Moved tests in a seperate folder
This commit is contained in:
Navan Chauhan
parent
0f0791037f
commit
b296e4d277
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@ -20,8 +20,7 @@ jobs:
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run: |
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python -m pip install --upgrade pip
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pip install mysql-connector mysql
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Fetch Latest Curie-CLI
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run: docker pull navanchauhan/curie-cli:latest
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- name: Run Database-Filler script
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run: cd app && python backend_test.py
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- name: Run Backend Test
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run: cd tests && python backednTest.py
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@ -20,12 +20,10 @@ jobs:
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run: |
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python -m pip install --upgrade pip
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pip install flake8 mysql-connector mysql
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint script with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 ./app/dbTestFiller.py --count --select=E9,F63,F7,F82 --show-source --statistics
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flake8 ./tests/dbTestFiller.py --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 ./app/dbTestFiller.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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flake8 ./tests/dbTestFiller.py --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Run Database-Filler script
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run: cd app && python dbTestFiller.py
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run: cd tests && python dbTestFiller.py
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@ -0,0 +1,100 @@
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import mysql.connector as con
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mycon = con.connect(host="navanspi.duckdns.org",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
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mycursor = mycon.cursor()
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# If we are running the CI on an actual server, try using the 6LU7 Mpro and Geraniin Job ID because Eucalyptol fails
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sql_select_Query = 'select * from curieweb where id="l9xo2isr98oepcia" LIMIT 1'
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mycursor.execute(sql_select_Query)
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records = mycursor.fetchall()
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def email(zi):
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import smtplib
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from email.mime.multipart import MIMEMultipart
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from email.mime.text import MIMEText
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from email.mime.base import MIMEBase
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from email import encoders
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fromaddr = "navanchauhan@gmail.com"
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toaddr = toEmail
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msg = MIMEMultipart()
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msg['From'] = fromaddr
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msg['To'] = toaddr
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msg['Subject'] = "Curie Web Results for Job ID " + str(jobID)
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body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description)
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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attachment = open((str(zi) + ".zip"), "rb")
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p = MIMEBase('application', 'octet-stream')
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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s = smtplib.SMTP('smtp.gmail.com', 587)
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s.starttls()
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s.login(fromaddr, 'ircd mday avbc tice')
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text = msg.as_string()
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s.sendmail(fromaddr, toaddr, text)
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s.quit()
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receptor_name = "protein.pdbqt"
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ligand_name = "ligand.pdbqt"
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description = "GitHub Action Test"
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#print(records[0])
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r = records[0]
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jobID = r[0]
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toEmail = r[1]
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targetB = r[2]
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if r[3] != None:
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receptor_name = str(r[3])
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if r[6] != None:
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ligand_name = str(r[6])
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ligandB = r[4]
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configB = r[7]
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date = r[8]
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if r[9] != None:
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description = r[9]
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import os
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cd = os.getcwd()
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f = os.path.join(cd,"static/uploads")
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#t = os.path.join(f,"receptor",target)
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#r = os.path.join(f,"ligands",ligand)
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#c = os.path.join(f,"configs",config)
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print(f)
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import tempfile
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from shutil import copy
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from shutil import make_archive
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with tempfile.TemporaryDirectory() as directory:
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print('The created temporary directory is %s' % directory)
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os.chdir(directory)
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# copy(t,os.getcwd())
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# copy(r,os.getcwd())
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# copy(c, os.getcwd())
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file = open(receptor_name,"wb")
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file.write(targetB)
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file.close()
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file = open(ligand_name,"wb")
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file.write(ligandB)
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file.close()
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file = open("config.txt","wb")
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file.write(configB)
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file.close()
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os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
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#copy("report.pdf",f)
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z = "Curie_Web_Result_"+str(jobID)
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zi = os.path.join(f,z)
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make_archive(zi, 'zip', directory)
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#copy(("Curie_Web_Result_"+str(jobID)),f)
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email(zi)
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#print((str(zi) + ".zip"))
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mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
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mycon.commit()
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@ -0,0 +1,69 @@
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import mysql.connector as con
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debug = False
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host = "navanspi.duckdns.org"
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done = 1
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if debug != False:
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host = "192.168.1.6"
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done = 0
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mycon = con.connect(host=host,user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
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mycursor = mycon.cursor()
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try:
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mycursor.execute("create table curieweb ( id varchar(16) primary key, email nvarchar(255) NOT NULL, protein LONGBLOB NOT NULL, protein_name VARCHAR(255), ligand_pdbqt LONGBLOB, ligand_smile VARCHAR(255), ligand_name VARCHAR(255), config LONGBLOB NOT NULL, date DATE, description VARCHAR(255), done TINYINT DEFAULT 0)")
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except con.ProgrammingError:
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print("Table Already Exists!")
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#try:
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# mycursor.execute("insert into curieweb values (1,'navanchauhan@gmail.com','lu.pdbqt','test.pdbqt','owo.txt',CURDATE(),'CURIE WEB TASK',0)")
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#except con.IntegrityError:
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# print("Duplicate Entry For Primary Key!")
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from random import choice, shuffle
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from string import digits, ascii_lowercase
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def gen_word(N, min_N_dig, min_N_low):
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choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
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choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
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chars = [choice(bet) for bet in choose_from]
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shuffle(chars)
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return ''.join(chars)
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def convertToBinaryData(filename):
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with open(filename, 'rb') as file:
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binaryData = file.read()
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return binaryData
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from os.path import basename
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ligand = convertToBinaryData("./files/Eucalyptol.pdbqt")
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receptor = convertToBinaryData("./files/6LU7.pdbqt")
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config = convertToBinaryData("./files/6LU7.txt")
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ligandName = "Eucalyptol"
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receptorName = "6LU7"
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sqlQuery = "insert into curieweb (id, email, protein, protein_name, ligand_pdbqt, ligand_name,date, config,done) values (%s,%s,%s,%s,%s,%s,CURDATE(),%s,%s) "
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jobID = gen_word(16, 1, 1)
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print("Succesfuly submitted Job ID:",jobID)
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insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
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try:
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mycursor.execute(sqlQuery,insert_tuple)
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except con.IntegrityError:
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print("Oops, Collision occured. Generating new Job ID and trying again.")
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jobID = gen_word(16, 1, 1)
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insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
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mycursor.execute(sqlQuery,insert_tuple)
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print("Removing Test Query")
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q = 'delete from curieweb where id="%s"' % (jobID)
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mycursor.execute(q)
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mycon.commit()
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print("Database working perfectly")
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,7 @@
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receptor=./targets/6LU7.pdbqt
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center_x=-9.7
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center_y=11.4
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center_z=68.9
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size_x=19.3
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size_y=29.9
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size_z=21.3
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@ -0,0 +1,22 @@
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REMARK Name =
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REMARK 3 active torsions:
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REMARK status: ('A' for Active; 'I' for Inactive)
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REMARK 1 A between atoms: C_1 and C_2
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REMARK 2 A between atoms: C_2 and C_11
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REMARK 3 A between atoms: C_6 and C_10
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REMARK x y z vdW Elec q Type
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REMARK _______ _______ _______ _____ _____ ______ ____
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ROOT
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ATOM 1 C UNL 1 0.937 -0.135 -0.034 0.00 0.00 +0.000 C
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ATOM 2 C UNL 1 2.469 -0.028 0.003 0.00 0.00 +0.000 C
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ATOM 3 C UNL 1 2.954 1.145 0.903 0.00 0.00 +0.000 C
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ATOM 4 C UNL 1 2.482 0.909 2.351 0.00 0.00 +0.000 C
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ATOM 5 C UNL 1 2.921 -0.490 2.797 0.00 0.00 +0.000 C
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ATOM 6 C UNL 1 3.781 -1.141 1.697 0.00 0.00 +0.000 C
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ATOM 7 O UNL 1 2.972 -1.282 0.511 0.00 0.00 +0.000 OA
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ATOM 8 C UNL 1 4.986 -0.243 1.358 0.00 0.00 +0.000 C
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ATOM 9 C UNL 1 4.494 1.151 0.952 0.00 0.00 +0.000 C
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ATOM 10 C UNL 1 4.237 -2.536 2.112 0.00 0.00 +0.000 C
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ATOM 11 C UNL 1 2.966 0.109 -1.444 0.00 0.00 +0.000 C
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ENDROOT
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TORSDOF 0
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