def modifyTransmute(self, elem, force = False, atomType=None):
"""
This method was originally a method of class mode and selectMode.
Transmute selected atoms into <elem> and with an optional <atomType>.
<elem> is an element number that selected atoms will be transmuted to.
<force>: boolean variable meaning keeping existing bond or not.
<atomType>: the optional hybrid bond type if the element support hybrid. --Huaicai[9/1/05]
"""
# now change selected atoms to the specified element
# [bruce 041215: this should probably be made available for any modes
# in which "selected atoms" are permitted, not just Select modes. #e]
from model.elements import PeriodicTable
if self.selatoms:
dstElem = PeriodicTable.getElement(elem)
for atm in self.selatoms.values():
atm.Transmute(dstElem, force = force, atomtype=atomType)
# bruce 041215 fix bug 131 by replacing low-level mvElement call
# with new higher-level method Transmute. Note that singlets
# can't be selected, so the fact that Transmute does nothing to
# them is not (presently) relevant.
#e status message?
# (Presently a.Transmute makes one per "error or refusal".)
self.o.gl_update()
if self.selmols: #bruce 060720 elif -> if, in case both atoms and chunks can be selected someday
dstElem = PeriodicTable.getElement(elem) #bruce 060720 fix typo dstElm -> dstElem to fix bug 2149
# but we have to decide if we want the behavior this now gives us, of transmuting inside selected chunks.
for mol in self.selmols[:]:
for atm in mol.atoms.values():
atm.Transmute(dstElem, force = force, atomtype=atomType)
# this might run on some killed singlets; should be ok
self.o.gl_update()
return
def update_hybrid_btngrp(self, buttonIndex = 0):
"""Update the buttons of the current element\'s hybridization types into hybrid_btngrp;
select the specified one if provided"""
elem = PeriodicTable.getElement(self.w.Element) # self.w.Element is atomic number
atypes = elem.atomtypes
if elem.name == 'Carbon':
self.setup_C_hybrid_buttons()
elif elem.name == 'Nitrogen':
self.setup_N_hybrid_buttons()
elif elem.name == 'Oxygen':
self.setup_O_hybrid_buttons()
elif elem.name == 'Sulfur':
self.setup_S_hybrid_buttons()
else:
self.hide_hybrid_btngrp()
self.elemGLPane.changeHybridType(None)
return
#if len(atypes) > 1:
# Prequisite: w.hybridComboBox has been updated at this moment.
b_name = self.bond_id2name[buttonIndex]
self.elemGLPane.changeHybridType(b_name)
self.elemGLPane.refreshDisplay(self.elm, self.displayMode)
self.theHybridizations.button(buttonIndex).setChecked(True)
self.set_hybrid_type(buttonIndex)
# Added Atomic Hybrids label. Mark 2007-05-30
self.atomic_hybrids_label.setText("Atomic Hybrids for " + elem.name + " :")
self.show_hybrid_btngrp()
def update_selection_filter_list(self):
"""Adds/removes the element selected in the MMKit to/from Atom Selection Filter
based on what modifier key is pressed (if any).
"""
eltnum = self.w.Element
if self.o.modkeys is None:
self.w.filtered_elements = []
self.w.filtered_elements.append(PeriodicTable.getElement(eltnum))
if self.o.modkeys == 'Shift':
if not PeriodicTable.getElement(eltnum) in self.w.filtered_elements[:]:
self.w.filtered_elements.append(PeriodicTable.getElement(eltnum))
elif self.o.modkeys == 'Control':
if PeriodicTable.getElement(eltnum) in self.w.filtered_elements[:]:
self.w.filtered_elements.remove(PeriodicTable.getElement(eltnum))
self.update_selection_filter_list_widget()
def fix_deprecated_elements( changed_atoms):
"""
scan for deprecated elements, and fix them
"""
fix_PAM3 = pref_fix_deprecated_PAM3_atoms()
fix_PAM5 = pref_fix_deprecated_PAM5_atoms()
deprecated_atoms = []
for atom in changed_atoms.itervalues():
deprecated_to = atom.element.deprecated_to
# an element symbol, or None, or 'remove'
if deprecated_to:
pam = atom.element.pam
assert pam in (MODEL_PAM3, MODEL_PAM5)
if pam == MODEL_PAM3:
fix = fix_PAM3
elif pam == MODEL_PAM5:
fix = fix_PAM5
else:
fix = False
if fix:
deprecated_atoms.append(atom)
elif debug_flags.DEBUG_DNA_UPDATER:
print "dna updater: debug_pref says don't alter deprecated atom %r" % (atom,)
continue
for atom in deprecated_atoms:
deprecated_to = atom.element.deprecated_to
# an element symbol, or 'remove'
if atom.display != diDEFAULT:
# Atoms of deprecated elements sometimes have funny display modes
# set by the DNA Duplex Generator. Remove these here.
# (This may be needed even after we fix the generator,
# due to old mmp files. REVIEW: can it ever cause harm?)
atom.setDisplay(diDEFAULT)
if deprecated_to == 'remove' or deprecated_to == 'X':
# (Atom.kill might be unideal behavior for 'remove',
# but that's only on Pl3 which never occurs AFAIK, so nevermind)
# Kill the atom (and make sure that new bondpoints get into a good enough position).
# REVIEW: does atom.kill make new bps immediately
# (review whether ok if more than one needs making on one base atom)
# or later
# (review whether it's still going to happen in the current master_updater call)? ####
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: kill deprecated atom %r" % (atom,)
summary_format = \
"Warning: dna updater killed [N] deprecated %s pseudoatom(s)" % \
(atom.element.symbol,)
env.history.deferred_summary_message( orangemsg(summary_format) )
atom.kill()
# TODO: worry about atom being a hotspot, or having a bondpoint which is a hotspot?
else:
# Transmute atom to a new element symbol -- assume its position,
# bonds, and bondpoints are all ok and need no changes.
# (Should be true of as 071119, since this is used only
# to make Ax and Ss PAM atoms from variant atomtypes
# used to mark them as being in special situations.)
#
# Use mvElement to avoid remaking existing bondpoints.
elt = PeriodicTable.getElement(deprecated_to)
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: transmute deprecated atom %r to element %s" % \
(atom, elt.symbol)
if dna_updater_warn_when_transmuting_deprecated_elements():
summary_format = \
"Warning: dna updater transmuted [N] %s to %s pseudoatom(s)" % \
(atom.element.symbol, elt.symbol )
env.history.deferred_summary_message( orangemsg(summary_format) )
# todo: refactor so orangemsg is replaced with a warning option
atom.mvElement(elt)
atom.make_enough_bondpoints()
# REVIEW: do this later, if atom classes should be corrected first
# to help this properly position bondpoints
# (or perhaps, first set correct atom classes, then do this,
# making sure it sets correct bondpoint classes,
# or that we correct them separately afterwards)
continue
return # from fix_deprecated_elements
def _readgms(assy, filename, isInsert=False):
"""
Read the atoms from a GAMESS DAT file into a single new chunk, which is returned,
unless there are no atoms in the file, in which case a warning is printed
and None is returned. (The new chunk (if returned) is in assy, but is not
yet added into any Group or Part in assy -- caller must do that.)
"""
fi = open(filename, "rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
ndix = {}
mol = Chunk(assy, nodename)
countdown = 0
equilibruim_found = False
atoms_found = False
for card in lines:
if failpat.search(
card): # GAMESS Aborted. No atom data will be found.
print card
break
# If this card is found:
# "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n"
# we know we have a successfully optimized structure/set of atoms.
# If this card is not found, the optimization failed for some reason.
# Atom positions begin soon after this card.
if card == "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n":
equilibruim_found = True
continue
# The atom positions we want ALWAYS begin 2 lines after this card:
# " COORDINATES OF ALL ATOMS ARE (ANGS)\n"
# which follows the previous card.
# This is one way to fix the problem mentioned above.
# I've commented the code below out since it needs further work to do what
# we need, and there is a chance we will not need this if GAMESS-US has
# the same number of lines (6) after the "EQUILIBRIUM" card above.
#
# P.S. The reason we do not just look for this card by itself is that there
# can be many of them. There is only one "EQUILIBRIUM" card, and the
# good atoms follow that card.
# 050624 Mark
if equilibruim_found:
if card == " COORDINATES OF ALL ATOMS ARE (ANGS)\n":
atoms_found = True
reading_atoms = True
countdown = 2
continue
if not equilibruim_found or not atoms_found:
continue
if countdown:
countdown -= 1
# print countdown, card # for debugging only.
continue
# The current card contains atom type and position.
n = 0
if reading_atoms:
if len(card) < 10:
reading_atoms = False # Finished reading atoms.
break
m = irecpat.match(card)
sym = capitalize(m.group(1))
try:
PeriodicTable.getElement(sym)
except:
env.history.message(
redmsg(
"Warning: GAMESS DAT file: unknown element %s in: %s" %
(sym, card)))
else:
xyz = map(float, (m.group(2), m.group(3), m.group(4)))
a = Atom(sym, A(xyz), mol)
ndix[n] = a
n += 1
# Don't return an empty chunk.
if not mol.atoms:
msg = "Warning: GAMESS file contains no equilibrium geometry. No atoms read into part."
env.history.message(redmsg(msg))
return None
# Need to compute and add bonds for this chunk. I'll ask Bruce how to best accomplish this.
# In the meantime, let's warn the user that no bonds have been formed since it
# is impossible to see this in vdW display mode.
# Mark 050623.
msg = "Warning: Equilibrium geometry found. Atoms read into part, but there are no bonds."
env.history.message(orangemsg(msg))
return mol
def _get_atomlist_from_gms_outfile(assy, filename):
"""
Read the atoms from a GAMESS OUT file into an atom list, which is returned,
unless there are no atoms in the file, in which case a warning is printed
and None is returned.
"""
fi = open(filename, "rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
newAtomList = []
countdown = 0
equilibruim_found = False
atoms_found = False
for card in lines:
if failpat.search(
card): # GAMESS Aborted. No atom data will be found.
print card
env.history.message(redmsg(card))
break
if noconvpat.search(card): # Geometry search is not converged.
print card
env.history.message(redmsg(card))
break
# If this card is found:
# "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n"
# we know we have a successfully optimized structure/set of atoms.
# If this card is not found, the optimization failed for some reason.
# Atom positions begin soon after this card.
if card == "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n":
equilibruim_found = True
continue
# The atom positions we want ALWAYS begin 2 lines after this card:
# " COORDINATES OF ALL ATOMS ARE (ANGS)\n"
# which follows the previous card.
# This is one way to fix the problem mentioned above.
# I've commented the code below out since it needs further work to do what
# we need, and there is a chance we will not need this if GAMESS-US has
# the same number of lines (6) after the "EQUILIBRIUM" card above.
#
# P.S. The reason we do not just look for this card by itself is that there
# can be many of them. There is only one "EQUILIBRIUM" card, and the
# good atoms follow that card.
# 050624 Mark
if equilibruim_found:
if card == " COORDINATES OF ALL ATOMS ARE (ANGS)\n":
atoms_found = True
reading_atoms = True
countdown = 2
continue
if not equilibruim_found or not atoms_found:
continue
if countdown:
countdown -= 1
# print countdown, card # for debugging only.
continue
# The current card contains atom type and position.
n = 0
if reading_atoms:
# print "_get_atomlist_from_gms_outfile:", card
if len(card) < 10:
reading_atoms = False # Finished reading atoms.
break
m = irecpat.match(card)
sym = capitalize(m.group(1))
try:
PeriodicTable.getElement(sym)
except:
env.history.message(
redmsg(
"Warning: GAMESS OUT file: unknown element %s in: %s" %
(sym, card)))
else:
xyz = map(float, (m.group(2), m.group(3), m.group(4)))
a = Atom(sym, A(xyz), mol)
newAtomList += [a]
# Let caller handle history msgs. Mark 050712
# if not newAtomList:
# msg = "Warning: GAMESS file contains no equilibrium geometry. No atoms read into part."
# env.history.message( redmsg(msg))
# return None
return newAtomList
def elementId(symbol):
return PeriodicTable.getElement(symbol).eltnum
from utilities.exception_classes import PluginBug
from utilities.constants import gensym
from utilities.prefs_constants import dnaDefaultStrand1Color_prefs_key
from utilities.prefs_constants import dnaDefaultStrand2Color_prefs_key
from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
from dna.model.Dna_Constants import getDuplexBasesPerTurn
##from dna.updater.dna_updater_prefs import pref_dna_updater_convert_to_PAM3plus5
from simulation.sim_commandruns import adjustSinglet
from model.elements import PeriodicTable
from model.Line import Line
from model.chem import Atom_prekill_prep
Element_Ae3 = PeriodicTable.getElement('Ae3')
from dna.model.Dna_Constants import basesDict, dnaDict
from dna.model.dna_model_constants import LADDER_END0
basepath_ok, basepath = find_plugin_dir("DNA")
if not basepath_ok:
env.history.message(orangemsg("The cad/plugins/DNA directory is missing."))
RIGHT_HANDED = -1
LEFT_HANDED = 1
from geometry.VQT import V, Q, norm, cross
from geometry.VQT import vlen
from Numeric import dot
def _readgms(assy, filename, isInsert=False):
"""
Read the atoms from a GAMESS DAT file into a single new chunk, which is returned,
unless there are no atoms in the file, in which case a warning is printed
and None is returned. (The new chunk (if returned) is in assy, but is not
yet added into any Group or Part in assy -- caller must do that.)
"""
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
ndix = {}
mol = Chunk(assy, nodename)
countdown = 0
equilibruim_found = False
atoms_found = False
for card in lines:
if failpat.search(card): # GAMESS Aborted. No atom data will be found.
print card
break
# If this card is found:
# "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n"
# we know we have a successfully optimized structure/set of atoms.
# If this card is not found, the optimization failed for some reason.
# Atom positions begin soon after this card.
if card == "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n":
equilibruim_found = True
continue
# The atom positions we want ALWAYS begin 2 lines after this card:
# " COORDINATES OF ALL ATOMS ARE (ANGS)\n"
# which follows the previous card.
# This is one way to fix the problem mentioned above.
# I've commented the code below out since it needs further work to do what
# we need, and there is a chance we will not need this if GAMESS-US has
# the same number of lines (6) after the "EQUILIBRIUM" card above.
#
# P.S. The reason we do not just look for this card by itself is that there
# can be many of them. There is only one "EQUILIBRIUM" card, and the
# good atoms follow that card.
# 050624 Mark
if equilibruim_found:
if card == " COORDINATES OF ALL ATOMS ARE (ANGS)\n":
atoms_found = True
reading_atoms = True
countdown = 2
continue
if not equilibruim_found or not atoms_found:
continue
if countdown:
countdown -= 1
# print countdown, card # for debugging only.
continue
# The current card contains atom type and position.
n = 0
if reading_atoms:
if len(card)<10:
reading_atoms = False # Finished reading atoms.
break
m=irecpat.match(card)
sym = capitalize(m.group(1))
try:
PeriodicTable.getElement(sym)
except:
env.history.message( redmsg( "Warning: GAMESS DAT file: unknown element %s in: %s" % (sym,card) ))
else:
xyz = map(float, (m.group(2),m.group(3), m.group(4)))
a = Atom(sym, A(xyz), mol)
ndix[n] = a
n += 1
# Don't return an empty chunk.
if not mol.atoms:
msg = "Warning: GAMESS file contains no equilibrium geometry. No atoms read into part."
env.history.message( redmsg(msg))
return None
# Need to compute and add bonds for this chunk. I'll ask Bruce how to best accomplish this.
# In the meantime, let's warn the user that no bonds have been formed since it
# is impossible to see this in vdW display mode.
# Mark 050623.
msg = "Warning: Equilibrium geometry found. Atoms read into part, but there are no bonds."
env.history.message( orangemsg(msg))
return mol
def populate(self, mol, height, width, z, bond_length, endings, position):
"""
Create a graphene sheet chunk.
"""
def add(element, x, y, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
num_atoms = len(mol.atoms)
bond_dict = {}
i = j = 0
y = -0.5 * height - 2 * bond_length
while y < 0.5 * height + 2 * bond_length:
i = 0
x = -0.5 * width - 2 * bond_length
while x < 0.5 * width + 2 * bond_length:
lst = []
for x1, y1 in quartet:
atm = add("C", x + x1 * bond_length, y + y1 * bond_length)
lst.append(atm)
bond_dict[(i, j)] = lst
bond_atoms(lst[0], lst[1], bond_constants.V_GRAPHITE)
bond_atoms(lst[1], lst[2], bond_constants.V_GRAPHITE)
bond_atoms(lst[2], lst[3], bond_constants.V_GRAPHITE)
i += 1
x += 3 * bond_length
j += 1
y += sqrt3 * bond_length
imax, jmax = i, j
for i in range(imax):
for j in range(jmax - 1):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i, j + 1)]
bond_atoms(lst1[0], lst2[1], bond_constants.V_GRAPHITE)
bond_atoms(lst1[3], lst2[2], bond_constants.V_GRAPHITE)
for i in range(imax - 1):
for j in range(jmax):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i + 1, j)]
bond_atoms(lst1[3], lst2[0], bond_constants.V_GRAPHITE)
# trim to dimensions
atoms = mol.atoms
for atm in atoms.values():
x, y, z = atm.posn()
xdim, ydim = width + bond_length, height + bond_length
# xdim, ydim = width + 0.5 * bond_length, height + 0.5 * bond_length
if (x < -0.5 * xdim or x > 0.5 * xdim or y < -0.5 * ydim
or y > 0.5 * ydim):
atm.kill()
def trimCarbons():
"""Trim all the carbons that only have one carbon neighbor.
"""
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
if TOROIDAL:
# This is for making electrical inductors. What would be
# really good here would be to break the bonds that are
# stretched by this and put back the bondpoints.
angstromsPerTurn = 6.0
for atm in atoms.values():
x, y, z = atm.posn()
r = (x**2 + y**2)**.5
if 0.25 * width <= r <= 0.5 * width:
angle = atan2(y, x)
zdisp = (angstromsPerTurn * angle) / (2 * pi)
atm.setposn(V(x, y, z + zdisp))
else:
atm.kill()
if endings == 1:
# hydrogen terminations
trimCarbons()
for atm in atoms.values():
atm.Hydrogenate()
elif endings == 2:
# nitrogen terminations
trimCarbons()
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
for atm in atoms.values():
atm.setposn(atm.posn() + position)
if num_atoms == len(mol.atoms):
raise Exception("Graphene sheet too small - no atoms added")
def populate(self, mol, height, width, z, bond_length, endings, position):
"""
Create a graphene sheet chunk.
"""
def add(element, x, y, atomtype='sp2'):
atm = Atom(element, V(x, y, z), mol)
atm.set_atomtype_but_dont_revise_singlets(atomtype)
return atm
num_atoms = len(mol.atoms)
bond_dict = { }
i = j = 0
y = -0.5 * height - 2 * bond_length
while y < 0.5 * height + 2 * bond_length:
i = 0
x = -0.5 * width - 2 * bond_length
while x < 0.5 * width + 2 * bond_length:
lst = [ ]
for x1, y1 in quartet:
atm = add("C", x + x1 * bond_length, y + y1 * bond_length)
lst.append(atm)
bond_dict[(i, j)] = lst
bonds.bond_atoms(lst[0], lst[1], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst[1], lst[2], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst[2], lst[3], bond_constants.V_GRAPHITE)
i += 1
x += 3 * bond_length
j += 1
y += sqrt3 * bond_length
imax, jmax = i, j
for i in range(imax):
for j in range(jmax - 1):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i, j+1)]
bonds.bond_atoms(lst1[0], lst2[1], bond_constants.V_GRAPHITE)
bonds.bond_atoms(lst1[3], lst2[2], bond_constants.V_GRAPHITE)
for i in range(imax - 1):
for j in range(jmax):
lst1 = bond_dict[(i, j)]
lst2 = bond_dict[(i+1, j)]
bonds.bond_atoms(lst1[3], lst2[0], bond_constants.V_GRAPHITE)
# trim to dimensions
atoms = mol.atoms
for atm in atoms.values():
x, y, z = atm.posn()
xdim, ydim = width + bond_length, height + bond_length
# xdim, ydim = width + 0.5 * bond_length, height + 0.5 * bond_length
if (x < -0.5 * xdim or x > 0.5 * xdim or y < -0.5 * ydim or y > 0.5 * ydim):
atm.kill()
def trimCarbons():
"""Trim all the carbons that only have one carbon neighbor.
"""
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
if TOROIDAL:
# This is for making electrical inductors. What would be
# really good here would be to break the bonds that are
# stretched by this and put back the bondpoints.
angstromsPerTurn = 6.0
for atm in atoms.values():
x, y, z = atm.posn()
r = (x**2 + y**2) ** .5
if 0.25 * width <= r <= 0.5 * width:
angle = atan2(y, x)
zdisp = (angstromsPerTurn * angle) / (2 * pi)
atm.setposn(V(x, y, z + zdisp))
else:
atm.kill()
if endings == 1:
# hydrogen terminations
trimCarbons()
for atm in atoms.values():
atm.Hydrogenate()
elif endings == 2:
# nitrogen terminations
trimCarbons()
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
for atm in atoms.values():
atm.setposn(atm.posn() + position)
if num_atoms == len(mol.atoms):
raise Exception("Graphene sheet too small - no atoms added")
from utilities.exception_classes import PluginBug
from utilities.constants import gensym
from utilities.prefs_constants import dnaDefaultStrand1Color_prefs_key
from utilities.prefs_constants import dnaDefaultStrand2Color_prefs_key
from utilities.prefs_constants import dnaDefaultSegmentColor_prefs_key
from dna.model.Dna_Constants import getDuplexBasesPerTurn
##from dna.updater.dna_updater_prefs import pref_dna_updater_convert_to_PAM3plus5
from simulation.sim_commandruns import adjustSinglet
from model.elements import PeriodicTable
from model.Line import Line
from model.chem import Atom_prekill_prep
Element_Ae3 = PeriodicTable.getElement('Ae3')
from dna.model.Dna_Constants import basesDict, dnaDict
from dna.model.dna_model_constants import LADDER_END0
basepath_ok, basepath = find_plugin_dir("DNA")
if not basepath_ok:
env.history.message(orangemsg("The cad/plugins/DNA directory is missing."))
RIGHT_HANDED = -1
LEFT_HANDED = 1
from geometry.VQT import V, Q, norm, cross
from geometry.VQT import vlen
from Numeric import dot
# - Remove Crossover needs to be offered when correct to do so, not otherwise
# - Pl position is wrong after either op, esp. Remove
# - Undo and Feature Help cmdnames are wrong (not working)
from utilities.constants import noop, average_value
from model.bond_constants import V_SINGLE
from model.bond_constants import atoms_are_bonded, find_bond
from model.bonds import bond_atoms_faster, bond_direction ##, bond_atoms
from utilities.Log import redmsg, greenmsg, quote_html ##, orangemsg
##from debug_prefs import debug_pref, Choice
import foundation.env as env
from utilities.GlobalPreferences import dna_updater_is_enabled
from model.elements import PeriodicTable
Element_Sj5 = PeriodicTable.getElement('Sj5')
Element_Ss5 = PeriodicTable.getElement('Ss5')
def crossover_menu_spec(atom, selatoms):
"""
Make a crossover-related menu_spec list for the two atoms in the
selatoms dict (atom.key -> atom), both Pl, for use in atom's context menu
(which must be one of the atoms in selatoms). If no menu commands are needed,
return [] (a valid empty menu_spec) or None.
Should be reasonably fast, but needn't be super-fast -- called once
whenever we construct a context menu for exactly two selected Pl atoms.
"""
assert len(selatoms) == 2
atoms = selatoms.values()
def fix_deprecated_elements(changed_atoms):
"""
scan for deprecated elements, and fix them
"""
fix_PAM3 = pref_fix_deprecated_PAM3_atoms()
fix_PAM5 = pref_fix_deprecated_PAM5_atoms()
deprecated_atoms = []
for atom in changed_atoms.itervalues():
deprecated_to = atom.element.deprecated_to
# an element symbol, or None, or 'remove'
if deprecated_to:
pam = atom.element.pam
assert pam in (MODEL_PAM3, MODEL_PAM5)
if pam == MODEL_PAM3:
fix = fix_PAM3
elif pam == MODEL_PAM5:
fix = fix_PAM5
else:
fix = False
if fix:
deprecated_atoms.append(atom)
elif debug_flags.DEBUG_DNA_UPDATER:
print "dna updater: debug_pref says don't alter deprecated atom %r" % (
atom, )
continue
for atom in deprecated_atoms:
deprecated_to = atom.element.deprecated_to
# an element symbol, or 'remove'
if atom.display != diDEFAULT:
# Atoms of deprecated elements sometimes have funny display modes
# set by the DNA Duplex Generator. Remove these here.
# (This may be needed even after we fix the generator,
# due to old mmp files. REVIEW: can it ever cause harm?)
atom.setDisplay(diDEFAULT)
if deprecated_to == 'remove' or deprecated_to == 'X':
# (Atom.kill might be unideal behavior for 'remove',
# but that's only on Pl3 which never occurs AFAIK, so nevermind)
# Kill the atom (and make sure that new bondpoints get into a good enough position).
# REVIEW: does atom.kill make new bps immediately
# (review whether ok if more than one needs making on one base atom)
# or later
# (review whether it's still going to happen in the current master_updater call)? ####
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: kill deprecated atom %r" % (atom, )
summary_format = \
"Warning: dna updater killed [N] deprecated %s pseudoatom(s)" % \
(atom.element.symbol,)
env.history.deferred_summary_message(orangemsg(summary_format))
atom.kill()
# TODO: worry about atom being a hotspot, or having a bondpoint which is a hotspot?
else:
# Transmute atom to a new element symbol -- assume its position,
# bonds, and bondpoints are all ok and need no changes.
# (Should be true of as 071119, since this is used only
# to make Ax and Ss PAM atoms from variant atomtypes
# used to mark them as being in special situations.)
#
# Use mvElement to avoid remaking existing bondpoints.
elt = PeriodicTable.getElement(deprecated_to)
if debug_flags.DEBUG_DNA_UPDATER_VERBOSE:
print "dna updater: transmute deprecated atom %r to element %s" % \
(atom, elt.symbol)
if dna_updater_warn_when_transmuting_deprecated_elements():
summary_format = \
"Warning: dna updater transmuted [N] %s to %s pseudoatom(s)" % \
(atom.element.symbol, elt.symbol )
env.history.deferred_summary_message(orangemsg(summary_format))
# todo: refactor so orangemsg is replaced with a warning option
atom.mvElement(elt)
atom.make_enough_bondpoints()
# REVIEW: do this later, if atom classes should be corrected first
# to help this properly position bondpoints
# (or perhaps, first set correct atom classes, then do this,
# making sure it sets correct bondpoint classes,
# or that we correct them separately afterwards)
continue
return # from fix_deprecated_elements
def elementId(symbol):
return PeriodicTable.getElement(symbol).eltnum
def build_struct(self, name, params, position, mol=None, createPrinted=False):
"""
Build a nanotube from the parameters in the Property Manger dialog.
"""
length, n, m, bond_length, zdist, xydist, \
twist, bend, members, endings, numwalls, spacing = params
# This can take a few seconds. Inform the user.
# 100 is a guess on my part. Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message(self.cmd + "This may take a moment...")
self.chirality = Chirality(n, m, bond_length)
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.chirality.xyz
if mol == None:
mol = Chunk(self.win.assy, name)
atoms = mol.atoms
mlimits = self.chirality.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.chirality.populate(mol, length + 4 * self.chirality.maxlen, members != 0)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (zdist + length) / length
atm.setposn(V(x, y, z))
length += zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.chirality.R
x *= (radius + 0.5 * xydist) / radius
y *= (radius - 0.5 * xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on nanotubes. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = bond_length
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if (z > .5 * (length + LENGTH_TWEAK) or
z < -.5 * (length + LENGTH_TWEAK)):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(bend) > pi / 360:
R = length / bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
# trim all the carbons that only have one carbon neighbor
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# if we're not picky about endings, we don't need to trim carbons
if endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.chirality.R)
if endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif endings == "Nitrogen":
# nitrogen terminations
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
if numwalls > 1:
n += int(spacing * 3 + 0.5) # empirical tinkering
params = (length, n, m, bond_length, zdist, xydist,
twist, bend, members, endings, numwalls-1, spacing)
self.build_struct(name, params, position, mol=mol, createPrinted=True)
return mol
def _init():
global _is_initialized
if (_is_initialized):
return
AMBER_AtomTypes["C"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CA"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CB"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CC"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CD"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CK"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CM"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CN"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CQ"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CR"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CT"] = PeriodicTable.getElement("C").find_atomtype("sp3")
AMBER_AtomTypes["CV"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CW"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["C*"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CY"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["CZ"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["C0"] = PeriodicTable.getElement("Ca").find_atomtype("?")
AMBER_AtomTypes["H"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H0"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HC"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H1"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H2"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H3"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HA"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H4"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H5"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HO"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HS"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HW"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HP"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HZ"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["F"] = PeriodicTable.getElement("F").find_atomtype("?")
AMBER_AtomTypes["Cl"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["Br"] = PeriodicTable.getElement("Br").find_atomtype("?")
AMBER_AtomTypes["I"] = PeriodicTable.getElement("I").find_atomtype("?")
AMBER_AtomTypes["IM"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["IB"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["MG"] = PeriodicTable.getElement("Mg").find_atomtype("?")
AMBER_AtomTypes["N"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NA"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NB"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NC"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N2"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N3"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["NT"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["N*"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NY"] = PeriodicTable.getElement("N").find_atomtype("sp")
AMBER_AtomTypes["O"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["O2"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["OW"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OH"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OS"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["P"] = PeriodicTable.getElement("P").find_atomtype("sp3(p)") #sp3(p) is 'sp3(phosphate)
AMBER_AtomTypes["S"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["SH"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["CU"] = PeriodicTable.getElement("Cu").find_atomtype("?")
AMBER_AtomTypes["FE"] = PeriodicTable.getElement("Fe").find_atomtype("?")
AMBER_AtomTypes["Li"] = PeriodicTable.getElement("Li").find_atomtype("?")
AMBER_AtomTypes["IP"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["Na"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["K"] = PeriodicTable.getElement("K").find_atomtype("?")
#AMBER_AtomTypes["Rb"] = PeriodicTable.getElement("Rb").find_atomtype("?")
#AMBER_AtomTypes["Cs"] = PeriodicTable.getElement("Cs").find_atomtype("?")
AMBER_AtomTypes["Zn"] = PeriodicTable.getElement("Zn").find_atomtype("?")
_is_initialized = True
def build_struct(self,
name,
params,
position,
mol=None,
createPrinted=False):
"""
Build a nanotube from the parameters in the Property Manger dialog.
"""
length, n, m, bond_length, zdist, xydist, \
twist, bend, members, endings, numwalls, spacing = params
# This can take a few seconds. Inform the user.
# 100 is a guess on my part. Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message(self.cmd + "This may take a moment...")
self.chirality = Chirality(n, m, bond_length)
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.chirality.xyz
if mol == None:
mol = Chunk(self.win.assy, name)
atoms = mol.atoms
mlimits = self.chirality.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.chirality.populate(mol, length + 4 * self.chirality.maxlen,
members != 0)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (zdist + length) / length
atm.setposn(V(x, y, z))
length += zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.chirality.R
x *= (radius + 0.5 * xydist) / radius
y *= (radius - 0.5 * xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on nanotubes. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = bond_length
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if (z > .5 * (length + LENGTH_TWEAK)
or z < -.5 * (length + LENGTH_TWEAK)):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(bend) > pi / 360:
R = length / bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
# trim all the carbons that only have one carbon neighbor
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# if we're not picky about endings, we don't need to trim carbons
if endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.chirality.R)
if endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif endings == "Nitrogen":
# nitrogen terminations
dstElem = PeriodicTable.getElement('N')
atomtype = dstElem.find_atomtype('sp2')
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(
greenmsg("%g seconds to build %d atoms" %
(t, len(atoms.values()))))
if numwalls > 1:
n += int(spacing * 3 + 0.5) # empirical tinkering
params = (length, n, m, bond_length, zdist, xydist, twist, bend,
members, endings, numwalls - 1, spacing)
self.build_struct(name,
params,
position,
mol=mol,
createPrinted=True)
return mol
def _get_atomlist_from_gms_outfile(assy, filename):
"""
Read the atoms from a GAMESS OUT file into an atom list, which is returned,
unless there are no atoms in the file, in which case a warning is printed
and None is returned.
"""
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
newAtomList = []
countdown = 0
equilibruim_found = False
atoms_found = False
for card in lines:
if failpat.search(card): # GAMESS Aborted. No atom data will be found.
print card
env.history.message( redmsg( card ))
break
if noconvpat.search(card): # Geometry search is not converged.
print card
env.history.message( redmsg( card ))
break
# If this card is found:
# "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n"
# we know we have a successfully optimized structure/set of atoms.
# If this card is not found, the optimization failed for some reason.
# Atom positions begin soon after this card.
if card == "1 ***** EQUILIBRIUM GEOMETRY LOCATED *****\n":
equilibruim_found = True
continue
# The atom positions we want ALWAYS begin 2 lines after this card:
# " COORDINATES OF ALL ATOMS ARE (ANGS)\n"
# which follows the previous card.
# This is one way to fix the problem mentioned above.
# I've commented the code below out since it needs further work to do what
# we need, and there is a chance we will not need this if GAMESS-US has
# the same number of lines (6) after the "EQUILIBRIUM" card above.
#
# P.S. The reason we do not just look for this card by itself is that there
# can be many of them. There is only one "EQUILIBRIUM" card, and the
# good atoms follow that card.
# 050624 Mark
if equilibruim_found:
if card == " COORDINATES OF ALL ATOMS ARE (ANGS)\n":
atoms_found = True
reading_atoms = True
countdown = 2
continue
if not equilibruim_found or not atoms_found:
continue
if countdown:
countdown -= 1
# print countdown, card # for debugging only.
continue
# The current card contains atom type and position.
n = 0
if reading_atoms:
# print "_get_atomlist_from_gms_outfile:", card
if len(card)<10:
reading_atoms = False # Finished reading atoms.
break
m=irecpat.match(card)
sym = capitalize(m.group(1))
try:
PeriodicTable.getElement(sym)
except:
env.history.message( redmsg( "Warning: GAMESS OUT file: unknown element %s in: %s" % (sym,card) ))
else:
xyz = map(float, (m.group(2),m.group(3), m.group(4)))
a = Atom(sym, A(xyz), mol)
newAtomList += [a]
# Let caller handle history msgs. Mark 050712
# if not newAtomList:
# msg = "Warning: GAMESS file contains no equilibrium geometry. No atoms read into part."
# env.history.message( redmsg(msg))
# return None
return newAtomList
def _init():
global _is_initialized
if (_is_initialized):
return
AMBER_AtomTypes["C"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CA"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CB"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CC"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CD"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CK"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CM"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CN"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CQ"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CR"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CT"] = PeriodicTable.getElement("C").find_atomtype("sp3")
AMBER_AtomTypes["CV"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CW"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["C*"] = PeriodicTable.getElement("C").find_atomtype("sp2")
AMBER_AtomTypes["CY"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["CZ"] = PeriodicTable.getElement("C").find_atomtype("sp")
AMBER_AtomTypes["C0"] = PeriodicTable.getElement("Ca").find_atomtype("?")
AMBER_AtomTypes["H"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H0"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HC"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H1"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H2"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H3"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HA"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H4"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["H5"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HO"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HS"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HW"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HP"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["HZ"] = PeriodicTable.getElement("H").find_atomtype("?")
AMBER_AtomTypes["F"] = PeriodicTable.getElement("F").find_atomtype("?")
AMBER_AtomTypes["Cl"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["Br"] = PeriodicTable.getElement("Br").find_atomtype("?")
AMBER_AtomTypes["I"] = PeriodicTable.getElement("I").find_atomtype("?")
AMBER_AtomTypes["IM"] = PeriodicTable.getElement("Cl").find_atomtype("?")
AMBER_AtomTypes["IB"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["MG"] = PeriodicTable.getElement("Mg").find_atomtype("?")
AMBER_AtomTypes["N"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NA"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NB"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NC"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N2"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["N3"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["NT"] = PeriodicTable.getElement("N").find_atomtype("sp3")
AMBER_AtomTypes["N*"] = PeriodicTable.getElement("N").find_atomtype("sp2")
AMBER_AtomTypes["NY"] = PeriodicTable.getElement("N").find_atomtype("sp")
AMBER_AtomTypes["O"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["O2"] = PeriodicTable.getElement("O").find_atomtype("sp2")
AMBER_AtomTypes["OW"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OH"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["OS"] = PeriodicTable.getElement("O").find_atomtype("sp3")
AMBER_AtomTypes["P"] = PeriodicTable.getElement("P").find_atomtype("sp3(p)") #sp3(p) is 'sp3(phosphate)
AMBER_AtomTypes["S"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["SH"] = PeriodicTable.getElement("S").find_atomtype("sp3") # ?
AMBER_AtomTypes["CU"] = PeriodicTable.getElement("Cu").find_atomtype("?")
AMBER_AtomTypes["FE"] = PeriodicTable.getElement("Fe").find_atomtype("?")
AMBER_AtomTypes["Li"] = PeriodicTable.getElement("Li").find_atomtype("?")
AMBER_AtomTypes["IP"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["Na"] = PeriodicTable.getElement("Na").find_atomtype("?")
AMBER_AtomTypes["K"] = PeriodicTable.getElement("K").find_atomtype("?")
#AMBER_AtomTypes["Rb"] = PeriodicTable.getElement("Rb").find_atomtype("?")
#AMBER_AtomTypes["Cs"] = PeriodicTable.getElement("Cs").find_atomtype("?")
AMBER_AtomTypes["Zn"] = PeriodicTable.getElement("Zn").find_atomtype("?")
_is_initialized = True
def _readpdb_new(assy,
filename,
isInsert = False,
showProgressDialog = False,
chainId = None):
"""
Read a Protein DataBank-format file into a single new chunk, which is
returned unless there are no atoms in the file, in which case a warning
is printed and None is returned. (The new chunk (if returned) is in assy,
but is not yet added into any Group or Part in assy -- caller must do that.)
Unless isInsert = True, set assy.filename to match the file we read,
even if we return None.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param isInsert: If True, the PDB file will be inserted into the current
assembly. If False (default), the PDB is opened as the
assembly.
@param isInsert: boolean
@param showProgressDialog: if True, display a progress dialog while reading
a file.
@type showProgressDialog: boolean
@return: A chunk containing the contents of the PDB file.
@rtype: L{Chunk}
@see: U{B{PDB File Format}<http://www.wwpdb.org/documentation/format23/v2.3.html>}
"""
from protein.model.Protein import is_water
def _finish_molecule():
"""
Perform some operations after reading entire PDB chain:
- rebuild (infer) bonds
- rename molecule to reflect a chain ID
- delete protein object if this is not a protein
- append the molecule to the molecule list
"""
if mol == water:
# Skip water, to be added explicitly at the end.
return
if mol.atoms:
###print "READING PDB ", (mol, numconects, chainId)
mol.name = pdbid.lower() + chainId
###idzialprint "SEQ = ", mol.protein.get_sequence_string()
###print "SEC = ", mol.protein.get_secondary_structure_string()
if mol.protein.count_c_alpha_atoms() == 0:
# If there is no C-alpha atoms, consider the chunk
# as a non-protein. But! Split it into individual
# hetero groups.
res_list = mol.protein.get_amino_acids()
assy.part.ensure_toplevel_group()
hetgroup = Group("Heteroatoms", assy, assy.part.topnode)
for res in res_list:
hetmol = Chunk(assy,
res.get_three_letter_code().replace(" ", "") + \
"[" + str(res.get_id()) + "]")
for atom in res.get_atom_list():
newatom = Atom(atom.element.symbol, atom.posn(), hetmol)
# New chunk - infer the bonds anyway (this is not
# correct, should first check connectivity read from
# the PDB file CONECT records).
inferBonds(hetmol)
hetgroup.addchild(hetmol)
mollist.append(hetgroup)
else:
#if numconects == 0:
# msg = orangemsg("PDB file has no bond info; inferring bonds")
# env.history.message(msg)
# # let user see message right away (bond inference can take significant
# # time) [bruce 060620]
# env.history.h_update()
# For protein - infer the bonds anyway.
inferBonds(mol)
mol.protein.set_chain_id(chainId)
mol.protein.set_pdb_id(pdbid)
if mol.atoms:
mollist.append(mol)
else:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
env.history.h_update()
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
mollist = []
# Lists of secondary structure tuples (res_id, chain_id)
helix = []
sheet = []
turn = []
dir, nodename = os.path.split(filename)
if not isInsert:
assy.filename = filename
ndix = {}
mol = Chunk(assy, nodename)
mol.protein = Protein()
# Create a chunk for water molecules.
water = Chunk(assy, nodename)
numconects = 0
comment_text = ""
_read_rosetta_info = False
# Create a temporary PDB ID - it should be later extracted from the
# file header.
pdbid = nodename.replace(".pdb","").lower()
atomname_exceptions = {
"HB":"H", #k these are all guesses -- I can't find this documented
# anywhere [bruce 070410]
"CA":"C", #k these are all guesses -- I can't find this documented
## "HE":"H", ### REVIEW: I'm not sure about this one --
### leaving it out means it's read as Helium,
# but including it erroneously might prevent reading an actual Helium
# if that was intended.
# Guess for now: include it for ATOM but not HETATM. (So it's
# specialcased below, rather than being included in this table.)
# (Later: can't we use the case of the 'E' to distinguish it from He?)
"HN":"H",
}
# Create and display a Progress dialog while reading the MMP file.
# One issue with this implem is that QProgressDialog always displays
# a "Cancel" button, which is not hooked up. I think this is OK for now,
# but later we should either hook it up or create our own progress
# dialog that doesn't include a "Cancel" button. --mark 2007-12-06
if showProgressDialog:
_progressValue = 0
_progressFinishValue = len(lines)
win = env.mainwindow()
win.progressDialog.setLabelText("Reading file...")
win.progressDialog.setRange(0, _progressFinishValue)
_progressDialogDisplayed = False
_timerStart = time.time()
for card in lines:
key = card[:6].lower().replace(" ", "")
if key in ["atom", "hetatm"]:
## sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
# bruce 080508 revision (guess at a bugfix for reading NE1-saved
# pdb files):
# get a list of atomnames to try; use the first one we recognize.
# Note that full atom name is in columns 13-16 i.e. card[12:16];
# see http://www.wwpdb.org/documentation/format2.3-0108-us.pdf,
# page 156. The old code only looked at two characters,
# card[12:14] == columns 13-14, and discarded ' ' and '_',
# and capitalized (the first character only). The code as I revised
# it on 070410 also discarded digits, and handled HB, HE, HN
# (guesses) using the atomname_exceptions dict.
name4 = card[12:16].replace(" ", "").replace("_", "")
name3 = card[12:15].replace(" ", "").replace("_", "")
name2 = card[12:14].replace(" ", "").replace("_", "")
chainId = card[21]
resIdStr = card[22:26].replace(" ", "")
if resIdStr != "":
resId = int(resIdStr)
else:
resId = 0
resName = card[17:20]
sym = card[77:78]
alt = card[16] # Alternate location indicator
if alt != ' ' and \
alt != 'A':
# Skip non-standard alternate location
# This is not very safe test, it should preserve
# the remaining atoms. piotr 080715
continue
###ATOM 131 CB ARG A 18 104.359 32.924 58.573 1.00 36.93 C
def nodigits(name):
for bad in "0123456789":
name = name.replace(bad, "")
return name
atomnames_to_try = [
name4, # as seems best according to documentation
name3,
name2, # like old code
nodigits(name4),
nodigits(name3),
nodigits(name2) # like code as revised on 070410
]
# First, look at 77-78 field - it should include an element symbol.
foundit = False
try:
PeriodicTable.getElement(sym)
except:
pass
else:
foundit = True
if not foundit:
for atomname in atomnames_to_try:
atomname = atomname_exceptions.get(atomname, atomname)
if atomname[0] == 'H' and key == "atom":
atomname = "H" # see comment in atomname_exceptions
sym = capitalize(atomname) # turns either 'he' or 'HE' into 'He'
try:
PeriodicTable.getElement(sym)
except:
# note: this typically fails with AssertionError
# (not e.g. KeyError) [bruce 050322]
continue
else:
foundit = True
break
pass
if not foundit:
msg = "Warning: Pdb file: will use Carbon in place of unknown element %s in: %s" \
% (name4, card)
print msg #bruce 070410 added this print
env.history.message( redmsg( msg ))
##e It would probably be better to create a fake atom, so the
# CONECT records would still work.
#bruce 080508 let's do that:
sym = "C"
# Better still might be to create a fake element,
# so we could write out the pdb file again
# (albeit missing lots of info). [bruce 070410 comment]
# Note: an advisor tells us:
# PDB files sometimes encode atomtypes,
# using C_R instead of C, for example, to represent sp2
# carbons.
# That particular case won't trigger this exception, since we
# only look at 2 characters [eventually, after trying more, as of 080508],
# i.e. C_ in that case. It would be better to realize this means
# sp2 and set the atomtype here (and perhaps then use it when
# inferring bonds, which we do later if the file doesn't have
# any bonds). [bruce 060614/070410 comment]
_is_water = is_water(resName, name4)
if _is_water:
tmpmol = mol
mol = water
# Now the element name is in sym.
xyz = map(float, [card[30:38], card[38:46], card[46:54]] )
n = int(card[6:11])
a = Atom(sym, A(xyz), mol)
ndix[n] = a
if not _is_water:
mol.protein.add_pdb_atom(a,
name4,
resId,
resName)
# Assign secondary structure.
if (resId, chainId) in helix:
mol.protein.assign_helix(resId)
if (resId, chainId) in sheet:
mol.protein.assign_strand(resId)
if (resId, chainId) in turn:
mol.protein.assign_turn(resId)
if mol == water:
mol = tmpmol
elif key == "conect":
try:
a1 = ndix[int(card[6:11])]
except:
#bruce 050322 added this level of try/except and its message;
# see code below for at least two kinds of errors this might
# catch, but we don't try to distinguish these here. BTW this
# also happens as a consequence of not finding the element
# symbol, above, since atoms with unknown elements are not
# created.
env.history.message( redmsg( "Warning: Pdb file: can't find first atom in CONECT record: %s" % (card,) ))
else:
for i in range(11, 70, 5):
try:
a2 = ndix[int(card[i:i+5])]
except ValueError:
# bruce 050323 comment:
# we assume this is from int('') or int(' ') etc;
# this is the usual way of ending this loop.
break
except KeyError:
#bruce 050322-23 added history warning for this,
# assuming it comes from ndix[] lookup.
env.history.message( redmsg( "Warning: Pdb file: can't find atom %s in: %s" % (card[i:i+5], card) ))
continue
bond_atoms(a1, a2)
numconects += 1
elif key == "ter":
# Finish the current molecule.
_finish_molecule()
# Discard the original molecule and create a new one.
mol = Chunk(assy, nodename)
mol.protein = Protein()
numconects = 0
elif key == "header":
# Extract PDB ID from the header string.
pdbid = card[62:66].lower()
comment_text += card
elif key == "compnd":
comment_text += card
elif key == "remark":
comment_text += card
elif key == "model":
# Check out the MODEL record, ignore everything other than MODEL 1.
# This behavior has to be optional and set via User Preference.
# piotr 080714
model_id = int(card[6:20])
if model_id > 1:
# Skip remaining part of the file.
break
elif key in ["helix", "sheet", "turn"]:
# Read secondary structure information.
if key == "helix":
begin = int(card[22:25])
end = int(card[34:37])
chainId = card[19]
for s in range(begin, end+1):
helix.append((s, chainId))
elif key == "sheet":
begin = int(card[23:26])
end = int(card[34:37])
chainId = card[21]
for s in range(begin, end+1):
sheet.append((s, chainId))
elif key == "turn":
begin = int(card[23:26])
end = int(card[34:37])
chainId = card[19]
for s in range(begin, end+1):
turn.append((s, chainId))
else:
if card[7:15] == "ntrials:":
_read_rosetta_info = True
comment_text += "Rosetta Scoring Analysis\n"
if _read_rosetta_info:
comment_text += card
if showProgressDialog: # Update the progress dialog.
_progressValue += 1
if _progressValue >= _progressFinishValue:
win.progressDialog.setLabelText("Building model...")
elif _progressDialogDisplayed:
win.progressDialog.setValue(_progressValue)
else:
_timerDuration = time.time() - _timerStart
if _timerDuration > 0.25:
# Display progress dialog after 0.25 seconds
win.progressDialog.setValue(_progressValue)
_progressDialogDisplayed = True
if showProgressDialog: # Make the progress dialog go away.
win.progressDialog.setValue(_progressFinishValue)
_finish_molecule()
if water.atoms:
# Check if there are any water molecules
water.name = "Solvent"
# The water should be hidden by default.
water.hide()
mollist.append(water)
return (mollist, comment_text)
def _readpdb(assy,
filename,
isInsert = False,
showProgressDialog = False,
chainId = None):
"""
Read a Protein DataBank-format file into a single new chunk, which is
returned unless there are no atoms in the file, in which case a warning
is printed and None is returned. (The new chunk (if returned) is in assy,
but is not yet added into any Group or Part in assy -- caller must do that.)
Unless isInsert = True, set assy.filename to match the file we read,
even if we return None.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param isInsert: If True, the PDB file will be inserted into the current
assembly. If False (default), the PDB is opened as the
assembly.
@param isInsert: boolean
@param showProgressDialog: if True, display a progress dialog while reading
a file.
@type showProgressDialog: boolean
@return: A chunk containing the contents of the PDB file.
@rtype: L{Chunk}
@see: U{B{PDB File Format}<http://www.wwpdb.org/documentation/format23/v2.3.html>}
"""
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
if not isInsert:
assy.filename = filename
ndix = {}
mol = Chunk(assy, nodename)
numconects = 0
atomname_exceptions = {
"HB":"H", #k these are all guesses -- I can't find this documented
# anywhere [bruce 070410]
## "HE":"H", ### REVIEW: I'm not sure about this one --
### leaving it out means it's read as Helium,
# but including it erroneously might prevent reading an actual Helium
# if that was intended.
# Guess for now: include it for ATOM but not HETATM. (So it's
# specialcased below, rather than being included in this table.)
# (Later: can't we use the case of the 'E' to distinguish it from He?)
"HN":"H",
}
# Create and display a Progress dialog while reading the MMP file.
# One issue with this implem is that QProgressDialog always displays
# a "Cancel" button, which is not hooked up. I think this is OK for now,
# but later we should either hook it up or create our own progress
# dialog that doesn't include a "Cancel" button. --mark 2007-12-06
if showProgressDialog:
_progressValue = 0
_progressFinishValue = len(lines)
win = env.mainwindow()
win.progressDialog.setLabelText("Reading file...")
win.progressDialog.setRange(0, _progressFinishValue)
_progressDialogDisplayed = False
_timerStart = time.time()
for card in lines:
key = card[:6].lower().replace(" ", "")
if key in ["atom", "hetatm"]:
## sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
# bruce 080508 revision (guess at a bugfix for reading NE1-saved
# pdb files):
# get a list of atomnames to try; use the first one we recognize.
# Note that full atom name is in columns 13-16 i.e. card[12:16];
# see http://www.wwpdb.org/documentation/format2.3-0108-us.pdf,
# page 156. The old code only looked at two characters,
# card[12:14] == columns 13-14, and discarded ' ' and '_',
# and capitalized (the first character only). The code as I revised
# it on 070410 also discarded digits, and handled HB, HE, HN
# (guesses) using the atomname_exceptions dict.
name4 = card[12:16].replace(" ", "").replace("_", "")
name3 = card[12:15].replace(" ", "").replace("_", "")
name2 = card[12:14].replace(" ", "").replace("_", "")
def nodigits(name):
for bad in "0123456789":
name = name.replace(bad, "")
return name
atomnames_to_try = [
name4, # as seems best according to documentation
name3,
name2, # like old code
nodigits(name4),
nodigits(name3),
nodigits(name2) # like code as revised on 070410
]
foundit = False
for atomname in atomnames_to_try:
atomname = atomname_exceptions.get(atomname, atomname)
if atomname == "HE" and key == "atom":
atomname = "H" # see comment in atomname_exceptions
sym = capitalize(atomname) # turns either 'he' or 'HE' into 'He'
try:
PeriodicTable.getElement(sym)
except:
# note: this typically fails with AssertionError
# (not e.g. KeyError) [bruce 050322]
continue
else:
foundit = True
break
pass
if not foundit:
msg = "Warning: Pdb file: will use Carbon in place of unknown element %s in: %s" \
% (name4, card)
print msg #bruce 070410 added this print
env.history.message( redmsg( msg ))
##e It would probably be better to create a fake atom, so the
# CONECT records would still work.
#bruce 080508 let's do that:
sym = "C"
# Better still might be to create a fake element,
# so we could write out the pdb file again
# (albeit missing lots of info). [bruce 070410 comment]
# Note: an advisor tells us:
# PDB files sometimes encode atomtypes,
# using C_R instead of C, for example, to represent sp2
# carbons.
# That particular case won't trigger this exception, since we
# only look at 2 characters [eventually, after trying more, as of 080508],
# i.e. C_ in that case. It would be better to realize this means
# sp2 and set the atomtype here (and perhaps then use it when
# inferring bonds, which we do later if the file doesn't have
# any bonds). [bruce 060614/070410 comment]
# Now the element name is in sym.
xyz = map(float, [card[30:38], card[38:46], card[46:54]] )
n = int(card[6:11])
a = Atom(sym, A(xyz), mol)
ndix[n] = a
elif key == "conect":
try:
a1 = ndix[int(card[6:11])]
except:
#bruce 050322 added this level of try/except and its message;
# see code below for at least two kinds of errors this might
# catch, but we don't try to distinguish these here. BTW this
# also happens as a consequence of not finding the element
# symbol, above, since atoms with unknown elements are not
# created.
env.history.message( redmsg( "Warning: Pdb file: can't find first atom in CONECT record: %s" % (card,) ))
else:
for i in range(11, 70, 5):
try:
a2 = ndix[int(card[i:i+5])]
except ValueError:
# bruce 050323 comment:
# we assume this is from int('') or int(' ') etc;
# this is the usual way of ending this loop.
break
except KeyError:
#bruce 050322-23 added history warning for this,
# assuming it comes from ndix[] lookup.
env.history.message( redmsg( "Warning: Pdb file: can't find atom %s in: %s" % (card[i:i+5], card) ))
continue
bond_atoms(a1, a2)
numconects += 1
if showProgressDialog: # Update the progress dialog.
_progressValue += 1
if _progressValue >= _progressFinishValue:
win.progressDialog.setLabelText("Building model...")
elif _progressDialogDisplayed:
win.progressDialog.setValue(_progressValue)
else:
_timerDuration = time.time() - _timerStart
if _timerDuration > 0.25:
# Display progress dialog after 0.25 seconds
win.progressDialog.setValue(_progressValue)
_progressDialogDisplayed = True
if showProgressDialog: # Make the progress dialog go away.
win.progressDialog.setValue(_progressFinishValue)
#bruce 050322 part of fix for bug 433: don't return an empty chunk
if not mol.atoms:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
return None
if numconects == 0:
msg = orangemsg("PDB file has no bond info; inferring bonds")
env.history.message(msg)
# let user see message right away (bond inference can take significant
# time) [bruce 060620]
env.history.h_update()
inferBonds(mol)
return mol
# - Remove Crossover needs to be offered when correct to do so, not otherwise
# - Pl position is wrong after either op, esp. Remove
# - Undo and Feature Help cmdnames are wrong (not working)
from utilities.constants import noop, average_value
from model.bond_constants import V_SINGLE
from model.bond_constants import atoms_are_bonded, find_bond
from model.bonds import bond_atoms_faster, bond_direction ##, bond_atoms
from utilities.Log import redmsg, greenmsg, quote_html ##, orangemsg
##from debug_prefs import debug_pref, Choice
import foundation.env as env
from utilities.GlobalPreferences import dna_updater_is_enabled
from model.elements import PeriodicTable
Element_Sj5 = PeriodicTable.getElement('Sj5')
Element_Ss5 = PeriodicTable.getElement('Ss5')
def crossover_menu_spec(atom, selatoms):
"""
Make a crossover-related menu_spec list for the two atoms in the
selatoms dict (atom.key -> atom), both Pl, for use in atom's context menu
(which must be one of the atoms in selatoms). If no menu commands are needed,
return [] (a valid empty menu_spec) or None.
Should be reasonably fast, but needn't be super-fast -- called once
whenever we construct a context menu for exactly two selected Pl atoms.
"""
assert len(selatoms) == 2
atoms = selatoms.values()
def build(self, name, assy, position, mol=None, createPrinted=False):
"""
Build a Peptide from the parameters in the Property Manger dialog.
"""
endPoint1, endPoint2 = self.getEndPoints()
cntAxis = endPoint2 - endPoint1
length = vlen(cntAxis)
# This can take a few seconds. Inform the user.
# 100 is a guess. --Mark 051103.
if not createPrinted:
# If it's a multi-wall tube, only print the "Creating" message once.
if length > 100.0:
env.history.message("This may take a moment...")
PROFILE = False
if PROFILE:
sw = Stopwatch()
sw.start()
xyz = self.xyz
if mol == None:
mol = Chunk(assy, name)
atoms = mol.atoms
mlimits = self.mlimits
# populate the tube with some extra carbons on the ends
# so that we can trim them later
self.populate(mol, length + 4 * self.maxlen)
# Apply twist and distortions. Bends probably would come
# after this point because they change the direction for the
# length. I'm worried about Z distortion because it will work
# OK for stretching, but with compression it can fail. BTW,
# "Z distortion" is a misnomer, we're stretching in the Y
# direction.
for atm in atoms.values():
# twist
x, y, z = atm.posn()
twistRadians = self.twist * z
c, s = cos(twistRadians), sin(twistRadians)
x, y = x * c + y * s, -x * s + y * c
atm.setposn(V(x, y, z))
for atm in atoms.values():
# z distortion
x, y, z = atm.posn()
z *= (self.zdist + length) / length
atm.setposn(V(x, y, z))
length += self.zdist
for atm in atoms.values():
# xy distortion
x, y, z = atm.posn()
radius = self.getRadius()
x *= (radius + 0.5 * self.xydist) / radius
y *= (radius - 0.5 * self.xydist) / radius
atm.setposn(V(x, y, z))
# Judgement call: because we're discarding carbons with funky
# valences, we will necessarily get slightly more ragged edges
# on Peptides. This is a parameter we can fiddle with to
# adjust the length. My thought is that users would prefer a
# little extra length, because it's fairly easy to trim the
# ends, but much harder to add new atoms on the end.
LENGTH_TWEAK = self.getBondLength()
# trim all the carbons that fall outside our desired length
# by doing this, we are introducing new singlets
for atm in atoms.values():
x, y, z = atm.posn()
if z > 0.5 * (length + LENGTH_TWEAK) or z < -0.5 * (length + LENGTH_TWEAK):
atm.kill()
# Apply bend. Equations are anomalous for zero bend.
if abs(self.bend) > pi / 360:
R = length / self.bend
for atm in atoms.values():
x, y, z = atm.posn()
theta = z / R
x, z = R - (R - x) * cos(theta), (R - x) * sin(theta)
atm.setposn(V(x, y, z))
def trimCarbons():
"""
Trim all the carbons that only have one carbon neighbor.
"""
for i in range(2):
for atm in atoms.values():
if not atm.is_singlet() and len(atm.realNeighbors()) == 1:
atm.kill()
trimCarbons()
# If we're not picky about endings, we don't need to trim carbons
if self.endings == "Capped":
# buckyball endcaps
addEndcap(mol, length, self.getRadius())
if self.endings == "Hydrogen":
# hydrogen terminations
for atm in atoms.values():
atm.Hydrogenate()
elif self.endings == "Nitrogen":
# nitrogen terminations.
# This option has been removed from the "Endings" combo box
# in the PM. 2008-05-02 --mark
dstElem = PeriodicTable.getElement("N")
atomtype = dstElem.find_atomtype("sp2")
for atm in atoms.values():
if len(atm.realNeighbors()) == 2:
atm.Transmute(dstElem, force=True, atomtype=atomtype)
# Translate structure to desired position
for atm in atoms.values():
v = atm.posn()
atm.setposn(v + position)
if PROFILE:
t = sw.now()
env.history.message(greenmsg("%g seconds to build %d atoms" % (t, len(atoms.values()))))
if self.numwalls > 1:
n += int(self.spacing * 3 + 0.5) # empirical tinkering
self.build(name, assy, endPoint1, endPoint2, position, mol=mol, createPrinted=True)
# Orient the Peptide.
if self.numwalls == 1:
# This condition ensures that MWCTs get oriented only once.
self._orient(mol, endPoint1, endPoint2)
return mol