def search_cocrystals(filter_solvents=True):
'''
Search the whole CSD for structures that contain two different molecules
with the specific settings
'''
start_time = time.clock()
csd = MoleculeReader('CSD')
entry_reader = EntryReader('CSD')
settings = search.Search.Settings()
settings.only_organic = True
settings.not_polymeric = True
settings.has_3d_coordinates = True
settings.no_disorder = True
settings.no_errors = True
settings.no_ions = True
settings.no_metals = True
pairs=[]
for entry in csd:
#if len(pairs)==100:
# break
if settings.test(entry):
mol = csd.molecule(entry.identifier)
mol.normalise_labels()
smi= mol.smiles
if smi != None:
smi = smi.split('.')
# We make sure that the structure consist of two different molecules
if len(Remove(smi)) == 2:
pairs.append(mol.identifier)
# clean the list from solvents
if filter_solvents:
print('Solvates and hydrates will be removed')
solvates=[]
name_dict={}
for mol1 in pairs:
mol = csd.molecule(mol1)
e=entry_reader.entry(mol1)
name_dict[mol1]=e.chemical_name
for i in range(0, (len(mol.components))):
if mol.components[i].smiles in clean_smiles.SOLVENT_SMILES:
solvates.append(mol.identifier)
solvates = Remove(solvates)
final_cocrystals = [x for x in pairs if x not in solvates]
#print(name_dict)
else:
final_cocrystals=pairs
# Clean the list from polymorphs
cocrystals = remove_polymorphs(final_cocrystals)
#print the time
end_time = time.clock()
name=[]
name= [name_dict[i] for i in cocrystals]
cocrystals_data= pd.concat([pd.DataFrame(cocrystals, columns=['csd_id']), pd.DataFrame(name, columns=['name'])], axis=1)
cocrystals_data=cocrystals_data.dropna(axis=0)
dataset_cocrystals = cocrystals_data[~cocrystals_data.name.str.contains("solvate")]
dataset_cocrystals = dataset_cocrystals[~dataset_cocrystals.name.str.contains("clathrate")]
print(end_time-start_time)
dataset_cocrystals.to_csv('new_all_cocrystals.csv',index=False)
return cocrystals
def get_entry(identifier, database="CSD"):
"""
input an identifier as a string and get the
ccdc.entry.Entry object
"""
csd_reader = EntryReader(database)
entry = csd_reader.entry(identifier)
return entry
def __init__(self):
d = "CSD_Drug_Subset_updated.gcd"
m = "MOF_subset.gcd"
self.drugs = self.get_refcodes(d)
self.mofs = self.get_refcodes(m)
self.subset = []
self.refcode = []
self.year = []
self.smiles = []
self.data = [
self.get_information(entry) for entry in EntryReader('CSD')
]
def run(self):
# inputs
with HotspotReader(self.args.hotspot_path) as reader:
hr = [
h for h in reader.read()
if h.identifier == self.args.hotspot_identifier
][0]
with MoleculeReader(self.args.docked_mols) as reader:
out = os.path.join(os.path.dirname(self.args.docked_mols),
"results_no_dummy.mol2")
with MoleculeWriter(out) as writer:
for mol in reader:
for atm in mol.atoms:
if atm.atomic_symbol == "Unknown":
mol.remove_atom(atm)
writer.write(mol)
self.args.docked_mols = out
entires = EntryReader(self.args.docked_mols)
# outputs
out_dir = os.path.join(os.path.dirname(self.args.docked_mols))
print(out_dir)
# process
hr = augmentation(hr, entires)
# 1) rescore
rescored = {e: score(hr, e) for e in entires}
ordered_rescored = OrderedDict(
sorted(rescored.items(), key=lambda item: item[1], reverse=True))
# 2) deduplicate: retain highest ranked pose only
out_dic = deduplicate(ordered_rescored)
# 3) output to dataframe ready for ccdc.descriptors API
df = pd.DataFrame({
"identifier": [e.identifier for e in out_dic.keys()],
"score":
list(out_dic.values()),
"activity": [activity_tag(e.identifier) for e in out_dic.keys()]
})
df.to_csv(os.path.join(out_dir, "rescored.csv"))
with EntryWriter(os.path.join(out_dir, "rescored.sdf")) as w:
for e in out_dic.keys():
w.write(e)
def gatherMatches(self):
"""
Set up as a raw string gather matches for now
TODO: create crystal flattener
:return:
"""
#Refine the hit list here to match group.
#TMP: right now im just going to return a list of identifiers
logger.info("Sending request for hits results\n\n")
#cellLib.displayHits(self.searchHits)
allHits = []
#TODO: cast to typem
## TMP str return
#line = ""
#for hit in self.searchHits:
# line += hit.crystal.to_string(format='sdf') +"\n"
#Quick + dirty format to just display on other side
for hit in self.searchHits:
#logger.info("Casting one hit " + hit.crystal.to_string(format='sdf'))
detailsImp = []
logger.info(hit.molecule.identifier)
logger.info("CCDC number: " + str(hit.entry.ccdc_number))
details = EntryReader('CSD').entry(hit.identifier)
detailsImp.append(hit.identifier) # refcode
logger.info(str(details.crystal.cell_lengths[0]))
detailsImp.append(str(details.crystal.cell_lengths[0]))
detailsImp.append(str(details.crystal.cell_lengths[1]))
detailsImp.append(str(details.crystal.cell_lengths[2]))
detailsImp.append(str(details.crystal.cell_angles[0]))
detailsImp.append(str(details.crystal.cell_angles[1]))
detailsImp.append(str(details.crystal.cell_angles[2]))
detailsImp.append(hit.crystal.formula)
#detailsImp.append(hit.crystal.lattice_centring)
allHits.append(detailsImp)
return allHits
def reportGenerator(filepath,refcode):
"""
:param filepath:
:param refcode:
:return:path to where generated html report can be found
"""
entry = EntryReader('csd').entry(refcode)
mol = entry.molecule
atoms = mol.atoms
bonds = mol.bonds
img = DiagramGenerator().image(mol)
doi = entry.publication.doi
if doi is None:
doi = ' '
else:
doi = '<a href="http://dx.doi.org/%s">%s</a>' % (doi, doi)
template_file_name = os.path.join(
os.path.dirname(__file__), 'simple_report_template.html'
)
template = unicode(open(template_file_name).read())
fileGenPath = os.path.join(filepath + refcode+ '.html')
with open(fileGenPath, 'w') as html:
s = template.format(
entry=entry,
molecule=mol,
image=img,
doi=doi,
synonyms='; '.join(s for s in entry.synonyms),
counts=dict(
natoms=len(atoms),
ndonors=len([a for a in atoms if a.is_donor]),
nacceptors=len([a for a in atoms if a.is_acceptor]),
nrot_bonds=len([b for b in bonds if b.is_rotatable]),
),
)
html.write(s.encode('utf8'))
return fileGenPath
def anal(self, queryTargetPath, normalizeFlag=False):
"""Perform geometrical analysis against the CCDC data source-"""
retD = {}
targetStructures = EntryReader(queryTargetPath)
for e in targetStructures:
mol = e.molecule
if normalizeFlag:
mol.assign_bond_types(which="unknown")
mol.standardise_aromatic_bonds()
mol.standardise_delocalised_bonds()
#
logger.info("begin analysis - for %s", queryTargetPath)
gam = self.__engine.analyse_molecule(mol)
bondOutliers = len(
[b for b in gam.analysed_bonds if b.unusual and b.enough_hits])
angleOutliers = len([
a for a in gam.analysed_angles if a.unusual and a.enough_hits
])
torsionOutliers = len([
t for t in gam.analysed_torsions if t.unusual and t.enough_hits
])
ringOutliers = len(
[r for r in gam.analysed_rings if r.unusual and r.enough_hits])
bL = self.__getBondAnalysis(gam)
aL = self.__getAngleAnalysis(gam)
tL = self.__getTorsionAnalysis(gam)
rL = self.__getRingAnalysis(gam)
retD = {
"bond_outliers": bondOutliers,
"angle_outliers": angleOutliers,
"torsion_outliers": torsionOutliers,
"ring_outliers": ringOutliers,
"bond_list": bL,
"angle_list": aL,
"torsion_list": tL,
"ring_list": rL,
}
return retD
def analyse_structures(user_gcd_input, user_csv_output):
if len(os.path.splitext(user_csv_output)[1]) == 0:
user_csv_output += ".csv"
with open(user_csv_output, 'w', newline='') as f:
writer = csv.writer(f)
writer.writerow(('Refcode', 'dimensionality', 'number in gcd file'))
csd_reader = EntryReader(user_gcd_input, 'CSD')
t2 = time.time()
n_structures = 0
n_mof = 0
n_non_mof = 0
for entry in csd_reader:
print('CSD entry: ' + str(entry.identifier))
n_structures += 1 # quick counter
count_polymers = 0
for component in entry.molecule.components:
if component.is_polymeric:
count_polymers += 1
if count_polymers > 1:
print('multiple polymer units present')
if entry.molecule.heaviest_component.is_polymeric:
n_mof += 1
framework = entry.molecule.heaviest_component
framework.remove_hydrogens(
) # next steps fail if any atoms in the unit do not have coordinates
entry.crystal.molecule = framework
fig = dimensionality(entry)
if fig == 0:
dimension = '0D non-MOF'
elif fig == 1:
dimension = '1D chain'
elif fig == 2:
dimension = '2D sheet'
elif fig == 3:
dimension = '3D framework'
else:
n_non_mof += 1
dimension = 'no polymeric bonds detected'
print('Framework dimensions for CSD entry % s: % s \n' %
(entry.identifier, dimension))
writer.writerow((entry.identifier, dimension, n_structures))
f.flush()
print('Total MOF subset size is: % d' % n_structures)
print('Entries recognised as polyermic is: % d' % n_mof)
print('Entries not recognised as polymeric (and ignored) is: % d' %
n_non_mof)
t3 = time.time()
overall_time_taken = str(t3 - t2)
print('total time elapsed for script % s' % overall_time_taken)
f.close()
def search(self,
queryTargetId,
queryTargetPath,
resultPath,
normalizeFlag=True,
maxHits=50,
searchType="similarity",
suppressMetals=False):
"""Search the CCDC database for similar or substructure matches for the input query molecule.
Args:
queryTargetId (str): query identifier
queryTargetPath (str): path to the query molfile (mol, sdf, mol2)
resultPath (str): output path to match results
normalizeFlag (bool, optional): do standard perceptions on matching molecules. Defaults to True.
maxHits (int, optional): maximum number of matches to return. Defaults to 50.
searchType (str, optional): search mode (substructure, similarity). Defaults to "similarity".
suppressMetals (bool, optional): filter structures containing metals. Defaults to False.
Returns:
(int): number of matches
"""
mU = MarshalUtil()
logger.info("Start search for target %s path %s result path %s",
queryTargetId, queryTargetPath, resultPath)
#
summaryList = []
#
targetDirPath = os.path.dirname(queryTargetPath)
cifTargetPath = os.path.join(targetDirPath, queryTargetId + ".cif")
#
targetStructures = EntryReader(queryTargetPath)
dirPath = os.path.join(resultPath, queryTargetId)
numHits = 0
for ii, e in enumerate(targetStructures, 1):
numHits = 0
startTime = time.time()
targetMol = e.molecule
if normalizeFlag:
targetMol.assign_bond_types(which="unknown")
targetMol.standardise_aromatic_bonds()
targetMol.standardise_delocalised_bonds()
#
logger.info("(%d) begin %s search - query id %s", ii, searchType,
queryTargetId)
if searchType == "similarity":
hits = self.__similaritySearch(targetMol,
suppressMetals=suppressMetals)
elif searchType == "substructure":
hits = self.__moleculeSubstructureSearch(
targetMol, suppressMetals=suppressMetals)
else:
hits = []
logger.info("(%d) completed search query id %s in %.3f seconds",
ii, queryTargetId,
time.time() - startTime)
if hits:
numHits += len(hits)
logger.info("(%d) search for %s matched %d: %r", ii,
queryTargetId, numHits,
[targetHit.identifier for targetHit in hits])
#
for targetHit in hits[:maxHits]:
#
hI = CcdcMatchIndexInst()
hI.setCsdVersion(csd_version())
hI.setCsdDirectory(csd_directory())
hI.setTargetId(queryTargetId)
hI.setTargetPath(queryTargetPath)
if mU.exists(cifTargetPath):
hI.setTargetCcPath(cifTargetPath)
hI.setIdentifier(targetHit.identifier)
hI.setMatchType(searchType)
try:
hI.setRFactor(targetHit.entry.r_factor)
hI.setChemicalName(targetHit.entry.chemical_name)
hI.setTemperature(targetHit.entry.temperature)
hI.setRadiationSource(targetHit.entry.radiation_source)
hI.setHasDisorder("N")
cit = targetHit.entry.publication
if cit.doi is not None:
hI.setCitationDOI(cit.doi)
if searchType == "similarity":
hI.setSimilarityScore(targetHit.similarity)
elif searchType == "substructure":
hI.setMatchedAtomLength(
len(targetHit.match_atoms()))
except Exception as e:
logger.exception("Failing with %s", str(e))
#
#
mU.mkdir(dirPath)
mol2L = []
if searchType == "substructure":
for jj, mc in enumerate(targetHit.match_components(),
1):
fp = os.path.join(
dirPath, queryTargetId + "_" +
targetHit.identifier + "_%03d" % jj + ".mol2")
mol2L.append(fp)
with MoleculeWriter(fp) as ofh:
ofh.write(mc)
# Replace the title line
with open(fp) as fin:
lines = fin.readlines()
lines[1] = lines[1].replace(
"00", targetHit.identifier)
#
with open(fp, "w") as fout:
fout.write("".join(lines))
#
fp = os.path.join(
dirPath, queryTargetId + "_" +
targetHit.identifier + "_%03d" % jj + ".sdf")
with MoleculeWriter(fp) as ofh:
ofh.write(mc)
# Replace the title line
with open(fp) as fin:
lines = fin.readlines()
lines[0] = lines[0].replace(
"00", targetHit.identifier)
#
with open(fp, "w") as fout:
fout.write("".join(lines))
#
# Check for multiple generated result files -
#
for jj, fp in enumerate(mol2L, 1):
logger.debug("(%d) adding component fp %s", jj, fp)
hI.setMatchNumber(jj)
hI.setMol2Path(fp)
tt = fp[:-4] + "sdf"
hI.setMolPath(tt)
summaryList.append(copy.deepcopy(hI.get()))
#
else:
hI.setMatchNumber(1)
summaryList.append(copy.deepcopy(hI.get()))
else:
logger.info("(%d) search for %s returns no matches", ii,
targetMol.identifier)
hits = None
#
if numHits > 0:
mU.mkdir(dirPath)
fp = os.path.join(dirPath, queryTargetId + "-index.json")
cmI = CcdcMatchIndex(indexFilePath=fp, verbose=self.__verbose)
cmI.load(summaryList)
cmI.writeIndex()
return numHits
entries = list(df.refcode)
from ccdc.search import TextNumericSearch
data = []
# for e in entries:
# query = TextNumericSearch()
# query.add_all_identifiers(e)
# hits = query.search()
# data.append(hits[0].entry.publication.doi)
# from pprint import pprint
#
# print len(data)
# print len(set(data))
from ccdc.diagram import DiagramGenerator
from ccdc.io import EntryReader
diagram_generator = DiagramGenerator()
diagram_generator.settings.font_size = 12
diagram_generator.settings.line_width = 1.6
diagram_generator.settings.image_width = 500
diagram_generator.settings.image_height = 500
csd_reader = EntryReader('CSD')
mols = set([csd_reader.entry(m) for m in entries])
for i, e in enumerate(mols):
img = diagram_generator.image(e)
img.save("hit{}.png".format(i))
class CSD_powder:
"""
CSD_powder class
#######################
this class calculates d_spacing, intensities and two theta for a specific crystal
Attributes
-------------
entry [ccdc entry reader method]
crystal_name str the name of a crystal of form 'AABHTZ'
Methods
---------------
__init__()
---------------
takes 2 arguments self,name [str]
sets crystal name
load_d_space()
---------------
uses name atr
calls ccdc PowderPattern class
calculates d_spacing using braggs law
returns d_space[list of d_spacing], intensities[list of peak intensities]
load_intensities()
------------------
uses name atr
calls ccdc PowderPattern class
returns list[intensities]
load_two_theta()
-------------------
uses name atr
calls ccdc PowderPattern class
returns list[two theta angles]
"""
def __init__(self):
self.entry = EntryReader('CSD')
def get_crystal_name(self):
return self.crystal_name
def set_crystal_name(self, value):
self.crystal_name = value
def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j, I in zip(two_t, intents):
if abs(l - j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(
I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas) / 2 # theta vals instead of 2theta
peak_radians = peak_thetas * np.pi / 180 # to radians
for peak in peak_radians:
d = self.wavelength / (2 * np.sin(peak)
) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space, intensity
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def get_data(self, option):
if option == 1:
d_space, intensities = self.load_d_space()
for i, j in zip(d_space, intensities):
print i, j
if option == 2:
"""all the data"""
x1 = self.load_intensities()
x2 = self.load_two_theta()
for i, j in zip(x1, x2):
print i, j
else:
sys.exit(1)
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from ccdc.io import EntryReader
import pandas as pd
mols = "./pharmit/query_results.sdf"
mols = EntryReader(mols)
smiles = []
name = []
rmsd = []
for m in mols:
smiles.append(m.molecule.smiles)
name.append(m.identifier)
rmsd.append(m.attributes["rmsd"])
df = pd.DataFrame({"smiles": smiles, "name": name, "rmsd": rmsd})
df.to_csv("pharmit.csv")
# entries= [(m.smiles, m.identifier) for m in mols]
#
# ligs =[]
#
# for i, entry in enumerate(entries):
# lig = Chem.MolFromSmiles(entry[0])
# name = ""
# for e in entry[1].split(" "):
def __init__(self):
self.entry = EntryReader('CSD')
formulas = open("formulas.txt", 'rb')
formulas_list = formulas.readlines()
new_formula_list = []
for formula_string in formulas_list:
formula_string = formula_string.rstrip('\n')
output_formula_list_item = []
fully_split_up = (list(split_text(formula_string)))
for index, index_item in enumerate(fully_split_up):
if index % 2 == 0:
output_formula_list_item.append(index_item +
fully_split_up[(index + 1)])
output_formula_list_item.sort()
new_formula_list.append(output_formula_list_item)
print new_formula_list
csd_entry_reader = EntryReader('CSD')
output = open("Results.txt", 'w')
for entry in csd_entry_reader:
for component in entry.molecule.components:
entry_formula = (component.formula).strip("(")
entry_formula = entry_formula.strip(")n")
entry_formula = (entry_formula).split(" ")
entry_formula.sort()
entry_formula = [i for i in entry_formula if re.search('[a-zA-Z]', i)]
print entry.identifier
if entry_formula in new_formula_list:
output.write(component.formula + "," + entry.identifier + "\n")
def __init__(self):
self.entry = EntryReader('CSD')
def __init__(self,name):
""
self.entry = EntryReader('CSD')
self.crystal_name = name
from ioAndInterfaces import ccdcCrystalToASE
from ccdc.io import EntryReader
from ase.io import write as ASEWrite
csdEntryReader = EntryReader('CSD')
aseCrystal = ccdcCrystalToASE(csdEntryReader.crystal('ABEBUF'))
ASEWrite('temp.xyz', aseCrystal)
def create_dataframe(base, run_id, pdbs):
format_dic = {
"asp": "ASP",
"chemscore": "Chemscore",
"goldscore": "Goldscore",
"plp": "PLP"
}
data = {
"pdb": [],
"runid": [],
"pose_id": [],
"pose_rank": [],
"dock_func": [],
"dock_fitness": [],
"rescore_func": [],
"rescore_fitness": [],
"gold_score": [],
"rmsd": [],
"rmsd_rank": []
}
pdbs = [
pdb for pdb in pdbs if os.path.isdir(os.path.join(base, pdb, run_id))
]
for pdb in tqdm(pdbs):
dpath = os.path.join(base, pdb, run_id)
funcs = [
d for d in os.listdir(dpath)
if not os.path.isfile(os.path.join(dpath, d))
]
for func in funcs:
ff_a, ff_b = process_ff_label(func)
s = [] # for the ranking
r = []
for i in range(1, 31):
pose = EntryReader(
os.path.join(dpath, func, "data",
f"ranked_{pdb}_ligand_m1_{i}.mol2"))[0]
attr = pose.attributes
score = float(attr["Gold.Score"].split("\n")[1][:5])
fit_score = {
k.split(".")[1]: attr[k]
for k in [a for a in attr.keys() if "Fitness" in a]
}
rmsd = attr["Gold.Reference.RMSD"]
data["pdb"].append(pdb)
data["runid"].append(run_id)
data["pose_id"].append(i)
data["dock_func"].append(ff_a)
data["dock_fitness"].append(float(fit_score[format_dic[ff_a]]))
data["gold_score"].append(score)
r.append(float(rmsd))
if ff_b is None:
data["rescore_func"].append(ff_a)
s.append(float(fit_score[format_dic[ff_a]]))
else:
data["rescore_func"].append(ff_b)
s.append(float(fit_score[format_dic[ff_b]]))
data["rescore_fitness"].extend(s)
data["pose_rank"].extend(rank_array(s))
data["rmsd"].extend(r)
data["rmsd_rank"].extend(rank_array(r))
return pd.DataFrame(data)
class CSD_powder:
"""
CSD_powder class
#######################
this class calculates d_spacing, intensities and two theta for a specific crystal
Attributes
-------------
entry [ccdc entry reader method]
crystal_name str the name of a crystal of form 'AABHTZ'
Methods
---------------
__init__()
---------------
takes 2 arguments self,name [str]
sets crystal name
load_d_space()
---------------
uses name atr
calls ccdc PowderPattern class
calculates d_spacing using braggs law
returns d_space[list of d_spacing], intensities[list of peak intensities]
load_intensities()
------------------
uses name atr
calls ccdc PowderPattern class
returns list[intensities]
load_two_theta()
-------------------
uses name atr
calls ccdc PowderPattern class
returns list[two theta angles]
"""
def __init__(self):
self.entry = EntryReader('CSD')
def get_crystal_name(self):
return self.crystal_name
def set_crystal_name(self,value):
self.crystal_name = value
def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j,I in zip(two_t,intents):
if abs(l-j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas)/2 # theta vals instead of 2theta
peak_radians = peak_thetas*np.pi/180 # to radians
for peak in peak_radians:
d = self.wavelength/(2*np.sin(peak)) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space,intensity
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def get_data(self,option):
if option == 1:
d_space,intensities = self.load_d_space()
for i,j in zip(d_space,intensities):
print i,j
if option == 2:
"""all the data"""
x1 = self.load_intensities()
x2 = self.load_two_theta()
for i,j in zip(x1,x2):
print i,j
else:
sys.exit(1)