From 9069ece776b62822e3b4e450468195d60db22101 Mon Sep 17 00:00:00 2001
From: cristinapaissoni <cristina.paissoni@gmail.com>
Date: Thu, 2 May 2019 15:51:42 +0200
Subject: [PATCH] Fixed files martiniFormFactor (#473)
---
.../martiniFormFactor_p2.py | 54 +++++++++----------
.../martiniFormFactor_p3.py | 36 ++++---------
2 files changed, 35 insertions(+), 55 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 162fdabe4..7c1884b08 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
@@ -7,6 +7,7 @@
from __future__ import division
import sys,logging
logging.basicConfig(format='%(levelname)-7s %(message)s',level=9)
+
# This is a simple and versatily option class that allows easy
# definition and parsing of options.
@@ -29,7 +30,6 @@ class Option:
self.value = [ self.func(i) for i in v ]
options = [
-
("-f", Option(str,1,None, "PDB Input file.\n\t\tDifferent chains (or chain breaks) should be separated by TER or named with different chain-ID.\n\t\tOnly one model is expected. ENDMDL is accepted only at the end of the file.")),
("-dat", Option(str,1,None,"Experimental Data Input file.\n\t\tEach line should contain momentum transfer (in inverse Ang) and non-zero intensity, separated by blanks or comma.\n\t\tIf momentum transfer is in inverse nm, use the option \"-unit nm\"")),
("-unit", Option(str,1,"Ang","Unit of the momentum transfer [Ang/nm]. Default: Ang")),
@@ -70,8 +70,6 @@ def help():
sys.exit()
-
-
#################################################
## 2 # HELPER FUNCTIONS, CLASSES AND SHORTCUTS ## -> @FUNC <-
#################################################
@@ -530,6 +528,7 @@ class Residue(list):
for i in self:
if i[0] == tag:
return i
+ return
if tag[1]:
return [i for i in self if tag[0] in i[0]] # Return partial matches
else:
@@ -631,6 +630,10 @@ class Chain:
def __eq__(self,other):
return (self.seq == other.seq and
self.breaks == other.breaks )
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
# Extract a residue by number or the list of residues of a given type
# This facilitates selecting residues for links, like chain["CYS"]
@@ -646,30 +649,27 @@ class Chain:
for i in self.cg():
if other == i[:4]:
return i
- else:
- for i in self.atoms():
- if other[:3] == i[:3]:
- return i
- else:
- return []
+ for i in self.atoms():
+ if other[:3] == i[:3]:
+ return i
+ return []
+ elif type(other) == slice:
+ # This implements the old __getslice__ method
+ i, j = other.start, other.stop
+ newchain = Chain(self.options, name=self.id)
+ # Extract the slices from all lists
+ for attr in self._attributes:
+ setattr(newchain, attr, getattr(self, attr)[i:j])
+ # Breaks that fall within the start and end of this chain need to be passed on.
+ # Residue numbering is increased by 20 bits!!
+ ch_sta, ch_end = newchain.residues[0][0][2], newchain.residues[-1][0][2]
+ newchain.breaks = [crack for crack in self.breaks if ch_sta < (crack << 20) < ch_end]
+ newchain.natoms = len(newchain.atoms())
+ # newchain.type()
+ # Return the chain slice
+ return newchain
return self.sequence[other]
- # Extract a piece of a chain as a new chain
- def __getslice__(self,i,j):
- newchain = Chain(self.options,name=self.id)
- # Extract the slices from all lists
- for attr in self._attributes:
- setattr(newchain, attr, getattr(self,attr)[i:j])
- # Breaks that fall within the start and end of this chain need to be passed on.
- # Residue numbering is increased by 20 bits!!
- # XXX I don't know if this works.
- ch_sta,ch_end = newchain.residues[0][0][2],newchain.residues[-1][0][2]
- newchain.breaks = [crack for crack in self.breaks if ch_sta < (crack<<20) < ch_end]
- newchain.natoms = len(newchain.atoms())
- newchain.type()
- # Return the chain slice
- return newchain
-
def _contains(self,atomlist,atom):
atnm,resn,resi,chn = atom
@@ -1056,7 +1056,6 @@ if __name__ == '__main__':
options = option_parser(args,options)
-
if options["-f"].value is None:
logging.error("No input PDB file. Try to use the option -h for help.")
sys.exit(1)
@@ -1065,11 +1064,8 @@ if __name__ == '__main__':
logging.error("No input data file. Try to use the option -h for help.")
sys.exit(1)
-
-
main(options)
-
stop = time.time()
stoploc = time.localtime(stop)
logging.info("\n\nEnded at time: {}:{}:{} of {}/{}/{}.".format(stoploc[3],stoploc[4],stoploc[5],stoploc[2],stoploc[1],stoploc[0]))
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 145fd540c..bb363def6 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
@@ -4,7 +4,6 @@
###################################
## 1 # OPTIONS AND DOCUMENTATION ## -> @DOC <-
###################################
-
import sys,logging
logging.basicConfig(format='%(levelname)-7s %(message)s',level=9)
@@ -528,8 +527,7 @@ class Residue(list):
for i in self:
if i[0] == tag:
return i
- else:
- return
+ return
if tag[1]:
return [i for i in self if tag[0] in i[0]] # Return partial matches
else:
@@ -631,6 +629,10 @@ class Chain:
def __eq__(self,other):
return (self.seq == other.seq and
self.breaks == other.breaks )
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
# Extract a residue by number or the list of residues of a given type
# This facilitates selecting residues for links, like chain["CYS"]
@@ -646,12 +648,10 @@ class Chain:
for i in self.cg():
if other == i[:4]:
return i
- else:
- for i in self.atoms():
- if other[:3] == i[:3]:
- return i
- else:
- return []
+ for i in self.atoms():
+ if other[:3] == i[:3]:
+ return i
+ return []
elif type(other) == slice:
# This implements the old __getslice__ method
i, j = other.start, other.stop
@@ -669,22 +669,6 @@ class Chain:
return newchain
return self.sequence[other]
- # Extract a piece of a chain as a new chain
- def __getslice__(self,i,j):
- newchain = Chain(self.options,name=self.id)
- # Extract the slices from all lists
- for attr in self._attributes:
- setattr(newchain, attr, getattr(self,attr)[i:j])
- # Breaks that fall within the start and end of this chain need to be passed on.
- # Residue numbering is increased by 20 bits!!
- # XXX I don't know if this works.
- ch_sta,ch_end = newchain.residues[0][0][2],newchain.residues[-1][0][2]
- newchain.breaks = [crack for crack in self.breaks if ch_sta < (crack<<20) < ch_end]
- newchain.natoms = len(newchain.atoms())
- newchain.type()
- # Return the chain slice
- return newchain
-
def _contains(self,atomlist,atom):
atnm,resn,resi,chn = atom
@@ -1079,7 +1063,7 @@ if __name__ == '__main__':
logging.error("No input data file. Try to use the option -h for help.")
sys.exit(1)
- main(options)
+ main(options)
stop = time.time()
stoploc = time.localtime(stop)
--
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