def visualize_orientation(direction, center=[0, 0, 0], scale=1.0, symmetric=False, color="green", color2="red"):
"""
Draw an arrow. Helper function for "helix_orientation" etc.
"""
from pymol import cgo
color_list = cmd.get_color_tuple(color)
color2_list = cmd.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([radius, 0.8, 0.8, 0.8])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([radius, 0.8, 0.8, 0.8])
obj.extend(color2_list)
coneend = cpv.add(end, cpv.scale(direction, 4.0 * radius))
if cmd.get_version()[1] >= 1.2:
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([radius * 1.75, 0.0])
obj.extend(color_list * 2)
obj.extend([1.0, 1.0]) # Caps
cmd.load_cgo(obj, get_unused_name("oriVec"), zoom=0)
def addSuccess(self, test):
if not (self.showAll and test.timings):
return super(PyMOLTestResult, self).addSuccess(test)
unittest.result.TestResult.addSuccess(self, test)
msg = 'ok (%s)' % ', '.join(
('%s: %.3fs' % (m, t) if m else '%.3fs' % t)
for (m, t) in test.timings)
self.stream.writeln(msg)
filename = os.getenv("PYMOLTESTTIMINGS",
os.path.join(pymol_test_dir, "timings.tab"))
with open(filename, "a") as handle:
for i, (m, t) in enumerate(test.timings):
version = cmd.get_version()
buildinfo = version[3:] or [0, "", 0]
print('\t'.join([
'%f' % time.time(),
'%012x' % uuid.getnode(),
'%f' % t,
type(test).__name__ + '.' + test._testMethodName,
str(m or i),
version[0],
buildinfo[1],
'%d' % buildinfo[2],
platform.platform(),
platform.node(),
]), file=handle)
def addSuccess(self, test):
if not (self.showAll and test.timings):
return super(PyMOLTestResult, self).addSuccess(test)
unittest.result.TestResult.addSuccess(self, test)
msg = 'ok (%s)' % ', '.join(
('%s: %.3fs' % (m, t) if m else '%.3fs' % t)
for (m, t) in test.timings)
self.stream.writeln(msg)
filename = os.getenv("PYMOLTESTTIMINGS",
os.path.join(pymol_test_dir, "timings.tab"))
with open(filename, "a") as handle:
for i, (m, t) in enumerate(test.timings):
version = cmd.get_version()
buildinfo = version[3:] or [0, "", 0]
print('\t'.join([
'%f' % time.time(),
'%012x' % uuid.getnode(),
'%f' % t,
type(test).__name__ + '.' + test._testMethodName,
str(m or i),
version[0],
buildinfo[1],
'%d' % buildinfo[2],
platform.platform(),
platform.node(),
]),
file=handle)
def test_version(self):
v = cmd.get_version()[:3]
# check types
self.assertTrue(isinstance(v[0], str))
self.assertTrue(isinstance(v[1], float))
self.assertTrue(isinstance(v[2], int))
# check that major of str and float match
self.assertEqual(int(v[0].split('.')[0]), int(v[1]))
def visualize_orientation(direction,
center=[0, 0, 0],
scale=1.0,
symmetric=False,
color='green',
color2='red'):
'''
Draw an arrow. Helper function for "helix_orientation" etc.
'''
from pymol import cgo
color_list = cmd.get_color_tuple(color)
color2_list = cmd.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([
radius,
0.8,
0.8,
0.8,
])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([
radius,
0.8,
0.8,
0.8,
])
obj.extend(color2_list)
coneend = cpv.add(end, cpv.scale(direction, 4.0 * radius))
if cmd.get_version()[1] >= 1.2:
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([
radius * 1.75,
0.0,
])
obj.extend(color_list * 2)
obj.extend([
1.0,
1.0, # Caps
])
cmd.load_cgo(obj, get_unused_name('oriVec'), zoom=0)
def testLoadPWG(self):
if sys.version_info[0] < 3:
import urllib2
else:
import urllib.request as urllib2
content_index = b'Hello World\n'
port = 8084
baseurl = 'http://localhost:%d' % port
def urlread(url):
handle = urllib2.urlopen(url, timeout=3.0)
try:
return handle.info(), handle.read()
finally:
handle.close()
with testing.mkdtemp() as rootdir:
filename = os.path.join(rootdir, 'index.html')
with open(filename, 'wb') as handle:
handle.write(content_index)
filename = os.path.join(rootdir, 'start.pwg')
with open(filename, 'w') as handle:
handle.write('root %s\n' % rootdir)
handle.write('port %d\n' % port)
handle.write('header add Test-Key Test-Value\n') # new in 2.4
cmd.load(filename)
header, content = urlread(baseurl)
self.assertEqual(header['Test-Key'], 'Test-Value')
self.assertEqual(content, content_index)
# Warning: can't call locking functions here, will dead-lock
# get_version is non-locking since 1.7.4
header, content = urlread(baseurl + '/apply/pymol.cmd.get_version')
content = content.decode('ascii', errors='ignore')
self.assertTrue(content, cmd.get_version()[0] in content)
def testLoadPWG(self):
if sys.version_info[0] < 3:
import urllib2
else:
import urllib.request as urllib2
content_index = b'Hello World\n'
port = 8084
baseurl = 'http://localhost:%d' % port
def urlread(url):
handle = urllib2.urlopen(url, timeout=3.0)
try:
return handle.read()
finally:
handle.close()
with testing.mkdtemp() as rootdir:
filename = os.path.join(rootdir, 'index.html')
with open(filename, 'wb') as handle:
handle.write(content_index)
filename = os.path.join(rootdir, 'start.pwg')
with open(filename, 'w') as handle:
handle.write('root %s\n' % rootdir)
handle.write('port %d\n' % port)
cmd.load(filename)
content = urlread(baseurl)
self.assertEqual(content, content_index)
# Warning: can't call locking functions here, will dead-lock
# get_version is non-locking since 1.7.4
content = urlread(baseurl + '/apply/pymol.cmd.get_version')
content = content.decode('ascii', errors='ignore')
self.assertTrue(content, cmd.get_version()[0] in content)
def sst(selection='(all)', raw='', state=-1, quiet=1):
'''
DESCRIPTION
Secondary structure assignment with SST.
http://lcb.infotech.monash.edu.au/sstweb/
SEE ALSO
dss, dssp, stride
'''
try:
import urllib2
except ImportError:
import urllib.request as urllib2
state, quiet = int(state), int(quiet)
ss_map = {
'C': 'L',
'E': 'S',
'G': 'H',
'H': 'H',
'I': 'H',
'g': 'H',
'h': 'H',
'i': 'H',
'3': 'L',
'4': 'L',
'5': 'L',
'T': 'L',
'-': 'L',
'|': 'L',
':': 'H',
}
ss_dict = {}
boundary = '192.168.1.80.500.9981.1375391031.267.10'
for model in cmd.get_object_list(selection):
pdbstr = cmd.get_pdbstr('%s & guide & (%s)' % (model, selection),
state)
body = '\r\n'.join([
'--' + boundary,
'Content-Disposition: form-data; name="sstverstr"',
'Content-Type: text/plain',
'',
'v1.6',
'--' + boundary,
'Content-Disposition: file; name="pdb_file"; filename="abc.pdb"',
'Content-Type: text/plain',
'',
pdbstr,
'--' + boundary + '--',
'',
])
body = body.encode('ascii', 'ignore')
try:
request = urllib2.Request(
data=body,
url='http://lcb.infotech.monash.edu.au/sstweb2/formaction.php')
request.add_header(
'User-agent',
'PyMOL ' + cmd.get_version()[0] + ' ' + cmd.sys.platform)
request.add_header('Content-type',
'multipart/form-data; boundary=%s' % boundary)
request.add_header('Content-length', len(body))
lines = urllib2.urlopen(request).readlines()
except urllib2.URLError:
print(' Error: URL request failed')
raise CmdException
if sys.version_info[0] > 2:
lines = (line.decode('ascii', 'ignore') for line in lines)
lines = iter(lines)
for line in lines:
if line.startswith('..........RESIDUE LEVEL'):
break
else:
if not quiet:
print(' Warning: SST assignment failed')
return
next(lines)
for line in lines:
if line.startswith('...................................END'):
break
chain = line[2].strip()
resi = line[3:9].strip()
ss = line[21]
ss_dict[model, chain, resi] = ss
_common_ss_alter(selection, ss_dict, ss_map, raw)
def save_pdb(filename,
selection='(all)',
state=-1,
symm=1,
ss=1,
aniso=0,
seqres=0,
quiet=1):
'''
DESCRIPTION
Save the coordinates of a selection as pdb including the
secondary structure information and, if possible, the unit
cell. The latter requires the selction of a single object
USAGE
save_pdb filename, selection [, state [, symm [, ss [, aniso ]]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
Note: to include the unit cell information you
need to select a single object
state = integer: state to save {default: -1 (current state)}
symm = 0 or 1: save symmetry info if possible {default: 1}
ss = 0 or 1: save secondary structure info {default: 1}
aniso = 0 or 1: save ANISO records {default: 0}
SEE ALSO
save
'''
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
symm, ss = int(symm), int(ss)
filename = cmd.exp_path(filename)
f = open(filename, 'w')
print('REMARK 200 Generated with PyMOL and psico'.ljust(80), file=f)
# Write sequence
if int(seqres):
f.write(get_pdb_seqres(selection))
# Write the CRYST1 line if possible
if symm:
try:
obj1 = cmd.get_object_list(selection)[0]
sym = cmd.get_symmetry(obj1)
if len(sym) != 7:
raise
f.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-10s%4d\n" %
tuple(sym + [1]))
if not quiet:
print(' Info: Wrote unit cell and space group info')
except:
if not quiet:
print(' Info: No crystal information')
# Write secondary structure
if ss:
try:
sss = get_pdb_sss(selection, state, quiet)
if not sss:
raise
f.write(sss)
if not quiet:
print(' Info: Wrote secondary structure info')
except:
if not quiet:
print(' Info: No secondary structure information')
# Write coordinates of selection
pdbstr = cmd.get_pdbstr(selection, state)
# fix END records
if state == 0 and cmd.get_version()[1] < 1.6:
pdbstr = '\n'.join(
line for line in pdbstr.splitlines() if line != 'END') + '\nEND\n'
# anisotropic b-factors
from . import pymol_version
if int(aniso) and pymol_version < 1.6 and \
cmd.get_model('first (%s)' % selection).atom[0].u_aniso[0] != 0.0:
def mergeaniso():
atom_it = iter(cmd.get_model(selection, state).atom)
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ['ATOM ', 'HETATM']:
yield 'ANISOU' + line[6:28] + \
''.join('%7.0f' % (u*1e4) for u in atom_it.next().u_aniso) + \
line[70:]
pdbstr = ''.join(mergeaniso())
f.write(pdbstr)
f.close()
if not quiet:
print('Wrote PDB to \'' + filename + '\'')
def modevectors( first_obj_frame, last_obj_frame, outname="modevectors", head=1.0,tail=0.3, head_length=1.5, headrgb="1.0,1.0,1.0",tailrgb="1.0,1.0,1.0",cutoff=4.0,skip=0,cut=0.5,atom="CA",stat="show",factor=1.0):
"""
Authors Sean Law & Srinivasa
Michigan State University
slaw_(at)_msu_dot_edu
Editor Sacha Yee
USAGE
While in PyMOL
Parameter Preset Type Description
first_obj_frame Undefined String Object name of the first structure. The mode vector will propagate from this structure. Defined by user.
last_obj_frame Undefined String Object name of the last structure. The mode vector (arrow head) will end at this structure. Defined by user.
outname modevectors String Name of object to store mode vectors in.
head 1.0 Float Radius for the circular base of the arrow head (cone)
tail 0.3 Float Radius for the cylinder of the arrow tail (cylinder)
head_length 1.5 Float Length of the arrow head (from the base of the cone to the tip of cone)
head_rgb 1.0,1.0,1.0 String RGB colour for the arrow head.
tail_rgb 1.0,1.0,1.0 String RGB colour for the arrow tail.
cutoff 4.0 Float Skips mode vectors that do not meet the cutoff distance (in Angstroms).
skip 0 Integer Denotes how many atoms to skip. No arrows will be created for skipped atoms.
cut 0.0 Float Truncates all arrow tail lengths (without disturbing the arrow head) (in Angstroms).
atom CA String Designates the atom to derive mode vectors from.
stat show String Keeps track and prints statistics (total modevectors, skipped, cutoff).
factor 1.0 Float Multiplies each mode vector length by a specified factor.
Values between 0 and 1 will decrease the relative mode vector length.
Values greater than 1 will increase the relative mode vector length.
"""
framefirst=cmd.get_model(first_obj_frame)
framelast=cmd.get_model(last_obj_frame)
objectname=outname
factor=float(factor)
arrow_head_radius=float(head)
arrow_tail_radius=float(tail)
arrow_head_length=float(head_length)
cutoff=float(cutoff)
skip=int(skip)
cut=float(cut)
atomtype=atom.strip('"[]()')
headrgb=headrgb.strip('" []()')
tailrgb=tailrgb.strip('" []()')
hr,hg,hb=map(float,headrgb.split(','))
tr,tg,tb=map(float,tailrgb.split(','))
version=cmd.get_version()
arrow=[]
arrowhead = []
arrowtail = []
x1 = []
y1 = []
z1 = []
x2 = []
y2 = []
z2 = []
exit_flag=False
##############################################################
# #
# Define an object called "tail" and store the tail and a #
# circular base of the triangle in this object. #
# #
##############################################################
skipcount=0
skipcounter=0
keepcounter=0
atom_lookup={}
for atom in framefirst.atom:
if atom.name == atomtype:
if skipcount == skip:
x1.append(atom.coord[0])
y1.append(atom.coord[1])
z1.append(atom.coord[2])
##########################################
# #
# Set atom_lookup for a specific atom #
# equal to ONE for the first input set. #
# This dictionary will be used as a #
# reference for the second set. #
# #
##########################################
current_atom="CHAIN "+atom.chain+" RESID "\
+atom.resi+" RESTYPE "\
+atom.resn+\
" ATMNAME "+atom.name
# print current_atom
atom_lookup[current_atom]=1
skipcount=0
keepcounter+=1
else:
# print skipcount
skipcount+=1
skipcounter+=1
skipcount=0
for atom in framelast.atom:
if atom.name == atomtype:
if skipcount == skip:
x2.append(atom.coord[0])
y2.append(atom.coord[1])
z2.append(atom.coord[2])
#########################################
# #
# Get atom information from second set #
# and compare with first set. All #
# atoms from this second set MUST be #
# found in the first set! Otherwise, #
# the script will exit with an error #
# since modevectors can only be created #
# by calculating values from identical #
# sources. #
# #
#########################################
current_atom="CHAIN "+atom.chain+" RESID "\
+atom.resi+" RESTYPE "\
+atom.resn+\
" ATMNAME "+atom.name
# print current_atom
if current_atom not in atom_lookup:
print "\nError: "+current_atom+" from \""\
+last_obj_frame+\
" \"is not found in \""+first_obj_frame+"\"."
print "\nPlease check your input and/or selections and try again."
exit_flag=True
break
skipcount=0
else:
skipcount+=1
if exit_flag == 1:
###########################################
# #
# Exit script because an atom cannot be #
# found in both input files #
# #
###########################################
return
cutoff_counter=0 # Track number of atoms failing to meet the cutoff
###################################################
# #
# Check that the two selections/PDB files contain #
# the same number of atoms. #
# #
###################################################
if len(x2) != len(x1):
print "\nError: \""+first_obj_frame+\
"\" and \""+last_obj_frame+\
"\" contain different number of residue/atoms."
print "\nPlease check your input and/or selections and try again."
return
else:
#Continue with representing modevectors!
#########################################
# #
# Delete old selection or object if it #
# exists so that it can be overwritten #
# #
#########################################
save_view=cmd.get_view(output=1,quiet=1)
cmd.delete(name=outname)
cmd.hide(representation="everything",selection=first_obj_frame)
cmd.hide(representation="everything",selection=last_obj_frame)
###################################################
# #
# Begin drawing arrow tails #
# #
###################################################
arrowtail = []
for mv in range(len(x1)):
vectorx=x2[mv]-x1[mv]
vectory=y2[mv]-y1[mv]
vectorz=z2[mv]-z1[mv]
length=sqrt(vectorx**2+vectory**2+vectorz**2)
if length < cutoff:
cutoff_counter+=1
continue
t=1.0-(cut/length)
x2[mv]=x1[mv]+factor*t*vectorx
y2[mv]=y1[mv]+factor*t*vectory
z2[mv]=z1[mv]+factor*t*vectorz
vectorx=x2[mv]-x1[mv]
vectory=y2[mv]-y1[mv]
vectorz=z2[mv]-z1[mv]
length=sqrt(vectorx**2+vectory**2+vectorz**2)
d=arrow_head_length # Distance from arrow tip to arrow base
t=1.0-(d/length)
tail = [
# Tail of cylinder
CYLINDER, x1[mv],y1[mv],z1[mv]\
,x1[mv]+(t+0.01)*vectorx,y1[mv]+(t+0.01)*vectory,z1[mv]+(t+0.01)*vectorz\
,arrow_tail_radius,tr,tg,tb,tr,tg,tb # Radius and RGB for each cylinder tail
]
arrow.extend(tail)
x=x1[mv]+t*vectorx
y=y1[mv]+t*vectory
z=z1[mv]+t*vectorz
dx=x2[mv]-x
dy=y2[mv]-y
dz=z2[mv]-z
seg=d/100
intfactor=int(factor)
if version < 1.1: #Version >= 1.1 has cone primitive
for i in range (100,0,-1): #i=100 is tip of cone
print i
t1=seg*i
t2=seg*(i+1)
radius=arrow_head_radius*(1.0-i/(100.0)) #Radius of each disc that forms cone
head=[
CYLINDER, x+t2*dx,y+t2*dy,z+t2*dz\
,x+t1*dx,y+t1*dy,z+t1*dz\
,radius,hr,hg,hb,hr,hg,hb # Radius and RGB for slice of arrow head
]
arrow.extend(head)
else:
head=[
CONE, x, y ,z, x+d*dx, y+d*dy, z+d*dz, arrow_head_radius, 0.0, hr, hg, hb, hr, hg, hb, 1.0, 1.0 ]
arrow.extend(head)
##############################################################
# #
# Load the entire object into PyMOL #
# #
# Print statistics if requested by user #
# #
##############################################################
if stat == "show":
natoms=skipcounter+keepcounter
print "\nTotal number of atoms = "+str(natoms)
print "Atoms skipped = "+str(skipcounter)
if keepcounter-cutoff_counter > 0:
print "Atoms counted = "+str(keepcounter-cutoff_counter)+" (see PyMOL object \""+outname+"\")"
else:
print "Atoms counted = "+str(keepcounter-cutoff_counter)+" (Empty CGO object not loaded)"
print "Atoms cutoff = "+str(cutoff_counter) #Note that cutoff occurs AFTER skipping!
if keepcounter-cutoff_counter > 0:
cmd.load_cgo(arrow,objectname) #Ray tracing an empty object will cause a segmentation fault. No arrows = Do not display in PyMOL!!!
cmd.show(representation="cartoon",selection=first_obj_frame)
cmd.cartoon("tube")
cmd.show(representation="cartoon",selection=last_obj_frame)
cmd.hide(representation="cartoon",selection=last_obj_frame)
cmd.bg_color(color="white")
cmd.set_view(save_view)
return
Date: October 30, 2015
Version: 1.0
License: Public Domain
"""
from pymol import cmd, stored
import re
try:
from collections import OrderedDict
_orderedDict = True
except ImportError:
_orderedDict = False
# PyMOL 1.7.4 introduces support for multi-letter chains, so we can afford to
# use a smaller alphabet. In earlier versions, use lower-case letters if needed
# (requires running `set ignore_case, 0`)
_long_chains = cmd.get_version()[1] >= 1.74
_default_base = 36 if _long_chains else 62
class OutOfChainsError(Exception):
def __init__(self,msg):
self.msg=msg
def __str__(self):
return str(self.msg)
class ChainSet(object):
"""
Base class for various methods to rename chains
Contains _chains, which maps from the renamed chain to a tuple with the
original (object,state,chain). All dict-like accessors work on ChainSets,
e.g.
def interpret_color(self, c):
if cmd.get_version()[1] < 1:
return cmd._interpret_color(str(c))
return cmd._interpret_color(cmd, str(c))
'''
(c) 2010 Thomas Holder
'''
from pymol import cmd, stored, CmdException
from chempy import cpv
import math
if cmd.get_version()[1] < 1.2:
def get_unused_name(name):
import random
return name + '%04d' % random.randint(0, 1000)
STATE = 1
else:
from pymol.cmd import get_unused_name
STATE = -1
def _vec_sum(vec_list):
# this is the same as
# return numpy.array(vec_list).sum(0).tolist()
vec = cpv.get_null()
for x in vec_list:
vec = cpv.add(vec, x)
return vec
def _mean_and_std(x):
# this is the same as
def sst(selection='(all)', raw='', state=-1, quiet=1):
'''
DESCRIPTION
Secondary structure assignment with SST.
http://lcb.infotech.monash.edu.au/sstweb/
SEE ALSO
dss, dssp, stride
'''
try:
import urllib2
except ImportError:
import urllib.request as urllib2
state, quiet = int(state), int(quiet)
ss_map = {
'C': 'L',
'E': 'S',
'G': 'H',
'H': 'H',
'I': 'H',
'g': 'H',
'h': 'H',
'i': 'H',
'3': 'L',
'4': 'L',
'5': 'L',
'T': 'L',
'-': 'L',
'|': 'L',
':': 'H',
}
ss_dict = {}
boundary = '192.168.1.80.500.9981.1375391031.267.10'
for model in cmd.get_object_list(selection):
pdbstr = cmd.get_pdbstr('%s & guide & (%s)' % (model, selection), state)
body = '\r\n'.join([
'--' + boundary,
'Content-Disposition: file; name="pdb_file"; filename="abc.pdb"',
'Content-Type: text/plain',
'',
pdbstr,
'--' + boundary + '--',
'',
])
try:
request = urllib2.Request(
'http://lcb.infotech.monash.edu.au/sstweb/formaction_pdbfile.php')
request.add_header('User-agent', 'PyMOL ' + cmd.get_version()[0] + ' ' +
cmd.sys.platform)
request.add_header('Content-type', 'multipart/form-data; boundary=%s' % boundary)
request.add_header('Content-length', len(body))
request.add_data(body)
lines = urllib2.urlopen(request).readlines()
except urllib2.URLError:
print(' Error: URL request failed')
raise CmdException
lines = iter(lines)
for line in lines:
if line.startswith('..........RESIDUE LEVEL'):
break
else:
if not quiet:
print(' Warning: SST assignment failed')
return
next(lines)
for line in lines:
if line.startswith('...................................END'):
break
chain = line[2].strip()
resi = line[3:9].strip()
ss = line[21]
ss_dict[model,chain,resi] = ss
_common_ss_alter(selection, ss_dict, ss_map, raw)
import time
import unittest
import itertools
import tempfile
import argparse
try:
import Image
except ImportError:
from PIL import Image
sys.modules['Image'] = Image
from pymol import cmd
from pymol.invocation import options
PYMOL_VERSION = cmd.get_version()
PYMOL_EDU = 'Edu' in PYMOL_VERSION[0]
is_win64bit = "Windows" in platform.system() and sys.maxsize > 2**32
usage = 'pymol [pymol options] %s [test options]' % (
os.path.basename(__file__))
parser = argparse.ArgumentParser("pymol", usage=usage)
parser.add_argument('--xml', action='store_true')
parser.add_argument('filenames', nargs='*', default=[])
parser.add_argument('--out', default=sys.stdout)
parser.add_argument('--offline', action='store_true')
parser.add_argument('--no-mmlibs', action='store_true')
parser.add_argument('--no-undo', action='store_true')
parser.add_argument('--verbosity', type=int, default=2)
have_dash_dash = __file__.startswith(sys.argv[0]) or '--run' in sys.argv
def diagnostics(filename='', compact=0, quiet=1):
'''
DESCRIPTION
Get system level diagnostics data
USAGE
diagnostics [ filename ]
ARGUMENTS
filename = str: If given, write output to text file
'''
import platform
import os
import re
import glob
import time
import textwrap
from pymol import invocation
from pymol import cmd, CmdException
compact, quiet = int(compact), int(quiet)
TZ = '%+05d' % (time.timezone / 36)
version = cmd.get_version()
body = u'PyMOL %s\n' % version[0]
if not compact:
if version[3]:
body += 'build date: %s %s\n' % (time.ctime(version[3]), TZ)
if version[4]:
body += 'git sha: %s\n' % version[4]
try:
# pymol conda package version
condameta = glob.glob(
os.path.join(sys.prefix, 'conda-meta',
'pymol-' + version[0] + '*.json'))
if condameta:
import json
d = json.load(open(condameta[0]))
body += 'conda build: %s %s\n' % (d.get('build'), d.get('schannel')
or d.get('channel'))
except BaseException as e:
print(e)
if not compact:
body += '\nLicense Information:\n'
body += 'Open-Source Build\n'
if not compact:
body += '\nOperating System:\n'
body += platform.platform() + '\n'
if platform.system() == 'Linux':
body += platform.version() + '\n'
if not compact:
body += '\nOpenGL Driver:\n'
renderer = cmd.get_renderer()
body += str(renderer[0] or '(none)') + '\n'
body += str(renderer[1] or '(none)') + '\n'
body += str(renderer[2] or '(none)') + '\n'
try:
from pymol.Qt import QtCore
body += '%s %s (Qt %s)\n' % (QtCore.__name__.split('.')[0],
QtCore.PYQT_VERSION_STR,
QtCore.QT_VERSION_STR)
except Exception as e:
body += '(%s)\n' % (e, )
if not compact:
body += '\nPython:\n'
body += '%s\n' % sys.version
body += 'prefix=%s\n' % _unicode(sys.prefix)
body += 'executable=%s\n' % _unicode(sys.executable)
body += u'filesystemencoding={}\n'.format(sys.getfilesystemencoding())
body += '\nStartup Scripts:\n'
pymolrc = invocation.get_user_config()
if pymolrc:
pymolrc = map(_unicode, pymolrc)
body += '\n'.join(pymolrc) + '\n'
else:
body += '(no pymolrc file found)\n'
body += '\nQt, Python and PyMOL Environment Variables:\n'
for key in sorted(os.environ):
if re.search(r'^PY|QT|^LANG',
key) and not (key == 'PYMOL_SCRIPTS'):
body += u'%s=%s\n' % (key, _unicode(os.environ[key]))
body += '\nPATH:\n'
body += textwrap.fill(_unicode(os.getenv('PATH', '')), 78) + '\n'
body += '\nDiagnostics collected on %s %s\n' % (time.ctime(), TZ)
if filename:
filename = cmd.exp_path(filename)
if not filename.endswith('.txt'):
raise CmdException('filename must have .txt extension')
with open(filename, 'w') as handle:
handle.write(body)
print('Diagnostics written to "%s"' % filename)
elif not quiet:
print(body.rstrip())
return body
A reference document with all commands can be generated with:
PyMOL> psico.helping.write_html_ref('psico-commands.html')
(c) 2010-2012 Thomas Holder <*****@*****.**>
Steffen Schmidt <*****@*****.**>
Max Planck Institute for Developmental Biology
License: BSD-2-Clause
'''
__version__ = '3.4'
try:
from pymol import cmd
pymol_version = cmd.get_version()[1]
except:
pymol_version = 1.6
__all__ = [
'aaindex',
'conservation',
'creating',
'editing',
'electrostatics',
'exporting',
'fasta',
'fitting',
'geometry',
'orientation',
'helping',
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: http://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
import time
import unittest
import itertools
import tempfile
import argparse
try:
import Image
except ImportError:
from PIL import Image
sys.modules['Image'] = Image
from pymol import cmd
from pymol.invocation import options
PYMOL_VERSION = cmd.get_version()
PYMOL_EDU = 'Edu' in PYMOL_VERSION[0]
is_win64bit = "Windows" in platform.system() and sys.maxsize > 2**32
usage = 'pymol [pymol options] %s [test options]' % (os.path.basename(__file__))
parser = argparse.ArgumentParser("pymol", usage=usage)
parser.add_argument('--xml', action='store_true')
parser.add_argument('filenames', nargs='*', default=[])
parser.add_argument('--out', default=sys.stdout)
parser.add_argument('--offline', action='store_true')
parser.add_argument('--no-mmlibs', action='store_true')
parser.add_argument('--verbosity', type=int, default=2)
have_dash_dash = __file__.startswith(sys.argv[0]) or '--run' in sys.argv
cliargs = parser.parse_known_args(None if have_dash_dash else [])[0]
def save_pdb(filename, selection="(all)", state=-1, symm=1, ss=1, aniso=0, quiet=1):
"""
DESCRIPTION
Save the coordinates of a selection as pdb including the
secondary structure information and, if possible, the unit
cell. The latter requires the selction of a single object
USAGE
save_pdb filename, selection [, state [, symm [, ss [, aniso ]]]]
ARGUMENTS
filename = string: file path to be written
selection = string: atoms to save {default: (all)}
Note: to include the unit cell information you
need to select a single object
state = integer: state to save {default: -1 (current state)}
symm = 0 or 1: save symmetry info if possible {default: 1}
ss = 0 or 1: save secondary structure info {default: 1}
aniso = 0 or 1: save ANISO records {default: 0}
SEE ALSO
save
"""
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
symm, ss = int(symm), int(ss)
filename = cmd.exp_path(filename)
f = open(filename, "w")
print >> f, "REMARK 200 Generated with PyMOL and psico".ljust(80)
# Write the CRYST1 line if possible
if symm:
try:
obj1 = cmd.get_object_list(selection)[0]
sym = cmd.get_symmetry(obj1)
if len(sym) != 7:
raise
f.write("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-10s%4d\n" % tuple(sym + [1]))
if not quiet:
print " Info: Wrote unit cell and space group info"
except:
if not quiet:
print " Info: No crystal information"
# Write secondary structure
if ss:
try:
sss = get_pdb_sss(selection, state, quiet)
if not sss:
raise
f.write(sss)
if not quiet:
print " Info: Wrote secondary structure info"
except:
if not quiet:
print " Info: No secondary structure information"
# Write coordinates of selection
pdbstr = cmd.get_pdbstr(selection, state)
# fix END records
if state == 0 and cmd.get_version()[1] < 1.6:
pdbstr = "\n".join(line for line in pdbstr.splitlines() if line != "END") + "\nEND\n"
# anisotropic b-factors
if int(aniso) and cmd.get_model("first (%s)" % selection).atom[0].u_aniso[0] != 0.0:
def mergeaniso():
atom_it = iter(cmd.get_model(selection, state).atom)
for line in pdbstr.splitlines(True):
yield line
if line[:6] in ["ATOM ", "HETATM"]:
yield "ANISOU" + line[6:28] + "".join("%7.0f" % (u * 1e4) for u in atom_it.next().u_aniso) + line[
70:
]
pdbstr = "".join(mergeaniso())
f.write(pdbstr)
f.close()
if not quiet:
print "Wrote PDB to '" + filename + "'"
Date: October 30, 2015
Version: 1.0
License: Public Domain
"""
from pymol import cmd, stored
import re
try:
from collections import OrderedDict
_orderedDict = True
except ImportError:
_orderedDict = False
# PyMOL 1.7.4 introduces support for multi-letter chains, so we can afford to
# use a smaller alphabet. In earlier versions, use lower-case letters if needed
# (requires running `set ignore_case, 0`)
_long_chains = cmd.get_version()[1] >= 1.74
_default_base = 36 if _long_chains else 62
class OutOfChainsError(Exception):
def __init__(self, msg):
self.msg = msg
def __str__(self):
return str(self.msg)
class ChainSet(object):
"""
Base class for various methods to rename chains
def diagnostics(filename='', compact=0, quiet=1):
'''
DESCRIPTION
Get system level diagnostics data
USAGE
diagnostics [ filename ]
ARGUMENTS
filename = str: If given, write output to text file
'''
import time
from pymol import invocation
from pymol import cmd, CmdException
compact, quiet = int(compact), int(quiet)
TZ = '%+05d' % (time.timezone / 36)
version = cmd.get_version()
body = u'PyMOL %s\n' % version[0]
if not compact:
if version[3]:
body += 'build date: %s %s\n' % (time.ctime(version[3]), TZ)
if version[4]:
body += 'git sha: %s\n' % version[4]
body += diagnostics_conda(version[0])
if not compact:
body += '\nLicense Information:\n'
body += 'Open-Source Build\n'
body += diagnostics_platform()
if not compact:
body += '\nOpenGL Driver:\n'
renderer = cmd.get_renderer()
body += str(renderer[0] or '(none)') + '\n'
body += str(renderer[1] or '(none)') + '\n'
body += str(renderer[2] or '(none)') + '\n'
body += diagnostics_qt()
if not compact:
body += diagnostics_python()
body += '\nStartup Scripts:\n'
pymolrc = invocation.get_user_config()
if pymolrc:
pymolrc = map(_unicode, pymolrc)
body += '\n'.join(pymolrc) + '\n'
else:
body += '(no pymolrc file found)\n'
body += diagnostics_env_vars()
body += '\nDiagnostics collected on %s %s\n' % (time.ctime(), TZ)
if filename:
filename = cmd.exp_path(filename)
if not filename.endswith('.txt'):
raise CmdException('filename must have .txt extension')
with open(filename, 'w') as handle:
handle.write(body)
print('Diagnostics written to "%s"' % filename)
elif not quiet:
print(body.rstrip())
return body
def interpret_color(self, c):
if cmd.get_version()[1] < 1:
return cmd._interpret_color(str(c))
return cmd._interpret_color(cmd, str(c))
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: http://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)'
def startup_pymod(app=None):
"""
Executed when clicking on the 'PyMod' item in PyMOL's plugin menu.
"""
if has_gui is None:
print(
"\n# No GUI library (either Tkinter or Qt bindings) was found. PyMod"
" can not be launched.")
return None
# Check if a PyMod main window is already open.
if pyqt_found:
try:
for widget in QtWidgets.QApplication.instance().topLevelWidgets():
if hasattr(widget,
"is_pymod_main_window") and widget.isVisible():
title = "PyMod Error"
message = (
"PyMod is already running. Please close its main"
" window or restart PyMOL in order to launch it again."
)
showerror(title, message)
return None
except Exception as e:
pass
# Checks if Python 3 is available.
if python_version != 3:
title = "Python Version Error"
message = "PyMod %s requires Python 3. Your current Python version is %s." % (
__pymod_version__, python_micro_version)
showerror(title, message)
return None
# Checks the PyMOL version.
pymol_version = float(".".join(cmd.get_version()[0].split(".")[0:2]))
if pymol_version < 2.3:
title = "PyMOL Version Error"
message = "PyMod %s requires a PyMOL version of 2.3 or higher. Your current PyMOL version is %s." % (
__pymod_version__, pymol_version)
showerror(title, message)
return None
# Checks for PyQt.
if not pyqt_found:
title = "Import Error"
message = "PyQt5 is not installed on your system. Please install it in order to use PyMod."
showerror(title, message)
return None
# Checks if NumPy and Biopython (PyMod core Python dependencies) are present before launching
# PyMod.
if not numpy_found:
title = "Import Error"
message = "NumPy is not installed on your system. Please install it in order to use PyMod."
showerror(title, message)
return None
if not biopython_found:
title = "Import Error"
message = "Biopython is not installed on your system. Please install it in order to use PyMod."
showerror(title, message)
return None
# Adds to the sys.path the directory where the PyMod module is located.
pymod_plugin_dirpath = os.path.dirname(__file__)
if os.path.isdir(pymod_plugin_dirpath):
sys.path.append(pymod_plugin_dirpath)
# Attempts to import MODELLER from the default sys.path.
modeller_spec = util.find_spec("modeller")
parallel_modeller = False # A flag, when set as 'True' MODELLER parallel jobs can be used.
# MODELLER can be imported.
if modeller_spec is not None:
parallel_modeller = True
# MODELLER can not be imported. Tries to import it from a PyMod conda
# pseudo-environment.
else:
# Adds to the sys.path the PyMod conda environment directory. Used to import
# modules fetched by conda within PyMod.
from pymod_lib import pymod_os_specific
pymod_env_dirpath = pymod_os_specific.get_pymod_cfg_paths()[3]
# Checks if a directory for a PyMod conda pseudo-environment exists.
if os.path.isdir(pymod_env_dirpath):
if sys.platform in ("linux", "darwin"):
conda_lib_dirpath_list = [
os.path.join(pymod_env_dirpath, "lib",
"python%s" % python_minor_version),
os.path.join(pymod_env_dirpath, "lib",
"python%s" % python_minor_version,
"lib-dynload"),
os.path.join(pymod_env_dirpath, "lib",
"python%s" % python_minor_version,
"site-packages")
]
path_extend_list = []
elif sys.platform == "win32":
dll_dirpath = os.path.join(pymod_env_dirpath, "Lib",
"site-packages")
conda_lib_dirpath_list = [
os.path.join(pymod_env_dirpath, "Library", "modeller",
"modlib"), dll_dirpath
]
path_extend_list = [
os.path.join(pymod_env_dirpath, "Scripts"),
pymod_env_dirpath, dll_dirpath
]
else:
conda_lib_dirpath_list = []
path_extend_list = []
# Add the environment directories to the sys.path of Python.
for conda_lib_dirpath in conda_lib_dirpath_list:
sys.path.append(conda_lib_dirpath)
# Also add new directories to the PATH to use the MODELLER DLLs.
if path_extend_list:
os.environ["PATH"] += os.pathsep.join(path_extend_list)
os.environ[
"HDF5_DISABLE_VERSION_CHECK"] = "1" # Prevents problems with hdf5 libraries versions.
# Edit the 'modslave.py' file of MODELLER in the PyMod environment directory
# (the user's original MODELLER files will remain untouched) so that the
# MODELLER version installed in the PyMod environment directory can be
# used to run parallel jobs. This operation will be performed only once,
# that is, the first time PyMod is launched after MODELLER has been
# installed through the GUI of the plugin.
try:
# Gets the installation directory of MODELLER. This can be acquired
# also if the MODELLER key is not valid.
from modeller import config
modeller_bin_dirpath = os.path.join(config.install_dir, "bin")
modslave_filepath = os.path.join(modeller_bin_dirpath,
"modslave.py")
modslave_bak_filepath = os.path.join(modeller_bin_dirpath,
"modslave.py.bak")
# Checks if the modslave file is present.
if os.path.isfile(modslave_filepath):
# Checks if the backup modslave file is present (if it already
# exists, then PyMod has already modified the original modslave
# file).
if not os.path.isfile(modslave_bak_filepath):
print(
"\n# Configuring the MODELLER modslave.py in the PyMod environment."
)
print("- modslave.py file found at: %s" %
modslave_filepath)
# Build a backup copy of the original modslave file.
print("- Backing up the modslave.py file.")
shutil.copy(modslave_filepath, modslave_bak_filepath)
# Gets the content from the old modslave file.
with open(modslave_filepath, "r") as m_fh:
modfile_lines = m_fh.readlines()
insert_idx = 1
for line_idx, line in enumerate(modfile_lines):
if line.startswith("import sys"):
print("- Found insert line")
insert_idx = line_idx + 1
break
# This will add the paths above also to the 'modslave.py'
# file, so that MODELLER can be imported in child processes.
import_lines = [
'\n# Added by the PyMod installer.\n',
'import os\n', 'import sys\n\n',
'conda_lib_dirpath_list = %s\n' %
repr(conda_lib_dirpath_list),
'path_extend_list = %s\n\n' %
repr(path_extend_list),
'for path in conda_lib_dirpath_list:\n',
' sys.path.append(path)\n',
'os.environ["PATH"] += os.pathsep.join(path_extend_list)\n',
'os.environ["HDF5_DISABLE_VERSION_CHECK"] = "1"\n',
'# End of the code inserted by PyMod.\n'
]
modfile_lines = modfile_lines[:
insert_idx] + import_lines + modfile_lines[
insert_idx:]
# Edits the modslave file.
with open(modslave_filepath, "w") as m_fh:
m_fh.writelines(modfile_lines)
print("- Finishing.")
parallel_modeller = True
except Exception as e:
print(
"- Could not import MODELLER from the PyMod environment: %s."
% e)
# Actually launches PyMod.
from pymod_lib import pymod_main
pymod_main.pymod_launcher(app=app,
pymod_plugin_name=pymod_plugin_name,
pymod_version=__pymod_version__,
pymod_revision=__revision__,
parallel_modeller=parallel_modeller)
A reference document with all commands can be generated with:
PyMOL> psico.helping.write_html_ref('psico-commands.html')
(c) 2010-2012 Thomas Holder <*****@*****.**>
Steffen Schmidt <*****@*****.**>
Max Planck Institute for Developmental Biology
License: BSD-2-Clause
'''
__version__ = '3.2'
try:
from pymol import cmd
pymol_version = cmd.get_version()[1]
except:
pymol_version = 1.6
__all__ = [
'aaindex',
'contactmap',
'contactmap_yang',
'conservation',
'creating',
'editing',
'electrostatics',
'exporting',
'fasta',
'fitting',
'geometry',
'''
Orientation, displacement and angle measurments of helices and domains.
(c) 2010-2012 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
'''
from pymol import cmd, CmdException
from chempy import cpv
if cmd.get_version()[1] < 1.2:
# legacy support to run this script standalone with PyMOL 0.99
def get_unused_name(name):
import random
return name + '%04d' % random.randint(0, 1000)
STATE = 1
else:
from pymol.cmd import get_unused_name
STATE = -1
def _vec_sum(vec_list):
# this is the same as
# return numpy.array(vec_list).sum(0).tolist()
vec = cpv.get_null()
for x in vec_list:
vec = cpv.add(vec, x)
return vec
def _common_orientation(selection, center, vec, visualize=1, scale=1.0, quiet=1):
if visualize:
def __init__(self, root, top, menuindex, Project_Dir, Install_Dir,
NRGsuite_Dir, OSid, PyMOL, Name, WINDOWWIDTH, WINDOWHEIGHT,
RootPrefs):
self.Name = Name
self.OSid = OSid
self.PyMOL = PyMOL
self.pymol_major_version = int(cmd.get_version()[0][0])
self.NRGsuite_Dir = NRGsuite_Dir
self.Install_Dir = Install_Dir
self.Project_Dir = Project_Dir
self.Folders = [self.NRGsuite_Dir]
if self.Project_Dir:
self.Folders.append(self.Project_Dir)
self.Set_Folders()
self.Validate_Folders()
self.Prefs = RootPrefs
self.Color_Green = '#CCFFCC'
self.Color_Grey = '#EDEDED'
self.Color_Gray = '#EDEDED'
self.Color_Blue = '#6699FF'
self.Color_Red = '#FF9999'
self.Color_White = '#FFFFFF'
self.Color_Black = '#000000'
self.root = root
self.root.title(self.Name)
self.top = top
self.menuindex = menuindex
if self.menuindex != -1:
self.Disable_MenuItem()
self.WINDOWWIDTH = WINDOWWIDTH
self.WINDOWHEIGHT = WINDOWHEIGHT
#self.root.geometry() # Interface DIMENSIONS
#self.root.maxsize(WINDOWWIDTH,WINDOWHEIGHT)
self.root.minsize(self.WINDOWWIDTH, self.WINDOWHEIGHT)
self.root.protocol('WM_DELETE_WINDOW', self.Quit)
General.CenterWindow(self.root, self.WINDOWWIDTH, self.WINDOWHEIGHT)
#==================================================================================
# SET the default fonts of the interface
#==================================================================================
FontType = self.Prefs.GetFontType()
FontSize = self.Prefs.GetFontSize()
self.font_Title = tkFont.Font(family=FontType,
size=FontSize,
weight=tkFont.BOLD)
self.font_Title_H = tkFont.Font(family=FontType,
size=FontSize + 1,
weight=tkFont.BOLD)
self.font_Text = tkFont.Font(family=FontType, size=FontSize)
self.font_Text_H = tkFont.Font(family=FontType, size=FontSize + 1)
self.font_Text_I = tkFont.Font(family=FontType,
size=FontSize,
slant=tkFont.ITALIC)
self.font_Text_U = tkFont.Font(family=FontType,
size=FontSize,
underline=True)
self.ChildWindow = None
self.ActiveFrame = None
self.Run = None
self.ProcessError = False
self.ProcessRunning = False
self.ProcessParsing = False
self.ProcessDone = False
self.ParseState = 10
self.SimulateState = -1
self.fMain = Frame(self.root)
self.fMain.pack(expand=True)
self.Def_Vars()
self.Init_Vars()
self.Frame_Main()
self.Build_Tabs()
self.MakeMenuBar()
self.After_Init()
self.Clean()
def modevectors(first_obj_frame,
last_obj_frame,
first_state=1,
last_state=1,
outname="modevectors",
head=0.5,
tail=0.1,
head_length=0.3,
headrgb="0,0,0",
tailrgb="0.0,0.0,0.0",
cutoff=4.0,
skip=0,
cut=0.5,
atom="CA",
stat="show",
factor=1.0,
notail=1):
"""
Authors Sean Law & Srinivasa
Michigan State University
slaw_(at)_msu_dot_edu
Editor Sacha Yee
USAGE
While in PyMOL
Parameter Preset Type Description
first_obj_frame Undefined String Object name of the first structure. The mode vector will propagate from this structure. Defined by user.
last_obj_frame Undefined String Object name of the last structure. The mode vector (arrow head) will end at this structure. Defined by user.
first_state 1 Integer Defines state of first object
last_state 1 Integer Defines state of last object
outname modevectors String Name of object to store mode vectors in.
head 1.0 Float Radius for the circular base of the arrow head (cone)
tail 0.3 Float Radius for the cylinder of the arrow tail (cylinder)
head_length 1.5 Float Length of the arrow head (from the base of the cone to the tip of cone)
head_rgb 1.0,1.0,1.0 String RGB colour for the arrow head.
tail_rgb 1.0,1.0,1.0 String RGB colour for the arrow tail.
cutoff 4.0 Float Skips mode vectors that do not meet the cutoff distance (in Angstroms).
skip 0 Integer Denotes how many atoms to skip. No arrows will be created for skipped atoms.
cut 0.0 Float Truncates all arrow tail lengths (without disturbing the arrow head) (in Angstroms).
atom CA String Designates the atom to derive mode vectors from.
stat show String Keeps track and prints statistics (total modevectors, skipped, cutoff).
factor 1.0 Float Multiplies each mode vector length by a specified factor.
Values between 0 and 1 will decrease the relative mode vector length.
Values greater than 1 will increase the relative mode vector length.
notail 0 Integer Hides tails and only uses cones (porcupine plot)
"""
framefirst = cmd.get_model(first_obj_frame, first_state)
framelast = cmd.get_model(last_obj_frame, last_state)
objectname = outname
factor = float(factor)
arrow_head_radius = float(head)
arrow_tail_radius = float(tail)
arrow_head_length = float(head_length)
cutoff = float(cutoff)
skip = int(skip)
cut = float(cut)
atomtype = atom.strip('"[]()')
objectname = objectname.strip('"[]()')
headrgb = headrgb.strip('" []()')
tailrgb = tailrgb.strip('" []()')
hr, hg, hb = list(map(float, headrgb.split(',')))
tr, tg, tb = list(map(float, tailrgb.split(',')))
version = cmd.get_version()[1]
arrow = []
arrowhead = []
arrowtail = []
x1 = []
y1 = []
z1 = []
x2 = []
y2 = []
z2 = []
exit_flag = False
##############################################################
# #
# Define an object called "tail" and store the tail and a #
# circular base of the triangle in this object. #
# #
##############################################################
skipcount = 0
skipcounter = 0
keepcounter = 0
atom_lookup = {}
for atom in framefirst.atom:
if atom.name == atomtype:
if skipcount == skip:
x1.append(atom.coord[0])
y1.append(atom.coord[1])
z1.append(atom.coord[2])
##########################################
# #
# Set atom_lookup for a specific atom #
# equal to ONE for the first input set. #
# This dictionary will be used as a #
# reference for the second set. #
# #
##########################################
current_atom = "CHAIN " + atom.chain + " RESID "\
+ atom.resi + " RESTYPE "\
+ atom.resn +\
" ATMNUM " + str(atom.index)
# print current_atom
atom_lookup['current_atom'] = 1
skipcount = 0
keepcounter += 1
else:
# print skipcount
skipcount += 1
skipcounter += 1
skipcount = 0
for atom in framelast.atom:
if atom.name == atomtype:
if skipcount == skip:
x2.append(atom.coord[0])
y2.append(atom.coord[1])
z2.append(atom.coord[2])
#########################################
# #
# Get atom information from second set #
# and compare with first set. All #
# atoms from this second set MUST be #
# found in the first set! Otherwise, #
# the script will exit with an error #
# since modevectors can only be created #
# by calculating values from identical #
# sources. #
# #
#########################################
current_atom = "CHAIN " + atom.chain + " RESID "\
+ atom.resi + " RESTYPE "\
+ atom.resn +\
" ATMNUM " + str(atom.index)
# print current_atom
if 'current_atom' not in atom_lookup:
print("\nError: " + current_atom + " from \""\
+ last_obj_frame +\
" \"is not found in \"" + first_obj_frame + "\".")
print(
"\nPlease check your input and/or selections and try again."
)
exit_flag = True
break
skipcount = 0
else:
skipcount += 1
if exit_flag == 1:
###########################################
# #
# Exit script because an atom cannot be #
# found in both input files #
# #
###########################################
return
cutoff_counter = 0 # Track number of atoms failing to meet the cutoff
###################################################
# #
# Check that the two selections/PDB files contain #
# the same number of atoms. #
# #
###################################################
if len(x2) != len(x1):
print("\nError: \"" + first_obj_frame +\
"\" and \"" + last_obj_frame +\
"\" contain different number of residue/atoms.")
print("\nPlease check your input and/or selections and try again.")
return
else:
# Continue with representing modevectors!
#########################################
# #
# Delete old selection or object if it #
# exists so that it can be overwritten #
# #
#########################################
save_view = cmd.get_view(output=1, quiet=1)
cmd.delete(objectname)
cmd.hide(representation="everything", selection=first_obj_frame)
cmd.hide(representation="everything", selection=last_obj_frame)
###################################################
# #
# Begin drawing arrow tails #
# #
###################################################
arrowtail = []
for mv in range(len(x1)):
vectorx = x2[mv] - x1[mv]
vectory = y2[mv] - y1[mv]
vectorz = z2[mv] - z1[mv]
length = sqrt(vectorx**2 + vectory**2 + vectorz**2)
if length < cutoff:
cutoff_counter += 1
continue
t = 1.0 - (cut / length)
x2[mv] = x1[mv] + factor * t * vectorx
y2[mv] = y1[mv] + factor * t * vectory
z2[mv] = z1[mv] + factor * t * vectorz
vectorx = x2[mv] - x1[mv]
vectory = y2[mv] - y1[mv]
vectorz = z2[mv] - z1[mv]
length = sqrt(vectorx**2 + vectory**2 + vectorz**2)
d = arrow_head_length # Distance from arrow tip to arrow base
t = 1.0 - (d / length)
if notail:
t = 0
tail = [
# Tail of cylinder
CYLINDER, x1[mv], y1[mv], z1[mv]\
, x1[mv] + (t + 0.01) * vectorx, y1[mv] + (t + 0.01) * vectory, z1[mv] + (t + 0.01) * vectorz\
, arrow_tail_radius, tr, tg, tb, tr, tg, tb # Radius and RGB for each cylinder tail
]
if notail == 0:
arrow.extend(tail)
x = x1[mv] + t * vectorx
y = y1[mv] + t * vectory
z = z1[mv] + t * vectorz
dx = x2[mv] - x
dy = y2[mv] - y
dz = z2[mv] - z
seg = d / 100
intfactor = int(factor)
if version < 1.1: # Version >= 1.1 has cone primitive
for i in range(100, 0, -1): # i=100 is tip of cone
print(i)
t1 = seg * i
t2 = seg * (i + 1)
radius = arrow_head_radius * (
1.0 - i / (100.0)) # Radius of each disc that forms cone
head = [
CYLINDER, x + t2 * dx, y + t2 * dy, z + t2 * dz\
, x + t1 * dx, y + t1 * dy, z + t1 * dz\
, radius, hr, hg, hb, hr, hg, hb # Radius and RGB for slice of arrow head
]
arrow.extend(head)
else:
head = [
CONE, x, y, z, x + d * dx, y + d * dy, z + d * dz,
arrow_head_radius, 0.0, hr, hg, hb, hr, hg, hb, 1.0, 1.0
]
arrow.extend(head)
##############################################################
# #
# Load the entire object into PyMOL #
# #
# Print statistics if requested by user #
# #
##############################################################
if stat == "show":
natoms = skipcounter + keepcounter
print("\nTotal number of atoms = " + str(natoms))
print("Atoms skipped = " + str(skipcounter))
if keepcounter - cutoff_counter > 0:
print("Atoms counted = " + str(keepcounter - cutoff_counter) +
" (see PyMOL object \"" + objectname + "\")")
else:
print("Atoms counted = " + str(keepcounter - cutoff_counter) +
" (Empty CGO object not loaded)")
print("Atoms cutoff = " +
str(cutoff_counter)) # Note that cutoff occurs AFTER skipping!
if keepcounter - cutoff_counter > 0:
cmd.delete(objectname)
cmd.load_cgo(
arrow, objectname
) # Ray tracing an empty object will cause a segmentation fault. No arrows = Do not display in PyMOL!!!
cmd.show(representation="cartoon", selection=first_obj_frame)
if (first_obj_frame != last_obj_frame):
cmd.show(representation="cartoon", selection=last_obj_frame)
cmd.hide(representation="cartoon", selection=last_obj_frame)
cmd.bg_color(color="white")
cmd.set_view(save_view)
return
def test_version(self):
v = cmd.get_version()
# check that all elements of v are the same, need to remove "." and strip trailing 0's
s = set(map(lambda s: str(s).replace('.', '').rstrip('0'), v))
self.assertEqual(len(s), 1)
