hpRefStruct/add_missing_loop.tcl at master · Perilla-lab/hpRefStruct · 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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
namespace eval ::hprefstruct:: {
        variable rosetta_bin /misc/chaoyi/src_builds/rosetta/rosetta_src_2018.42.60459_bundle/main/source/bin/rosetta_scripts.linuxgccrelease
        variable rosetta_db /misc/chaoyi/src_builds/rosetta/rosetta_src_2018.42.60459_bundle/main/database/
        variable molprobity_path /home/chaoyi/builds/Molprobity/build/bin
        variable AA_path /misc/chaoyi/src_builds/hpRefStruct/test/building_missing_loops/AAs_pdb
        proc check_install { } {
                if { ![file isfile $::hprefstruct::rosetta_bin] } { error "Cannot find $::hprefstruct::rosetta_bin" }
                if { ![file isdirectory $::hprefstruct::rosetta_db] } { error "Cannot find $::hprefstruct::rosetta_db" }
                if { ![file isdirectory $::hprefstruct::molprobity_path] } { error "Cannot find $::hprefstruct::molprobity_path" }
                if { ![file isdirectory $::hprefstruct::AA_path] } { error "Cannot find $::hprefstruct::AA_path" }
        }
        check_install
}

proc ::hprefstruct::identify_missing { pdb } {
        set ip [open $pdb r]
        set tmp [list]
        while { [gets $ip oline] >= 0 } {
                if { [regexp -- "REMARK 465" $oline] } {
                        if [string is integer -strict [string range $oline 25 25]] {
				if { ![info exists chn] } {
					set chn [string range $oline 19 19]
					set tmp2 [list $chn]
					eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
				} elseif { $chn == [string range $oline 19 19] } {
					eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
				} else {
					lappend tmp $tmp2
					set chn [string range $oline 19 19]
					set tmp2 [list $chn]
					eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
				}
                        }
                }
        }
	lappend tmp $tmp2
        close $ip
        return $tmp
}

proc ::hprefstruct::separate_chain { pdb } {
	set id [mol new $pdb]
	set ary [::hprefstruct::identify_missing $pdb]
	if { [llength $ary] == 0 } {
		error "Cannot find missing residue record in $pdb ..."
	} else {
		foreach i $ary {
			set chn [lindex $i 0]
			set sel [atomselect $id "protein and chain $chn"]
			set list1 [lrange $i 1 end]
			set l2 [::hprefstruct::find_cons [lsort -u -integer [$sel get resid]]]
			set tmp 0
			foreach {i j} $l2 {
				set flna [lindex [split $pdb .] 0].chain-$chn.$tmp.pdb
#				[atomselect $id "protein and chain $chn and resid $i to $j"] writepdb $flna
				# to do: use tcl to realize sed
#				exec sed -i "1d;\$d" $flna
				incr tmp
			}
			::hprefstruct::build_segments $chn $list1
#			::hprefstruct::sort_list [lindex [split $pdb .] 0] $chn $list1 $l2
		}
	}
	mol delete $id
}

proc ::hprefstruct::build_segments { chn list1 } {
        set list1-1 [list]
        set list1-2 [list]
        foreach {i j} $list1 {
                lappend list1-1 $i
                lappend list1-2 $j
        }
        set l1 [::hprefstruct::find_cons ${list1-1}]
	set count 0
	foreach {i j} $l1 {
                set start [lsearch ${list1-1} $i]
                set end [lsearch ${list1-1} $j]
		for {set k $start} {$k <= $end} {incr k} {
			set pdb "AAs_pdb/[lindex ${list1-2} $k].pdb"
			file copy -force $pdb temp
			set resid [lindex ${list1-1} $k]
	                exec sed -i "s/ A / $chn /g" temp
                        exec sed -i "s/   1   /$resid   /g" temp
                        exec cat temp >> $chn.build.$count.pdb
		}
		incr count
	}
}

proc ::hprefstruct::sort_list { name chn list1 l2 } {
	set list1-1 [list]
        set list1-2 [list]
        foreach {i j} $list1 {
	        lappend list1-1 $i
                lappend list1-2 $j
	}
	set l1 [::hprefstruct::find_cons ${list1-1}]
	set loop [open "loop_chain-$chn.loop" w]
	file delete $chn.pdb
	if { [llength $l1] > [llength $l2] } {
		set start [lsearch ${list1-1} [lindex $l1 0]]
		set end [lsearch ${list1-1} [lindex $l1 1]]
		puts $loop "LOOP [lindex $l1 0] [expr [lindex $l1 1] + 1] [expr [lindex $l1 1] + 1] 0 1"
		foreach {i j} [lrange $l1 2 end-2] {
			puts $loop "LOOP [expr [lindex $l1 $i] - 1] [expr [lindex $l1 $j] + 1] [expr [lindex $l1 $j] + 1] 0 1"
		}
		puts $loop "LOOP [expr [lindex $l1 end-1] - 1] [lindex $l1 end] [expr [lindex $l1 end-1] - 1] 0 1"
		close $loop
		for {set i $start} {$i <= $end} {incr i} {
			set pdb "AAs_pdb/[lindex ${list1-2} $i].pdb"
			file copy -force $pdb temp
			set resid [lindex ${list1-1} $i]
			exec sed -i "s/ A / $chn /g" temp
			exec sed -i "s/   1   /$resid  /g" temp
			exec cat temp >> $chn.pdb
		}
		set l1_ [lrange $l1 2 end]
		set k 0
		foreach {i j} ${l1_} {
			exec cat $name.chain-$chn.$k.pdb >> $chn.pdb
			set start [lsearch ${list1-1} $i]
			set end [lsearch ${list1-1} $j]
			for {set l $start} {$l <= $end} {incr l} {
				set pdb "AAs_pdb/[lindex ${list1-2} $l].pdb"
				file copy -force $pdb temp
				set resid [lindex ${list1-1} $l]
                        	exec sed -i "s/ A / $chn /g" temp
                        	exec sed -i "s/   1   /  $resid   /g" temp
                        	exec cat temp >> $chn.pdb
			}
			incr k
		}

	}
	set id [mol new $chn.pdb]
	[atomselect $id all] writepdb $chn.pdb
	mol delete $id
}


proc ::hprefstruct::find_cons { list } {
	set tmp [lindex $list 0]
	set x [lindex $list 0]
	for { set i 1 } { $i < [llength $list] } { incr i } {
		if { [lindex $list $i] == [expr $x + 1] } {
			incr x
			continue
		} else {
			lappend tmp [lindex $list $i-1] [lindex $list $i]
			set x [lindex $list $i]
		}
	}
	lappend tmp [lindex $list end]
	return $tmp
}

proc ::hprefstruct::get_seq { pdb chain } {
        set ip [open $pdb r]
        set tmp [list]
        while { [gets $ip oline] >= 0 } {
                if { [regexp -- "REMARK 465" $oline] } {
                        if [string is integer -strict [string range $oline 25 25]] {
                                if { ![info exists chn] } {
                                        set chn [string range $oline 19 19]
                                        set tmp2 [list $chn]
                                        eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
                                } elseif { $chn == [string range $oline 19 19] } {
                                        eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
                                } else {
                                        lappend tmp $tmp2
                                        set chn [string range $oline 19 19]
                                        set tmp2 [list $chn]
                                        eval lappend tmp2 [string range $oline 22 25] [string range $oline 15 17]
                                }
                        }
                }
        }
}

proc ::hprefstruct::get_chain { pdb } {
	set id [mol new $pdb]
        set chn [lsort -u [[atomselect $id protein] get chain]]
	mol delete $id
	return $chn
}

proc ::hprefstruct::edit_chain { chain miss } {
	variable AA_path

}

set x [::hprefstruct::identify_missing 6vsb.pdb]
puts [lindex $x 0]
#puts [lindex $x 1]
#puts [lindex $x 2]
::hprefstruct::separate_chain 6vsb.pdb