"""
Created on 01 March 2016
@author: Mojtaba Haghighatlari
"""
from __future__ import print_function
from builtins import range
import warnings
import os
import time
import pandas as pd
from lxml import objectify, etree
from chemml.utils import std_datetime_str
from chemml.utils import bool_formatter
from chemml.utils import tot_exec_time_str
class Dragon(object):
"""
An interface to Dragon 6 and 7 chemoinformatics software. Dragon is a commercial software and
you should provide
Parameters
----------
version: int, optional (default=7)
The version of available Dragon on the user's system. (available versions: 6 or 7)
Weights: list, optional (default=["Mass","VdWVolume","Electronegativity","Polarizability","Ionization","I-State"])
A list of weights to be used
blocks: list, optional (default = list(range(1,31)))
A list of integers as descriptor blocks' id. There are totally 29 and 30 blocks available in
version 6 and 7, respectively.
This module is not atimed to cherry pick descriptors in each block.
For doing so, please use Script Wizard in Drgon GUI.
external: boolean, optional (default=False)
If True, include external variables at the end of each saved file.
Notes
-----
The documentation for the rest of parameters can be found in the following links:
- http://www.talete.mi.it/help/dragon_help/index.html
- https://chm.kode-solutions.net/products_dragon_tutorial.php
In the current version, we recommend the user to use this class with the following parameters:
molInput = 'file'
molfile = path to one SMILES representation file with .smi format or a dictionary of many filepaths
script = 'new'
Examples
--------
>>> import pandas as pd
>>> from chemml.chem import Dragon
>>> drg = Dragon()
>>> drg.script_wizard(script='new', output_directory='./')
>>> drg.run()
>>> df = drg.convert_to_csv(remove=True)
>>> df = df.drop(['No.','NAME'], axis=1)
"""
def __init__(self,
version=7,
molFile='required_required',
molInput="file",
CheckUpdates=True,
SaveLayout=True,
PreserveTemporaryProjects=True,
ShowWorksheet=False,
Decimal_Separator=".",
Missing_String="NaN",
DefaultMolFormat="1",
HelpBrowser="/usr/bin/xdg-open",
RejectUnusualValence=False,
Add2DHydrogens=False,
MaxSRforAllCircuit="19",
MaxSR="35",
MaxSRDetour="30",
MaxAtomWalkPath="2000",
LogPathWalk=True,
LogEdge=True,
Weights=("Mass", "VdWVolume", "Electronegativity", "Polarizability", "Ionization",
"I-State"),
SaveOnlyData=False,
SaveLabelsOnSeparateFile=False,
SaveFormatBlock="%b-%n.txt",
SaveFormatSubBlock="%b-%s-%n-%m.txt",
SaveExcludeMisVal=False,
SaveExcludeAllMisVal=False,
SaveExcludeConst=False,
SaveExcludeNearConst=False,
SaveExcludeStdDev=False,
SaveStdDevThreshold="0.0001",
SaveExcludeCorrelated=False,
SaveCorrThreshold="0.95",
SaveExclusionOptionsToVariables=False,
SaveExcludeMisMolecules=False,
SaveExcludeRejectedMolecules=False,
blocks=list(range(1, 31)),
molInputFormat="SMILES",
SaveStdOut=False,
SaveProject=False,
SaveProjectFile="Dragon_project.drp",
SaveFile=True,
SaveType="singlefile",
SaveFilePath="Dragon_descriptors.txt",
logMode="file",
logFile="Dragon_log.txt",
external=False,
fileName=None,
delimiter=",",
consecutiveDelimiter=False,
MissingValue="NaN",
RejectDisconnectedStrucuture=False,
RetainBiggestFragment=False,
DisconnectedCalculationOption="0",
RoundCoordinates=True,
RoundWeights=True,
RoundDescriptorValues=True,
knimemode=False):
if version in (6, 7):
self.version = version
else:
msg = "Only version 6 and 7 are available through this module."
raise ValueError(msg)
self.molFile = molFile
self.molInput = molInput
self.CheckUpdates = CheckUpdates
self.PreserveTemporaryProjects = PreserveTemporaryProjects
self.SaveLayout = SaveLayout
self.ShowWorksheet = ShowWorksheet
self.Decimal_Separator = Decimal_Separator
self.Missing_String = Missing_String
self.DefaultMolFormat = DefaultMolFormat
self.HelpBrowser = HelpBrowser
self.RejectUnusualValence = RejectUnusualValence
self.Add2DHydrogens = Add2DHydrogens
self.MaxSRforAllCircuit = MaxSRforAllCircuit
self.MaxSR = MaxSR
self.MaxSRDetour = MaxSRDetour
self.MaxAtomWalkPath = MaxAtomWalkPath
self.LogPathWalk = LogPathWalk
self.LogEdge = LogEdge
self.Weights = Weights
self.SaveOnlyData = SaveOnlyData
self.SaveLabelsOnSeparateFile = SaveLabelsOnSeparateFile
self.SaveFormatBlock = SaveFormatBlock
self.SaveFormatSubBlock = SaveFormatSubBlock
self.SaveExcludeMisVal = SaveExcludeMisVal
self.SaveExcludeAllMisVal = SaveExcludeAllMisVal
self.SaveExcludeConst = SaveExcludeConst
self.SaveExcludeNearConst = SaveExcludeNearConst
self.SaveExcludeStdDev = SaveExcludeStdDev
self.SaveStdDevThreshold = SaveStdDevThreshold
self.SaveExcludeCorrelated = SaveExcludeCorrelated
self.SaveCorrThreshold = SaveCorrThreshold
self.SaveExclusionOptionsToVariables = SaveExclusionOptionsToVariables
self.SaveExcludeMisMolecules = SaveExcludeMisMolecules
self.SaveExcludeRejectedMolecules = SaveExcludeRejectedMolecules
self.blocks = blocks
self.molInputFormat = molInputFormat
self.SaveStdOut = SaveStdOut
self.SaveProject = SaveProject
self.SaveProjectFile = SaveProjectFile
self.SaveFile = SaveFile
self.SaveType = SaveType
self.SaveFilePath = SaveFilePath
self.logMode = logMode
self.logFile = logFile
self.external = external
self.fileName = fileName
self.delimiter = delimiter
self.consecutiveDelimiter = consecutiveDelimiter
self.MissingValue = MissingValue
self.RejectDisconnectedStrucuture = RejectDisconnectedStrucuture
self.RetainBiggestFragment = RetainBiggestFragment
self.DisconnectedCalculationOption = DisconnectedCalculationOption
self.RoundCoordinates = RoundCoordinates
self.RoundWeights = RoundWeights
self.RoundDescriptorValues = RoundDescriptorValues
self.knimemode = knimemode
def script_wizard(self, script='new', output_directory='./'):
"""
The script_wizard is designed to build a Dragon script file. The name and
the functionality of this function is the same as available Script wizard
in the Dragon Graphic User Interface.
Note: All reported nodes are mandatory, except the <EXTERNAL> tag
Note: Script for version 7 doesn't support fingerprints block
Parameters
----------
script: string, optional (default="new")
If "new" start creating a new script from scratch. If you want to load an existing script,
pass the filename with drs format.
output_directory: string, optional (default = './')
the path to the working directory to store output files.
dragon: xml element
Dragon script in xml format.
drs: string
Dragon script file name
data_path: string
The path+name of saved data file in any format. If saveType is 'block'
or 'subblock' data_path is just the path to the directory that all data
files have been saved.
Returns
-------
class parameters
"""
self.output_directory = output_directory
if not os.path.exists(self.output_directory):
os.makedirs(self.output_directory)
if script == 'new':
if self.version == 6:
self.dragon = objectify.Element(
"DRAGON",
version="%i.0.0" % self.version,
script_version="1",
generation_date=std_datetime_str('date').replace('-', '/'))
OPTIONS = objectify.SubElement(self.dragon, "OPTIONS")
OPTIONS.append(
objectify.Element("CheckUpdates", value=bool_formatter(self.CheckUpdates)))
OPTIONS.append(objectify.Element("SaveLayout", value=bool_formatter(self.SaveLayout)))
OPTIONS.append(
objectify.Element("ShowWorksheet", value=bool_formatter(self.ShowWorksheet)))
OPTIONS.append(objectify.Element("Decimal_Separator", value=self.Decimal_Separator))
OPTIONS.append(objectify.Element("Missing_String", value=self.Missing_String))
OPTIONS.append(objectify.Element("DefaultMolFormat", value=self.DefaultMolFormat))
OPTIONS.append(objectify.Element("HelpBrowser", value=self.HelpBrowser))
OPTIONS.append(
objectify.Element(
"RejectUnusualValence", value=bool_formatter(self.RejectUnusualValence)))
OPTIONS.append(
objectify.Element("Add2DHydrogens", value=bool_formatter(self.Add2DHydrogens)))
OPTIONS.append(objectify.Element("MaxSRforAllCircuit", value=self.MaxSRforAllCircuit))
OPTIONS.append(objectify.Element("MaxSR", value=self.MaxSR))
OPTIONS.append(objectify.Element("MaxSRDetour", value=self.MaxSRDetour))
OPTIONS.append(objectify.Element("MaxAtomWalkPath", value=self.MaxAtomWalkPath))
OPTIONS.append(objectify.Element("LogPathWalk", value=bool_formatter(self.LogPathWalk)))
OPTIONS.append(objectify.Element("LogEdge", value=bool_formatter(self.LogEdge)))
Weights = objectify.SubElement(OPTIONS, "Weights")
for weight in self.Weights:
if weight not in [
"Mass", "VdWVolume", "Electronegativity", "Polarizability", "Ionization",
"I-State"
]:
msg = "'%s' is not a valid weight type." % weight
raise ValueError(msg)
Weights.append(objectify.Element('weight', name=weight))
OPTIONS.append(
objectify.Element("SaveOnlyData", value=bool_formatter(self.SaveOnlyData)))
OPTIONS.append(
objectify.Element(
"SaveLabelsOnSeparateFile", value=bool_formatter(self.SaveLabelsOnSeparateFile)))
OPTIONS.append(objectify.Element("SaveFormatBlock", value=self.SaveFormatBlock))
OPTIONS.append(objectify.Element("SaveFormatSubBlock", value=self.SaveFormatSubBlock))
OPTIONS.append(
objectify.Element("SaveExcludeMisVal", value=bool_formatter(self.SaveExcludeMisVal)))
OPTIONS.append(
objectify.Element(
"SaveExcludeAllMisVal", value=bool_formatter(self.SaveExcludeAllMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeConst", value=bool_formatter(self.SaveExcludeConst)))
OPTIONS.append(
objectify.Element(
"SaveExcludeNearConst", value=bool_formatter(self.SaveExcludeNearConst)))
OPTIONS.append(
objectify.Element("SaveExcludeStdDev", value=bool_formatter(self.SaveExcludeStdDev)))
OPTIONS.append(objectify.Element("SaveStdDevThreshold", value=self.SaveStdDevThreshold))
OPTIONS.append(
objectify.Element(
"SaveExcludeCorrelated", value=bool_formatter(self.SaveExcludeCorrelated)))
OPTIONS.append(objectify.Element("SaveCorrThreshold", value=self.SaveCorrThreshold))
OPTIONS.append(
objectify.Element(
"SaveExclusionOptionsToVariables",
value=bool_formatter(self.SaveExclusionOptionsToVariables)))
OPTIONS.append(
objectify.Element(
"SaveExcludeMisMolecules", value=bool_formatter(self.SaveExcludeMisMolecules)))
OPTIONS.append(
objectify.Element(
"SaveExcludeRejectedMolecules",
value=bool_formatter(self.SaveExcludeRejectedMolecules)))
DESCRIPTORS = objectify.SubElement(self.dragon, "DESCRIPTORS")
for i in self.blocks:
if i < 1 or i > 29:
msg = "block id must be in range 1 to 29."
raise ValueError(msg)
DESCRIPTORS.append(objectify.Element('block', id="%i" % i, SelectAll="true"))
MOLFILES = objectify.SubElement(self.dragon, "MOLFILES")
MOLFILES.append(objectify.Element("molInput", value=self.molInput))
# if self.molInput == "stdin":
# if self.molInputFormat not in ['SYBYL', 'MDL', 'HYPERCHEM', 'SMILES', 'MACROMODEL']:
# msg = "'%s' is not a valid molInputFormat. Formats:['SYBYL','MDL','HYPERCHEM','SMILES','MACROMODEL']" % self.molInputFormat
# raise ValueError(msg)
# MOLFILES.append(objectify.Element("molInputFormat", value=self.molInputFormat))
if self.molInput == "file":
if isinstance(self.molFile, dict):
for f in range(1, len(self.molFile) + 1):
MOLFILES.append(objectify.Element("molFile", value=self.molFile[f]['file']))
elif isinstance(self.molFile, str):
MOLFILES.append(objectify.Element("molFile", value=self.molFile))
else:
msg = 'Variable molInput can be either a string or a list'
raise ValueError(msg)
else:
msg = "The molInput value must be 'file'. 'stdin' is not supported through ChemML"
raise ValueError(msg)
OUTPUT = objectify.SubElement(self.dragon, "OUTPUT")
OUTPUT.append(objectify.Element("SaveStdOut", value=bool_formatter(self.SaveStdOut)))
OUTPUT.append(objectify.Element("SaveProject", value=bool_formatter(self.SaveProject)))
if self.SaveProject:
OUTPUT.append(objectify.Element("SaveProjectFile", value=self.SaveProjectFile))
OUTPUT.append(objectify.Element("SaveFile", value=bool_formatter(self.SaveFile)))
if self.SaveFile:
OUTPUT.append(objectify.Element(
"SaveType", value=self.SaveType)) # value = "[singlefile/block/subblock]"
OUTPUT.append(
objectify.Element(
"SaveFilePath", value=self.output_directory + self.SaveFilePath)
) #Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.
OUTPUT.append(objectify.Element("logMode",
value=self.logMode)) # value = [none/stderr/file]
if self.logMode == "file":
OUTPUT.append(
objectify.Element("logFile", value=self.output_directory + self.logFile))
if self.external:
EXTERNAL = objectify.SubElement(self.dragon, "EXTERNAL")
EXTERNAL.append(objectify.Element("fileName", value=self.fileName))
EXTERNAL.append(objectify.Element("delimiter", value=self.delimiter))
EXTERNAL.append(
objectify.Element(
"consecutiveDelimiter", value=bool_formatter(self.consecutiveDelimiter)))
EXTERNAL.append(objectify.Element("MissingValue", value=self.MissingValue))
self._save_script()
elif self.version == 7:
self.dragon = objectify.Element(
"DRAGON",
version="%i.0.0" % self.version,
description="Dragon7 - FP1 - MD5270",
script_version="1",
generation_date=std_datetime_str('date').replace('-', '/'))
OPTIONS = objectify.SubElement(self.dragon, "OPTIONS")
OPTIONS.append(
objectify.Element("CheckUpdates", value=bool_formatter(self.CheckUpdates)))
OPTIONS.append(
objectify.Element(
"PreserveTemporaryProjects",
value=bool_formatter(self.PreserveTemporaryProjects)))
OPTIONS.append(objectify.Element("SaveLayout", value=bool_formatter(self.SaveLayout)))
# OPTIONS.append(objectify.Element("ShowWorksheet", value = bool_formatter(self.ShowWorksheet)))
OPTIONS.append(objectify.Element("Decimal_Separator", value=self.Decimal_Separator))
if self.Missing_String == "NaN": self.Missing_String = "na"
OPTIONS.append(objectify.Element("Missing_String", value=self.Missing_String))
OPTIONS.append(objectify.Element("DefaultMolFormat", value=self.DefaultMolFormat))
# OPTIONS.append(objectify.Element("HelpBrowser", value = self.HelpBrowser))
OPTIONS.append(
objectify.Element(
"RejectDisconnectedStrucuture",
value=bool_formatter(self.RejectDisconnectedStrucuture)))
OPTIONS.append(
objectify.Element(
"RetainBiggestFragment", value=bool_formatter(self.RetainBiggestFragment)))
OPTIONS.append(
objectify.Element(
"RejectUnusualValence", value=bool_formatter(self.RejectUnusualValence)))
OPTIONS.append(
objectify.Element("Add2DHydrogens", value=bool_formatter(self.Add2DHydrogens)))
OPTIONS.append(
objectify.Element(
"DisconnectedCalculationOption", value=self.DisconnectedCalculationOption))
OPTIONS.append(objectify.Element("MaxSRforAllCircuit", value=self.MaxSRforAllCircuit))
# OPTIONS.appendm(objectify.Element("MaxSR", value = self.MaxSR))
OPTIONS.append(objectify.Element("MaxSRDetour", value=self.MaxSRDetour))
OPTIONS.append(objectify.Element("MaxAtomWalkPath", value=self.MaxAtomWalkPath))
OPTIONS.append(
objectify.Element("RoundCoordinates", value=bool_formatter(self.RoundCoordinates)))
OPTIONS.append(
objectify.Element("RoundWeights", value=bool_formatter(self.RoundWeights)))
OPTIONS.append(objectify.Element("LogPathWalk", value=bool_formatter(self.LogPathWalk)))
OPTIONS.append(objectify.Element("LogEdge", value=bool_formatter(self.LogEdge)))
Weights = objectify.SubElement(OPTIONS, "Weights")
for weight in self.Weights:
if weight not in [
"Mass", "VdWVolume", "Electronegativity", "Polarizability", "Ionization",
"I-State"
]:
msg = "'%s' is not a valid weight type." % weight
raise ValueError(msg)
Weights.append(objectify.Element('weight', name=weight))
OPTIONS.append(
objectify.Element("SaveOnlyData", value=bool_formatter(self.SaveOnlyData)))
OPTIONS.append(
objectify.Element(
"SaveLabelsOnSeparateFile", value=bool_formatter(self.SaveLabelsOnSeparateFile)))
OPTIONS.append(objectify.Element("SaveFormatBlock", value=self.SaveFormatBlock))
OPTIONS.append(objectify.Element("SaveFormatSubBlock", value=self.SaveFormatSubBlock))
OPTIONS.append(
objectify.Element("SaveExcludeMisVal", value=bool_formatter(self.SaveExcludeMisVal)))
OPTIONS.append(
objectify.Element(
"SaveExcludeAllMisVal", value=bool_formatter(self.SaveExcludeAllMisVal)))
OPTIONS.append(
objectify.Element("SaveExcludeConst", value=bool_formatter(self.SaveExcludeConst)))
OPTIONS.append(
objectify.Element(
"SaveExcludeNearConst", value=bool_formatter(self.SaveExcludeNearConst)))
OPTIONS.append(
objectify.Element("SaveExcludeStdDev", value=bool_formatter(self.SaveExcludeStdDev)))
OPTIONS.append(objectify.Element("SaveStdDevThreshold", value=self.SaveStdDevThreshold))
OPTIONS.append(
objectify.Element(
"SaveExcludeCorrelated", value=bool_formatter(self.SaveExcludeCorrelated)))
OPTIONS.append(objectify.Element("SaveCorrThreshold", value=self.SaveCorrThreshold))
OPTIONS.append(
objectify.Element(
"SaveExclusionOptionsToVariables",
value=bool_formatter(self.SaveExclusionOptionsToVariables)))
OPTIONS.append(
objectify.Element(
"SaveExcludeMisMolecules", value=bool_formatter(self.SaveExcludeMisMolecules)))
OPTIONS.append(
objectify.Element(
"SaveExcludeRejectedMolecules",
value=bool_formatter(self.SaveExcludeRejectedMolecules)))
OPTIONS.append(
objectify.Element(
"RoundDescriptorValues", value=bool_formatter(self.RoundDescriptorValues)))
DESCRIPTORS = objectify.SubElement(self.dragon, "DESCRIPTORS")
for i in self.blocks:
if i < 1 or i > 30:
msg = "block id must be in range 1 to 30."
raise ValueError(msg)
DESCRIPTORS.append(objectify.Element('block', id="%i" % i, SelectAll="true"))
MOLFILES = objectify.SubElement(self.dragon, "MOLFILES")
MOLFILES.append(objectify.Element("molInput", value=self.molInput))
# if self.molInput == "stdin":
# if self.molInputFormat not in [
# 'SYBYL', 'MDL', 'HYPERCHEM', 'SMILES', 'CML', 'MACROMODEL'
# ]:
# msg = "'%s' is not a valid molInputFormat. Formats:['SYBYL','MDL','HYPERCHEM','SMILES','CML','MACROMODEL']" % self.molInputFormat
# raise ValueError(msg)
# MOLFILES.append(objectify.Element("molInputFormat", value=self.molInputFormat))
if self.molInput == "file":
if isinstance(self.molFile, dict):
for f in range(1, len(self.molFile) + 1):
MOLFILES.append(objectify.Element("molFile", value=self.molFile[f]['file']))
elif isinstance(self.molFile, str):
MOLFILES.append(objectify.Element("molFile", value=self.molFile))
else:
msg = 'Variable molFile can be either a string or a list'
raise ValueError(msg)
else:
msg = "The molInput value must be 'file'. 'stdin' is not supported through ChemML"
raise ValueError(msg)
OUTPUT = objectify.SubElement(self.dragon, "OUTPUT")
OUTPUT.append(objectify.Element("knimemode", value=bool_formatter(self.knimemode)))
OUTPUT.append(objectify.Element("SaveStdOut", value=bool_formatter(self.SaveStdOut)))
OUTPUT.append(objectify.Element("SaveProject", value=bool_formatter(self.SaveProject)))
if self.SaveProject:
OUTPUT.append(objectify.Element("SaveProjectFile", value=self.SaveProjectFile))
OUTPUT.append(objectify.Element("SaveFile", value=bool_formatter(self.SaveFile)))
if self.SaveFile:
OUTPUT.append(objectify.Element(
"SaveType", value=self.SaveType)) # value = "[singlefile/block/subblock]"
OUTPUT.append(
objectify.Element(
"SaveFilePath", value=self.output_directory + self.SaveFilePath)
) #Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.
OUTPUT.append(objectify.Element("logMode",
value=self.logMode)) # value = [none/stderr/file]
if self.logMode == "file":
OUTPUT.append(
objectify.Element("logFile", value=self.output_directory + self.logFile))
if self.external:
EXTERNAL = objectify.SubElement(self.dragon, "EXTERNAL")
EXTERNAL.append(objectify.Element("fileName", value=self.fileName))
EXTERNAL.append(objectify.Element("delimiter", value=self.delimiter))
EXTERNAL.append(
objectify.Element(
"consecutiveDelimiter", value=bool_formatter(self.consecutiveDelimiter)))
EXTERNAL.append(objectify.Element("MissingValue", value=self.MissingValue))
self._save_script()
else:
doc = etree.parse(script)
self.dragon = etree.tostring(doc) # dragon script : dragon
self.dragon = objectify.fromstring(self.dragon)
objectify.deannotate(self.dragon)
etree.cleanup_namespaces(self.dragon)
if self.dragon.attrib['version'][0] not in ['6', '7']:
msg = "Dragon script is not labeled to the newest vesions of Dragon, 6 or 7. This may causes some problems."
warnings.warn(msg, RuntimeWarning)
mandatory_nodes = ['OPTIONS', 'DESCRIPTORS', 'MOLFILES', 'OUTPUT']
reported_nodes = [element.tag for element in self.dragon.iterchildren()]
if not set(reported_nodes).issuperset(set(mandatory_nodes)):
msg = "Dragon script doesn't contain all required nodes, which are:%s" % str(
mandatory_nodes)
raise ValueError(msg)
self.drs = script
self.data_path = self.dragon.OUTPUT.SaveFilePath.attrib['value']
return self
def _save_script(self):
# objectify.deannotate(self.dragon)
etree.cleanup_namespaces(self.dragon)
self.drs_name = 'Dragon_script.drs'
with open(os.path.join(self.output_directory, self.drs_name), 'w') as outfile:
outfile.write(etree.tostring(self.dragon, pretty_print=True).decode())
def printout(self):
objectify.deannotate(self.dragon)
etree.cleanup_namespaces(self.dragon)
print(objectify.dump(self.dragon))
def run(self):
t0 = time.time()
print("running Dragon%i ..." % self.version)
os_ret = os.system('nohup dragon%sshell -s %s' %
(self.version, os.path.join(self.output_directory, self.drs_name)))
if os_ret != 0:
msg = "Oops, dragon%ishell command didn't work! Are you sure Dragon%i software is installed on your machine?" % (
self.version, self.version)
raise ImportError(msg)
# execution time
tmp_str = tot_exec_time_str(t0)
print("... Dragon job completed in %s"%tmp_str)
# print subprocess.check_output(['nohup dragon%sshell -s %s'%(self.version,self.drs)])
def convert_to_csv(self, remove=True):
"""
This function converts the tab-delimited txt file from Dragon to pandas dataframe.
Note that this process might require large memory based on the number of data points and features.
Parameters
----------
remove: bool, optional (default = True)
if True, the original descriptors file (Dragon_descriptors.txt) will be removed.
Returns
-------
pandas.DataFrame
The 2D dataframe of the descriptors. Note that the first two columns are 'No.' and 'NAME'.
"""
# convert to csv file
t0 = time.time()
print("converting output file to csv format ...")
df = pd.read_csv(self.data_path, sep=None, engine='python')
# df = df.drop(['No.', 'NAME'], axis=1)
# execution time
tmp_str = tot_exec_time_str(t0)
# remove original tab delimited file
if remove:
os.remove(self.data_path)
self.data_path = None
print("... conversion completed in %s"%tmp_str)
return df
