def make_gaussian_cube_atoms(session):
from chimerax.map import Volume
from chimerax.map_data.gaussian.gaussian_grid import GaussianGrid
glist = [m.data for m in session.models
if isinstance(m, Volume) and isinstance(m.data, GaussianGrid)]
slist = []
for g in glist:
atoms = g.gc.atoms
if atoms:
from chimerax.atomic import AtomicStructure, Element
s = AtomicStructure(session)
r = s.new_residue('UNK', 'A', 1)
for i, (n,q,x,y,z) in enumerate(atoms):
e = Element.get_element(n)
a = s.new_atom(e.name, e)
b = bohr_radius = 0.5291772108 # Angstroms
a.coord = (b*x,b*y,b*z)
a.serial_number = i
r.add_atom(a)
s.connect_structure()
slist.append(s)
session.models.add(slist)
session.logger.info('Created %d atomic models for %d Gaussian Cube files'
% (len(slist), len(glist)))
def duplicate(session, selection, newModel=True):
# dict for unique models, residues, and atoms
models = {}
# dict for just models and atoms
atom_list = {}
for atom in selection:
if atom.structure not in models:
models[atom.structure] = {}
atom_list[atom.structure] = []
if atom.residue not in models[atom.structure]:
models[atom.structure][atom.residue] = []
models[atom.structure][atom.residue].append(atom)
atom_list[atom.structure].append(atom)
for model in models:
if newModel:
struc = AtomicStructure(session,
name="copy of %s" % model.atomspec)
else:
struc = model
offset = len(model.atoms)
for res in models[model]:
residue = struc.new_residue(res.name, res.chain_id, res.number)
for atom in models[model][res]:
dup_atom = struc.new_atom(atom.name, atom.element)
dup_atom.coord = atom.coord
dup_atom.serial_number = len(struc.atoms)
res.add_atom(dup_atom)
for i, atom1 in enumerate(atom_list[model]):
atom1.selected = False
if newModel:
struc.atoms[i].selected = True
struc.atoms[i].color = atom1.color
struc.atoms[i].radius = atom1.radius
struc.atoms[i].draw_mode = atom1.draw_mode
else:
struc.atoms[i + offset].selected = True
struc.atoms[i + offset].color = atom1.color
struc.atoms[i + offset].radius = atom1.radius
struc.atoms[i + offset].draw_mode = atom1.draw_mode
for j, atom2 in enumerate(atom_list[model][:i]):
if atom2 in atom1.neighbors:
if newModel:
struc.new_bond(struc.atoms[i], struc.atoms[j])
else:
struc.new_bond(struc.atoms[i + offset],
struc.atoms[j + offset])
if newModel:
session.models.add([struc])
session.triggers.activate_trigger(SELECTION_CHANGED, None)
def _read_block(session, stream):
# First line should be an integer count of the number of
# atoms in the block. Each block gets turned into an
# AtomicStructure instance.
count_line = stream.readline()
if not count_line:
return None
try:
count = int(count_line)
except ValueError:
# XXX: Should emit an error message
return None
from chimerax.atomic import AtomicStructure
s = AtomicStructure(session)
# Next line is a comment line
s.comment = stream.readline().strip()
# There should be "count" lines of atoms.
from numpy import array, float64
residue = s.new_residue("UNK", 'A', 1)
element_count = {}
for n in range(count):
atom_line = stream.readline()
if not atom_line:
# XXX: Should emit an error message
return None
parts = atom_line.split()
if len(parts) != 4:
# XXX: Should emit an error message
return None
# Extract available data
element = parts[0]
xyz = [float(v) for v in parts[1:]]
# Convert to required initializers
# XXX: May need to convert element to usable form
n = element_count.get(element, 0) + 1
name = element + str(n)
element_count[element] = n
# Create atom
atom = s.new_atom(name, element)
atom.coord = array(xyz, dtype=float64)
residue.add_atom(atom)
s.connect_structure()
s.new_atoms() # tell structure it needs to update
return s
def _prep_add(session,
structures,
unknowns_info,
template,
need_all=False,
**prot_schemes):
global _serial
_serial = None
atoms = []
type_info_for_atom = {}
naming_schemas = {}
idatm_type = {} # need this later; don't want a recomp
hydrogen_totals = {}
# add missing OXTs of "real" C termini;
# delete hydrogens of "fake" N termini after protonation
# and add a single "HN" back on, using same dihedral as preceding residue;
# delete extra hydrogen of "fake" C termini after protonation
logger = session.logger
real_N, real_C, fake_N, fake_C = determine_termini(session, structures)
logger.info("Chain-initial residues that are actual N"
" termini: %s" % ", ".join([str(r) for r in real_N]))
logger.info("Chain-initial residues that are not actual N"
" termini: %s" % ", ".join([str(r) for r in fake_N]))
logger.info("Chain-final residues that are actual C"
" termini: %s" % ", ".join([str(r) for r in real_C]))
logger.info("Chain-final residues that are not actual C"
" termini: %s" % ", ".join([str(r) for r in fake_C]))
for rc in real_C:
complete_terminal_carboxylate(session, rc)
# ensure that N termini are protonated as N3+ (since Npl will fail)
from chimerax.atomic import Sequence
for nter in real_N + fake_N:
n = nter.find_atom("N")
if not n:
continue
# if residue wasn't templated, leave atom typing alone
if Sequence.protein3to1(n.residue.name) == 'X':
continue
if not (n.residue.name == "PRO" and n.num_bonds >= 2):
n.idatm_type = "N3+"
coordinations = {}
for struct in structures:
pbg = struct.pseudobond_group(struct.PBG_METAL_COORDINATION,
create_type=None)
if not pbg:
continue
for pb in pbg.pseudobonds:
for a in pb.atoms:
if not need_all and a.structure not in structures:
continue
if not a.element.is_metal:
coordinations.setdefault(a, []).append(pb.other_atom(a))
remaining_unknowns = {}
type_info_class = type_info['H'].__class__
from chimerax.atomic import Residue
for struct in structures:
for atom in struct.atoms:
if atom.element.number == 0:
res = atom.residue
struct.delete_atom(atom)
idatm_lookup = {}
if template:
template_lookup = {}
from chimerax.atomic import TmplResidue
get_template = TmplResidue.get_template
for res in struct.residues:
if get_template(res.name):
continue
try:
exemplar = template_lookup[res.name]
except KeyError:
from chimerax.mmcif import find_template_residue
tmpl = find_template_residue(session, res.name)
if not tmpl:
continue
from chimerax.atomic import AtomicStructure
s = AtomicStructure(session)
r = exemplar = template_lookup[res.name] = s.new_residue(
res.name, 'A', 1)
atom_map = {}
for ta in tmpl.atoms:
if ta.element.number > 1:
a = s.new_atom(ta.name, ta.element)
a.coord = ta.coord
r.add_atom(a)
atom_map[ta] = a
for tnb in ta.neighbors:
if tnb in atom_map:
s.new_bond(a, atom_map[tnb])
for a in res.atoms:
ea = exemplar.find_atom(a.name)
if ea:
a.idatm_type = ea.idatm_type
for r in template_lookup.values():
r.structure.delete()
template_lookup.clear()
for atom in struct.atoms:
atom_type = atom.idatm_type
idatm_type[atom] = atom_type
if atom_type in type_info:
# don't want to ask for idatm_type in middle
# of hydrogen-adding loop (since that will
# force a recomp), so remember here
type_info_for_atom[atom] = type_info[atom_type]
# if atom is in standard residue but has missing bonds to
# heavy atoms, skip it instead of incorrectly protonating
# (or possibly throwing an error if e.g. it's planar)
# also
# UNK/N residues will be missing some or all of their side-chain atoms, so
# skip atoms that would otherwise be incorrectly protonated due to their
# missing neighbors
truncated = \
atom.is_missing_heavy_template_neighbors(no_template_okay=True) \
or \
(atom.residue.name in ["UNK", "N"] and atom.residue.polymer_type != Residue.PT_NONE
and unk_atom_truncated(atom)) \
or \
(atom.residue.polymer_type == Residue.PT_NUCLEIC and atom.name == "P"
and atom.num_explicit_bonds < 4)
if truncated:
session.logger.warning(
"Not adding hydrogens to %s because it is missing heavy-atom"
" bond partners" % atom)
type_info_for_atom[atom] = type_info_class(
4, atom.num_bonds, atom.name)
else:
atoms.append(atom)
# sulfonamide nitrogens coordinating a metal
# get an additional hydrogen stripped
if coordinations.get(atom, []) and atom.element.name == "N":
if "Son" in [nb.idatm_type for nb in atom.neighbors]:
orig_ti = type_info[atom_type]
type_info_for_atom[atom] = orig_ti.__class__(
orig_ti.geometry, orig_ti.substituents - 1,
orig_ti.description)
continue
if atom in unknowns_info:
type_info_for_atom[atom] = unknowns_info[atom]
atoms.append(atom)
continue
remaining_unknowns.setdefault(atom.residue.name,
set()).add(atom.name)
# leave remaining unknown atoms alone
type_info_for_atom[atom] = type_info_class(4, atom.num_bonds,
atom.name)
for rname, atom_names in remaining_unknowns.items():
names_text = ", ".join([nm for nm in atom_names])
atom_text, obj_text = ("atoms",
"them") if len(atom_names) > 1 else ("atom",
"it")
logger.warning(
"Unknown hybridization for %s (%s) of residue type %s;"
" not adding hydrogens to %s" %
(atom_text, names_text, rname, obj_text))
naming_schemas.update(
determine_naming_schemas(struct, type_info_for_atom))
if need_all:
from chimerax.atomic import AtomicStructure
for struct in [
m for m in session.models if isinstance(m, AtomicStructure)
]:
if struct in structures:
continue
for atom in struct.atoms:
idatm_type[atom] = atom.idatm_type
if atom.idatm_type in type_info:
type_info_for_atom[atom] = type_info[atom.idatm_type]
for atom in atoms:
if atom not in type_info_for_atom:
continue
bonding_info = type_info_for_atom[atom]
total_hydrogens = bonding_info.substituents - atom.num_bonds
for bonded in atom.neighbors:
if bonded.element.number == 1:
total_hydrogens += 1
hydrogen_totals[atom] = total_hydrogens
schemes = {}
# HIS and CYS treated as 'unspecified'; use built-in typing
for scheme_type, res_names, res_check, typed_atoms in [
('his', ["HID", "HIE", "HIP"], None, []),
('asp', asp_res_names, _asp_check, asp_prot_names),
('glu', glu_res_names, _glu_check, glu_prot_names),
('lys', ["LYS", "LYN"], _lys_check, ["NZ"]),
('cys', ["CYM"], _cys_check, ["SG"])
]:
scheme = prot_schemes.get(scheme_type + '_scheme', None)
if scheme is None:
by_name = True
scheme = {}
else:
by_name = False
if not scheme:
for s in structures:
for r in s.residues:
if r.name in res_names and res_check and res_check(r):
if by_name:
scheme[r] = r.name
elif scheme_type != 'his':
scheme[r] = res_names[0]
# unset any explicit typing...
for ta in typed_atoms:
a = r.find_atom(ta)
if a:
a.idatm_type = None
else:
for r in scheme.keys():
if res_check and not res_check(r, scheme[r]):
del scheme[r]
schemes[scheme_type] = scheme
# create dictionary keyed on histidine residue with value of another
# dictionary keyed on the nitrogen atoms with boolean values: True
# equals should be protonated
his_Ns = {}
for r, protonation in schemes["his"].items():
delta = r.find_atom("ND1")
epsilon = r.find_atom("NE2")
if delta is None or epsilon is None:
# find the ring, etc.
rings = r.structure.rings()
for ring in rings:
if r in rings.atoms.residues:
break
else:
continue
# find CG by locating CB-CG bond
ring_bonds = ring.bonds
for ra in ring.atoms:
if ra.element.name != "C":
continue
for ba, b in zip(ra.neighbors, ra.bonds):
if ba.element.name == "C" and b not in ring_bonds:
break
else:
continue
break
else:
continue
nitrogens = [a for a in ring.atoms if a.element.name == "N"]
if len(nitrogens) != 2:
continue
if ra in nitrogens[0].neighbors:
delta, epsilon = nitrogens
else:
epsilon, delta = nitrogens
if protonation == "HID":
his_Ns.update({delta: True, epsilon: False})
elif protonation == "HIE":
his_Ns.update({delta: False, epsilon: True})
elif protonation == "HIP":
his_Ns.update({delta: True, epsilon: True})
else:
continue
for n, do_prot in his_Ns.items():
if do_prot:
type_info_for_atom[n] = type_info["Npl"]
n.idatm_type = idatm_type[n] = "Npl"
else:
type_info_for_atom[n] = type_info["N2"]
n.idatm_type = idatm_type[n] = "N2"
for r, protonation in schemes["asp"].items():
_handle_acid_protonation_scheme_item(r, protonation, asp_res_names,
asp_prot_names, type_info,
type_info_for_atom)
for r, protonation in schemes["glu"].items():
_handle_acid_protonation_scheme_item(r, protonation, glu_res_names,
glu_prot_names, type_info,
type_info_for_atom)
for r, protonation in schemes["lys"].items():
nz = r.find_atom("NZ")
if protonation == "LYS":
it = 'N3+'
else:
it = 'N3'
ti = type_info[it]
if nz is not None:
type_info_for_atom[nz] = ti
# avoid explicitly setting type if possible
if nz.idatm_type != it:
nz.idatm_type = it
for r, protonation in schemes["cys"].items():
sg = r.find_atom("SG")
if protonation == "CYS":
it = 'S3'
else:
it = 'S3-'
ti = type_info[it]
if sg is not None:
type_info_for_atom[sg] = ti
# avoid explicitly setting type if possible
if sg.idatm_type != it:
sg.idatm_type = it
return atoms, type_info_for_atom, naming_schemas, idatm_type, \
hydrogen_totals, his_Ns, coordinations, fake_N, fake_C
def get_rotamers(session,
res,
phi=None,
psi=None,
cis=False,
res_type=None,
rot_lib="Dunbrack",
log=False):
"""Takes a Residue instance and optionally phi/psi angles (if different from the Residue), residue
type (e.g. "TYR"), and/or rotamer library name. Returns a list of AtomicStructure instances (sublass of
AtomicStructure). The AtomicStructure are each a single residue (a rotamer) and are in descending
probability order. Each has an attribute "rotamer_prob" for the probability and "chis" for the
chi angles.
"""
res_type = res_type or res.name
if res_type == "ALA" or res_type == "GLY":
raise NoResidueRotamersError("No rotamers for %s" % res_type)
if not isinstance(rot_lib, RotamerLibrary):
rot_lib = session.rotamers.library(rot_lib)
# check that the residue has the n/c/ca atoms needed to position the rotamer
# and to ensure that it is an amino acid
from chimerax.atomic import Residue
match_atoms = {}
for bb_name in Residue.aa_min_backbone_names:
match_atoms[bb_name] = a = res.find_atom(bb_name)
if a is None:
raise LimitationError("%s missing from %s; needed to position CB" %
(bb_name, res))
match_atoms["CB"] = res.find_atom("CB")
if not phi and not psi:
phi, psi = res.phi, res.psi
omega = res.omega
cis = False if omega is None or abs(omega) > 90 else True
if log:
def _info(ang):
if ang is None:
return "none"
return "%.1f" % ang
if match_atoms["CA"].alt_locs:
al_info = " (alt loc %s)" % match_atoms["CA"].alt_loc
else:
al_info = ""
session.logger.info("%s%s: phi %s, psi %s %s" %
(res, al_info, _info(phi), _info(psi),
"cis" if cis else "trans"))
session.logger.status("Retrieving rotamers from %s library" %
rot_lib.display_name)
res_template_func = rot_lib.res_template_func
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
session.logger.status("Rotamers retrieved from %s library" %
rot_lib.display_name)
mapped_res_type = rot_lib.res_name_mapping.get(res_type, res_type)
template = rot_lib.res_template_func(mapped_res_type)
tmpl_N = template.find_atom("N")
tmpl_CA = template.find_atom("CA")
tmpl_C = template.find_atom("C")
tmpl_CB = template.find_atom("CB")
if match_atoms['CB']:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("C", "CA", "CB")
], [tmpl_C, tmpl_CA, tmpl_CB]
else:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("N", "CA", "C")
], [tmpl_N, tmpl_CA, tmpl_C]
from chimerax.geometry import align_points
from numpy import array
xform, rmsd = align_points(array([fa.coord for fa in tmpl_match_atoms]),
array([ta.coord for ta in res_match_atoms]))
n_coord = xform * tmpl_N.coord
ca_coord = xform * tmpl_CA.coord
cb_coord = xform * tmpl_CB.coord
info = Residue.chi_info[mapped_res_type]
bond_cache = {}
angle_cache = {}
from chimerax.atomic.struct_edit import add_atom, add_dihedral_atom, add_bond
structs = []
middles = {}
ends = {}
for i, rp in enumerate(params):
s = AtomicStructure(session, name="rotamer %d" % (i + 1))
structs.append(s)
r = s.new_residue(mapped_res_type, 'A', 1)
registerer = "swap_res get_rotamers"
AtomicStructure.register_attr(session,
"rotamer_prob",
registerer,
attr_type=float)
s.rotamer_prob = rp.p
AtomicStructure.register_attr(session, "chis", registerer)
s.chis = rp.chis
rot_N = add_atom("N", tmpl_N.element, r, n_coord)
rot_CA = add_atom("CA", tmpl_CA.element, r, ca_coord, bonded_to=rot_N)
rot_CB = add_atom("CB", tmpl_CB.element, r, cb_coord, bonded_to=rot_CA)
todo = []
for j, chi in enumerate(rp.chis):
n3, n2, n1, new = info[j]
b_len, angle = _len_angle(new, n1, n2, template, bond_cache,
angle_cache)
n3 = r.find_atom(n3)
n2 = r.find_atom(n2)
n1 = r.find_atom(n1)
new = template.find_atom(new)
a = add_dihedral_atom(new.name,
new.element,
n1,
n2,
n3,
b_len,
angle,
chi,
bonded=True)
todo.append(a)
middles[n1] = [a, n1, n2]
ends[a] = [a, n1, n2]
# if there are any heavy non-backbone atoms bonded to template
# N and they haven't been added by the above (which is the
# case for Richardson proline parameters) place them now
for tnnb in tmpl_N.neighbors:
if r.find_atom(tnnb.name) or tnnb.element.number == 1:
continue
tnnb_coord = xform * tnnb.coord
add_atom(tnnb.name, tnnb.element, r, tnnb_coord, bonded_to=rot_N)
# fill out bonds and remaining heavy atoms
from chimerax.geometry import distance, align_points
done = set([rot_N, rot_CA])
while todo:
a = todo.pop(0)
if a in done:
continue
tmpl_A = template.find_atom(a.name)
for bonded, bond in zip(tmpl_A.neighbors, tmpl_A.bonds):
if bonded.element.number == 1:
continue
rbonded = r.find_atom(bonded.name)
if rbonded is None:
# use middles if possible...
try:
p1, p2, p3 = middles[a]
conn = p3
except KeyError:
p1, p2, p3 = ends[a]
conn = p2
t1 = template.find_atom(p1.name)
t2 = template.find_atom(p2.name)
t3 = template.find_atom(p3.name)
xform = align_points(
array([t.coord for t in [t1, t2, t3]]),
array([p.coord for p in [p1, p2, p3]]))[0]
pos = xform * template.find_atom(bonded.name).coord
rbonded = add_atom(bonded.name,
bonded.element,
r,
pos,
bonded_to=a)
middles[a] = [rbonded, a, conn]
ends[rbonded] = [rbonded, a, conn]
if a not in rbonded.neighbors:
add_bond(a, rbonded)
if rbonded not in done:
todo.append(rbonded)
done.add(a)
return structs
class MolecularDynamicsTool(HtmlToolInstance):
'''
# Properties for the tool
'''
SESSION_ENDURING = False
SESSION_SAVE = False
CUSTOM_SCHEME = "kmd"
def __init__(self, session, tool_name):
super().__init__(session,
tool_name,
size_hint=(500, 500),
show_http_in_help=False)
self.display_name = DISPLAY_NAME
self._build_ui()
self.atomStruct = None
self.atomLocation = []
self.surfacePositions = []
self.attributeFile = False
# Loads the html view to be shown
def _build_ui(self):
html_file = os.path.join(os.path.dirname(__file__), "dynamics.html")
self.html_view.setUrl(pathlib.Path(html_file).as_uri())
# This is to delete the model from the view
def delete(self):
super(HtmlToolInstance, self).delete()
self.deleteModel()
'''
# This handles when a window.location becomes kmd:<command>
#
# @param url - The command
'''
def handle_scheme(self, url):
command = url.path()
if command.startswith("log"):
self.session.logger.info(command[len("log_"):])
elif command == "Open":
self.openFile()
elif command.startswith("FrameChange"):
frame = int(command[len("FrameChange_T_"):])
self.changeModel(frame, command[12] == 'T')
elif command == "MovieDone":
movie_encode(self.session, output=[self.movieName], format="h264")
elif command == "MovieStart":
fileName, filt = QFileDialog.getSaveFileName(
caption="Save Movie", filter="MP4 File (*.mp4)")
if fileName == "":
return
if fileName[-4:] != ".mp4":
fileName = fileName + ".mp4"
self.movieName = fileName
movie_record(self.session)
self.html_view.runJavaScript("startMovie()")
elif command == "Attribute":
self.loadAttributeFile()
else:
self.session.logger.info("Unknown Command: " + str(url))
def loadAttributeFile(self):
fileName, filt = QFileDialog.getOpenFileName(
caption="Open Attribute File", filter="Attribute File (*.dat)")
if fileName == "":
return
fileObj = open(fileName)
lines = fileObj.readlines()[3:]
fileObj.close()
mapVals = {}
for line in lines:
parts = line.split('\t')[1:]
mapVals[int(parts[0][1:])] = float(parts[1])
maxValue = max(mapVals.values())
minValue = min(mapVals.values())
midValue = (maxValue + minValue) / 2
# Color from min (blue) to mid (white) to max (red)
for key in mapVals.keys():
value = mapVals[key]
per = (value - minValue) / (midValue - minValue) - 1
color = abs(per) * 255
colorSet = [255, 255 - color, 255 - color, 255
] if per > 0 else [255 - color, 255 - color, 255, 255]
colorSet = array(colorSet)
self.atomStruct.residues[key - 1].ribbon_color = colorSet
self.atomStruct.residues[key - 1].atoms.colors = colorSet
js = "attributeName = '" + fileName.split(
"/")[-1] + "';updateDisplay()"
self.html_view.runJavaScript(js)
self.attributeFile = True
if self.atomStruct.surfaces() != []:
run(self.session,
"color #" + self.atomStruct.surfaces()[0].id_string +
" fromatoms",
log=False)
# This is to remove model for changing
def deleteModel(self):
if self.atomStruct == None:
return
if self.atomStruct.deleted:
return
if self.atomStruct.surfaces() != []:
self.session.models.remove([self.atomStruct.surfaces()[0]])
self.session.models.remove([self.atomStruct])
self.attributeFile = False
self.atomStruct = None
self.atomLocation = []
self.surfacePositions = []
js = "modelName = null; frameCount = 0; reset();"
self.html_view.runJavaScript(js)
# This is to move the atoms
def changeModel(self, frame, surf):
locs = self.atomLocation[frame]
atms = self.atomStruct.atoms
atms.coords = locs
if surf:
### Need to recalculate the surfce here
if self.atomStruct.surfaces() == []:
surface(self.session, atoms=self.atomStruct.atoms)
else:
surfPos = self.surfacePositions[frame]
if surfPos is None:
self.session.models.remove([self.atomStruct.surfaces()[0]])
surface(self.session, atoms=self.atomStruct.atoms)
self.surfacePositions[frame] = self.atomStruct.surfaces(
)[0]
else:
self.session.models.remove([self.atomStruct.surfaces()[0]])
self.atomStruct.add([surfPos])
###
run(self.session,
"color #" + self.atomStruct.surfaces()[0].id_string +
" fromatoms",
log=False)
elif self.atomStruct.surfaces() != []:
self.session.models.remove([self.atomStruct.surfaces()[0]])
# This opens a file
def openFile(self):
fileName, filt = QFileDialog.getOpenFileName(
caption="Open PDB Trajectory File", filter="PDB File (*.pdb)")
if fileName == "":
return
if self.atomStruct != None:
self.deleteModel()
# This create a simple Oxygen atom
# Need to get this to display
self.atomStruct = AtomicStructure(self.session)
myFile = open(fileName)
coords = []
prevRes = None
res = None
modelNum = -1
for line in myFile:
if line.startswith("MODEL"):
modelNum = modelNum + 1
coords = []
prevRes = None
res = None
elif line.startswith("ENDMDL"):
self.atomLocation.append(array(coords))
elif line.startswith("ATOM"):
x = float(line[30:38].strip())
y = float(line[38:46].strip())
z = float(line[46:54].strip())
name = line[12:16].strip()
resName = line[17:20].strip()
chain = line[21]
resSeq = line[22:26].strip()
element = line[76:78].strip()
if element == "H":
continue
coords.append([x, y, z])
if modelNum != 0:
continue
if resName + resSeq != prevRes:
prevRes = resName + resSeq
res = self.atomStruct.new_residue(resName, chain,
int(resSeq))
atom = self.atomStruct.new_atom(name, element)
atom.coord = array([x, y, z], dtype=float64)
res.add_atom(atom)
myFile.close()
self.atomStruct.connect_structure()
self.session.models.add([self.atomStruct])
for i in range(len(self.atomLocation)):
self.surfacePositions.append(None)
self.atomStruct.atoms.coords = self.atomLocation[0]
fileName = fileName.split("/")[-1]
js = "modelName = '" + fileName + "'; frameCount = " + str(
len(self.atomLocation)) + "; reset();"
self.html_view.runJavaScript(js)
run(self.session, "lighting full", log=False)
def _read_block(session, stream, line_number):
# XYZ files are stored in blocks, with each block representing
# a set of atoms. This function reads a single block
# and builds a ChimeraX AtomStructure instance containing
# the atoms listed in the block.
# First line should be an integer count of the number of
# atoms in the block.
count_line = stream.readline()
if not count_line:
# Reached EOF, normal termination condition
return None, line_number
line_number += 1
try:
count = int(count_line)
except ValueError:
session.logger.error("line %d: atom count missing" % line_number)
return None, line_number
# Create the AtomicStructure instance for atoms in this block.
# All atoms in the structure are placed in one residue
# since XYZ format does not partition atoms into groups.
from chimerax.atomic import AtomicStructure
from numpy import array, float64
s = AtomicStructure(session)
residue = s.new_residue("UNK", 'A', 1)
# XYZ format supplies the atom element type only, but
# ChimeraX keeps track of both the element type and
# a unique name for each atom. To construct the unique
# atom name, the # 'element_count' dictionary is used
# to track the number of atoms of each element type so far,
# and the current count is used to build unique atom names.
element_count = {}
# Next line is a comment line
s.comment = stream.readline().strip()
line_number += 1
# There should be "count" lines of atoms.
for n in range(count):
atom_line = stream.readline()
if not atom_line:
session.logger.error("line %d: atom data missing" % line_number)
return None, line_number
line_number += 1
# Extract available data
parts = atom_line.split()
if len(parts) != 4:
session.logger.error("line %d: atom data malformatted" %
line_number)
return None, line_number
# Convert to required parameters for creating atom.
# Since XYZ format only required atom element, we
# create a unique atom name by putting a number after
# the element name.
xyz = [float(v) for v in parts[1:]]
element = parts[0]
n = element_count.get(element, 0) + 1
name = element + str(n)
element_count[element] = n
# Create atom in AtomicStructure instance 's',
# set its coordinates, and add to residue
atom = s.new_atom(name, element)
atom.coord = array(xyz, dtype=float64)
residue.add_atom(atom)
# Use AtomicStructure method to add bonds based on interatomic distances
s.connect_structure()
# Updating state such as atom types while adding atoms iteratively
# is unnecessary (and generally incorrect for partial structures).
# When all atoms have been added, the instance is notified to
# tell it to update internal state.
s.new_atoms()
# Return AtomicStructure instance and current line number
return s, line_number
def _make_structure(self, block):
from numpy import array
from .maestro import IndexAttribute
if self.atomic:
from chimerax.atomic import AtomicStructure as SC
else:
from chimerax.atomic import Structure as SC
from chimerax.atomic import Element
atoms = block.get_sub_block("m_atom")
if atoms is None:
print("No m_atom block found")
return None
bonds = block.get_sub_block("m_bond")
s = SC(self.session, auto_style=self.auto_style)
SC.register_attr(self.session, "viewdockx_data", "ViewDockX")
residue_map = {}
atom_map = {}
for row in range(atoms.size):
attrs = atoms.get_attribute_map(row)
index = attrs[IndexAttribute]
# Get residue data and create if necessary
res_seq = attrs["i_m_residue_number"]
insert_code = attrs.get("s_m_insertion_code", None)
if not insert_code:
insert_code = ' '
chain_id = attrs.get("s_m_chain_name", ' ')
res_key = (chain_id, res_seq, insert_code)
try:
r = residue_map[res_key]
except KeyError:
res_name = attrs.get("s_m_pdb_residue_name", "UNK")
r = s.new_residue(res_name, chain_id, res_seq, insert_code)
residue_map[res_key] = r
rgb = attrs.get("s_m_ribbon_color_rgb", None)
if rgb:
r.ribbon_color = self._get_color(rgb)
# Get atom data and create
try:
name = attrs["s_m_pdb_atom_name"]
except KeyError:
name = attrs.get("s_m_atom_name", "")
name = name.strip()
atomic_number = attrs.get("i_m_atomic_number", 6)
element = Element.get_element(atomic_number)
if not name:
name = element.name
a = s.new_atom(name, element)
a.coord = array([atoms.get_attribute("r_m_x_coord", row),
atoms.get_attribute("r_m_y_coord", row),
atoms.get_attribute("r_m_z_coord", row)])
try:
a.bfactor = attrs["r_m_pdb_tfactor"]
except (KeyError, TypeError):
a.bfactor = 0.0
try:
a.occupancy = attrs["r_m_pdb_occupancy"]
except (KeyError, TypeError):
a.occupancy = 1.0
rgb = attrs.get("s_m_color_rgb", None)
if rgb:
a.color = self._get_color(rgb)
# Add atom to residue and to atom map for bonding later
r.add_atom(a)
atom_map[index] = a
if bonds is None or bonds.size == 0:
s.connect_structure()
else:
for row in range(bonds.size):
attrs = bonds.get_attribute_map(row)
fi = attrs["i_m_from"]
ti = attrs["i_m_to"]
if ti < fi:
# Bonds are reported in both directions. We only need one.
continue
afi = atom_map[fi]
ati = atom_map[ti]
b = s.new_bond(afi, ati)
b.order = attrs["i_m_order"]
return s
def _make_structure(self):
"""Build ChimeraX structure and reset structure data cache"""
try:
if self._molecule is None:
return
if self.atomic:
from chimerax.atomic import AtomicStructure as SC
else:
from chimerax.atomic import Structure as SC
# Create structure
s = SC(self.session, auto_style=self.auto_style)
s.name = self._molecule.mol_name
SC.register_attr(self.session, "viewdockx_data", "ViewDockX")
s.viewdockx_data = self._data
if self._molecule.charge_type:
s.charge_model = self._molecule.charge_type
if self._molecule.mol_type:
s.mol2_type = self._molecule.mol_type
if self._molecule.mol_comment:
s.mol2_comment = self._molecule.mol_comment
# Create residues
substid2residue = {}
for subst_data in self._substs:
# ChimeraX limitation: 4-letter residue type
name = subst_data.subst_name[:4]
chain = subst_data.chain
if chain is None or chain == "****":
chain = ''
residue = s.new_residue(name, chain, subst_data.subst_id)
substid2residue[subst_data.subst_id] = residue
# Create atoms
atomid2atom = {}
from numpy import array, float64
for atom_data in self._atoms:
name = atom_data.atom_name
element = atom_data.atom_type
if '.' in element:
element = element.split('.')[0]
atom = s.new_atom(name, element)
atom.coord = array([atom_data.x, atom_data.y, atom_data.z],
dtype=float64)
if atom_data.charge is not None:
atom.charge = atom_data.charge
try:
residue = substid2residue[atom_data.subst_id]
except KeyError:
# Must not have been a substructure section
residue = s.new_residue("UNK", '', atom_data.subst_id)
substid2residue[atom_data.subst_id] = residue
residue.add_atom(atom)
atomid2atom[atom_data.atom_id] = atom
# Create bonds
for bond_data in self._bonds:
try:
origin = atomid2atom[bond_data.origin_atom_id]
target = atomid2atom[bond_data.target_atom_id]
except KeyError:
self.session.logger.warning("bad atom index in bond")
else:
s.new_bond(origin, target)
self.structures.append(s)
finally:
self._reset_structure()
def read_sdf(session, stream, file_name):
path = stream.name if hasattr(stream, 'name') else None
structures = []
nonblank = False
state = "init"
from chimerax.core.errors import UserError
from chimerax.atomic.struct_edit import add_atom
from chimerax.atomic import AtomicStructure, Element, Bond, Atom, AtomicStructure
from numpy import array
Bond.register_attr(session, "order", "SDF format", attr_type=float)
Atom.register_attr(session, "charge", "SDF format", attr_type=float)
AtomicStructure.register_attr(session, "charge_model", "SDF format", attr_type=str)
try:
for l in stream:
line = l.strip()
nonblank = nonblank or line
if state == "init":
state = "post header 1"
mol_name = line
elif state == "post header 1":
state = "post header 2"
elif state == "post header 2":
state = "counts"
elif state == "counts":
if not line:
break
state = "atoms"
serial = 1
anums = {}
atoms = []
try:
num_atoms = int(l[:3].strip())
num_bonds = int(l[3:6].strip())
except ValueError:
raise UserError("Atom/bond counts line of MOL/SDF file '%s' is botched" % file_name)
from chimerax.atomic.structure import is_informative_name
name = mol_name if is_informative_name(mol_name) else file_name
s = AtomicStructure(session, name=name)
structures.append(s)
r = s.new_residue("UNL", " ", 1)
elif state == "atoms":
num_atoms -= 1
if num_atoms == 0:
if num_bonds:
state = "bonds"
else:
state = "properties"
try:
x = float(l[:10].strip())
y = float(l[10:20].strip())
z = float(l[20:30].strip())
elem = l[31:34].strip()
except ValueError:
s.delete()
raise UserError("Atom line of MOL/SDF file '%s' is not x y z element...: '%s'"
% (file_name, l))
element = Element.get_element(elem)
if element.number == 0:
# lone pair of somesuch
atoms.append(None)
continue
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
a = add_atom("%s%d" % (element.name, anum), element, r, array([x,y,z]), serial_number=serial)
serial += 1
atoms.append(a)
elif state == "bonds":
num_bonds -= 1
if num_bonds == 0:
state = "properties"
try:
a1_index = int(l[:3].strip())
a2_index = int(l[3:6].strip())
order = float(l[6:9].strip())
except ValueError:
raise UserError("Bond line of MOL/SDF file '%s' is not a1 a2 order...: '%s'"
% (file_name, 1))
a1 = atoms[a1_index-1]
a2 = atoms[a2_index-1]
if not a1 or not a2:
continue
s.new_bond(a1, a2).order = order
elif state == "properties":
if not s.atoms:
raise UserError("No atoms found for compound '%s' in MOL/SDF file '%s'" % (name, file_name))
if line.split() == ["M", "END"]:
state = "data"
reading_data = None
elif state == "data":
if line == "$$$$":
nonblank = False
state = "init"
elif reading_data == "charges":
data_item = line.strip()
if data_item:
try:
data.append(float(data_item))
except ValueError:
try:
index, charge = data_item.split()
index = int(index) - 1
charge = float(charge)
except ValueError:
raise UserError("Charge data (%s) in %s data is not either a floating-point"
" number or an atom index and a floating-point number" % (data_item,
orig_data_name))
else:
if not indexed_charges:
# for indexed charges, the first thing is a count
data.pop()
indexed_charges = True
data.append((index, charge))
else:
if not indexed_charges and len(atoms) != len(data):
raise UserError("Number of charges (%d) in %s data not equal to number of atoms"
" (%d)" % (len(data), orig_data_name, len(atoms)))
if indexed_charges:
for a in atoms:
# charge defaults to 0.0, so don't need to set non-indexed
for index, charge in data:
atoms[index].charge = charge
else:
for a, charge in zip(atoms, data):
a.charge = charge
if "mmff94" in data_name:
s.charge_model = "MMFF94"
reading_data = None
elif reading_data == "cid":
data_item = line.strip()
if data_item:
try:
cid = int(data_item)
except ValueError:
raise UserError("PubChem CID (%s) is %s data is not an integer" % (data_item,
orid_data_name))
s.name = "pubchem:%d" % cid
s.prefix_html_title = False
s.get_html_title = lambda *args, cid=cid: 'PubChem entry <a href="https://pubchem.ncbi.nlm.nih.gov/compound/%d">%d</a>' % (cid, cid)
s.has_formatted_metadata = lambda *args: False
reading_data = None
elif line.startswith('>'):
try:
lp = line.index('<')
rp = line[lp+1:].index('>') + lp + 1
except (IndexError, ValueError):
continue
orig_data_name = line[lp+1:rp]
data_name = orig_data_name.lower()
if data_name.endswith("charges") and "partial" in data_name:
reading_data = "charges"
indexed_charges = False
data = []
elif data_name == "pubchem_compound_cid":
reading_data = "cid"
except BaseException:
for s in structures:
s.delete()
raise
finally:
stream.close()
if nonblank and state not in ["data", "init"]:
if structures:
session.logger.warning("Extraneous text after final $$$$ in MOL/SDF file '%s'" % file_name)
else:
raise UserError("Unexpected end of file (parser state: %s) in MOL/SDF file '%s'"
% (state, file_name))
return structures, ""
class MolecularDynamicsTool(HtmlToolInstance):
'''
# Properties for the tool
'''
SESSION_ENDURING = False
SESSION_SAVE = False
CUSTOM_SCHEME = "kmd"
def __init__(self, session, tool_name):
super().__init__(session,
tool_name,
size_hint=(500, 500),
show_http_in_help=False)
self.display_name = DISPLAY_NAME
self._build_ui()
self.atomStruct = None
self.atomLocation = []
self.surfacePositions = []
self.attributeFile = False
# Loads the html view to be shown
def _build_ui(self):
html_file = os.path.join(os.path.dirname(__file__), "dynamics.html")
self.html_view.setUrl(pathlib.Path(html_file).as_uri())
# This is to delete the model from the view
def delete(self):
super(HtmlToolInstance, self).delete()
self.deleteModel()
'''
# This handles when a window.location becomes kmd:<command>
#
# @param url - The command
'''
def handle_scheme(self, url):
command = url.path()
if command.startswith("log"):
self.session.logger.info(command[len("log_"):])
elif command == "Open":
self.openFile()
elif command.startswith("FrameChange"):
frame = int(command[len("FrameChange_T_"):])
self.changeModel(frame, command[12] == 'T')
elif command == "MovieDone":
movie_encode(self.session, output=[self.movieName], format="h264")
elif command == "MovieStart":
fileName, filt = QFileDialog.getSaveFileName(
caption="Save Movie", filter="MP4 File (*.mp4)")
if fileName == "":
return
if fileName[-4:] != ".mp4":
fileName = fileName + ".mp4"
self.movieName = fileName
movie_record(self.session)
self.html_view.runJavaScript("startMovie()")
elif command == "Attribute":
self.loadAttributeFile()
else:
self.session.logger.info("Unknown Command: " + str(url))
def loadAttributeFile(self):
fileName, filt = QFileDialog.getOpenFileName(
caption="Open Attribute File", filter="Attribute File (*.dat)")
if fileName == "":
return
fileObj = open(fileName)
lines = fileObj.readlines()[3:]
fileObj.close()
mapVals = {}
for line in lines:
parts = line.split('\t')[1:]
mapVals[int(parts[0][1:])] = float(parts[1])
maxValue = max(mapVals.values())
minValue = min(mapVals.values())
midValue = (maxValue + minValue) / 2
# Color from min (blue) to mid (white) to max (red)
for key in mapVals.keys():
value = mapVals[key]
per = (value - minValue) / (midValue - minValue) - 1
color = abs(per) * 255
colorSet = [255, 255 - color, 255 - color, 255
] if per > 0 else [255 - color, 255 - color, 255, 255]
colorSet = array(colorSet)
self.atomStruct.residues[key - 1].ribbon_color = colorSet
self.atomStruct.residues[key - 1].atoms.colors = colorSet
js = "attributeName = '" + fileName.split(
"/")[-1] + "';updateDisplay()"
self.html_view.runJavaScript(js)
self.attributeFile = True
if self.atomStruct.surfaces() != []:
run(self.session,
"color #" + self.atomStruct.surfaces()[0].id_string +
" fromatoms",
log=False)
# This is to remove model for changing
def deleteModel(self):
if self.atomStruct == None:
return
if self.atomStruct.deleted:
return
if self.atomStruct.surfaces() != []:
self.session.models.remove([self.atomStruct.surfaces()[0]])
self.session.models.remove([self.atomStruct])
self.attributeFile = False
self.atomStruct = None
self.atomLocation = []
self.surfacePositions = []
js = "modelName = null; frameCount = 0; reset();"
self.html_view.runJavaScript(js)
# This is to move the atoms
def changeModel(self, frame, surf):
locs = self.atomLocation[frame]
atms = self.atomStruct.atoms
atms.coords = locs
if surf:
### Need to recalculate the surfce here
if self.atomStruct.surfaces() == []:
surface(self.session, atoms=self.atomStruct.atoms)
else:
surfPos = self.surfacePositions[frame]
if surfPos is None:
self.session.models.remove([self.atomStruct.surfaces()[0]])
surface(self.session, atoms=self.atomStruct.atoms)
self.surfacePositions[frame] = self.atomStruct.surfaces(
)[0]
else:
self.session.models.remove([self.atomStruct.surfaces()[0]])
self.atomStruct.add([surfPos])
###
run(self.session,
"color #" + self.atomStruct.surfaces()[0].id_string +
" fromatoms",
log=False)
elif self.atomStruct.surfaces() != []:
self.session.models.remove([self.atomStruct.surfaces()[0]])
# This opens a file
def openFile(self):
fileName, filt = QFileDialog.getOpenFileName(caption="Open Trajectory File",
filter="PDB File (*.pdb);;" \
"H5 Trajectory File (*.h5);;" \
"HDF5 Trajectory File (*.hdf5)" \
"GRO Topology File (*.gro)"
)
print(fileName)
print(filt)
if fileName == "":
return
if filt == "(*.gro)":
gro_fileName = fileName
fileName, filt = QFileDialog.getOpenFileName(caption="Open Trajectory File",
filter="XTC Trajectory File (*.xtc);;" \
"TRR Trajectory File (*.trr);;" \
)
print(fileName)
print(filt)
else:
gro_fileName = None
if self.atomStruct != None:
self.deleteModel()
# This create a simple Oxygen atom
# Need to get this to display
self.atomStruct = AtomicStructure(self.session)
if filt in ["(*.xtc)", "(*.trr)"]:
trj = mdtraj.load(fileName, topology=gro_fileName)
else:
trj = mdtraj.load(fileName)
trj.atom_slice(trj.topology.select("not element H"))
table, bond_table = trj.topology.to_dataframe()
table.rename(columns={
"name": "atomname",
"resName": "residue_name",
"chainID": "chain_id",
"resSeq": "pos"
},
inplace=True)
table["pos"] = table["pos"].astype(int)
xyz = trj.xyz[0]
table["loc"] = [array(x, dtype=float64) for x in xyz]
res_infos = table[["residue_name", "chain_id", "pos"
]].drop_duplicates(keep="first").to_dict("records")
for res in res_infos:
residue = self.atomStruct.new_residue(**res)
qry = ' and '.join(
['{} == {}'.format(k, v) for k, v in res.items()])
res_atoms = table.query(qry)[["name", "element",
"loc"]].to_dict("records")
for a in res_atoms:
atom = self.atomStruct.new_atom({
"name": a["name"],
"element": a["element"]
})
atom.coord = a["loc"]
residue.add_atom(atom)
for frame in range(1, trj.n_frames):
xyz = trj.xyz[frame]
self.atomLocation.append(array(xyz, dtype=float64))
self.atomStruct.connect_structure()
self.session.models.add([self.atomStruct])
for i in range(len(self.atomLocation)):
self.surfacePositions.append(None)
self.atomStruct.atoms.coords = self.atomLocation[0]
fileName = fileName.split("/")[-1]
js = "modelName = '" + fileName + "'; frameCount = " + str(
len(self.atomLocation)) + "; reset();"
self.html_view.runJavaScript(js)
run(self.session, "lighting full", log=False)