(($((DCD_frames*$end_percent/100))-1))

######################
#  Derived settings  #
######################

DCD_filename=$(basename "$DCD_file")
DCD_filename_noext="${DCD_file%.*}"

output_prefix=${DCD_filename_noext}"-"stride${stride}
if [[ $start_percent != '0' ]] || [[ $end_percent != '100' ]]; then
    output_prefix=$output_prefix-percent${start_percent}to${end_percent}
fi

PDB_traj=${output_prefix}".pdb"
temp=${output_prefix}".temp.pdb"

###########################
#  Check file extensions  #
###########################

if [[ $DCD_filename != *.dcd ]]; then
    echo "DCD file should have .dcd extension."
    exit
fi

if [[ $PSF_file != *.psf ]]; then
    echo "PSF file should have .psf extension."
    exit
fi

#############################
#  Use catdcd to make PDBs  #
#############################

echo "Converting DCD file to PDB file."
echo catdcd -o ${PDB_traj} -otype pdb -stride ${stride} -stype psf -s ${PSF_file} ${DCD_file}
catdcd -o ${PDB_traj} -otype pdb -stride ${stride} -stype psf -s ${PSF_file} -first $start_frame -last $end_frame ${DCD_file}

############################
#  Fix up PDBs with regex  #
############################

echo "Using regex to fix the PDB trajectory file."
cat ${PDB_traj} | perl -pe 's{^[^A].*$}{$n=$n+1; "ENDMDL\nMODEL     $n"}e' | sed 1d | sed '$d' >$temp
cat $temp | perl -pe 's/(ATOM +\d+)    [41]/\1  N  /' | perl -pe 's/(ATOM +\d+)    2/\1  CA /' | perl -pe 's/(ATOM +\d+)    3/\1  C  /' | perl -pe 's/(ATOM +\d+) +\d+ +(\w)/\1  \2SC \2/' >${PDB_traj}
rm -f $temp