Answers

#!/usr/bin/env python3
import pymysql.cursors

# Set parameters
dbname   = "biodb"
dbhost   = "pandora"
dbuser   = "xxxx"   # Ask a demonstrator
dbpass   = "xxxx"   # Ask a demonstrator
port     = 3306

# Create SQL statement to find number of human protein entries
sql      = "select count(*) from protein where source = 'Homo sapiens'"

# Connect to the database
db = pymysql.connect(host=dbhost, port=port, user=dbuser, passwd=dbpass, db=dbname)

# Create a cursor and execute the SQL on it
cursor = db.cursor()
nrows  = cursor.execute(sql)

# We know there is only one row returned to fetch it and print the data
data   = cursor.fetchone()
print ("There were ", data[0], " rows")

#!/usr/bin/env python3
import pymysql.cursors

# Set parameters
dbname   = "biodb"
dbhost   = "pandora"
dbuser   = "xxxx"   # Ask a demonstrator
dbpass   = "xxxx"   # Ask a demonstrator
port     = 3306

# Create SQL statement to find information for PDB entry 1DM5
sql      = "select source, resolution, description from protein where pdb_code = '1DM5'"

# Connect to the database
db = pymysql.connect(host=dbhost, port=port, user=dbuser, passwd=dbpass, db=dbname)

# Create a cursor and execute the SQL on it
cursor = db.cursor()
nrows  = cursor.execute(sql)

# We know there is only one row returned to fetch it and print the data
data   = cursor.fetchone()

src   = data[0]
resol = data[1]
desc  = data[2]

print ("PDB Code:     1DM5")
print ("Species:     ", src)
print ("Resolution:  ", resol)
print ("Description: ", desc)

This version uses repeated calls to cursor.fetchone()

#!/usr/bin/env python3
import pymysql.cursors

# Set parameters
dbname   = "biodb"
dbhost   = "pandora"
dbuser   = "xxxx"   # Ask a demonstrator
dbpass   = "xxxx"   # Ask a demonstrator
port     = 3306

# Create SQL statement to find information for proteins from Leishmania
sql = "select pdb_code, resolution, name from protein where source = 'LEISHMANIA MAJOR'"

# Connect to the database
db = pymysql.connect(host=dbhost, port=port, user=dbuser, passwd=dbpass, db=dbname)

# Create a cursor and execute the SQL on it
cursor = db.cursor()
nrows  = cursor.execute(sql)

# Use repeated calls to cursor.fetchone()
data = cursor.fetchone()
while data is not None:
    pdb   = data[0]
    resol = data[1]
    name  = data[2]

    print (pdb, " ", resol, " ", name)
    data = cursor.fetchone()

This version uses the preferred method if using the cursor as an iterator.

#!/usr/bin/env python3
import pymysql.cursors

# Set parameters
dbname   = "biodb"
dbhost   = "pandora"
dbuser   = "xxxx"   # Ask a demonstrator
dbpass   = "xxxx"   # Ask a demonstrator
port     = 3306

# Create SQL statement to find information for proteins from Leishmania
sql = "select pdb_code, resolution, name from protein where source = 'LEISHMANIA MAJOR'"

# Connect to the database
db = pymysql.connect(host=dbhost, port=port, user=dbuser, passwd=dbpass, db=dbname)

# Create a cursor and execute the SQL on it
cursor = db.cursor()
nrows  = cursor.execute(sql)

# Using the cursor as an iterator
for data in cursor:
    pdb   = data[0]
    resol = data[1]
    name  = data[2]

    print (pdb, " ", resol, " ", name)