projects
/
django_unres.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
a2e1f49
)
saxs input data normalization and plot for input pdb
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Thu, 25 Jan 2018 20:50:47 +0000
(21:50 +0100)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Thu, 25 Jan 2018 20:50:47 +0000
(21:50 +0100)
django_simple/todo/jobfiles.py
patch
|
blob
|
history
django_simple/todo/models.py
patch
|
blob
|
history
django_simple/todo/templates/details.html
patch
|
blob
|
history
django_simple/todo/templates/details1.html
patch
|
blob
|
history
files/pbs8.csh
patch
|
blob
|
history
files/pbs8_new.csh
patch
|
blob
|
history
files/plot_saxs.py
patch
|
blob
|
history
diff --git
a/django_simple/todo/jobfiles.py
b/django_simple/todo/jobfiles.py
index
df2ce65
..
d9b8c7c
100644
(file)
--- a/
django_simple/todo/jobfiles.py
+++ b/
django_simple/todo/jobfiles.py
@@
-398,13
+398,20
@@
CUTOFF=7.00000 WCORR4=0.00000"""
f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
if instance.saxs_data != '':
f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
if instance.saxs_data != '':
+ saxs_r=[]
+ saxs_P=[]
+ saxs_norm=0
fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
lines=instance.saxs_data.split('\n')
for line in lines:
tmp=line.split()
if len(tmp)==2:
f.write(tmp[0]+' '+tmp[1]+'\n')
fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
lines=instance.saxs_data.split('\n')
for line in lines:
tmp=line.split()
if len(tmp)==2:
f.write(tmp[0]+' '+tmp[1]+'\n')
- fsaxs.write(tmp[0]+' '+tmp[1]+'\n')
+ saxs_r.append(tmp[0])
+ saxs_P.append(float(tmp[1]))
+ saxs_norm += float(tmp[1])
+ for r,p in zip(saxs_r,saxs_P):
+ fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
fsaxs.close()
f.write(w+'\n')
fsaxs.close()
f.write(w+'\n')
diff --git
a/django_simple/todo/models.py
b/django_simple/todo/models.py
index
1c07a2c
..
765e3c6
100644
(file)
--- a/
django_simple/todo/models.py
+++ b/
django_simple/todo/models.py
@@
-83,7
+83,7
@@
class Task(models.Model):
#saxs
scal_rad = models.FloatField(default=1.0)
#saxs
scal_rad = models.FloatField(default=1.0)
- wsaxs = models.FloatField(default=100.0)
+ wsaxs = models.FloatField(default=1000.0)
saxs_data = models.TextField(max_length=10000,default='')
saxs_data = models.TextField(max_length=10000,default='')
diff --git
a/django_simple/todo/templates/details.html
b/django_simple/todo/templates/details.html
index
b567e6e
..
3484627
100644
(file)
--- a/
django_simple/todo/templates/details.html
+++ b/
django_simple/todo/templates/details.html
@@
-513,7
+513,7
@@
Created {{ task.created_date }}
{% if task.saxs_data != "" %}
<li class="list-group-item task-item">
<div class="col-md-2"> P(r) of input SAXS data and
{% if task.saxs_data != "" %}
<li class="list-group-item task-item">
<div class="col-md-2"> P(r) of input SAXS data and
- calculated for 5 models </div>
+ calculated for 5 models and the input pdb</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
width="500"> </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
width="500"> </div>
diff --git
a/django_simple/todo/templates/details1.html
b/django_simple/todo/templates/details1.html
index
e1f4578
..
5681fd9
100644
(file)
--- a/
django_simple/todo/templates/details1.html
+++ b/
django_simple/todo/templates/details1.html
@@
-513,7
+513,7
@@
Created {{ task.created_date }}
{% if task.saxs_data != "" %}
<li class="list-group-item task-item">
<div class="col-md-2"> P(r) of input SAXS data and
{% if task.saxs_data != "" %}
<li class="list-group-item task-item">
<div class="col-md-2"> P(r) of input SAXS data and
- calculated for 5 models </div>
+ calculated for 5 models and the input pdb</div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
width="500"> </div>
<div class="col-md-10"> <img
src="/myfiles/download-file/{{task.jobdirname}}/saxs.png"
width="500"> </div>
diff --git
a/files/pbs8.csh
b/files/pbs8.csh
index
82e7143
..
f413281
100755
(executable)
--- a/
files/pbs8.csh
+++ b/
files/pbs8.csh
@@
-78,16
+78,21
@@
end
/users2/local/pymol_1.6/pymol -c ../files/model.pml
/users2/local/pymol_1.6/pymol -c ../files/model.pml
-awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
-/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
-rm tmp.pdb
-
-/users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
-/users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
-/users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
-/users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
-/users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
-rm plik1.pdb
+if ( `grep -c pdbref file.inp` ) then
+ awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+ /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
+ rm tmp.pdb
+
+ /users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
+ /users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
+ /users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
+ /users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
+ /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+ if (-e saxs.data) then
+ awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
+ endif
+ rm plik1.pdb
+endif
if (-e saxs.data) then
awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
if (-e saxs.data) then
awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
diff --git
a/files/pbs8_new.csh
b/files/pbs8_new.csh
index
67dcc8c
..
1713c99
100755
(executable)
--- a/
files/pbs8_new.csh
+++ b/
files/pbs8_new.csh
@@
-78,16
+78,21
@@
end
/users2/local/pymol_1.6/pymol -c ../files/model.pml
/users2/local/pymol_1.6/pymol -c ../files/model.pml
-awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
-/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
-rm tmp.pdb
-
-/users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
-/users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
-/users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
-/users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
-/users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
-rm plik1.pdb
+if ( `grep -c pdbref file.inp` ) then
+ awk '{printf "%s%s%s\n",substr($0,0,21)," ",substr($0,23)}' plik.pdb > tmp.pdb
+ /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp.pdb > plik1.pdb
+ rm tmp.pdb
+
+ /users2/local/bin/tmscore MODEL1.pdb plik1.pdb > tmscore1.out
+ /users2/local/bin/tmscore MODEL2.pdb plik1.pdb > tmscore2.out
+ /users2/local/bin/tmscore MODEL3.pdb plik1.pdb > tmscore3.out
+ /users2/local/bin/tmscore MODEL4.pdb plik1.pdb > tmscore4.out
+ /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out
+ if (-e saxs.data) then
+ awk -f ../files/saxs_dist.awk plik1.pdb > plik_saxs.data
+ endif
+ rm plik1.pdb
+endif
if (-e saxs.data) then
awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
if (-e saxs.data) then
awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data
diff --git
a/files/plot_saxs.py
b/files/plot_saxs.py
index
292550b
..
d1ff7f6
100755
(executable)
--- a/
files/plot_saxs.py
+++ b/
files/plot_saxs.py
@@
-7,6
+7,7
@@
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import numpy as np
import sys
import matplotlib.cm as cm
import numpy as np
import sys
+import os.path
x,y= np.loadtxt('saxs.data',usecols=(0,1),unpack=True)
x1,y1= np.loadtxt('MODEL1_saxs.data',usecols=(0,2),unpack=True)
x,y= np.loadtxt('saxs.data',usecols=(0,1),unpack=True)
x1,y1= np.loadtxt('MODEL1_saxs.data',usecols=(0,2),unpack=True)
@@
-26,5
+27,10
@@
plt.plot(x2,y2,'-',color='lime')
plt.plot(x3,y3,'-',color='blue')
plt.plot(x4,y4,'-',color='magenta')
plt.plot(x5,y5,'-',color='cyan')
plt.plot(x3,y3,'-',color='blue')
plt.plot(x4,y4,'-',color='magenta')
plt.plot(x5,y5,'-',color='cyan')
-plt.legend(['reference','MODEL1','MODEL2','MODEL3','MODEL4','MODEL5'])
+if os.path.isfile('plik_saxs.data'):
+ x6,y6= np.loadtxt('plik_saxs.data',usecols=(0,2),unpack=True)
+ plt.plot(x6,y6,'--',color='black')
+ plt.legend(['reference','MODEL1','MODEL2','MODEL3','MODEL4','MODEL5','input pdb'])
+else:
+ plt.legend(['reference','MODEL1','MODEL2','MODEL3','MODEL4','MODEL5'])
plt.savefig('saxs.png')
plt.savefig('saxs.png')