def test_single_row(self, rw_data):
myDataList = []
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.appendAttribute("details")
aCat.append([1, 2, 3, 4, 5, 6, 7, 'data_my_big_data_file'])
aCat.append([1, 2, 3, 4, 5, 6, 7, 'loop_my_big_data_loop'])
aCat.append([1, 2, 3, 4, 5, 6, 7, 'save_my_big_data_saveframe'])
aCat.append([1, 2, 3, 4, 5, 6, 7, '_category.item'])
curContainer.append(aCat)
bCat = curContainer.getObj("pdbx_seqtool_mapping_ref")
print("----attribute list %r\n" % bCat.getAttributeList())
row = bCat.getRow(0)
print("----ROW %r\n" % row)
with open(str(rw_data['pathOutputFile2']), "w") as ofh:
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
assert len(myDataList) == 1
def testSingleRow(self):
"""Test case - read /write single row and null row in data file
"""
try:
#
myDataList = []
# ofh = open(self.__pathOutputFile1, "w")
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.appendAttribute("details")
aCat.append([1, 2, 3, 4, 5, 6, 7, "data_my_big_data_file"])
aCat.append([1, 2, 3, 4, 5, 6, 7, "loop_my_big_data_loop"])
aCat.append([1, 2, 3, 4, 5, 6, 7, "save_my_big_data_saveframe"])
aCat.append([1, 2, 3, 4, 5, 6, 7, "_category.item"])
# aCat.dumpIt()
curContainer.append(aCat)
#
bCat = curContainer.getObj("pdbx_seqtool_mapping_ref")
logger.debug("----attribute list %r", bCat.getAttributeList())
row = bCat.getRow(0)
logger.debug("----ROW %r", row)
#
with open(self.__pathOutputFile2, "w") as ofh:
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
self.assertEqual(len(myDataList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
class CIF(object):
"""
This class uses the mmcif library to create an mmCIF-like object
Each object has one container, with a container ID and a list of DataCategory objects
"""
DUMMY_CONTAINER_ID = "emd_0000"
def __init__(self, cif_name_name):
self.filename = cif_name_name
# self.__dataList needed for PDBxWriter
self.__dataList = []
self.__container_id = None
self.__container = None
self.__dataMap = {}
def write(self):
"""
Given a file name, a pdbx writer is used to write data stored in self.__dataList
:return written: a boolean; True when pdf writer is finished
"""
written = False
if self.filename:
ofh = open(self.filename, "w")
pdbx_writer = PdbxWriter(ofh)
pdbx_writer.write(self.__dataList)
ofh.close()
written = True
return written
def add_container(self, container_id):
"""
This method provides the basic functionality to set up a container
:param container_id: a string; an mmcif category e.g. 'emd_admin'
:return:
"""
added = False
self.__container_id = container_id
self.__container = DataContainer(container_id)
self.__dataMap[container_id] = len(self.__dataList)
self.__dataList.append(self.__container)
if self.__container is not None:
added = True
return added
def prepare_container(self, container_id):
"""
Creates a container is it doesn't exist using either provided value or the dummy value
:param container_id: a string; an mmcif category e.g. 'emd_admin'
:return:
"""
if not self.__container:
if container_id is None:
container_id = self.DUMMY_CONTAINER_ID
return self.add_container(container_id)
def add_category(self, category_id, items):
"""
This method creates a data category object, adds all items to it and appends it to the container
:param category_id: a string; an mmcif category e.g. 'emd_admin'
:param items: a list of strings; each element in the list is an item of mmcif category as defined by category_id
:return: a list of strings; each element represents a value for the corresponding element in data_items
"""
category = DataCategory(category_id)
for item in items:
category.appendAttribute(item)
self.__container.append(category)
#
# def update_single_row_value(self, category_id, item_name, row, value):
# """Update value in single row
# """
# catObj = self.__container.getObj(category_id)
# if catObj is None:
# return
# #
# catObj.setValue(value, item_name, row)
#
# def update_multiple_rows_value(self, category_id, item_name, value):
# """Update value in multiple rows
# """
# cat_obj = self.__container.getObj(category_id)
# if cat_obj is None:
# return
# #
# row_no = cat_obj.getRowCount()
# for row in range(0, row_no):
# cat_obj.setValue(value, item_name, row)
def insert_data(self, category_id, data_list):
"""
This method appends the data in data_list to the container labeled category_id
:param category_id: a string; an mmcif category e.g. 'emd_admin'
:param data_list:
:return:
"""
cat_obj = self.__container.getObj(category_id)
if cat_obj is None:
return
if any(isinstance(el, list) for el in data_list):
# print(data_list)
for data_ord in data_list[0]:
new_list = []
ord_index = data_list[0].index(data_ord)
new_list.append(ord_index)
new_list.append(data_list[1][ord_index])
# print(new_list)
cat_obj.append(new_list)
else:
cat_obj.append(data_list)
def insert_data_into_category(self, category_id, data_items, data_list):
"""
Helper method: calls two other methods, one to add a category and its items into a container and
another to insert the data for the category items
:param category_id: a string; an mmcif category e.g. 'emd_admin'
:param data_items: a list of strings; each element in the list is an item of mmcif category as defined by category_id
:param data_list: a list of strings; each element represents a value for the corresponding element in data_items
:return:
"""
# print('INSERT DATA INTO CATEGORY:', category_id, data_items, data_list)
self.add_category(category_id, data_items)
self.insert_data(category_id, data_list)
def __writeModel(self, targetId, targetObj, fitFD, fitXyzMapD,
fitAtomUnMappedL, matchD, modelId, modelPath):
"""Write the chemical component model for the input chemical component Id and associated atom mapping and
feature details --
ComponentAtomDetails = namedtuple("ComponentAtomDetails", "index atNo name aType x y z fCharge")
AlignAtomMap = namedtuple("AlignAtomMap", "refId refAtIdx refAtNo refAtName fitId fitAtIdx fitAtNo fitAtName")
AlignAtomUnMapped = namedtuple("AlignAtomUnMapped", "fitId fitAtIdx fitAtNo fitAtType fitAtName fitAtFormalCharge x y z fitNeighbors")
"""
try:
unMappedTypeD = defaultdict(int)
hAtomPrefix = "HEX"
variantType = self.__getBuildVariant(targetId)
#
if not self.__testUnMappedProtonation(fitAtomUnMappedL):
logger.info(
"Unmapped non-hydrogen atoms target %r model %r unMapped count (%d)",
targetId, modelId, len(fitAtomUnMappedL))
return False, variantType
# Get atom partners for the unmapped atoms
fitAtMapD = {}
for refAtName, fAtTup in fitXyzMapD.items():
fitAtMapD[fAtTup.atName] = refAtName
if fitAtomUnMappedL:
# Check if neighbors are all mapped
ok = True
for fitUnTup in fitAtomUnMappedL:
for nAtName in fitUnTup.fitNeighbors:
if nAtName not in fitAtMapD:
ok = False
logger.info(
"Missing mapped neighbor for %r target %r model %r",
nAtName, targetId, modelId)
break
if not ok:
return False, variantType
else:
logger.debug("%s match has unmapped protonation", modelId)
variantType = "tautomer_protomer"
#
#
kList = ["xyz", "SMILES", "SMILES_STEREO", "InChI", "InChIKey"]
for k in kList:
if k not in fitFD:
logger.error(
"Fit feature dictionary for %s missing key %s",
targetId, k)
return False, variantType
# ------------
dataContainer = DataContainer(modelId)
#
myContainer = targetObj
dbName = myContainer.getName()
if dbName.upper() != targetId.upper():
logger.info("mismatch datablock (%r) and targetId (%r)",
dbName, targetId)
cObj = None
if myContainer.exists("chem_comp"):
cObj = myContainer.getObj("chem_comp")
#
#
catName = "pdbx_chem_comp_model"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(catName, attributeNameList=["id", "comp_id"]))
#
parentId = targetId.split("|")[0]
wObj = dataContainer.getObj(catName)
wObj.setValue(modelId, "id", 0)
wObj.setValue(parentId, "comp_id", 0)
#
# -------- ---------
catName = "pdbx_chem_comp_model_atom"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(catName,
attributeNameList=[
"model_id", "atom_id", "type_symbol",
"charge", "model_Cartn_x",
"model_Cartn_y", "model_Cartn_z",
"ordinal_id"
]))
wObj = dataContainer.getObj(catName)
#
if myContainer.exists("chem_comp_atom"):
cObj = myContainer.getObj("chem_comp_atom")
#
# Only write the mapped atoms in case we are missing hydrogens in the mapping
#
jj = 0
for ii in range(cObj.getRowCount()):
atName = cObj.getValue("atom_id", ii)
atType = cObj.getValue("type_symbol", ii)
if atName not in fitXyzMapD:
unMappedTypeD[atType] += 1
continue
fitXyz = fitXyzMapD[atName]
#
# fCharge = cObj.getValue("charge", ii)
#
wObj.setValue(modelId, "model_id", jj)
wObj.setValue(atName, "atom_id", jj)
wObj.setValue(atType, "type_symbol", jj)
#
wObj.setValue(fitXyz.atFormalCharge, "charge", jj)
wObj.setValue("%.4f" % fitXyz.x, "model_Cartn_x", jj)
wObj.setValue("%.4f" % fitXyz.y, "model_Cartn_y", jj)
wObj.setValue("%.4f" % fitXyz.z, "model_Cartn_z", jj)
wObj.setValue(jj + 1, "ordinal_id", jj)
jj += 1
#
# Add the unmapped atoms ...
# AlignAtomUnMapped = namedtuple("AlignAtomUnMapped", "fitId fitAtIdx fitAtNo fitAtType fitAtName fitNeighbors")
ii = wObj.getRowCount()
for jj, uTup in enumerate(fitAtomUnMappedL):
refAtomName = hAtomPrefix + str(jj)
wObj.setValue(modelId, "model_id", ii)
wObj.setValue(refAtomName, "atom_id", ii)
wObj.setValue(uTup.fitAtType, "type_symbol", ii)
wObj.setValue(uTup.fitAtFormalCharge, "charge", ii)
wObj.setValue("%.4f" % uTup.x, "model_Cartn_x", ii)
wObj.setValue("%.4f" % uTup.y, "model_Cartn_y", ii)
wObj.setValue("%.4f" % uTup.z, "model_Cartn_z", ii)
wObj.setValue(ii + 1, "ordinal_id", ii)
# -------- ---------
catName = "pdbx_chem_comp_model_bond"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(catName,
attributeNameList=[
"model_id", "atom_id_1", "atom_id_2",
"value_order", "ordinal_id"
]))
wObj = dataContainer.getObj(catName)
#
if myContainer.exists("chem_comp_bond"):
cObj = myContainer.getObj("chem_comp_bond")
#
jj = 0
for ii in range(cObj.getRowCount()):
at1 = cObj.getValue("atom_id_1", ii)
if at1 not in fitXyzMapD:
continue
at2 = cObj.getValue("atom_id_2", ii)
if at2 not in fitXyzMapD:
continue
bType = cObj.getValue("value_order", ii)
#
wObj.setValue(modelId, "model_id", jj)
wObj.setValue(at1, "atom_id_1", jj)
wObj.setValue(at2, "atom_id_2", jj)
wObj.setValue(bType, "value_order", jj)
wObj.setValue(jj + 1, "ordinal_id", jj)
jj += 1
#
ii = wObj.getRowCount()
for jj, uTup in enumerate(fitAtomUnMappedL):
at1 = hAtomPrefix + str(jj)
for nAt in uTup.fitNeighbors:
at2 = fitAtMapD[nAt]
wObj.setValue(modelId, "model_id", ii)
wObj.setValue(at1, "atom_id_1", ii)
wObj.setValue(at2, "atom_id_2", ii)
wObj.setValue("SING", "value_order", ii)
wObj.setValue(ii + 1, "ordinal_id", ii)
# -------- ---------
catName = "pdbx_chem_comp_model_descriptor"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(
catName,
attributeNameList=["model_id", "type", "descriptor"]))
wObj = dataContainer.getObj(catName)
#
ii = 0
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("SMILES", "type", ii)
wObj.setValue(fitFD["SMILES"], "descriptor", ii)
ii += 1
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("SMILES_CANONICAL", "type", ii)
wObj.setValue(fitFD["SMILES_STEREO"], "descriptor", ii)
ii += 1
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("InChI", "type", ii)
wObj.setValue(fitFD["InChI"], "descriptor", ii)
ii += 1
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("InChIKey", "type", ii)
wObj.setValue(fitFD["InChIKey"], "descriptor", ii)
#
# -------- ---------
if matchD["queryId"] is not None:
catName = "pdbx_chem_comp_model_reference"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(catName,
attributeNameList=[
"model_id", "db_name", "db_code"
]))
wObj = dataContainer.getObj(catName)
ii = 0
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("COD", "db_name", ii)
wObj.setValue(matchD["queryId"], "db_code", ii)
#
featureD = {}
v = matchD["rValue"]
vS = str(v)
if v is not None and len(vS) > 0:
featureD["r_factor"] = "%.3f" % float(v)
#
v = matchD["diffrnTemp"]
vS = str(v)
# remove string artifacts from temperature string ...
if v is not None and len(vS) > 0:
tV = vS.upper()
try:
if tV.endswith("DEG.C"):
tV = tV.replace("AT", "")
tV = tV.replace("DEG.C", "")
tV = float(tV.strip())
tV = tV + 273.15
else:
tV = tV.replace("AT", "")
tV = tV.replace("K", "")
tV = float(tV.strip())
featureD["experiment_temperature"] = tV
except Exception as e:
logger.exception(
"Temperature conversion fails for %s (%r) with %s",
modelId, vS, tV)
#
v = matchD["publicationDOI"]
vS = str(v)
if v is not None and len(vS) > 0:
featureD["publication_doi"] = v
#
v = matchD["version"]
vS = str(v)
if v is not None and len(vS) > 0:
featureD["cod_version"] = v
#
if matchD["radiationSource"] and "neutron" in matchD[
"radiationSource"]:
featureD["neutron_radiation_experiment"] = True
if matchD["hasDisorder"] in ["Y"]:
featureD["has_disorder"] = True
#
if len(unMappedTypeD) == 1 and "H" in unMappedTypeD:
logger.info("model %r heavy_atoms_only", modelId)
featureD["heavy_atoms_only"] = True
else:
featureD["all_atoms_have_sites"] = True
# -------- ---------
catName = "pdbx_chem_comp_model_feature"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(catName,
attributeNameList=[
"model_id", "feature_name",
"feature_value"
]))
wObj = dataContainer.getObj(catName)
#
fKeyList = [
"experiment_temperature", "publication_doi", "r_factor",
"csd_version"
]
ii = 0
for fKey in fKeyList:
if fKey in featureD:
wObj.setValue(modelId, "model_id", ii)
wObj.setValue(fKey, "feature_name", ii)
wObj.setValue(str(featureD[fKey]), "feature_value", ii)
ii += 1
#
boolKeyList = [
"has_disorder", "neutron_radiation_experiment",
"heavy_atoms_only", "all_atoms_have_sites"
]
for fKey in boolKeyList:
if fKey in featureD:
if featureD[fKey]:
wObj.setValue(modelId, "model_id", ii)
wObj.setValue(fKey, "feature_name", ii)
wObj.setValue("Y", "feature_value", ii)
ii += 1
#
if variantType:
wObj.setValue(modelId, "model_id", ii)
wObj.setValue(variantType + "_match", "feature_name", ii)
wObj.setValue("Y", "feature_value", ii)
ii += 1
# -------- ---------
catName = "pdbx_chem_comp_model_audit"
if not dataContainer.exists(catName):
dataContainer.append(
DataCategory(
catName,
attributeNameList=["model_id", "action_type", "date"]))
wObj = dataContainer.getObj(catName)
#
ii = 0
wObj.setValue(modelId, "model_id", ii)
wObj.setValue("Initial release", "action_type", ii)
wObj.setValue(self.__getToday(), "date", ii)
# wObj.setValue('RCSB', 'processing_site', ii)
# wObj.setValue('JDW', 'annotator', ii)
# wObj.setValue('?', 'details', ii)
#
mU = MarshalUtil(workPath=self.__cachePath)
ok = mU.doExport(modelPath, [dataContainer], fmt="mmcif")
return ok, variantType
except Exception as e:
logger.exception("Failing for %r with %s", targetId, str(e))
return False, ""
def __buildCif(self, rD, containerName="vrpt"):
""" Construct a mmCIF data category objects for the input
extracted data.
Args:
rD (dict): extracted data organized by category.
containerName (str) : data block name
Returns:
containers (list): data container list
"""
#
curContainer = DataContainer(containerName)
for elName in rD:
catName = elName
if (not rD[elName]) or (not self.__attribD[catName]) or (
catName in ["programs"]):
continue
hasOrdinal = "ordinal" in self.__attribD[catName]
rowList = rD[elName]
# Find the unique attribute content across the rowlist and the ordinal value
atS = set()
for ii, rowD in enumerate(rowList, 1):
if hasOrdinal:
rowD["ordinal"] = ii
if "icode" in rowD:
rowD["icode"] = str(rowD["icode"]).strip()
if "altcode" in rowD:
rowD["altcode"] = str(rowD["altcode"]).strip()
atS.update(rowD.keys())
attributeNameList = list(atS)
#
# Set a reasonable order for these attributes
#
sD = {ky: self.__atOrdD[ky] for ky in attributeNameList}
srtAtL = [
tup[0]
for tup in sorted(sD.items(), key=operator.itemgetter(1))
]
logger.debug("Category %s sorted attributes %r", catName, srtAtL)
aCat = DataCategory(catName, srtAtL, rowList)
curContainer.append(aCat)
#
# Adjust schema names -
#
atD = self.__dictionaryMap["attributes"]
for catName in curContainer.getObjNameList():
catObj = curContainer.getObj(catName)
atNameList = catObj.getAttributeList()
mapD = {}
mapCatName = self.__dictionaryMap["categories"][
catName] if catName in self.__dictionaryMap[
"categories"] else catName
for atName in atNameList:
mapD[atName] = atD[(catName, atName)]["at"] if (
catName, atName) in atD else atName
catObj.renameAttributes(mapD)
catObj.setName(mapCatName)
#
# Map provenance items from programs.properties -
#
catObj = curContainer.getObj("program")
if catObj and catObj.hasAttribute("properties"):
for iRow in range(catObj.getRowCount()):
pV = catObj.getValue("properties", iRow)
pVL = [v.strip() for v in pV.split(",")]
nL = [
self.__atMap[ky] if ky in self.__atMap else ky
for ky in pVL
]
catObj.setValue(",".join(nL), "properties", iRow)
# logger.info("Row %r properties %r" % (iRow, pV))
#
return [curContainer]
class mmCIFUtil:
"""Using pdbx mmCIF utility to parse mmCIF file"""
def __init__(self, verbose=False, log=sys.stderr, filePath=None): # pylint: disable=unused-argument
# self.__verbose = verbose
self.__lfh = log
self.__filePath = filePath
self.__dataList = []
self.__dataMap = {}
self.__container = None
self.__blockID = None
self.__read()
#
def __read(self):
if not self.__filePath:
return
#
try:
ifh = open(self.__filePath, "r")
pRd = PdbxReader(ifh)
pRd.read(self.__dataList)
ifh.close()
if self.__dataList:
self.__container = self.__dataList[0]
self.__blockID = self.__container.getName()
idx = 0
for container in self.__dataList:
self.__dataMap[container.getName()] = idx
idx += 1
#
#
except Exception as e:
self.__lfh.write("Read %s failed %s.\n" %
(self.__filePath, str(e)))
#
def GetBlockID(self):
"""Return first block ID"""
return self.__blockID
def GetValueAndItemByBlock(self, blockName, catName):
"""Get category values and item names"""
dList = []
iList = []
if blockName not in self.__dataMap:
return dList, iList
#
catObj = self.__dataList[self.__dataMap[blockName]].getObj(catName)
if not catObj:
return dList, iList
#
iList = catObj.getAttributeList()
rowList = catObj.getRowList()
for row in rowList:
tD = {}
for idxIt, itName in enumerate(iList):
if row[idxIt] != "?" and row[idxIt] != ".":
tD[itName] = row[idxIt]
#
if tD:
dList.append(tD)
#
#
return dList, iList
def GetValueAndItem(self, catName):
dList, iList = self.GetValueAndItemByBlock(self.__blockID, catName)
return dList, iList
def GetValue(self, catName):
"""Get category values based on category name 'catName'. The results are stored
in a list of dictionaries with item name as key
"""
dList, _iList = self.GetValueAndItemByBlock(self.__blockID, catName)
return dList
def GetSingleValue(self, catName, itemName):
"""Get the first value of item name 'itemName' from 'itemName' item in 'catName' category."""
text = ""
dlist = self.GetValue(catName)
if dlist:
if itemName in dlist[0]:
text = dlist[0][itemName]
return text
#
def UpdateSingleRowValue(self, catName, itemName, row, value):
"""Update value in single row"""
catObj = self.__container.getObj(catName)
if catObj is None:
return
#
catObj.setValue(value, itemName, row)
def UpdateMultipleRowsValue(self, catName, itemName, value):
"""Update value in multiple rows"""
catObj = self.__container.getObj(catName)
if catObj is None:
return
#
rowNo = catObj.getRowCount()
for row in range(0, rowNo):
catObj.setValue(value, itemName, row)
#
def AddBlock(self, blockID):
"""Add Data Block"""
self.__container = DataContainer(blockID)
self.__blockID = blockID
self.__dataMap[blockID] = len(self.__dataList)
self.__dataList.append(self.__container)
def AddCategory(self, categoryID, items):
"""Add Category"""
category = DataCategory(categoryID)
for item in items:
category.appendAttribute(item)
#
self.__container.append(category)
def RemoveCategory(self, categoryID):
return self.__container.remove(categoryID)
def InsertData(self, categoryID, dataList):
""""""
catObj = self.__container.getObj(categoryID)
if catObj is None:
return
#
for data in dataList:
catObj.append(data)
#
def WriteCif(self, outputFilePath=None):
"""Write out cif file"""
if not outputFilePath:
return
#
ofh = open(outputFilePath, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(self.__dataList)
ofh.close()
def GetCategories(self):
return self.__container.getObjNameList()
def GetAttributes(self, category):
return self.__container.getObj(category).getAttributeList()
def category_as_dict(self, category, block=None):
if block is None:
block = self.__blockID
values, attributes = self.GetValueAndItemByBlock(block, category)
data = [[x[y] if y in x else None for y in attributes] for x in values]
return {category: {"Items": attributes, "Values": data}}
def block_as_dict(self, block=None):
if block is None:
block = self.__blockID
data = {}
for category in self.GetCategories():
data.update(self.category_as_dict(category, block=block))
return data