Skip to content

Commit

Permalink
Add selection keywords checking + silent option (do not print TBL file)
Browse files Browse the repository at this point in the history
  • Loading branch information
@mtrellet
mtrellet committed Aug 21, 2017
1 parent 09d3c58 commit 212ec96
Show file tree
Hide file tree
Showing 2 changed files with 86 additions and 42 deletions.
6 changes: 6 additions & 0 deletions haddock_tbl_validation/distance-or_malformed.tbl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
assign ( resid 201 and name C18 ) ( resid 93 and name HG2+ ) 4.66 4.66 1.0
or
( resid 201 and name C22 ) ( resid 93 and HG2+ )
or
( resid 205 and name C22 ) ( resid 93 and name HG2+ )

122 changes: 80 additions & 42 deletions haddock_tbl_validation/validate_tbl.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import argparse
import os


def check_parenthesis(file):
open_parenthesis = re.compile('[\(]')
close_parenthesis = re.compile('[\)]')
Expand All @@ -16,29 +17,34 @@ def check_parenthesis(file):
for march in quotation_marks.finditer(file):
quote += 1
if opened != closed:
raise Exception("Problem with TBL file parentheses (%d opening for %d closing parentheses)" % (opened, closed))
raise Exception("Problem with TBL file parentheses (%d opening for %d "
"closing parentheses)" % (opened, closed))
if quote % 2 != 0:
raise Exception("Problem with TBL file, odd number of quotation marks (%d quotation marks)" % quote)
raise Exception("Problem with TBL file, odd number of quotation marks "
"(%d quotation marks)" % quote)


def validate_tbl(restraints, pcs = False):
def validate_tbl(restraints, pcs=False):
# List of selection keywords
selectors = ('name', 'resn', 'atom', 'resi', 'attr', 'segi')
output = ""
parentmatch = re.compile('[\(\)]')
# Global mode is activated outside any assign statement
mode = "global"
# Remove any carriage return/new line caracters
lines = restraints.replace('\r','').split("\n")
lines = restraints.replace('\r', '').split("\n")
# Line number
lnr = 0
# Temporary line storage for future output
tmp_output = None

for l in lines:
lnr+=1
lnr += 1
# Take everything which is before putative "!" (comment) caracter
if l.find("!") > -1:
if l.find("!") > -1:
l = l[:l.find("!")]
# Remove whitespaces and merge with previous line if in OR statement for AIR restraints
# Remove whitespaces and merge with previous line if in OR statement
# for AIR restraints
if mode != "format":
l = l.strip()
else:
Expand All @@ -49,7 +55,7 @@ def validate_tbl(restraints, pcs = False):
continue
# Check if all "" are closed
if l.count('"') % 2 > 0:
raise Exception('Unclosed " at line %d for line: %s' % (lnr,l))
raise Exception('Unclosed " at line %d for line: %s' % (lnr, l))
if mode in ("global", "postglobal"):
# Start of an assign statement
if l.lower().startswith("assi"):
Expand All @@ -58,7 +64,7 @@ def validate_tbl(restraints, pcs = False):
output += tmp_output
mode = "assign"
selections = []
# assign is the only caracter of the line, check following lines
# assign is the only caracter of the line,check following lines
if l.find("(") == -1:
continue
# Reset temporary buffer
Expand All @@ -68,14 +74,17 @@ def validate_tbl(restraints, pcs = False):
mode = "postassign"
selections = []
l = l[len("or"):]
# Case where "OR" statement is the only one on the line (rest of selection at the next line)
# Case where "OR" statement is the only one on the line
# (rest of selection at the next line)
if l == "":
continue
# We are not treating an assign params (postglobal) or at the end (global)
# and no "OR" restraint is present -> ERROR
# We are not treating an assign params (postglobal) or at the
# end (global) and no "OR" restraint is present -> ERROR
else:
raise Exception("Invalid TBL file: Unknown statement (line %d): %s" % (lnr, l))
# We check if the selection is made over two lines (thanks to "segid" keyword)
raise Exception("Invalid TBL file: Unknown statement "
"(line %d): %s" % (lnr, l))
# We check if the selection is made over two lines
# (thanks to "segid" keyword)
if mode == "postassign":
if l.count("segid") == 1:
mode = "format"
Expand All @@ -87,11 +96,12 @@ def validate_tbl(restraints, pcs = False):
matched = False
# We are looking for parenthesis as start of the selections
if mode in ("assign", "postassign"):
# Ambiguous restraint for two different pairs of atoms (ex: THR 1 B <-> ALA 2 A OR GLY 2 B <-> ASP 10 A )
# Ambiguous restraint for two different pairs of atoms
# (ex: THR 1 B <-> ALA 2 A OR GLY 2 B <-> ASP 10 A )
pos = l.find("(")
if pos != -1:
matched = True
l = l[pos+1:]
l = l[pos + 1:]
# We look for an "OR" selection
if mode == "postassign":
mode = "postsel"
Expand All @@ -115,8 +125,20 @@ def validate_tbl(restraints, pcs = False):
else:
mode = "assign"
matched = True
# Get back the parentheses content
s += l[:match.start()]
# print l[:match.start()]
# Get back the parentheses content and check
# for selection keywords
nb_and_or = l[:match.start()].count("and") + \
l[:match.start()].count("or")
nb_kwd = 0
for kwd in selectors:
nb_kwd += l[:match.start()].count(kwd)
if len(l[:match.start()]) and nb_kwd == nb_and_or + 1:
s += l[:match.start()]
elif len(l[:match.start()]):
raise Exception("Invalid selection syntax in-term "
"%s (stopped at line %d)" %
(l[:match.start()], lnr))
selections.append(s)
s = None
# Get the rest of the line
Expand All @@ -138,8 +160,10 @@ def validate_tbl(restraints, pcs = False):
# Selection parsed for "OR" line
if mode == "postassign":
if len(selections) != postselections:
raise Exception("Invalid TBL file: wrong number of selections: in-term %d, cross-term %d (stopped at line %d)" % (postselections, len(selections), lnr))
tmp_output +=" or"
raise Exception("Invalid TBL file: wrong number of selections:"
" in-term %d, cross-term %d (stopped at line "
"%d)" % (postselections, len(selections), lnr))
tmp_output += " or"
for s in selections:
tmp_output += "\t(%s)\n" % s
# We let the possibility for other "OR"
Expand All @@ -153,34 +177,37 @@ def validate_tbl(restraints, pcs = False):
if len(selections) == 5:
types = (" %.3f", " %.3f")
else:
raise Exception("Invalid TBL file: wrong number of selections (must be 5 in PCS mode)")
raise Exception("Invalid TBL file: wrong number of "
"selections (must be 5 in PCS mode)")
else:
if len(selections) == 2:
types = (" %.3f", " %.3f", " %.3f")
elif len(selections) == 4:
elif len(selections) == 4:
types = (" %.3f", " %.3f", " %.3f", " %d")
elif len(selections) == 5:
raise Exception("Invalid TBL file: wrong number of selections (can be 5 only in PCS mode)")
elif len(selections) == 6:
elif len(selections) == 5:
raise Exception("Invalid TBL file: wrong number of "
"selections (can be 5 only in PCS mode)")
elif len(selections) == 6:
types = (" %.3f", " %.3f")
else:
check_parenthesis(restraints)
raise Exception("Invalid TBL file: wrong number of selections (must be 2,4 or 6)")
raise Exception("Invalid TBL file: wrong number of "
"selections (must be 2,4 or 6)")
postselections = len(selections)
numbers = []
# Distance restraints parsing
if mode == "numbers":
ll = l.split()
for num in ll:
if len(numbers) == len(types):
if len(numbers) == len(types):
break
numbers.append(float(num))
if len(numbers) == len(types):
if len(numbers) == len(types):
tmp_output = "assign "
for s in selections:
for s in selections:
tmp_output += "\t(%s)\n" % s
tmp_output = tmp_output[:-len("\n")]
for n,t in zip(numbers,types):
for n, t in zip(numbers, types):
tmp_output += t % n
tmp_output += "\n"
mode = "postglobal"
Expand All @@ -192,7 +219,9 @@ def validate_tbl(restraints, pcs = False):
mode = "global"
# If mode is not back to global, something has not been processed properly
if mode != "global":
raise Exception("Invalid TBL file: Malformed ASSIGN statement (line %d), use --quick to check for putative syntax issues" % lastassign)
raise Exception("Invalid TBL file: Malformed ASSIGN statement "
"(line %d), use --quick to check for putative syntax "
"issues" % lastassign)
if not len(output.strip()):
raise Exception("Invalid or empty TBL file")

Expand All @@ -203,18 +232,24 @@ def validate_tbl(restraints, pcs = False):
output = output.replace("\n", "", 1)
return output


if __name__ == '__main__':
parser = argparse.ArgumentParser(description="This script validates a restraint file (*.tbl).\n")

parser.add_argument("file",
help="TBL file to be validated")
parser = argparse.ArgumentParser(description="This script validates a "
"restraint file (*.tbl).\n")

parser.add_argument("--pcs", action='store_true',
help="PCS mode")
parser.add_argument("file", help="TBL file to be validated")

parser.add_argument("--pcs", action='store_true', help="PCS mode")

parser.add_argument("--quick", action='store_true',
help="Check global formatting before going line by line (opening/closing parenthesis and quotation marks")

help="Check global formatting before going line by "
"line (opening/closing parenthesis and "
"quotation marks")

parser.add_argument("--silent", action='store_true',
help="Only output errors, do not output TBL file "
"at the end")

args = parser.parse_args()

if (args.quick):
Expand All @@ -225,7 +260,10 @@ def validate_tbl(restraints, pcs = False):
if os.path.exists(args.file):
tbldata = open(args.file).read()
# Parse and process the restraints
print validate_tbl(tbldata, args.pcs)
if args.silent:
validate_tbl(tbldata, args.pcs)
else:
print validate_tbl(tbldata, args.pcs)
else:
raise Exception("TBL file %s does not exist, check the path" % args.file)
raise Exception("TBL file %s does not exist, check the path" %
args.file)

0 comments on commit 212ec96

Please sign in to comment.