def preprocess_COMPND(self, compnd_list):
entity = self.struct.cifdb.confirm_table("entity")
entity_keywords = self.struct.cifdb.confirm_table("entity_keywords")
for compnd in compnd_list:
erow = mmCIF.mmCIFRow()
ekrow = mmCIF.mmCIFRow()
setmaps(compnd, "MOLECULE", erow, "pdbx_description")
if erow:
entity.append(erow)
setmaps(compnd, "FRAGMENT", ekrow, "pdbx_fragment")
setmaps(compnd, "EC", ekrow, "pdbx_ec")
setmaps(compnd, "MUTATION", ekrow, "pdbx_mutation")
if ekrow:
entity_keywords.append(ekrow)
def preprocess_COMPND(self, compnd_list):
entity = self.struct.cifdb.confirm_table("entity")
entity_keywords = self.struct.cifdb.confirm_table("entity_keywords")
for compnd in compnd_list:
erow = mmCIF.mmCIFRow()
ekrow = mmCIF.mmCIFRow()
setmaps(compnd, "MOLECULE", erow, "pdbx_description")
if erow:
entity.append(erow)
setmaps(compnd, "FRAGMENT", ekrow, "pdbx_fragment")
setmaps(compnd, "EC", ekrow, "pdbx_ec")
setmaps(compnd, "MUTATION", ekrow, "pdbx_mutation")
if ekrow:
entity_keywords.append(ekrow)
def preprocess_EXPDTA(self, expdta_list):
for technique, details in expdta_list:
self.struct.experimental_method = technique
break
exptl = self.struct.cifdb.confirm_table("exptl")
for (technique, details) in expdta_list:
row = mmCIF.mmCIFRow({"method": technique})
if details:
row["details"] = details
exptl.append(row)
def preprocess_EXPDTA(self, expdta_list):
for technique, details in expdta_list:
self.struct.experimental_method = technique
break
exptl = self.struct.cifdb.confirm_table("exptl")
for (technique, details) in expdta_list:
row = mmCIF.mmCIFRow({"method": technique})
if details:
row["details"] = details
exptl.append(row)
def set_single(self, table_name, col_name, val):
"""Utility function for setting a table where there should only be a
single row of data.
"""
if val == None:
return
table = self.confirm_table(table_name)
if len(table):
table[0][col_name] = val
else:
row = mmCIF.mmCIFRow()
table.append(row)
row[col_name] = val
def set_single(self, table_name, col_name, val):
"""Utility function for setting a table where there should only be a
single row of data.
"""
if val == None:
return
table = self.confirm_table(table_name)
if len(table):
table[0][col_name] = val
else:
row = mmCIF.mmCIFRow()
table.append(row)
row[col_name] = val
def preprocess_AUTHOR(self, author_list):
audit_author = self.struct.cifdb.confirm_table("audit_author")
for author in author_list:
audit_author.append(mmCIF.mmCIFRow({"name": author}))
def preprocess_KEYWDS(self, keywds_list):
struct_keywords = self.struct.cifdb.confirm_table("struct_keywords")
for keywds in keywds_list:
struct_keywords.append(mmCIF.mmCIFRow({"text": keywds}))
def preprocess_SOURCE(self, source_list):
entity_src_nat = self.struct.cifdb.confirm_table("entity_src_nat")
entity_src_gen = self.struct.cifdb.confirm_table("entity_src_gen")
for source in source_list:
nrow = mmCIF.mmCIFRow()
grow = mmCIF.mmCIFRow()
setmaps(source, "FRAGMENT",
grow, "pdbx_gene_src_fragment")
setmaps(source, "ORGANISM_SCIENTIFIC",
grow, "pdbx_gene_src_scientific_name")
setmaps(source, "ORGANISM_COMMON",
grow, "pdbx_gene_src_common_name")
setmaps(source, "GENUS",
grow, "pdbx_gene_src_genus")
setmaps(source, "GENUS",
grow, "pdbx_gene_src_genus")
setmaps(source, "SPECIES",
grow, "pdbx_gene_src_species")
setmaps(source, "STRAIN",
grow, "pdbx_gene_src_strain")
setmaps(source, "VARIANT",
grow, "pdbx_gene_src_variant")
setmaps(source, "CELL_LINE",
grow, "pdbx_gene_src_cell_line")
setmaps(source, "ATCC",
grow, "pdbx_gene_src_atcc")
setmaps(source, "ORGAN",
grow, "pdbx_gene_src_organ")
setmaps(source, "TISSUE",
grow, "pdbx_gene_src_tissue")
setmaps(source, "CELL",
grow, "pdbx_gene_src_cell")
setmaps(source, "ORGANELLE",
grow, "pdbx_gene_src_organelle")
setmaps(source, "SECRETION",
nrow, "pdbx_secretion")
setmaps(source, "CELLULAR_LOCATION",
grow, "pdbx_gene_src_cellular_location")
setmaps(source, "PLASMID",
nrow, "pdbx_plasmid_name")
setmaps(source, "GENE",
grow, "pdbx_gene_src_gene")
setmaps(source, "EXPRESSION_SYSTEM",
grow, "pdbx_host_org_scientific_name")
setmaps(source, "EXPRESSION_SYSTEM_COMMON",
grow, "pdbx_host_org_common_name")
setmaps(source, "EXPRESSION_SYSTEM_GENUS",
grow, "pdbx_host_org_genus")
setmaps(source, "EXPRESSION_SYSTEM_SPECIES",
grow, "pdbx_host_org_species")
setmaps(source, "EXPRESSION_SYSTEM_STRAIN",
grow, "pdbx_host_org_strain")
setmaps(source, "EXPRESSION_SYSTEM_VARIANT",
grow, "pdbx_host_org_variant")
setmaps(source, "EXPRESSION_SYSTEM_CELL_LINE",
grow, "pdbx_host_org_cell_line")
setmaps(source, "EXPRESSION_SYSTEM_ATCC_NUMBER",
grow, "pdbx_host_org_atcc")
setmaps(source, "EXPRESSION_SYSTEM_ORGAN",
grow, "pdbx_host_org_organ")
setmaps(source, "EXPRESSION_SYSTEM_TISSUE",
grow, "pdbx_host_org_tissue")
setmaps(source, "EXPRESSION_SYSTEM_CELL",
grow, "pdbx_host_org_cell")
setmaps(source, "EXPRESSION_SYSTEM_ORGANELLE",
grow, "pdbx_host_org_organelle")
setmaps(source, "EXPRESSION_SYSTEM_CELLULAR_LOCATION",
grow, "pdbx_host_org_cellular_location")
setmaps(source, "EXPRESSION_SYSTEM_VECTOR_TYPE",
grow, "pdbx_host_org_vector_type")
setmaps(source, "EXPRESSION_SYSTEM_VECTOR",
grow, "pdbx_host_org_vector")
setmaps(source, "EXPRESSION_SYSTEM_PLASMID",
grow, "plasmid")
setmaps(source, "EXPRESSION_SYSTEM_GENE",
grow, "pdbx_host_org_gene")
setmaps(source, "OTHER_DETAILS",
grow, "pdbx_description")
if nrow:
entity_src_nat.append(nrow)
if grow:
entity_src_gen.append(grow)
def preprocess_AUTHOR(self, author_list):
audit_author = self.struct.cifdb.confirm_table("audit_author")
for author in author_list:
audit_author.append(mmCIF.mmCIFRow({"name": author}))
def preprocess_KEYWDS(self, keywds_list):
struct_keywords = self.struct.cifdb.confirm_table("struct_keywords")
for keywds in keywds_list:
struct_keywords.append(mmCIF.mmCIFRow({"text": keywds}))
def preprocess_SOURCE(self, source_list):
entity_src_nat = self.struct.cifdb.confirm_table("entity_src_nat")
entity_src_gen = self.struct.cifdb.confirm_table("entity_src_gen")
for source in source_list:
nrow = mmCIF.mmCIFRow()
grow = mmCIF.mmCIFRow()
setmaps(source, "FRAGMENT", grow, "pdbx_gene_src_fragment")
setmaps(source, "ORGANISM_SCIENTIFIC", grow,
"pdbx_gene_src_scientific_name")
setmaps(source, "ORGANISM_COMMON", grow,
"pdbx_gene_src_common_name")
setmaps(source, "GENUS", grow, "pdbx_gene_src_genus")
setmaps(source, "GENUS", grow, "pdbx_gene_src_genus")
setmaps(source, "SPECIES", grow, "pdbx_gene_src_species")
setmaps(source, "STRAIN", grow, "pdbx_gene_src_strain")
setmaps(source, "VARIANT", grow, "pdbx_gene_src_variant")
setmaps(source, "CELL_LINE", grow, "pdbx_gene_src_cell_line")
setmaps(source, "ATCC", grow, "pdbx_gene_src_atcc")
setmaps(source, "ORGAN", grow, "pdbx_gene_src_organ")
setmaps(source, "TISSUE", grow, "pdbx_gene_src_tissue")
setmaps(source, "CELL", grow, "pdbx_gene_src_cell")
setmaps(source, "ORGANELLE", grow, "pdbx_gene_src_organelle")
setmaps(source, "SECRETION", nrow, "pdbx_secretion")
setmaps(source, "CELLULAR_LOCATION", grow,
"pdbx_gene_src_cellular_location")
setmaps(source, "PLASMID", nrow, "pdbx_plasmid_name")
setmaps(source, "GENE", grow, "pdbx_gene_src_gene")
setmaps(source, "EXPRESSION_SYSTEM", grow,
"pdbx_host_org_scientific_name")
setmaps(source, "EXPRESSION_SYSTEM_COMMON", grow,
"pdbx_host_org_common_name")
setmaps(source, "EXPRESSION_SYSTEM_GENUS", grow,
"pdbx_host_org_genus")
setmaps(source, "EXPRESSION_SYSTEM_SPECIES", grow,
"pdbx_host_org_species")
setmaps(source, "EXPRESSION_SYSTEM_STRAIN", grow,
"pdbx_host_org_strain")
setmaps(source, "EXPRESSION_SYSTEM_VARIANT", grow,
"pdbx_host_org_variant")
setmaps(source, "EXPRESSION_SYSTEM_CELL_LINE", grow,
"pdbx_host_org_cell_line")
setmaps(source, "EXPRESSION_SYSTEM_ATCC_NUMBER", grow,
"pdbx_host_org_atcc")
setmaps(source, "EXPRESSION_SYSTEM_ORGAN", grow,
"pdbx_host_org_organ")
setmaps(source, "EXPRESSION_SYSTEM_TISSUE", grow,
"pdbx_host_org_tissue")
setmaps(source, "EXPRESSION_SYSTEM_CELL", grow,
"pdbx_host_org_cell")
setmaps(source, "EXPRESSION_SYSTEM_ORGANELLE", grow,
"pdbx_host_org_organelle")
setmaps(source, "EXPRESSION_SYSTEM_CELLULAR_LOCATION", grow,
"pdbx_host_org_cellular_location")
setmaps(source, "EXPRESSION_SYSTEM_VECTOR_TYPE", grow,
"pdbx_host_org_vector_type")
setmaps(source, "EXPRESSION_SYSTEM_VECTOR", grow,
"pdbx_host_org_vector")
setmaps(source, "EXPRESSION_SYSTEM_PLASMID", grow, "plasmid")
setmaps(source, "EXPRESSION_SYSTEM_GENE", grow,
"pdbx_host_org_gene")
setmaps(source, "OTHER_DETAILS", grow, "pdbx_description")
if nrow:
entity_src_nat.append(nrow)
if grow:
entity_src_gen.append(grow)
