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fix formatting

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elichad
2022-04-01 09:35:04 +00:00
parent 3796862169
commit 4fa9ee2d02
1 changed files with 150 additions and 78 deletions
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lib/galaxy/datatypes/molecules.py
+150 -78
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@@ -2,8 +2,6 @@ import logging
import os
import re
from attr import Attribute
from galaxy.datatypes import metadata
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.data import (
@@ -71,7 +69,119 @@ class GenericMolFile(Text):
return 'text/plain'
def get_element_symbols(self):
return ["Ac", "Ag", "Al", "Am", "Ar", "As", "At", "Au", "B ", "Ba", "Be", "Bh", "Bi", "Bk", "Br", "C ", "Ca", "Cd", "Ce", "Cf", "Cl", "Cm", "Co", "Cr", "Cs", "Cu", "Ds", "Db", "Dy", "Er", "Es", "Eu", "F ", "Fe", "Fm", "Fr", "Ga", "Gd", "Ge", "H ", "He", "Hf", "Hg", "Ho", "Hs", "I ", "In", "Ir", "K ", "Kr", "La", "Li", "Lr", "Lu", "Md", "Mg", "Mn", "Mo", "Mt", "N ", "Na", "Nb", "Nd", "Ne", "Ni", "No", "Np", "O ", "Os", "P ", "Pa", "Pb", "Pd", "Pm", "Po", "Pr", "Pt", "Pu", "Ra", "Rb", "Re", "Rf", "Rg", "Rh", "Rn", "Ru", "S ", "Sb", "Sc", "Se", "Sg", "Si", "Sm", "Sn", "Sr", "Ta", "Tb", "Tc", "Te", "Th", "Ti", "Tl", "Tm", "U ", "V ", "W ", "Xe", "Y ", "Yb", "Zn", "Zr"]
return [
"Ac",
"Ag",
"Al",
"Am",
"Ar",
"As",
"At",
"Au",
"B ",
"Ba",
"Be",
"Bh",
"Bi",
"Bk",
"Br",
"C ",
"Ca",
"Cd",
"Ce",
"Cf",
"Cl",
"Cm",
"Co",
"Cr",
"Cs",
"Cu",
"Ds",
"Db",
"Dy",
"Er",
"Es",
"Eu",
"F ",
"Fe",
"Fm",
"Fr",
"Ga",
"Gd",
"Ge",
"H ",
"He",
"Hf",
"Hg",
"Ho",
"Hs",
"I ",
"In",
"Ir",
"K ",
"Kr",
"La",
"Li",
"Lr",
"Lu",
"Md",
"Mg",
"Mn",
"Mo",
"Mt",
"N ",
"Na",
"Nb",
"Nd",
"Ne",
"Ni",
"No",
"Np",
"O ",
"Os",
"P ",
"Pa",
"Pb",
"Pd",
"Pm",
"Po",
"Pr",
"Pt",
"Pu",
"Ra",
"Rb",
"Re",
"Rf",
"Rg",
"Rh",
"Rn",
"Ru",
"S ",
"Sb",
"Sc",
"Se",
"Sg",
"Si",
"Sm",
"Sn",
"Sr",
"Ta",
"Tb",
"Tc",
"Te",
"Th",
"Ti",
"Tl",
"Tm",
"U ",
"V ",
"W ",
"Xe",
"Y ",
"Yb",
"Zn",
"Zr",
]
class MOL(GenericMolFile):
@@ -768,16 +878,13 @@ class Cell(GenericMolFile):
# enhanced metadata
try:
ase_data = ase_io.read(dataset.file_name, format="castep-cell")
except ValueError:
except ValueError as e:
log.error("Could not read CELL structure data: %s", unicodify(e))
raise
try:
atom_data = [
str(sym) + str(pos)
for sym, pos in zip(
ase_data.get_chemical_symbols(), ase_data.get_positions()
)
str(sym) + str(pos) for sym, pos in zip(ase_data.get_chemical_symbols(), ase_data.get_positions())
]
chemical_formula = ase_data.get_chemical_formula()
pbc = ase_data.get_pbc()
@@ -826,11 +933,7 @@ class Cell(GenericMolFile):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.info = self.get_dataset_info(dataset.metadata)
structure_string = (
"structure"
if dataset.metadata.number_of_molecules == 1
else "structures"
)
structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
dataset.blurb = f"CASTEP CELL file containing {dataset.metadata.number_of_molecules} {structure_string}"
else:
@@ -845,7 +948,7 @@ class Cell(GenericMolFile):
info_list = []
info_list.append(f"Chemical formula:\n{metadata.chemical_formula}")
if metadata.is_periodic:
info_list.append(f"Periodic:\nYes")
info_list.append("Periodic:\nYes")
info_list.append(
f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x,2)) for x in metadata.lattice_parameters])}"
)
@@ -959,7 +1062,7 @@ class CIF(GenericMolFile):
try:
ase_data = ase_io.read(dataset.file_name, index=":", format="cif")
log.warning(str(ase_data))
except ValueError:
except ValueError as e:
log.error("Could not read CIF structure data: %s", unicodify(e))
raise
@@ -970,12 +1073,7 @@ class CIF(GenericMolFile):
try:
for block in ase_data:
atom_data.append(
[
str(sym) + str(pos)
for sym, pos in zip(
block.get_chemical_symbols(), block.get_positions()
)
]
[str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
)
chemical_formula.append(block.get_chemical_formula())
pbc = block.get_pbc()
@@ -991,16 +1089,14 @@ class CIF(GenericMolFile):
dataset.metadata.number_of_molecules = len(ase_data)
dataset.metadata.atom_data = atom_data
dataset.metadata.number_of_atoms = [
len(atoms) for atoms in dataset.metadata.atom_data
]
dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
dataset.metadata.chemical_formula = chemical_formula
dataset.metadata.is_periodic = is_periodic
dataset.metadata.lattice_parameters = list(lattice_parameters)
log.warning("metadata is: %s", dataset.metadata)
else:
# simple metadata
dataset.metadata.number_of_molecules = count_special_lines(r'^data_', dataset.file_name)
dataset.metadata.number_of_molecules = count_special_lines(r"^data_", dataset.file_name)
"""with open(dataset.file_name) as f:
cell = f.read()
try:
@@ -1032,11 +1128,7 @@ class CIF(GenericMolFile):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.info = self.get_dataset_info(dataset.metadata)
structure_string = (
"structure"
if dataset.metadata.number_of_molecules == 1
else "structures"
)
structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
dataset.blurb = f"CIF file containing {dataset.metadata.number_of_molecules} {structure_string}"
else:
@@ -1052,7 +1144,7 @@ class CIF(GenericMolFile):
if metadata.number_of_molecules == 1:
info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
if metadata.is_periodic[0]:
info_list.append(f"Periodic:\nYes")
info_list.append("Periodic:\nYes")
info_list.append(
f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x,2)) for x in metadata.lattice_parameters[0]])}"
)
@@ -1064,7 +1156,7 @@ class CIF(GenericMolFile):
formulae = "\n".join(metadata.chemical_formula)
info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
info = "\n--\n".join(info_list)
#else:
# else:
# info = f"Atoms in file:\n{metadata.number_of_atoms}"
return info
@@ -1187,11 +1279,7 @@ class XYZ(GenericMolFile):
atoms.append(atom)
blocks.append({
"number_of_atoms":n_atoms,
"comment": comment,
"atom_data":atoms
})
blocks.append({"number_of_atoms": n_atoms, "comment": comment, "atom_data": atoms})
return blocks
@@ -1205,7 +1293,7 @@ class XYZ(GenericMolFile):
# ASE recommend always parsing as extended xyz
ase_data = ase_io.read(dataset.file_name, index=":", format="extxyz")
log.warning(str(ase_data))
except ValueError:
except ValueError as e:
log.error("Could not read XYZ structure data: %s", unicodify(e))
raise
@@ -1216,12 +1304,7 @@ class XYZ(GenericMolFile):
try:
for block in ase_data:
atom_data.append(
[
str(sym) + str(pos)
for sym, pos in zip(
block.get_chemical_symbols(), block.get_positions()
)
]
[str(sym) + str(pos) for sym, pos in zip(block.get_chemical_symbols(), block.get_positions())]
)
chemical_formula.append(block.get_chemical_formula())
pbc = block.get_pbc()
@@ -1237,9 +1320,7 @@ class XYZ(GenericMolFile):
dataset.metadata.number_of_molecules = len(ase_data)
dataset.metadata.atom_data = atom_data
dataset.metadata.number_of_atoms = [
len(atoms) for atoms in dataset.metadata.atom_data
]
dataset.metadata.number_of_atoms = [len(atoms) for atoms in dataset.metadata.atom_data]
dataset.metadata.chemical_formula = chemical_formula
dataset.metadata.is_periodic = is_periodic
dataset.metadata.lattice_parameters = list(lattice_parameters)
@@ -1249,23 +1330,15 @@ class XYZ(GenericMolFile):
with open(dataset.file_name) as f:
xyz_lines = f.readlines()
blocks = self.read_blocks(xyz_lines)
dataset.metadata.number_of_molecules=len(blocks)
dataset.metadata.atom_data=[
block["atom_data"] for block in blocks
]
dataset.metadata.number_of_atoms=[
block["number_of_atoms"] for block in blocks
]
dataset.metadata.number_of_molecules = len(blocks)
dataset.metadata.atom_data = [block["atom_data"] for block in blocks]
dataset.metadata.number_of_atoms = [block["number_of_atoms"] for block in blocks]
def set_peek(self, dataset, is_multi_byte=False):
if not dataset.dataset.purged:
dataset.peek = get_file_peek(dataset.file_name)
dataset.info = self.get_dataset_info(dataset.metadata)
structure_string = (
"structure"
if dataset.metadata.number_of_molecules == 1
else "structures"
)
structure_string = "structure" if dataset.metadata.number_of_molecules == 1 else "structures"
dataset.blurb = f"XYZ file containing {dataset.metadata.number_of_molecules} {structure_string}"
else:
dataset.peek = "file does not exist"
@@ -1280,7 +1353,7 @@ class XYZ(GenericMolFile):
if metadata.number_of_molecules == 1:
info_list.append(f"Chemical formula:\n{metadata.chemical_formula[0]}")
if metadata.is_periodic[0]:
info_list.append(f"Periodic:\nYes")
info_list.append("Periodic:\nYes")
info_list.append(
f"Lattice parameters in axis-angle format:\n{', '.join([str(round(x,2)) for x in metadata.lattice_parameters[0]])}"
)
@@ -1292,7 +1365,7 @@ class XYZ(GenericMolFile):
formulae = "\n".join(metadata.chemical_formula)
info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
info = "\n--\n".join(info_list)
#else:
# else:
# TODO: message along the lines of "ask your admin to install ase"?
# info = f"Atoms in file:\n{metadata.number_of_atoms}"
@@ -1376,10 +1449,10 @@ class ExtendedXYZ(XYZ):
# extract column properties
# these have the format 'Properties="<name>:<type>:<number>:..."' in the comment line
# e.g. Properties="species:S:1:pos:R:3:vel:R:3:select:I:1"
properties=re.search(r'Properties=\"?([a-zA-Z0-9:]+)\"?',comment)
if properties is None: # re.search returned None
properties = re.search(r"Properties=\"?([a-zA-Z0-9:]+)\"?", comment)
if properties is None: # re.search returned None
raise ValueError(f"Could not find column properties in line: {comment}")
properties = [s.split(":") for s in re.findall(r'[a-zA-Z]+:[SIRL]:[0-9]+', properties.group(1))]
properties = [s.split(":") for s in re.findall(r"[a-zA-Z]+:[SIRL]:[0-9]+", properties.group(1))]
total_columns = sum([int(s[2]) for s in properties])
for _ in range(n_atoms):
@@ -1387,41 +1460,40 @@ class ExtendedXYZ(XYZ):
atom = atom.split()
if len(atom) != total_columns:
raise ValueError(f"Expected {total_columns} columns but found {len(atom)}: {atom}")
index=0
index = 0
# check that atom data adheres to correct column format as specified by the properties
# none of this is stored permanently as it's not needed for metadata
# but the processing will raise errors if the format is incorrect
for property in properties:
to_check = atom[index:index+int(property[2])]
to_check = atom[index : index + int(property[2])]
for i in to_check:
if property[1] == "S": #string
if property[1] == "S": # string
# check that any element symbols are correct, otherwise ignore strings
if property[0].lower()=="species" and i.lower().capitalize() not in self.get_element_symbols():
if (
property[0].lower() == "species"
and i.lower().capitalize() not in self.get_element_symbols()
):
raise ValueError(f"{i} is not a valid element symbol")
elif property[1] == "L": #logical
elif property[1] == "L": # logical
if not re.match(r"(?:[tT]rue|TRUE|T)\b|(?:[fF]alse|FALSE|F)\b", i):
raise ValueError(f"{i} is not a valid logical element.")
elif property[1] == "I": #integer
elif property[1] == "I": # integer
int(i)
elif property[1] == "R": #float
elif property[1] == "R": # float
float(i)
else:
raise ValueError(f"Could not recognise property type {property[1]}.")
index+=int(property[2])
index += int(property[2])
atoms.append(atom)
blocks.append({
"number_of_atoms":n_atoms,
"comment": comment,
"atom_data":atoms
})
blocks.append({"number_of_atoms": n_atoms, "comment": comment, "atom_data": atoms})
return blocks
def set_peek(self, dataset, is_multi_byte=False):
super().set_peek(dataset, is_multi_byte)
dataset.blurb = "Extended "+dataset.blurb
dataset.blurb = "Extended " + dataset.blurb
class grd(Text):