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add command line input
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Patrick Li committed Jun 20, 2024
1 parent cebe7b5 commit 0cb7acb
Showing 1 changed file with 133 additions and 57 deletions.
190 changes: 133 additions & 57 deletions autosolvate/multicomponent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -248,66 +248,142 @@ def build(self):
docker.run(system)

def startmulticomponent(argumentList):
# options = "hm:s:o:c:b:a:t:l:p:"
# long_options = ["help", "pdb_prefix", "solvent", "output", "totalcharge",
# "cubesize", "amberhome","closeness","solventoff","solventfrcmod"]
# arguments, values = getopt.getopt(argumentList, options, long_options)
r"""
Wrap function that parses command line options for autosolvate multicomponent module,
generate solvent box and related force field parameters.
Parameters
----------
argumentList: list
The list contains the command line options to specify solute, solvent, and other options
related to structure and force field parameter generation.
Command line option definitions
-m, --main solute xyz file
-s, --solvent name of solvent (water, methanol, chloroform, nma)
-o, --output prefix of the output file names
-c, --charge formal charge of solute
-u, --spinmultiplicity spin multiplicity of solute
-g, --chargemethod name of charge fitting method (bcc, resp)
-b, --cubesize size of solvent cube in angstroms
-r, --srunuse option to run inside a slurm job
-e, --gaussianexe name of the Gaussian quantum chemistry package executable used to generate electrostatic potential needed for RESP charge fitting
-d, --gaussiandir path to the Gaussian package
-a, --amberhome path to the AMBER molecular dynamics package root directory. Definition of the environment variable $AMBERHOME
-t, --closeness Solute-solvent closeness setting, for acetonitrile tolerance parameter in packmol in Å, for water, methanol, nma, chloroform the scaling factor in tleap, setting to 'automated' will automatically set this parameter based on solvent.
-l, --solventoff path to the custom solvent .off library file. Required if the user want to use some custom solvent other than the 5 solvents contained in AutoSolvate (TIP3P water, methanol, NMA, chloroform, MeCN)
-p, --solventfrcmod path to the custom solvent .frcmod file. Required if the user wants to use some custom solvent other than the 5 solvents contained in AutoSolvate.
-h, --help short usage description
Returns
-------
None
Generates the structure files and save as ```.pdb```. Generates the MD parameter-topology and coordinates files and saves as ```.prmtop``` and ```.inpcrd```
"""
#print(argumentList)
options = "hm:s:o:c:b:g:u:re:d:a:t:l:p:"
long_options = ["help", "main", "solvent", "output", "charge", "cubesize", "chargemethod", "spinmultiplicity", "srunuse","gaussianexe", "gaussiandir", "amberhome", "closeness","solventoff","solventfrcmod"]
arguments, values = getopt.getopt(argumentList, options, long_options)
solutexyz=""
solvent='water'
slu_netcharge=0
cube_size=54
charge_method="bcc"
slu_spinmult=1
outputFile=""
srun_use=False
amberhome=None
gaussianexe=None
gaussiandir=None
closeness=0.8
solvent_off=""
solvent_frcmod=""
#print(arguments)
#print(values)
for currentArgument, currentValue in arguments:
if currentArgument in ("-h", "--help"):
print('Usage: autosolvate boxgen [OPTIONS]')
print(' -m, --main solute xyz file')
print(' -s, --solvent_lists solvent xyz files, separated by slash. (ex. water.pdb/acetonitrile.pdb)')
# print(' -o, --output prefix of the output file names') # not currently supporting this option
print(' -c, --charge formal charge of solute')
print(' -u, --spinmultiplicity spin multiplicity of solute')
print(' -g, --chargemethod name of charge fitting method (bcc, resp)') # currently only support bcc
print(' -b, --cubesize size of solvent cube in angstroms')
# print(' -r, --srunuse option to run inside a slurm job') # not currently supporting this option
# print(' -e, --gaussianexe name of the Gaussian quantum chemistry package executable') # not currently supporting gaussian
# print(' -d, --gaussiandir path to the Gaussian package') # not currently supporting gaussian
# print(' -a, --amberhome path to the AMBER molecular dynamics package root directory') # not currently supporting amberhome
print(' -t, --closeness Solute-solvent closeness setting')
# print(' -l, --solventoff path to the custom solvent .off library file') # not currently supporting this option
# print(' -p, --solventfrcmod path to the custom solvent .frcmod file') # not currently supporting this option
print(' -h, --help short usage description')
exit()
elif currentArgument in ("-m", "--main"):
print ("Main/solutexyz", currentValue)
solutexyz=str(currentValue)
elif currentArgument in ("-s", "--solvent"):
print ("Solvent:", currentValue)
solvent=str(currentValue)
elif currentArgument in ("-o", "--output"):
print ("Output:", currentValue)
outputFile=str(currentValue)
elif currentArgument in ("-c", "--charge"):
print ("Charge:", currentValue)
slu_netcharge=int(currentValue)
elif currentArgument in ("-b", "--cubesize"):
print ("Cubesize:", currentValue)
cube_size=float(currentValue)
elif currentArgument in ("-g", "--chargemethod"):
print ("Chargemethod:", currentValue)
charge_method=str(currentValue)
elif currentArgument in ("-u", "--spinmultiplicity"):
print ("Spinmultiplicity:", currentValue)
slu_spinmult=int(currentValue)
elif currentArgument in ("-r", "--srunuse"):
print("usign srun")
srun_use=True
elif currentArgument in ("-e","--gaussianexe"):
print("Gaussian executable name:", currentValue)
gaussianexe = currentValue
elif currentArgument in ("-d","--gaussiandir"):
print("Gaussian package directory:", currentValue)
gaussiandir = currentValue
elif currentArgument in ("-a","--amberhome"):
print("Amber home directory:", currentValue)
amberhome = currentValue
elif currentArgument in ("-t", "--closeness"):
print("Solute-Solvente closeness parameter", currentValue)
closeness = currentValue
elif currentArgument in ("-l", "--solventoff"):
print("Custom solvent .off library path:", currentValue)
solvent_off = currentValue
elif currentArgument in ("-p", "--solventfrcmod"):
print("Custom solvent .frcmmod file path:", currentValue)
solvent_frcmod = currentValue

# pdb_prefix= ''
# totalcharge='Default'
# solvent = "water"
# solvent_frcmod = ""
# solvent_off = ""
# slv_count = 210*8
# cube_size = 54
# closeness = "automated"
# outputFile = ""
# amberhome = '$AMBERHOME/bin/'
# for currentArgument, currentValue in arguments:
# if currentArgument in ("-h", "--help"):
# print('Usage: autosolvate_metal boxgen [OPTIONS]')
# print(' -m, --pdb_prefix prefix of pdb file name not include _mcpb')
# print(' -s, --solvent name of solvent')
# print(' -o, --output prefix of the output file names')
# print(' -c, --charge formal charge of solute')
# print(' -b, --cubesize size of solvent cube in angstroms')
# print(' -a, --amberhome path to the AMBER molecular dynamics package root directory')
# print(' -t, --closeness Solute-solvent closeness setting')
# print(' -l, --solventoff path to the custom solvent .off library file')
# print(' -p, --solventfrcmod path to the custom solvent .frcmod file')
# print(' -h, --help short usage description')
# exit()
# elif currentArgument in ('-m','-pdb_prefix'):
# pdb_prefix = str(currentValue)
# elif currentArgument in ("-s", "--solvent"):
# solvent=str(currentValue)
# elif currentArgument in ("-o", "--output"):
# print ("Output:", currentValue)
# outputFile=str(currentValue)
# elif currentArgument in ("-c", "--charge"):
# print ("Charge:", currentValue)
# totalcharge=str(currentValue)
# elif currentArgument in ("-b", "--cubesize"):
# print ("Cubesize:", currentValue)
# cube_size=float(currentValue)
# elif currentArgument in ("-a","--amberhome"):
# print("Amber home directory:", currentValue)
# amberhome = currentValue
# elif currentArgument in ("-t", "--closeness"):
# print("Solute-Solvente closeness parameter", currentValue)
# closeness = currentValue
# elif currentArgument in ("-l", "--solventoff"):
# print("Custom solvent .off library path:", currentValue)
# solvent_off = currentValue
# elif currentArgument in ("-p", "`````--solventfrcmod"):
# print("Custom solvent .frcmmod file path:", currentValue)
# solvent_frcmod = currentValue
print('DEBUGGING MULTICOMPONENT')
if solutexyz == "":
print("Error! Solute xyzfile must be provided!\nExiting...")
exit()
elif not os.path.exists(solutexyz):
print("Error! Solute xyzfile path ", solutexyz, " does not exist!\nExiting...")
exit()

try:
_, ext = os.path.splitext(solutexyz)
pybel.readfile(ext[1:], solutexyz).__next__()
except:
print("Error! Solute structure file format issue!")
print(solutexyz," cannot be opened with openbabel.\n Exiting...")
exit()

global WORKING_DIR
WORKING_DIR = os.getcwd()

builder = MixtureBuilder()
builder.add_solute('naphthalene_neutral.xyz')
builder.add_solvent('acetonitrile.pdb')
builder.add_solvent('water.pdb')
builder.add_solute(solutexyz, charge=slu_netcharge, spinmult=slu_spinmult)
for s in solvent.split("/"):
builder.add_solvent(s)
builder.build()


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