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distancetoatom.py
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distancetoatom.py
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'''
distancetoatom.py
Described at: https://www.pymolwiki.org/Distancetoatom
##################################################
Prints all distanced between the specified atom/coordinate/center
and all atoms within cutoff distance that are part of the selection.
All coordinates and distances can be saved in a csv-style text file report
and can be appended to a (custom) atom property, if defined.
##################################################
Author : Andreas Warnecke, Jared Sampson
email: [email protected], [email protected]
Date: June 2014
License: BSD2
Version: 1.0
##################################################
VERSION NOTES:
1.0 2014 First release
'''
from __future__ import print_function
import sys
from pymol import cmd
from pymol import stored
from chempy import cpv
from pymol import cmd
def get_coord(v):
if not isinstance(v, str):
try:
return v[:3]
except:
return False
if v.startswith('['):
return cmd.safe_list_eval(v)[:3]
try:
if cmd.count_atoms(v)==1:
# atom coordinates
return cmd.get_atom_coords(v)
else:
# more than one atom --> use "center"
# alt check!
if cmd.count_atoms('(alt *) and not (alt "")')!=0:
print("distancetoatom: warning! alternative coordinates found for origin, using center!")
view_temp=cmd.get_view()
cmd.zoom(v)
v=cmd.get_position()
cmd.set_view(view_temp)
return v
except:
return False
def distancetoatom(
origin='pk1',
cutoff=10,
filename=None,
selection='all',
state=0,
property_name='p.dist',
coordinates=0,
decimals=3,
sort=1,
quiet=1
):
'''
DESCRIPTION
distancetoatom.py
Described at: https://www.pymolwiki.org/Distancetoatom
Prints all distanced between the specified atom/coordinate/center
and all atoms within cutoff distance that are part of the selection.
All coordinates and distances can be saved in a csv-style text file report
and can be appended to a (custom) atom property, if defined.
USAGE
distancetoatom [ origin [, cutoff [, filename [, selection
[, state [, property_name [, coordinates [, decimals [, sort
[, quiet ]]]]]]]]]]
ARGUMENTS
NAME TYPE FUNCTION
origin: <list> defines the coordinates for the origin and can be:
<str> 1. a list with coordinates [x,y,z]
2. a single atom selection string {default='pk1'}
3. a multi-atom selection string (center will be used)
cutoff <float> sets the maximum distance {default: 10}
filename <str> filename for optional output report. {default=None}
set to e.g. 'report.txt' to create a report
(omit or set to '', None, 0 or False to disable)
selection <str> can be used to define/limit the measurment to specific
sub-selections {default='all'}
state <int> object state, {default=0} # = current
property_name <str> the distance will be stored in this property {p.dist}
set "" to disable
coordinates <int> toggle whether atom coordinated will be reported {0}
decimals <int> decimals for coordinates and distance:
default = 3 # = max. PDB resolution
sort <int> Sorting by distance?
1: ascending (default)
0: no sorting (by names)
-1: descending
quiet <bool> toggle verbosity
'''
# keyword check
try:
selection = '(%s)'%selection
ori=get_coord(origin)
if not ori:
print("distancetoatom: aborting - check input for 'origin'!")
return False
cutoff = abs(float(cutoff))
filename = str(filename)
state = abs(int(state))
if (not int(state)):
state=cmd.get_state()
cmd.set('state', state) # distance by state
property_name = str(property_name)
decimals = abs(int(decimals))
sort = int(sort)
coordinates=bool(int(coordinates))
quiet=bool(int(quiet))
except:
print('distancetoatom: aborting - input error!')
return False
# round origin
ori = [round(x,decimals) for x in ori]
# report?
if filename in ['', '0', 'False', 'None']:
filename=False
else:
try:
report=open(filename,'w') # file for writing
except:
print('distancetoatom: Unable to open report file! - Aborting!')
return False
# temporary name for pseudoatom
tempname = cmd.get_unused_name('temp_name')
tempsel = cmd.get_unused_name('temp_sel')
#origin
cmd.pseudoatom(object=tempname, resi=1, pos=ori)
# select atoms within cutoff
cmd.select(tempsel, '(%s around %f) and (%s) and state %d' %(tempname, cutoff, selection, state))
cmd.delete(tempname)
# single atom ori and part of selection
# avoid double reporting!
single_atom_ori=False
try:
if cmd.count_atoms('(%s) and (%s) and (%s)'%(selection, tempsel, origin))==1:
single_atom_ori=True
except: pass
# pass= coordinates or multi-atom or single, not selected --> report ori
# atom list
stored.temp=[]
cmd.iterate(tempsel, 'stored.temp.append([model, segi, chain, resn, resi, name, alt])')
# custom properties? # conditional disabling
if (property_name==''): property_name=False
if ((cmd.get_version()[1]<1.7) and (property_name not in ['b','q'])):
property_name=False
# calculate the distances, creating list
distance_list=[]
if (not single_atom_ori):
distance_list.append(['ORIGIN: '+str(origin), ori[0], ori[1], ori[2], 0.0])
for atom in stored.temp:
atom_name = ('/%s/%s/%s/%s`%s/%s`%s'%(atom[0], atom[1], atom[2], atom[3], atom[4], atom[5], atom[6]))
atom_xyz = [round(x, decimals) for x in cmd.get_atom_coords(atom_name)]
atom_dist = round(cpv.distance(ori, atom_xyz), decimals)
distance_list.append([atom_name,atom_xyz[0],atom_xyz[1],atom_xyz[2], atom_dist])
# create property with distance (can be used for coloring, labeling etc)
if property_name:
try:
cmd.alter(atom_name, '%s=%f'%(property_name, atom_dist))
except:
# I'm not sure alter raises exceptions if the property is illegal
property_name=False
# sort list, if selected
if sort>0: distance_list.sort(key=lambda dist: dist[4])
elif sort<0: distance_list.sort(key=lambda dist: dist[4], reverse=True)
# add header
distance_list=[['Atom Macro ID',
'x-coord',
'y-coord',
'z-coord',
'distance_to_origin']
]+distance_list
if ((not quiet) and (filename)):
# Hijack stdout to print to file and console
class logboth(object):
def __init__(self, *files):
self.files = files
def write(self, obj):
for f in self.files:
f.write(obj)
originalstdout = sys.stdout
sys.stdout = logboth(sys.stdout, report)
for entry in distance_list:
if coordinates:
output= '%s, %s, %s, %s, %s' %(entry[0],entry[1],entry[2],entry[3],entry[4]) #csv style
else:
output= '%s, %s' %(entry[0],entry[4]) #csv style
if (not quiet):
print(output)
elif filename:
report.write(output+'\n')
# restore regular stdout
if ((not quiet) and (filename)): sys.stdout = originalstdout
# close file
if filename: report.close()
if (not quiet):
if property_name: print('Distances saved to property: %s' %str(property_name))
else: print('Distances NOT saved to property (illegal custom property)')
# remove temp. selection
cmd.delete(tempsel)
# return list for potential use:
if coordinates:
if len(distance_list)>2: # prevents crash if list is otherwise empty
distance_list2=list(map(distance_list.__getitem__, [1,4]))
return distance_list2
else: return distance_list
else:
return distance_list
################################################################################
cmd.extend( 'distancetoatom', distancetoatom );
cmd.auto_arg[0]['distancetoatom']=[lambda: cmd.Shortcut(['all', '[0,0,0]', 'pk1']), 'origin=', ',']
cmd.auto_arg[1]['distancetoatom']=[lambda: cmd.Shortcut(['7']), 'cutoff=', ',']
cmd.auto_arg[2]['distancetoatom']=[lambda: cmd.Shortcut(['None','distancetoatom_report.txt']), 'filename=', ',']
cmd.auto_arg[3]['distancetoatom']=[lambda: cmd.Shortcut(['selection=all, state=0, property_name=p.dist, coordinates=0, decimals=3, sort=1']), 'remaining (defaults)...', '']
################################################################################