From 591f456def2674f828f47eabd058778283f7870c Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Thu, 11 Apr 2019 16:49:12 +0200
Subject: [PATCH] some lgtm fixes for python scripts
---
.../TUTORIAL_SAXS-AACG/martiniFormFactor_p2.py | 13 +++----------
.../TUTORIAL_SAXS-AACG/martiniFormFactor_p3.py | 11 +++--------
2 files changed, 6 insertions(+), 18 deletions(-)
diff --git a/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p2.py b/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p2.py
index 71ffd26f0..162fdabe4 100644
--- a/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p2.py
+++ b/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p2.py
@@ -7,9 +7,6 @@
from __future__ import division
import sys,logging
logging.basicConfig(format='%(levelname)-7s %(message)s',level=9)
-import os.path
-import re
-
# This is a simple and versatily option class that allows easy
# definition and parsing of options.
@@ -286,7 +283,6 @@ def aver(b):
# [ name, resname, resid, chain, x, y, z ]
def mapCG(r):
p = CoarseGrained.mapping[r[0][1]] # Mapping for this residue
- flat_p = [item for sublist in p for item in sublist]
# Get the atom_name, mass, coordinates (x,y,z), atom id for all atoms in the residue
a = [(i[0],CoarseGrained.mass.get(i[0][0],0),i[4:7],i[7]) for i in r]
# Store weight, coordinate and index for atoms that match a bead
@@ -301,7 +297,7 @@ def mapCG(r):
#######################
## 4 # STRUCTURE I/O ## -> @IO <-
#######################
-import logging,math,random,sys
+import math,sys
#----+---------+
## A | PDB I/O |
@@ -534,8 +530,6 @@ class Residue(list):
for i in self:
if i[0] == tag:
return i
- else:
- return
if tag[1]:
return [i for i in self if tag[0] in i[0]] # Return partial matches
else:
@@ -826,7 +820,7 @@ class Chain:
#############
## 8 # MAIN # -> @MAIN <-
#############
-import sys,logging,random,math,os,re
+import sys,math
def main(options):
# Check whether to read from a gro/pdb file or from stdin
@@ -1049,7 +1043,7 @@ def main(options):
if __name__ == '__main__':
- import sys,logging,time
+ import sys,time
start = time.time()
stloc = time.localtime(start)
@@ -1060,7 +1054,6 @@ if __name__ == '__main__':
logging.error("NO INPUT! Try to use the option -h for help.")
sys.exit(1)
- options = options
options = option_parser(args,options)
diff --git a/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p3.py b/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p3.py
index 5830224dd..145fd540c 100644
--- a/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p3.py
+++ b/user-doc/tutorials/others/isdb-2/TUTORIAL_SAXS-AACG/martiniFormFactor_p3.py
@@ -7,8 +7,6 @@
import sys,logging
logging.basicConfig(format='%(levelname)-7s %(message)s',level=9)
-import os.path
-import re
# This is a simple and versatily option class that allows easy
@@ -283,7 +281,6 @@ def aver(b):
# [ name, resname, resid, chain, x, y, z ]
def mapCG(r):
p = CoarseGrained.mapping[r[0][1]] # Mapping for this residue
- flat_p = [item for sublist in p for item in sublist]
# Get the atom_name, mass, coordinates (x,y,z), atom id for all atoms in the residue
a = [(i[0],CoarseGrained.mass.get(i[0][0],0),i[4:7],i[7]) for i in r]
# Store weight, coordinate and index for atoms that match a bead
@@ -298,7 +295,7 @@ def mapCG(r):
#######################
## 4 # STRUCTURE I/O ## -> @IO <-
#######################
-import logging,math,random,sys
+import math,sys
#----+---------+
## A | PDB I/O |
@@ -671,7 +668,6 @@ class Chain:
# Return the chain slice
return newchain
return self.sequence[other]
- return self.sequence[other]
# Extract a piece of a chain as a new chain
def __getslice__(self,i,j):
@@ -839,7 +835,7 @@ class Chain:
#############
## 8 # MAIN # -> @MAIN <-
#############
-import sys,logging,random,math,os,re
+import sys,math
def main(options):
# Check whether to read from a gro/pdb file or from stdin
@@ -1062,7 +1058,7 @@ def main(options):
if __name__ == '__main__':
- import sys,logging,time
+ import sys,time
start = time.time()
stloc = time.localtime(start)
@@ -1073,7 +1069,6 @@ if __name__ == '__main__':
logging.error("NO INPUT! Try to use the option -h for help.")
sys.exit(1)
- options = options
options = option_parser(args,options)
if options["-f"].value is None:
--
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