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recipes.py
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recipes.py
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"""This module describes the commandline or python commands for all the
phases of pymemdyn. It consists of:
- Init
- Minimization
- Equilibration
- Relaxation
- Collecting results
"""
import os
import protein
class BasicInit(object):
def __init__(self, **kwargs):
# First we make a list of ordered steps
self.steps = ["pdb2gmx", "set_itp", "clean_itp", "concat", "set_protein_height", "editconf",
"set_protein_size", "editconf2", "set_protein_size2",
"set_popc", "editconf3", "editconf4", "make_topol",
"editconf5", "solvate", "set_protein_height2", "set_water",
"editconf6", "editconf7", "editconf8",
"solvate2", "count_lipids", "make_topol2",
"make_topol_lipids", "make_ffoplsaanb", "set_grompp",
"set_chains", "make_ndx", "grompp", "trjconv",
"get_charge", "genion", "grompp2", "trjconv2",
"grompp3", "trjconv3", "clean_pdb"]
# And then we define each step
self.recipe = \
{"pdb2gmx": {"gromacs": "pdb2gmx", # 1
"options": {"src": "",
"tgt": "proteinopls.pdb",
"top": "protein.top"}},
"set_itp": {"command": "set_itp", # 2
"options": {"src": "protein.top",
"tgt": "protein.itp"}},
"clean_itp": {"command": "clean_itp",
"options": {"src_files": []}},
"concat": {"command": "concat", # 3
"options": {"src": "proteinopls.pdb",
"tgt": ""}},
"set_protein_height": {"command": "set_protein_height", # 4
"options": {"src": "proteinopls.pdb"}},
"editconf": {"gromacs": "editconf", # 5
"options": {"src": "proteinopls.pdb",
"tgt": "proteinopls.pdb",
"dist": ""}},
"set_protein_size": {"command": "set_protein_size", # 6
"options": {"src": "proteinopls.pdb",
"dir": "xy"}},
"editconf2": {"gromacs": "editconf", # 7
"options": {"src": "proteinopls.pdb",
"tgt": "proteinopls.pdb",
"dist": ""}},
"set_protein_size2": {"command": "set_protein_size", # 8
"options": {"src": "proteinopls.pdb",
"dir": "z"}},
"set_popc": {"command": "set_popc", # 9
"options": {"tgt": "popc.pdb"}},
"editconf3": {"gromacs": "editconf", # 10
"options": {"src": "proteinopls.pdb",
"tgt": "proteinopls.pdb",
"box": "",
"angles": ["90", "90", "120"],
"bt": "tric"}},
"editconf4": {"gromacs": "editconf", # 11
"options": {"src": "popc.pdb",
"tgt": "popc.gro",
"box": ""}},
"make_topol": {"command": "make_topol", # 12
"options": {}},
"editconf5": {"gromacs": "editconf", # 13
"options": {"src": "proteinopls.pdb",
"tgt": "proteinopls.pdb",
"translate_z": ""}},
"solvate": {"gromacs": "solvate", # 14
"options": {"cp": "proteinopls.pdb",
"cs": "popc.gro",
"tgt": "protpopc.pdb",
"top": "topol.top"}},
"set_protein_height2": {"command": "set_protein_height", # 15
"options": {"src": "protpopc.pdb",
"solvate2": "True"}},
"set_water": {"command": "set_water", # 16
"options": {"tgt": "water.pdb"}},
"editconf6": {"gromacs": "editconf", # 17
"options": {"src": "water.pdb",
"tgt": "water.gro",
"box": ""}},
"editconf7": {"gromacs": "editconf", # 18
"options": {"src": "protpopc.pdb",
"tgt": "protpopc.pdb",
"box": "",
"angles": ["90", "90", "120"],
"bt": "tric"}},
"editconf8": {"gromacs": "editconf", # 19
"options": {"src": "protpopc.pdb",
"tgt": "protpopc.pdb",
"translate_z": ""}},
"solvate2": {"gromacs": "solvate", # 20
"options": {"cp": "protpopc.pdb",
"cs": "water.gro",
"tgt": "tmp.pdb",
"top": "topol.top"}},
"count_lipids": {"command": "count_lipids", # 21
"options": {"src": "tmp.pdb",
"tgt": "popc.pdb"}},
"make_topol2": {"command": "make_topol", # 22
"options": {}},
"make_topol_lipids": {"command": "make_topol_lipids"}, # 23
"make_ffoplsaanb": {"command": "make_ffoplsaanb", # 24
"options": {}},
"set_grompp": {"command": "set_grompp", # 25
"options": {"steep.mdp": "steep.mdp",
"popc.itp": "popc.itp",
"spc.itp": "spc.itp",
"ions.itp": "ions.itp",
"ffoplsaabon_mod.itp": "ffoplsaabon_mod.itp",
"ffoplsaa_mod.itp": "ffoplsaa_mod.itp"}},
"set_chains": {"command": "set_chains", # 26
"options": {"src": "proteinopls.pdb"}},
"make_ndx": {"command": "make_ndx", # 27
"options": {"src": "tmp.pdb",
"tgt": "index.ndx"}},
"grompp": {"gromacs": "grompp", # 28
"options": {"src": "steep.mdp",
"src2": "tmp.pdb",
"tgt": "topol.tpr",
"top": "topol.top",
"index": "index.ndx"}},
"trjconv": {"gromacs": "trjconv", # 29
"options": {"src": "tmp.pdb",
"src2": "topol.tpr",
"tgt": "tmp.pdb",
"pbc": "mol",
"index": "index.ndx"},
"input": "1\n0\n"},
"get_charge": {"command": "get_charge", # 30
"options": {"src": "steep.mdp",
"src2": "tmp.pdb",
"tgt": "topol.tpr",
"top": "topol.top",
"index": "index.ndx"}},
"genion": {"gromacs": "genion", # 31
"options": {"src": "topol.tpr",
"tgt": "output.pdb",
"src2": "topol.top",
"index": "index.ndx",
"np": "",
"nn": ""},
"input": " SOL \n"},
"grompp2": {"gromacs": "grompp", # 32
"options": {"src": "steep.mdp",
"src2": "output.pdb",
"tgt": "topol.tpr",
"top": "topol.top"}},
"trjconv2": {"gromacs": "trjconv", # 33
"options": {"src": "output.pdb",
"src2": "topol.tpr",
"tgt": "output.pdb",
"trans": [],
"pbc": "mol"},
"input": "0\n"},
"grompp3": {"gromacs": "grompp", # 34
"options": {"src": "steep.mdp",
"src2": "output.pdb",
"tgt": "topol.tpr",
"top": "topol.top"}},
"trjconv3": {"gromacs": "trjconv", # 35
"options": {"src": "output.pdb",
"src2": "topol.tpr",
"tgt": "hexagon.pdb",
"ur": "compact",
"pbc": "mol"},
"input": "1\n0\n"},
"clean_pdb": {"command": "clean_pdb", # 36
"options": {"src": "hexagon.pdb",
"tgt": "hexagon.pdb"}}
}
self.breaks = \
{"pdb2gmx": {"src": "membrane_complex.complex.proteins.pdb_his"},
"concat": {"tgt": "membrane_complex.complex"},
"editconf": {"dist": "membrane_complex.box_height"},
"editconf2": {"dist": "membrane_complex.box_width"},
"editconf3": {"box": "membrane_complex.trans_box_size"},
"editconf4": {"box": "membrane_complex.bilayer_box_size"},
"editconf5": {"translate_z": "membrane_complex.complex.center_z"},
"editconf6": {"box": "membrane_complex.embeded_box_size"},
"editconf7": {"box": "membrane_complex.protein_box_size"},
"editconf8": {"translate_z": "membrane_complex.complex.center_z"},
"genion": {"nn": "membrane_complex.complex.positive_charge",
"np": "membrane_complex.complex.negative_charge"},
"make_topol": {"complex": "membrane_complex.complex"},
"make_topol2": {"complex": "membrane_complex.complex"},
"make_ffoplsaanb": {"complex": "membrane_complex.complex"},
"trjconv2": {"trans": "membrane_complex.complex.trans"}
}
if kwargs["membrane_complex"].proteins.chains:
for chain in kwargs["membrane_complex"].proteins.chains:
self.recipe["clean_itp"]["options"]["src_files"].append(
f"protein_Protein_chain_{chain}.itp")
if kwargs["debugFast"] or False:
self.recipe["set_grompp"]["options"]["steep.mdp"] = "steepDEBUG.mdp"
# This recipe modifies the previous one taking ligands into account
class LigandInit(BasicInit):
def __init__(self, **kwargs):
super(LigandInit, self).__init__(**kwargs)
if kwargs["membrane_complex"]:
for var, value in vars(kwargs["membrane_complex"]).items():
if isinstance(value, protein.Ligand):
self.steps.insert(9, f"genrestr_{var}")
self.recipe[f"genrestr_{var}"] = \
{"gromacs": "genrestr",
"options": {"src": "",
"tgt": f"posre_{var}.itp",
"index": f"ligand_{var}_ha.ndx",
"forces": ["1000", "1000", "1000"]},
"input": "3\n"}
self.steps.insert(9, f"make_ndx_{var}")
self.recipe[f"make_ndx_{var}"] = \
{"gromacs": "make_ndx",
"options": {"src": "",
"tgt": f"ligand_{var}_ha.ndx",
var: True},
"input": "! a H*\nq\n"}
self.breaks[f"make_ndx_{var}"] = \
{"src": f"membrane_complex.complex.{var}.pdb"}
self.breaks[f"genrestr_{var}"] = \
{"src": f"membrane_complex.complex.{var}.pdb"}
##########################################################################
# Minimization #
##########################################################################
class BasicMinimization(object):
def __init__(self, **kwargs):
self.steps = ["set_stage_init", "mdrun"]
self.recipe = {
"set_stage_init": {"command": "set_stage_init", # 1
"options": {"src_dir": "",
"src_files": ["topol.tpr"],
"tgt_dir": "Rmin",
"repo_files": ["steep.mdp"]}},
"mdrun": {"gromacs": "mdrun", # 2
"options": {"dir": "Rmin",
"src": "topol.tpr",
"tgt": "traj.trj",
"energy": "ener.edr",
"conf": "confout.gro",
"log": "md.log"}},
}
self.breaks = {}
if kwargs["debugFast"] or False:
self.recipe["set_stage_init"]["options"]["repo_files"] = \
["eqDEBUG.mdp"]
##########################################################################
# Equilibration #
##########################################################################
class BasicEquilibration(object):
def __init__(self, **kwargs):
self.steps = ["clean_itp", "editconf", "make_ndx", "set_grompp", "set_stage_init", "grompp",
"set_stage_init2", "mdrun"]
self.recipe = {
"clean_itp": {"command": "clean_itp",
"options": {"src_files": ["protein.itp"]}},
"editconf": {"gromacs": "editconf", # 1
"options": {"src": "Rmin/confout.gro",
"tgt": "min.pdb"}},
"make_ndx": {"command": "make_ndx", # 2
"options": {"src": "min.pdb",
"tgt": "index.ndx"}},
"set_grompp": {"command": "set_grompp", # 3
"options": {"eq.mdp": "eq.mdp"}},
"set_stage_init": {"command": "set_stage_init", # 4
"options": {"src_dir": "",
"src_files": ["eq.mdp"],
"tgt_dir": "eq"}},
"grompp": {"gromacs": "grompp", # 5
"options": {"src": "eq.mdp",
"src2": "min.pdb",
"top": "topol.top",
"tgt": "topol.tpr",
"tgt_top": "eq/processed.top", # DEBUGGING
"index": "index.ndx"}},
"set_stage_init2": {"command": "set_stage_init", # 6
"options": {"src_dir": "",
"src_files": ["topol.tpr",
"posre.itp"],
"tgt_dir": "eq"}},
"mdrun": {"gromacs": "mdrun", # 7
"options": {"dir": "eq",
"src": "topol.tpr",
"tgt": "traj.trr",
"energy": "ener.edr",
"conf": "confout1000.gro",
"traj": "traj.xtc",
"log": "md_eq1000.log"}},
}
self.breaks = {}
if kwargs["membrane_complex"].proteins.chains:
for chain in kwargs["membrane_complex"].proteins.chains:
self.recipe["set_stage_init2"]["options"]["src_files"].append(
f"posre_Protein_chain_{chain}.itp")
if kwargs["membrane_complex"]:
for var, value in vars(kwargs["membrane_complex"]).items():
if isinstance(value, protein.Ligand) or isinstance(value, protein.CrystalWaters) or isinstance(value, protein.Ions):
self.recipe["set_stage_init2"]["options"]["src_files"].append(
f"posre_{var}.itp")
if kwargs["debugFast"] or False:
self.recipe["grompp"]["options"]["src"] = "Rmin/eqDEBUG.mdp"
self.recipe["set_stage_init"]["options"]["src_files"] = \
["eqDEBUG.mdp"]
#class LigandEquilibration(BasicEquilibration):
# def __init__(self, **kwargs):
# super(LigandEquilibration, self).__init__(**kwargs)
# if kwargs["membrane_complex"]:
# for var, value in vars(kwargs["membrane_complex"]).items():
# if isinstance(value, protein.Ligand):
# self.steps.insert(2, "genrestr")
# self.recipe["genrestr"] = \
# {"gromacs": "genrestr",
# "options": {"src": "Rmin/topol.tpr",
# "tgt": "protein_ca200.itp",
# "index": "index.ndx",
# "forces": ["200", "200", "200"]},
# "input": "3\n"}
##########################################################################
# Relaxation #
##########################################################################
class BasicRelax(object):
def __init__(self, **kwargs):
self.steps = []
self.recipe = {}
for const in range(800, 0, -200):
self.steps.extend(["relax{0}".format(const),
"set_stage_init{0}".format(const),
"grompp{0}".format(const),
"mdrun{0}".format(const)])
tgt_dir = "eq/{0}".format(const)
src_dir = "eq"
self.recipe["relax%d" % const] = \
{"command": "relax", # 1, 4, 7, 10
"options": {"const": const,
"src_dir": src_dir,
"tgt_dir": tgt_dir,
"posres": [],
"mdp": "eq.mdp"}}
self.recipe["set_stage_init%d" % const] = \
{"command": "set_stage_init", # 4
"options": {"src_dir": "",
"src_files": ["topol.top",
"ffoplsaa_mod.itp",
"ffoplsaanb_mod.itp",
"ffoplsaabon_mod.itp",
"protein.itp",
"popc.itp",
"ions.itp",
"spc.itp"],
"tgt_dir": "eq/{0}".format(const)}}
self.recipe["grompp%d" % const] = \
{"gromacs": "grompp", # 2, 5, 8, 11
"options": {"src": os.path.join(tgt_dir, "eq{0}.mdp".format(const)),
"src2": os.path.join(src_dir, "confout{0}.gro".format(const+200)),
"top": os.path.join(tgt_dir, "topol.top"),
"tgt": os.path.join(tgt_dir, "topol.tpr"),
"tgt_top": os.path.join(tgt_dir, "processed.top"), # DEBUGGING
"index": "index.ndx"}}
self.recipe["mdrun%d" % const] = \
{"gromacs": "mdrun", # 3, 6, 9, 12
"options": {"dir": tgt_dir,
"src": "topol.tpr",
"tgt": "traj.trr",
"energy": "ener.edr",
"conf": "../confout{0}.gro".format(const),
"traj": "traj.xtc",
"log": "md_eq{0}.log".format(const)}}
for chain in kwargs["membrane_complex"].proteins.chains:
self.recipe[f"set_stage_init{const}"]["options"]["src_files"].append(f"protein_Protein_chain_{chain}.itp")
for var, value in vars(kwargs["membrane_complex"]).items():
if isinstance(value, protein.Ligand) or isinstance(value, protein.CrystalWaters) or isinstance(value, protein.Ions):
self.recipe[f"relax{const}"]["options"]["posres"].append(f"posre_{var}.itp")
self.recipe[f"set_stage_init{const}"]["options"]["src_files"].append(f"{var}.itp")
# TODO: add section for copying .itp for oligomers (posre is handled in relax)
self.breaks = {}
if kwargs["debugFast"] or False:
for i in [x for x in self.recipe.keys() if x.startswith("relax")]:
self.recipe[i]["options"]["mdp"] = "eqDEBUG.mdp"
# class LigandRelax(BasicRelax):
# def __init__(self, **kwargs):
# super(LigandRelax, self).__init__(**kwargs)
# if kwargs["membrane_complex"]:
# for var, value in vars(kwargs["membrane_complex"]).items():
# if isinstance(value, protein.Ligand):
# self.recipe["relax800"]["options"]["posres"].append(f"posre_{var}.itp")
##########################################################################
# C-Alpha Atoms Relaxation #
##########################################################################
class BasicCARelax(object):
def __init__(self, **kwargs):
self.steps = ["set_stage_init", "set_stage_init2", "restrain_ca", "grompp", "mdrun"]
self.recipe = {
"set_stage_init": {"command": "set_stage_init", # 1
"options": {"src_dir": "eq",
"tgt_dir": "eqProd",
"src_files": ["confout200.gro"],
"repo_files": ["eqCA.mdp"]}},
"set_stage_init2": {"command": "set_stage_init", # 1
"options": {"src_dir": "eq/200",
"tgt_dir": "eqProd",
"src_files": ["topol.top",
"ffoplsaa_mod.itp",
"ffoplsaanb_mod.itp",
"ffoplsaabon_mod.itp",
"protein.itp",
"posre.itp",
"popc.itp",
"ions.itp",
"spc.itp"]}},
"restrain_ca": {"command": "restrain_ca",
"options": {"src_files": ["eqProd/posre.itp"],
"index": "index.ndx"}},
# "genrestr": {"gromacs": "genrestr", # 2
# "options": {"src": "Rmin/topol.tpr",
# "tgt": "posre.itp",
# "index": "index.ndx",
# "forces": ["200"] * 3},
# "input": "3\n"},
"grompp": {"gromacs": "grompp", # 3
"options": {"src": "eqProd/eqCA.mdp",
"src2": "eqProd/confout200.gro",
"top": "eqProd/topol.top",
"tgt": "eqProd/topol.tpr",
"tgt_top": "eqProd/processed.top", # DEBUGGING
"index": "index.ndx"}},
"mdrun": {"gromacs": "mdrun", # 4
"options": {"dir": "eqProd",
"src": "topol.tpr",
"tgt": "traj.trr",
"energy": "ener.edr",
"conf": "confout.gro",
"traj": "traj.xtc",
"log": "md_eqProd.log"}},
}
self.breaks = {}
for chain in kwargs["membrane_complex"].proteins.chains:
self.recipe[f"set_stage_init2"]["options"]["src_files"].extend([f"protein_Protein_chain_{chain}.itp", f"posre_Protein_chain_{chain}.itp"])
self.recipe[f"restrain_ca"]["options"]["src_files"].extend([f"eqProd/posre_Protein_chain_{chain}.itp"])
for var, value in vars(kwargs["membrane_complex"]).items():
if isinstance(value, protein.Ligand) or isinstance(value, protein.CrystalWaters) or isinstance(value, protein.Ions):
self.recipe[f"set_stage_init2"]["options"]["src_files"].extend([f"{var}.itp", f"posre_{var}.itp"])
if kwargs["debugFast"] or False:
self.recipe["set_stage_init"]["options"]["src_files"] = \
["confout.gro", "eqDEBUG.mdp"]
self.recipe["grompp"]["options"]["src"] = "eqProd/eqDEBUG.mdp"
if kwargs["full_relax"] != True:
self.steps.remove("mdrun")
##########################################################################
# Ballesteros-Weinstein Restrained Relaxation #
##########################################################################
class BasicBWRelax(object):
def __init__(self, **kwargs):
self.steps = ["getbw","set_stage_init", "grompp", "mdrun"]
self.recipe = {
"getbw": {"command": "getbw", # 1
"options": {"src": "proteinopls.pdb"}},
"set_stage_init": {"command": "set_stage_init", # 2
"options": {"src_dir": "eq",
"tgt_dir": "eqProd",
"src_files": ["confout200.gro",
"../disre.itp"],
"repo_files": ["dres.mdp"]}},
"grompp": {"gromacs": "grompp", # 3
"options": {"src": "eqProd/dres.mdp",
"src2": "eqProd/confout200.gro",
"top": "topol.top",
"tgt": "eqProd/topol.tpr",
"tgt_top": "eqProd/processed.top", # DEBUGGING
"index": "index.ndx"}},
"mdrun": {"gromacs": "mdrun", # 4
"options": {"dir": "eqProd",
"src": "topol.tpr",
"tgt": "traj.trr",
"energy": "ener.edr",
"conf": "confout.gro",
"traj": "traj.xtc",
"log": "md_eqBW.log"}},
}
self.breaks = {}
if kwargs["debugFast"] or False:
self.recipe["set_stage_init"]["options"]["src_files"] = \
["confout.gro", "eqDEBUG.mdp"]
self.recipe["grompp"]["options"]["src"] = "eqProd/eqDEBUG.mdp"
if kwargs["full_relax"] != True:
self.steps.remove("mdrun")
##########################################################################
# Collect All Results & Output #
##########################################################################
class BasicCollectResults(object):
def __init__(self, **kwargs):
"""
This recipe navigates through the output of *GROMACS*, generating and
collecting various files and logs, and finally putting it all together
in a tar file.
Provides a list of *steps* as the order to execute the recipe.
dict *recipe* as the variables to pass to functions.
dict *breaks* as points where object calling can put their vars.
"""
self.breaks = {}
self.steps = ["trjcat", "trjconv", "rms1", "rms2",
"rms3", "rmsf", "tot_ener", "temp", "pressure",
"volume", "set_stage_init", "grompp",
"set_end", "set_end_2", "set_end_3",
"set_end_4", "set_end_5", "set_end_6",
"tar_it"]
self.recipe = {"trjcat":
{"gromacs": "trjcat", # 1
"options": {"dir1": "eq",
"dir2": "eqProd",
"name": "traj.xtc",
"tgt": "traj_EQ.xtc"},
"input": "c\n" * 6},
"trjconv":
{"gromacs": "trjconv", # 2
"options": {"src": "traj_EQ.xtc",
"src2": "topol.tpr",
"tgt": "traj_pymol.xtc",
"ur": "compact",
"skip": "2",
"pbc": "mol"},
"input": "1\n0\n"},
"rms1":
{"gromacs": "rms", # 4
"options": {"src": "eq/topol.tpr",
"src2": "traj_EQ.xtc",
"tgt": "rmsd-all-atom-vs-start.xvg"},
"input": "1\n1\n"},
"rms2":
{"gromacs": "rms", # 5
"options": {"src": "eq/topol.tpr",
"src2": "traj_EQ.xtc",
"tgt": "rmsd-backbone-vs-start.xvg"},
"input": "4\n4\n"},
"rms3":
{"gromacs": "rms", # 6
"options": {"src": "eq/topol.tpr",
"src2": "traj_EQ.xtc",
"tgt": "rmsd-calpha-vs-start.xvg"},
"input": "3\n3\n"},
"rmsf":
{"gromacs": "rmsf", # 7
"options": {"src": "eq/topol.tpr",
"src2": "traj_EQ.xtc",
"tgt": "rmsf-per-residue.xvg"},
"input": "1\n"},
"set_stage_init": {"command": "set_stage_init", # 2
"options": {"tgt_dir": ".",
"repo_files": ["prod.mdp"]}},
"grompp": {"gromacs": "grompp", # 3
"options": {"src": "prod.mdp",
"src2": "eq/confout200.gro",
"top": "topol.top",
"tgt": "topol.tpr",
"tgt_top": "prod.top", # DEBUGGING
"index": "index.ndx"}},
"set_end":
{"command": "set_stage_init", # 12
"options": {"src_dir": "eqProd",
"src_files": ["confout.gro",
"processed.top",
"dres.mdp",
"eqCA.mdp"],
"repo_files": ["prod.mdp",
"README.md",
"load_gpcr.pml"],
"tgt_dir": "finalOutput"}},
"set_end_2":
{"command": "set_stage_init", # 14
"options": {"src_dir": "",
"src_files": [
"log.log",
"hexagon.pdb",
"index.ndx",
"traj_EQ.xtc",
"ener_EQ.edr",
"traj_pymol.xtc",
"prod.top"],
"tgt_dir": "finalOutput"}},
"set_end_3":
{"command": "set_stage_init", # 15
"options": {"src_dir": "",
"src_files": ["tot_ener.xvg",
"tot_ener.log",
"temp.xvg",
"temp.log",
"pressure.xvg",
"pressure.log",
"volume.xvg",
"volume.log",
"rmsd-all-atom-vs-start.xvg",
"rmsd-calpha-vs-start.xvg",
"rmsd-backbone-vs-start.xvg",
"rmsf-per-residue.xvg"],
"tgt_dir": "finalOutput/reports"}},
"set_end_4":
{"command": "set_stage_init", # 16
"options": {"src_dir": "eq",
"src_files": ["md_eq1000.log",
"confout1000.gro",
"confout800.gro",
"confout600.gro",
"confout400.gro",
"confout200.gro",],
"tgt_dir": "finalOutput/logs"}},
"set_end_5":
{"command": "set_stage_init", # 17
"options": {"src_dir": "eq",
"src_files": [
"{0}/md_eq{0}.log".format(
const)
for const in
range(800, 0, -200)],
"tgt_dir": "finalOutput/logs"}},
"set_end_6":
{"command": "set_stage_init", # 18
"options": {"src_dir": "eqProd",
"src_files": ["md_eqBW.log",
"md_eqCA.log"],
"tgt_dir": "finalOutput/logs"}},
"tar_it":
{"command": "tar_out", # 19
"options": {"src_dir": "finalOutput",
"tgt": "MD_output.tgz"}},
}
options = {"tot_ener": "Total-Energy\n",
"temp": "Temperature\n",
"pressure": "Pressure\n",
"volume": "Volume\n"} # 8 to 11
for option, gro_key in options.items():
self.recipe[option] = \
{"gromacs": "energy",
"options": {"src": "ener_EQ.edr",
"tgt": "{0}.xvg".format(option),
"log": "{0}.log".format(option)},
"input": gro_key}
if kwargs["full_relax"] != True:
self.recipe["trjcat"]["options"]["dir2"] = ""
self.steps.remove("set_stage_init")
self.steps.remove("grompp")
class BasicCACollectResults(BasicCollectResults):
def __init__(self, **kwargs):
super(BasicCACollectResults, self).__init__(**kwargs)
self.steps.insert(2, "eneconv")
self.recipe["eneconv"] = \
{"gromacs": "eneconv",
"options": {"dir1": "eq",
"dir2": "eqProd",
"name": "ener.edr",
"tgt": "ener_EQ.edr"},
"input": "y\nc\nc\nc\nc\nc\nc\n"}
class BasicBWCollectResults(BasicCollectResults):
def __init__(self, **kwargs):
super(BasicBWCollectResults, self).__init__(**kwargs)
self.steps.insert(14, "set_end_BW")
self.recipe["set_end_BW"] = \
{"command": "set_stage_init",
"options": {"src_dir": "",
"src_files": ["tot_ener2.xvg",
"tot_ener2.log",
"temp2.xvg",
"temp2.log",
"pressure2.xvg",
"pressure2.log",
"volume2.xvg",
"volume2.log"],
"tgt_dir": "finalOutput/reports"}}
self.steps.insert(10, "volume2")
self.steps.insert(10, "pressure2")
self.steps.insert(10, "temp2")
self.steps.insert(10, "tot_ener2")
options2 = {"tot_ener2": "Total-Energy\n",
"temp2": "Temperature\n",
"pressure2": "Pressure\n",
"volume2": "Volume\n"}
for option, gro_key in options2.items():
self.recipe[option] = \
{"gromacs": "energy",
"options": {"src": "eqProd/ener.edr",
"tgt": "{0}.xvg".format(option),
"log": "{0}.log".format(option)},
"input": gro_key}
self.steps.insert(2, "eneconv")
self.recipe["eneconv"] = \
{"gromacs": "eneconv",
"options": {"dir1": "eq",
"dir2": "",
"name": "ener.edr",
"tgt": "ener_EQ.edr"},
"input": "y\nc\nc\nc\nc\nc\nc\n"}