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 _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
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
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)