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Output performed with loggers. Adds options --no-print. (#12)

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Output performed with loggers.  Adds --quiet and --verbose options.
This commit is contained in:
Toni G
2016-04-29 08:21:35 +02:00
committed by Matvey Adzhigirey
parent ca6224433a
commit 5fbbdd4868
23 changed files with 4987 additions and 217 deletions
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29
propka/bonds.py
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@@ -5,6 +5,7 @@ from __future__ import print_function
import pickle,sys,os,math,propka.calculations
import pkg_resources
from propka.lib import info, warning
class bondmaker:
def __init__(self):
@@ -111,14 +112,14 @@ class bondmaker:
""" Finds bonds proteins based on the way atoms
normally bond in proteins"""
print('++++ Side chains ++++')
info('++++ Side chains ++++')
# side chains
for chain in protein.chains:
for residue in chain.residues:
if residue.resName.replace(' ','') not in ['N+','C-']:
self.find_bonds_for_side_chain(residue.atoms)
print('++++ Backbones ++++')
info('++++ Backbones ++++')
# backbone
last_residues = []
for chain in protein.chains:
@@ -128,12 +129,12 @@ class bondmaker:
self.connect_backbone(chain.residues[i-1], chain.residues[i])
last_residues.append(chain.residues[i])
print('++++ terminal oxygen ++++')
info('++++ terminal oxygen ++++')
# terminal OXT
for last_residue in last_residues:
self.find_bonds_for_terminal_oxygen(last_residue)
print('++++ cysteines ++++')
info('++++ cysteines ++++')
# Cysteines
for chain in protein.chains:
for i in range(0,len(chain.residues)):
@@ -349,9 +350,9 @@ class bondmaker:
ylen = ymax-ymin
zlen = zmax-zmin
#print('x range: [%6.2f;%6.2f] %6.2f'%(xmin,xmax,xlen))
#print('y range: [%6.2f;%6.2f] %6.2f'%(ymin,ymax,ylen))
#print('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
#info('x range: [%6.2f;%6.2f] %6.2f'%(xmin,xmax,xlen))
#info('y range: [%6.2f;%6.2f] %6.2f'%(ymin,ymax,ylen))
#info('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
# how many boxes do we need in each dimension?
# NOTE: math.ceil() returns an int in python3 and a float in
@@ -361,9 +362,9 @@ class bondmaker:
self.no_box_y = max(1, int(math.ceil(ylen/box_size)))
self.no_box_z = max(1, int(math.ceil(zlen/box_size)))
#print('No. box x: %6.2f'%self.no_box_x)
#print('No. box y: %6.2f'%self.no_box_y)
#print('No. box z: %6.2f'%self.no_box_z)
#info('No. box x: %6.2f'%self.no_box_x)
#info('No. box y: %6.2f'%self.no_box_y)
#info('No. box z: %6.2f'%self.no_box_z)
# initialize boxes
self.boxes = {}
@@ -400,7 +401,7 @@ class bondmaker:
# No box exists for this coordinate
pass
#print(atom,'->',key,':',len(self.boxes[key]))
#info(atom,'->',key,':',len(self.boxes[key]))
return
@@ -415,7 +416,7 @@ class bondmaker:
if atom1 == atom2:
return
#print('making bond for',atom1,atom2)
#info('making bond for',atom1,atom2)
if not atom1 in atom2.bonded_atoms:
atom2.bonded_atoms.append(atom1)
@@ -465,12 +466,12 @@ if __name__ == '__main__':
import protein, pdb, sys,os
arguments = sys.argv
if len(arguments) != 2:
print('Usage: bonds.py <pdb_file>')
info('Usage: bonds.py <pdb_file>')
sys.exit(0)
filename = arguments[1]
if not os.path.isfile(filename):
print('Error: Could not find \"%s\"'%filename)
info('Error: Could not find \"%s\"' % filename)
sys.exit(1)
pdblist = pdb.readPDB(filename)