Enum (class) – inherits from Enum class
-bondcycle_collective Check to see if, when considered as a collective, this -set of bondrecs leads to one or more cyclic bondchain; if so, longest bonds that +set of bondrecs leads to one or more cyclic bondchains; if so, longest bonds that break bondcycles are removed from bondrecs list and resulting list is returned
bdf (pandas.DataFrame) – bonds data frame
+bdf (pandas.DataFrame) – bonds data frame, sorted in ascending order by bondlength
list of bond records that results in no new bondcycles
@@ -4706,26 +4701,6 @@makes_bondcycle checks the current ‘bondchain’ index lists to see if a bond between aidx and bidx (global atom indices) would generate a C-C’ bondcycle, which they do if they have the same ‘bondchain’ attribute, shorter than the minimum allowable bondcycle length, if this is not -1
-aidx (int) – global index of an atom
bidx (int) – global index of another atom
True if a bond betwen aidx and bidx would form a C-C’ bondcycle
-bool
-
self.bond_templates:BondTemplateList=[]
self.symmetry_relateds=[]
self.stereocenters=[] # list of atomnames
- self.stereoisomers:dict(str,Molecule)={}
+ self.stereoisomers={}
self.nconformers=0
self.conformers_dict={}
self.conformers=[] # just a list of gro file basenames
@@ -1013,7 +1013,7 @@ Source code for HTPolyNet.molecule
overall_maximum=(-1.e9,-1,-1)
coord_trials={}
for myH,myHnm in myHpartners.items(): # keys are globalIdx's, values are names
- coord_trials[myH]:dict[TopoCoord]={}
+ coord_trials[myH]={}
Rh=TC.get_R(myH)
logger.debug(f' Rh {myH} {Rh} {Rh.dtype}')
Rih=Ri-Rh
diff --git a/_modules/HTPolyNet/software.html b/_modules/HTPolyNet/software.html
index f6ebafd..3131cad 100644
--- a/_modules/HTPolyNet/software.html
+++ b/_modules/HTPolyNet/software.html
@@ -42,7 +42,6 @@ Source code for HTPolyNet.software
import logging
import os
from HTPolyNet.stringthings import my_logger
-# from GPUtil import getGPUs
logger=logging.getLogger(__name__)
diff --git a/_modules/HTPolyNet/topocoord.html b/_modules/HTPolyNet/topocoord.html
index 8e99e82..5f8def1 100644
--- a/_modules/HTPolyNet/topocoord.html
+++ b/_modules/HTPolyNet/topocoord.html
@@ -53,6 +53,7 @@ Source code for HTPolyNet.topocoord
from HTPolyNet.matrix4 import Matrix4
from HTPolyNet.gromacs import grompp_and_mdrun,mdp_get, mdp_modify, gmx_energy_trace
import HTPolyNet.projectfilesystem as pfs
+# import HTPolyNet.polybonds as pb
logger=logging.getLogger(__name__)
@@ -65,9 +66,9 @@ Source code for HTPolyNet.topocoord
:type Enum: class
"""
passed = 0
- failed_pierced_ring = 1 # does this bond-candidate pierce a ring?
- failed_shortcircuit = 2 # does this bond-candidate result in short-circuit?
- failed_bondcycle = 3 # does this bond-candidate create a bondcycle on its own?
+ failed_pierced_ring = 1 # candidate bond pierces a ring
+ failed_shortcircuit = 2 # candidate bond creates a short-circuit
+ # failed_bondcycle = 3 # Bondcycles are handled collectively
unset = 99
@@ -102,6 +103,7 @@ Source code for HTPolyNet.topocoord
self.grxattr=[]
self.idx_lists={}
self.idx_lists['bondchain']=[]
+ # self.polybondchainmanager=pb.PolyBondChainManager()
if grofilename!='':
self.read_gro(grofilename,wrap_coords=wrap_coords)
else:
@@ -1463,8 +1465,8 @@ Source code for HTPolyNet.topocoord
# j=int(j)
if self.makes_shortcircuit(i,j):
return BTRC.failed_shortcircuit,0
- if self.makes_bondcycle(i,j):
- return BTRC.failed_bondcycle,0
+ # if self.makes_bondcycle(i,j):
+ # return BTRC.failed_bondcycle,0
if self.pierces_ring(i,j,pbc=pbc,show_piercings=show_piercings):
return BTRC.failed_pierced_ring,0
# logger.debug(f'passed: {i:>7d} {j:>7d} {rij:>6.3f} nm')
@@ -1699,89 +1701,150 @@ Source code for HTPolyNet.topocoord
# logger.debug(f'post {msg} chains {self.idx_lists["bondchain"]} {cnms}')
-
-[docs]
- def makes_bondcycle(self,aidx,bidx):
- """makes_bondcycle checks the current 'bondchain' index lists to see if a bond between aidx and bidx (global atom indices) would generate a C-C' bondcycle, which they do if they have the same 'bondchain' attribute, shorter than the minimum allowable bondcycle length, if this is not -1
-
- :param aidx: global index of an atom
- :type aidx: int
- :param bidx: global index of another atom
- :type bidx: int
- :return: True if a bond betwen aidx and bidx would form a C-C' bondcycle
- :rtype: bool
- """
- # is there a bondchain with aidx as head and bidx as tail, or vice versa?
- for c in self.idx_lists['bondchain']:
- if (aidx==c[0] and bidx==c[-1]) or (aidx==c[-1] and bidx==c[0]):
- if self.min_bondcycle_length==-1 or len(c)<self.min_bondcycle_length:
- return True
- return False
+ # def makes_bondcycle(self,aidx,bidx):
+ # """makes_bondcycle checks the current 'bondchain' index lists to see if a bond between aidx and bidx (global atom indices) would generate a C-C' bondcycle, which they do if they have the same 'bondchain' attribute, shorter than the minimum allowable bondcycle length, if this is not 0
+ # :param aidx: global index of an atom
+ # :type aidx: int
+ # :param bidx: global index of another atom
+ # :type bidx: int
+ # :return: True if a bond betwen aidx and bidx would form a C-C' bondcycle
+ # :rtype: bool
+ # """
+ # # is there a bondchain with aidx as head and bidx as tail, or vice versa?
+ # for c in self.idx_lists['bondchain']:
+ # if (aidx==c[0] and bidx==c[-1]) or (aidx==c[-1] and bidx==c[0]):
+ # if self.min_bondcycle_length<=0 or len(c)<self.min_bondcycle_length:
+ # return True
+ # return False
[docs]
def bondcycle_collective(self,bdf:pd.DataFrame):
"""bondcycle_collective Check to see if, when considered as a collective, this
- set of bondrecs leads to one or more cyclic bondchain; if so, longest bonds that
+ set of bondrecs leads to one or more cyclic bondchains; if so, longest bonds that
break bondcycles are removed from bondrecs list and resulting list is returned
- :param bdf: bonds data frame
+ :param bdf: bonds data frame, sorted in ascending order by bondlength
:type bdf: pandas.DataFrame
:return: list of bond records that results in no new bondcycles
:rtype: list
"""
- def addlink(chainlist,i,j):
- i_cidx=(-1,-1)
- j_cidx=(-1,-1)
- for cidx,c in enumerate(chainlist):
- if i in c:
- i_cidx=(cidx,c.index(i))
- if j in c:
- j_cidx=(cidx,c.index(j))
- logger.debug(f'i {i_cidx} j {j_cidx}')
- if not (i_cidx==(-1,-1) or (j_cidx==(-1,-1))):
- # logger.debug(f'bondcycle_collective: {i} is in bondchain {i_cidx[0]} at {i_cidx[1]}')
- # logger.debug(f'bondcycle_collective: {j} is in bondchain {j_cidx[0]} at {j_cidx[1]}')
- if i_cidx[0]==j_cidx[0]:
- # cyclized!
- logger.debug(f'bondchain {i_cidx[0]} is cyclized!')
- return i_cidx[0],True
- old_head,old_tail=(i_cidx,j_cidx) if i_cidx[1]==0 else (j_cidx,i_cidx)
- chainlist[old_tail[0]].extend(chainlist[old_head[0]])
- # logger.debug(f'new bondchain {old_tail[0]} {chainlist[old_tail[0]]}')
- chainlist.remove(chainlist[old_head[0]])
- return old_tail[0],False
- else: # this bond involves one atom in a bondchain and another that is not; no way this can be a cyclization, but we have to return somthing
- return i_cidx[0] if i_cidx[0]!=-1 else j_cidx[0],False
-
- # kb=bondrecs.copy()
- # logger.debug(f'checking set of {bdf.shape[0]} bonds for nascent cycles')
+ class working_bondlist:
+ def __init__(self,my_idx,idx_list):
+ self.idx=my_idx
+ self.atidx_list=idx_list
+ self.added_bonds=[]
+ self.is_new_cycle=False
+ def idx_of(self,ai):
+ return self.atidx_list.index(ai)
+ def is_head(self,ai):
+ return self.idx_of(ai)==0
+ def len(self):
+ return len(self.atidx_list)
+ def is_tail(self,ai):
+ return self.idx_of(ai)==self.len()-1
+ def addbond(self,bidx):
+ self.added_bonds.append(bidx)
+ def cycletag(self):
+ self.is_new_cycle=True
+ def merge(self,other):
+ self.atidx_list.extend(other.atidx_list)
+ other.atidx_list=[]
+ self.added_bonds.extend(other.added_bonds)
+ other.added_bonds=[]
+ other.absorber=self
+
+ def addlink(bondchains,b_idx,ai,aj):
+ ibl=None
+ jbl=None
+ for bl in bondchains:
+ if ai in bl.idx_list:
+ ibl=bl
+ if aj in bl.idx_list:
+ jbl=bl
+ if not ibl or not jbl:
+ # must not be a system that can form bondchains
+ return
+ logger.debug(f'i-atom {ai} is in bondchain {ibl.idx} (length {len(ibl)}) at index {ibl.idx_of(ai)}')
+ logger.debug(f'j-atom {aj} is in bondchain {jbl.idx} (length {len(jbl)}) at index {jbl.idx_of(aj)}')
+ if ibl==jbl:
+ # same bondchain
+ assert (ibl.is_head(ai) and ibl.is_tail(aj)) or (ibl.is_tail(ai) and ibl.is_head(aj))
+ ibl.cycletag()
+ ibl.addbond(b_idx)
+ logger.debug(f'bondchain {ibl.idx} is cyclized!')
+ # return dict(makescycle=True,cyclizedchain=i_cidx["bondchainidx"])
+ # otherwise, we unify the two bondchains
+ # case 1: atom i is the head of its bondchain
+ else:
+ if ibl.is_head(ai):
+ assert jbl.is_tail(aj)
+ jbl.addbond(b_idx)
+ jbl.merge(ibl)
+ else:
+ assert ibl.is_tail(ai) and jbl.is_head(aj)
+ ibl.addbond(b_idx)
+ ibl.merge(jbl)
+
+ logger.debug(f'Checking set of {bdf.shape[0]} bonds for C-C bondcycles')
new_bdf=bdf.copy()
new_bdf['remove-to-uncyclize']=[False for _ in range(new_bdf.shape[0])]
- chains=deepcopy(self.idx_lists['bondchain'])
- assert id(chains) != id(self.idx_lists['bondchain'])
- if not chains:
+ if len(self.idx_lists['bondchain'])==0:
return new_bdf
- cyclized_chains={}
- chains_of_bonds=[]
- for i,r in bdf.iterrows():
- chain_idx,cyclized=addlink(chains,r.ai,r.aj)
- # logger.debug(f'bond {i} {r.ai}-{r.aj} ({r.reactantName}) adds to bondchain {chain_idx}')
- chains_of_bonds.append(chain_idx)
- if cyclized and not chain_idx in cyclized_chains:
- cyclized_chains[chain_idx]=[]
- assert len(chains_of_bonds)==bdf.shape[0]
+ # make a working copy of the bondchains structure from its snapshot
+ bondchains=[working_bondlist(i,self.idx_lists['bondchain'][i]) for i in range(len(self.idx_lists['bondchain']))]
+ # add links to placeholder bondchain structure one at a time and note any cyclization that occurs along the way
for i,r in bdf.iterrows():
- # logger.debug(f'compiling bonds of cyclized chains: bond {i}')
- cidx=chains_of_bonds[i]
- # logger.debug(f'compiling bonds of cyclized chains: cidx {chains_of_bonds[i]}')
- if cidx in cyclized_chains:
- cyclized_chains[cidx].append(i)
- for k,v in cyclized_chains.items():
- if self.min_bondcycle_length==-1 or len(v)<self.min_bondcycle_length:
- lb=v[-1] # last bondrec in list
- new_bdf.loc[lb,'remove-to-uncyclize']=True
+ addlink(bondchains,i,r.ai,r.aj)
+ for bl in bondchains:
+ if bl.is_new_cycle:
+ logger.debug(f'Bondchain {bl.idx} ({"-".join([str(x) for x in bl.atidx_list])}) is a new cycle')
+ logger.debug(f'-> Cycle length is {bl.len()} reacted C=C bonds')
+ if self.min_bondcycle_length<=0 or bl.len()<self.min_bondcycle_length:
+ longest_bond_index=max(bl.added_bonds) # remember, bdf is sorted by bondlength
+ logger.debug(f'-> limit is {self.min_bondcycle_length}, so we will break the longest added bond')
+ logger.debug(f'-> bond index {longest_bond_index} is the longest added bond in the cycle')
+ new_bdf.loc[longest_bond_index,'remove-to-uncyclize']=True
+
+ # if rdict.get('makescycle',False):
+ # chains_of_bonds[i]=rdict["cyclizedchain"]
+ # cyclized_chains.append(rdict["cyclizedchain"])
+ # else:
+ # if rdict.get('retainedchain',-1)>-1:
+ # # a chain merger happened
+ # chains_of_bonds[i]=rdict["retainedchain"]
+ # for k in chains_of_bonds.keys():
+ # if chains_of_bonds[k]==rdict["removedchain"]:
+ # chains_of_bonds[k]=rdict["retainedchain"]
+ # else:
+ # # no chain merger happened; do nothing
+ # pass
+ # # for each bondcycle, identify the new bonds that collectively cause the cyclization
+ # cyclizing_bonds={}
+ # for k,v in chains_of_bonds.items():
+ # if v in cyclized_chains:
+ # if not v in cyclizing_bonds:
+ # cyclizing_bonds[v]=[]
+ # cyclizing_bonds[v].append(k)
+
+ # for cycleidx,newbonds in cyclizing_bonds.items():
+ # cyclelength=len(chains[cycleidx])
+ # # # logger.debug(f'bond {i} {r.ai}-{r.aj} ({r.reactantName}) adds to bondchain {chain_idx}')
+ # # chains_of_bonds.append(chain_idx)
+ # # if cyclized and not chain_idx in cyclized_chains:
+ # # cyclized_chains[chain_idx]=[]
+ # # assert len(chains_of_bonds)==bdf.shape[0]
+ # for i,r in bdf.iterrows():
+ # # logger.debug(f'compiling bonds of cyclized chains: bond {i}')
+ # cidx=chains_of_bonds[i]
+ # # logger.debug(f'compiling bonds of cyclized chains: cidx {chains_of_bonds[i]}')
+ # if cidx in cyclized_chains:
+ # cyclized_chains[cidx].append(i)
+ # for k,v in cyclized_chains.items():
+ # if self.min_bondcycle_length<=0 or len(v)<self.min_bondcycle_length:
+ # lb=v[-1] # last bondrec in list
+ # new_bdf.loc[lb,'remove-to-uncyclize']=True
return new_bdf
diff --git a/genindex.html b/genindex.html
index 279705b..c1d9568 100644
--- a/genindex.html
+++ b/genindex.html
@@ -539,8 +539,6 @@ E
F
- finished (HTPolyNet.curecontroller.cure_step attribute)
- flip_stereocenters() (HTPolyNet.molecule.Molecule method)
@@ -1067,8 +1065,6 @@
M
- (HTPolyNet.topology.Topology method)
- - makes_bondcycle() (HTPolyNet.topocoord.TopoCoord method)
-
- makes_shortcircuit() (HTPolyNet.topocoord.TopoCoord method)
- map_from_templates() (HTPolyNet.topocoord.TopoCoord method)
diff --git a/objects.inv b/objects.inv
index 0995ebf..d2e51b9 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 0b920fc..1c53a30 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["HTPolyNetPackage", "example-tutorials/index", "example-tutorials/postsim_analyses/index", "example-tutorials/shortbuilds/1-polymethylstyrene/configuration", "example-tutorials/shortbuilds/1-polymethylstyrene/index", "example-tutorials/shortbuilds/1-polymethylstyrene/introduction", "example-tutorials/shortbuilds/1-polymethylstyrene/monomer", "example-tutorials/shortbuilds/1-polymethylstyrene/reactions", "example-tutorials/shortbuilds/1-polymethylstyrene/results", "example-tutorials/shortbuilds/1-polymethylstyrene/run", "example-tutorials/shortbuilds/2-DGEBA-PACM/configuration", "example-tutorials/shortbuilds/2-DGEBA-PACM/index", "example-tutorials/shortbuilds/2-DGEBA-PACM/introduction", "example-tutorials/shortbuilds/2-DGEBA-PACM/monomers", "example-tutorials/shortbuilds/2-DGEBA-PACM/reactions", "example-tutorials/shortbuilds/2-DGEBA-PACM/results", "example-tutorials/shortbuilds/2-DGEBA-PACM/run", "example-tutorials/shortbuilds/3-VE-STY/configuration", "example-tutorials/shortbuilds/3-VE-STY/index", "example-tutorials/shortbuilds/3-VE-STY/introduction", "example-tutorials/shortbuilds/3-VE-STY/reactions", "example-tutorials/shortbuilds/3-VE-STY/results", "example-tutorials/shortbuilds/3-VE-STY/run", "example-tutorials/shortbuilds/index", "index", "install", "references/index", "user-guide/configs/configs-for-analyze", "user-guide/configs/configs-for-postsim", "user-guide/configs/configs-for-run", "user-guide/configuration-files", "user-guide/index", "user-guide/molecular-structure-inputs", "user-guide/program-flow", "user-guide/usage"], "filenames": ["HTPolyNetPackage.rst", "example-tutorials/index.rst", "example-tutorials/postsim_analyses/index.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/configuration.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/index.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/introduction.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/monomer.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/reactions.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/results.rst", "example-tutorials/shortbuilds/1-polymethylstyrene/run.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/configuration.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/index.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/introduction.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/monomers.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/reactions.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/results.rst", "example-tutorials/shortbuilds/2-DGEBA-PACM/run.rst", "example-tutorials/shortbuilds/3-VE-STY/configuration.rst", "example-tutorials/shortbuilds/3-VE-STY/index.rst", "example-tutorials/shortbuilds/3-VE-STY/introduction.rst", "example-tutorials/shortbuilds/3-VE-STY/reactions.rst", "example-tutorials/shortbuilds/3-VE-STY/results.rst", "example-tutorials/shortbuilds/3-VE-STY/run.rst", "example-tutorials/shortbuilds/index.rst", "index.rst", "install.rst", "references/index.rst", "user-guide/configs/configs-for-analyze.rst", "user-guide/configs/configs-for-postsim.rst", "user-guide/configs/configs-for-run.rst", "user-guide/configuration-files.rst", "user-guide/index.rst", "user-guide/molecular-structure-inputs.rst", "user-guide/program-flow.rst", "user-guide/usage.rst"], "titles": ["HTPolyNet package", "Example Tutorials", "Examples Using
htpolynet postsim and analyze", "The Configuration File", "Poly(4-methyl styrene)", "Introduction", "Monomer: 4-methylstyrene", "Reactions", "Results", "Running the Build", "The Configuration File", "DGEBA-PACM Thermoset", "Introduction", "Monomers", "Reactions", "Results", "Running the Build", "The Configuration File", "BisGMA-Styrene Thermoset", "Introduction", "Reactions", "Results", "Running the Build", "Examples Using htpolynet run", "HTPolyNet", "Installation and Prerequisites", "References", "Configuration Files for htpolynet analyze", "Configuration Files for htpolynet postsim", "Configuration Files for htpolynet run", "Configuration Files", "User Guide", "Molecular Structure Inputs", "Program Flow", "Usage"], "terms": {"driver": [0, 5, 12], "cli": 0, "sourc": [0, 25, 34], "command": [0, 2, 5, 6, 8, 9, 12, 13, 16, 19, 21, 22, 24, 25, 27, 28, 29, 32, 34], "line": [0, 2, 8, 13, 15, 21, 24, 27, 29, 34], "interfac": [0, 27, 28, 34], "fetch_exampl": 0, "arg": [0, 9], "handl": [0, 9, 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"proj-0-plots"]], "Running the Build": [[9, "running-the-build"], [16, "running-the-build"], [22, "running-the-build"]], "Console output": [[9, "console-output"]], "A Note About FutureWarnings": [[9, "a-note-about-futurewarnings"]], "DGEBA-PACM Thermoset": [[11, "dgeba-pacm-thermoset"]], "Monomers": [[13, "monomers"]], "DGEBA": [[13, "dgeba"]], "PACM": [[13, "pacm"]], "BisGMA-Styrene Thermoset": [[18, "bisgma-styrene-thermoset"]], "Building bisGMA": [[20, "building-bisgma"]], "Cure reactions": [[20, "cure-reactions"]], "Monomer-monomer reactions in the bisGMA/styrene system": [[20, "id4"]], "Examples Using htpolynet run": [[23, "examples-using-htpolynet-run"]], "HTPolyNet": [[24, "htpolynet"]], "Citation": [[24, "citation"]], "Indices and tables": [[24, "indices-and-tables"]], "Installation and Prerequisites": [[25, "installation-and-prerequisites"]], "Software Prequisites": [[25, "software-prequisites"]], "Installation": [[25, "installation"]], "Notes": [[25, "notes"]], "Compilation of AmberTools": [[25, "compilation-of-ambertools"]], "Compilation of Gromacs": [[25, "compilation-of-gromacs"]], "Compilation of obabel": [[25, "compilation-of-obabel"]], "Other Prequisites": [[25, "other-prequisites"]], "References": [[26, "references"]], "Cited Works": [[26, "cited-works"]], "Other Reference Material": [[26, "other-reference-material"]], "Configuration Files for htpolynet analyze": [[27, "configuration-files-for-htpolynet-analyze"]], "Simple examples": [[27, "simple-examples"]], "Shortcut analyses": [[27, "shortcut-analyses"]], "Configuration Files for htpolynet postsim": [[28, "configuration-files-for-htpolynet-postsim"]], "Configuration Files for htpolynet run": [[29, "configuration-files-for-htpolynet-run"]], "All the details": [[29, "all-the-details"]], "A Simple Configuration Example: Polymerizing styrene": [[29, "a-simple-configuration-example-polymerizing-styrene"]], "Configuration Files": [[30, "configuration-files"]], "By type:": [[30, null]], "User Guide": [[31, "user-guide"]], "Molecular Structure Inputs": [[32, "molecular-structure-inputs"]], "Program Flow": [[33, "program-flow"]], "The Connect-Update-Relax-Equilibrate (CURE) algorithm": [[33, "the-connect-update-relax-equilibrate-cure-algorithm"]], "Identifying allowable bonds: Bondsearch filters": [[33, "bondsearch-filters"]], "Usage": [[34, "usage"]], "Typical Usage": [[34, "typical-usage"]], "The HTPolyNet Directory Structure": [[34, "the-htpolynet-directory-structure"]], "HTPolyNet Subcommand Summaries": [[34, "htpolynet-subcommand-summaries"]], "htpolynet run": [[34, "htpolynet-run"]], "htpolynet parameterize": [[34, "htpolynet-parameterize"]], "htpolynet info": [[34, "htpolynet-info"]], "htpolynet plots": [[34, "htpolynet-plots"]], "htpolynet fetch-example": [[34, "htpolynet-fetch-example"]], "htpolynet input-check": [[34, "htpolynet-input-check"]], "htpolynet postsim": [[34, "htpolynet-postsim"]], "htpolynet analyze": [[34, "htpolynet-analyze"]]}, "indexentries": {"analyze (class in htpolynet.analyze)": [[0, "HTPolyNet.analyze.Analyze"]], "analyzeconfiguration (class in htpolynet.analyze)": [[0, "HTPolyNet.analyze.AnalyzeConfiguration"]], "analyzedensity (class in htpolynet.analyze)": [[0, "HTPolyNet.analyze.AnalyzeDensity"]], "analyzeffv (class in htpolynet.analyze)": [[0, "HTPolyNet.analyze.AnalyzeFFV"]], "btrc (class in htpolynet.topocoord)": [[0, "HTPolyNet.topocoord.BTRC"]], "bondtemplate (class in htpolynet.bondtemplate)": [[0, "HTPolyNet.bondtemplate.BondTemplate"]], "bondlist (class in htpolynet.bondlist)": [[0, "HTPolyNet.bondlist.Bondlist"]], "checkpoint (class in htpolynet.checkpoint)": [[0, "HTPolyNet.checkpoint.Checkpoint"]], "command (class in htpolynet.command)": [[0, "HTPolyNet.command.Command"]], "configuration (class in htpolynet.configuration)": [[0, "HTPolyNet.configuration.Configuration"]], "coordinates (class in htpolynet.coordinates)": [[0, "HTPolyNet.coordinates.Coordinates"]], "curecontroller (class in htpolynet.curecontroller)": [[0, "HTPolyNet.curecontroller.CureController"]], "curestate (class in htpolynet.curecontroller)": [[0, "HTPolyNet.curecontroller.CureState"]], "gaffparameterize() (in module htpolynet.ambertools)": [[0, "HTPolyNet.ambertools.GAFFParameterize"]], "grx_attributes (in module htpolynet.coordinates)": [[0, "HTPolyNet.coordinates.GRX_ATTRIBUTES"]], "htpolynet.ambertools": [[0, "module-HTPolyNet.ambertools"]], "htpolynet.analyze": [[0, "module-HTPolyNet.analyze"]], "htpolynet.banner": [[0, "module-HTPolyNet.banner"]], "htpolynet.bondlist": [[0, "module-HTPolyNet.bondlist"]], "htpolynet.bondtemplate": [[0, "module-HTPolyNet.bondtemplate"]], "htpolynet.checkpoint": [[0, "module-HTPolyNet.checkpoint"]], "htpolynet.command": [[0, "module-HTPolyNet.command"]], "htpolynet.configuration": [[0, "module-HTPolyNet.configuration"]], "htpolynet.coordinates": [[0, "module-HTPolyNet.coordinates"]], "htpolynet.counttime": [[0, "module-HTPolyNet.countTime"]], "htpolynet.curecontroller": [[0, "module-HTPolyNet.curecontroller"]], "htpolynet.dataframetools": [[0, "module-HTPolyNet.dataframetools"]], "htpolynet.driver": [[0, "module-HTPolyNet.driver"]], "htpolynet.expandreactions": [[0, "module-HTPolyNet.expandreactions"]], "htpolynet.gromacs": [[0, "module-HTPolyNet.gromacs"]], "htpolynet.inputcheck": [[0, "module-HTPolyNet.inputcheck"]], "htpolynet.linkcell": [[0, "module-HTPolyNet.linkcell"]], "htpolynet.matrix4": [[0, "module-HTPolyNet.matrix4"]], "htpolynet.molecule": [[0, "module-HTPolyNet.molecule"]], "htpolynet.plot": [[0, "module-HTPolyNet.plot"]], "htpolynet.postsim": [[0, "module-HTPolyNet.postsim"]], "htpolynet.projectfilesystem": [[0, "module-HTPolyNet.projectfilesystem"]], "htpolynet.reaction": [[0, "module-HTPolyNet.reaction"]], "htpolynet.ring": [[0, "module-HTPolyNet.ring"]], "htpolynet.runtime": [[0, "module-HTPolyNet.runtime"]], "htpolynet.software": [[0, "module-HTPolyNet.software"]], "htpolynet.stringthings": [[0, "module-HTPolyNet.stringthings"]], "htpolynet.topocoord": [[0, "module-HTPolyNet.topocoord"]], "htpolynet.topology": [[0, "module-HTPolyNet.topology"]], "htpolynet.unused_symmetry_stuff": [[0, "module-HTPolyNet.unused_symmetry_stuff"]], "htpolynet.utils": [[0, "module-HTPolyNet.utils"]], "linkcell (class in htpolynet.linkcell)": [[0, "HTPolyNet.linkcell.Linkcell"]], "matrix4 (class in htpolynet.matrix4)": [[0, "HTPolyNet.matrix4.Matrix4"]], "molecule (class in htpolynet.molecule)": [[0, "HTPolyNet.molecule.Molecule"]], "new() (htpolynet.molecule.molecule class method)": [[0, "HTPolyNet.molecule.Molecule.New"]], "newmolecule() (htpolynet.configuration.configuration method)": [[0, "HTPolyNet.configuration.Configuration.NewMolecule"]], "postsimanneal (class in htpolynet.postsim)": [[0, "HTPolyNet.postsim.PostSimAnneal"]], "postsimdeform (class in htpolynet.postsim)": [[0, "HTPolyNet.postsim.PostSimDeform"]], "postsimladder (class in htpolynet.postsim)": [[0, "HTPolyNet.postsim.PostSimLadder"]], "postsimmd (class in htpolynet.postsim)": [[0, "HTPolyNet.postsim.PostSimMD"]], "postsimconfiguration (class in htpolynet.postsim)": [[0, "HTPolyNet.postsim.PostsimConfiguration"]], "projectfilesystem (class in htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.ProjectFileSystem"]], "reaction (class in htpolynet.reaction)": [[0, "HTPolyNet.reaction.Reaction"]], "reactionbond (class in htpolynet.bondtemplate)": [[0, "HTPolyNet.bondtemplate.ReactionBond"]], "ring (class in htpolynet.ring)": [[0, "HTPolyNet.ring.Ring"]], "ringlist (class in htpolynet.ring)": [[0, "HTPolyNet.ring.RingList"]], "runtime (class in htpolynet.runtime)": [[0, "HTPolyNet.runtime.Runtime"]], "runtimelibrary (class in htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary"]], "segment (class in htpolynet.ring)": [[0, "HTPolyNet.ring.Segment"]], "software (class in htpolynet.software)": [[0, "HTPolyNet.software.Software"]], "title (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.Title"]], "topocoord (class in htpolynet.topocoord)": [[0, "HTPolyNet.topocoord.TopoCoord"]], "topology (class in htpolynet.topology)": [[0, "HTPolyNet.topology.Topology"]], "add_bonds() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.add_bonds"]], "add_enumerated_angles() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.add_enumerated_angles"]], "add_enumerated_dihedrals() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.add_enumerated_dihedrals"]], "add_length_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.add_length_attribute"]], "add_length_attribute() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.add_length_attribute"]], "add_restraints() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.add_restraints"]], "add_restraints() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.add_restraints"]], "adjacency_matrix() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.adjacency_matrix"]], "adjust_charges() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.adjust_charges"]], "adjust_charges() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.adjust_charges"]], "all_atoms() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.all_atoms"]], "allowed_keys (htpolynet.analyze.analyze attribute)": [[0, "HTPolyNet.analyze.Analyze.allowed_keys"]], "ambertools": [[0, "module-ambertools"]], "ambertools (htpolynet.software.software attribute)": [[0, "HTPolyNet.software.Software.ambertools"]], "analyze": [[0, "module-analyze"]], "analyze() (in module htpolynet.analyze)": [[0, "HTPolyNet.analyze.analyze"]], "analyze_sea() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.analyze_sea"]], "append() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.append"]], "are_bonded() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.are_bonded"]], "are_bonded() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.are_bonded"]], "are_cellndx_neighbors() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.are_cellndx_neighbors"]], "are_ldx_neighbors() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.are_ldx_neighbors"]], "as_list() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.as_list"]], "atom_count() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.atom_count"]], "atomcount() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.atomcount"]], "atomcount() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.atomcount"]], "atoms_w_same_attribute_as() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.atoms_w_same_attribute_as"]], "attenuate_bond_parameters() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.attenuate_bond_parameters"]], "attenuate_bond_parameters() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.attenuate_bond_parameters"]], "attenuate_pair_parameters() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.attenuate_pair_parameters"]], "attenuate_pair_parameters() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.attenuate_pair_parameters"]], "banner": [[0, "module-banner"]], "banner() (in module htpolynet.banner)": [[0, "HTPolyNet.banner.banner"]], "basename() (htpolynet.curecontroller.cure_step method)": [[0, "HTPolyNet.curecontroller.cure_step.basename"]], "bond_source_check() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.bond_source_check"]], "bondchain_expand_reactions() (in module htpolynet.expandreactions)": [[0, "HTPolyNet.expandreactions.bondchain_expand_reactions"]], "bondchainlist_update() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.bondchainlist_update"]], "bondcycle_collective() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.bondcycle_collective"]], "bondlist": [[0, "module-bondlist"]], "bondtemplate": [[0, "module-bondtemplate"]], "bondtest() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.bondtest"]], "bondtest_df() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.bondtest_df"]], "build (htpolynet.reaction.reaction_stage attribute)": [[0, "HTPolyNet.reaction.reaction_stage.build"]], "build_interresidue_graph() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.build_interresidue_graph"]], "build_mdp() (htpolynet.postsim.postsimanneal method)": [[0, "HTPolyNet.postsim.PostSimAnneal.build_mdp"]], "build_mdp() (htpolynet.postsim.postsimdeform method)": [[0, "HTPolyNet.postsim.PostSimDeform.build_mdp"]], "build_mdp() (htpolynet.postsim.postsimladder method)": [[0, "HTPolyNet.postsim.PostSimLadder.build_mdp"]], "build_mdp() (htpolynet.postsim.postsimmd method)": [[0, "HTPolyNet.postsim.PostSimMD.build_mdp"]], "build_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.build_plots"]], "calculate_maximum_conversion() (htpolynet.configuration.configuration method)": [[0, "HTPolyNet.configuration.Configuration.calculate_maximum_conversion"]], "cap (htpolynet.reaction.reaction_stage attribute)": [[0, "HTPolyNet.reaction.reaction_stage.cap"]], "cap_bondsearch (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cap_bondsearch"]], "cap_equilibrate (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cap_equilibrate"]], "cap_relax 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"HTPolyNet.topocoord.TopoCoord.center_coords"]], "cfg (htpolynet.runtime.runtime attribute)": [[0, "HTPolyNet.runtime.Runtime.cfg"]], "check_your_topology() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.check_your_topology"]], "checkbox() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.checkbox"]], "checkbox() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.checkbox"]], "checkin() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.checkin"]], "checkin() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.checkin"]], "checkout() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.checkout"]], "checkout() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.checkout"]], "checkpoint": [[0, "module-checkpoint"]], "claim_parent() 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"HTPolyNet.curecontroller.cure_step.cure_bondsearch"]], "cure_drag (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_drag"]], "cure_equilibrate (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_equilibrate"]], "cure_relax (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_relax"]], "cure_step (class in htpolynet.curecontroller)": [[0, "HTPolyNet.curecontroller.cure_step"]], "cure_update (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_update"]], "curecontroller": [[0, "module-curecontroller"]], "curedict_defaults (htpolynet.curecontroller.curecontroller attribute)": [[0, "HTPolyNet.curecontroller.CureController.curedict_defaults"]], "cwd() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.cwd"]], "dataframetools": [[0, "module-dataframetools"]], 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"HTPolyNet.curecontroller.CureController.default_equilibration_sequence"]], "default_filename (htpolynet.checkpoint.checkpoint attribute)": [[0, "HTPolyNet.checkpoint.Checkpoint.default_filename"]], "default_params (htpolynet.analyze.analyze attribute)": [[0, "HTPolyNet.analyze.Analyze.default_params"]], "default_params (htpolynet.analyze.analyzedensity attribute)": [[0, "HTPolyNet.analyze.AnalyzeDensity.default_params"]], "default_params (htpolynet.analyze.analyzeffv attribute)": [[0, "HTPolyNet.analyze.AnalyzeFFV.default_params"]], "default_params (htpolynet.postsim.postsimanneal attribute)": [[0, "HTPolyNet.postsim.PostSimAnneal.default_params"]], "default_params (htpolynet.postsim.postsimdeform attribute)": [[0, "HTPolyNet.postsim.PostSimDeform.default_params"]], "default_params (htpolynet.postsim.postsimladder attribute)": [[0, "HTPolyNet.postsim.PostSimLadder.default_params"]], "default_params (htpolynet.postsim.postsimmd attribute)": [[0, "HTPolyNet.postsim.PostSimMD.default_params"]], "delete_atoms() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.delete_atoms"]], "delete_atoms() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.delete_atoms"]], "delete_atoms() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.delete_atoms"]], "delete_atoms() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.delete_atoms"]], "density() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.density"]], "density_evolution() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.density_evolution"]], "density_from_gro() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.density_from_gro"]], "detect_rings() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.detect_rings"]], "determine_sequence() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.determine_sequence"]], "df_typeorder() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.df_typeorder"]], "dfrotate() (in module htpolynet.coordinates)": [[0, "HTPolyNet.coordinates.dfrotate"]], "diag_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.diag_plots"]], "diagnostics_graphs() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.diagnostics_graphs"]], "do() (htpolynet.analyze.analyze method)": [[0, "HTPolyNet.analyze.Analyze.do"]], "do() (htpolynet.postsim.postsimmd method)": [[0, "HTPolyNet.postsim.PostSimMD.do"]], "do_e_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.do_E_plots"]], "do_capping() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.do_capping"]], "do_cure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_cure"]], "do_densification() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_densification"]], "do_initialization() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_initialization"]], "do_iter() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.do_iter"]], "do_postcure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_postcure"]], "do_precure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_precure"]], "do_tg_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.do_tg_plots"]], "do_workflow() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_workflow"]], "driver": [[0, "module-driver"]], "dup_check() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.dup_check"]], "enablecheckpoint() (in module htpolynet.checkpoint)": [[0, "HTPolyNet.checkpoint.enableCheckpoint"]], "encluster() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.encluster"]], "enumerate_1_4_pairs() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.enumerate_1_4_pairs"]], "equilibrate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.equilibrate"]], "exists() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.exists"]], "exists() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.exists"]], "expandreactions": [[0, "module-expandreactions"]], "extract_molecule_reactions() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.extract_molecule_reactions"]], "failed_bondcycle (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.failed_bondcycle"]], "failed_pierced_ring (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.failed_pierced_ring"]], "failed_shortcircuit (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.failed_shortcircuit"]], "fcc() (htpolynet.coordinates.coordinates class method)": [[0, "HTPolyNet.coordinates.Coordinates.fcc"]], "fetch_example() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.fetch_example"]], "fetch_molecule_files() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.fetch_molecule_files"]], "filter() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.filter"]], "find_sacrificial_h() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.find_sacrificial_H"]], "find_template() (in module htpolynet.topocoord)": [[0, "HTPolyNet.topocoord.find_template"]], "finished (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.finished"]], "flip_stereocenters() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.flip_stereocenters"]], "flip_stereocenters() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.flip_stereocenters"]], "fromdataframe() (htpolynet.bondlist.bondlist class method)": [[0, "HTPolyNet.bondlist.Bondlist.fromDataFrame"]], "from_ex() (htpolynet.topology.topology class method)": [[0, "HTPolyNet.topology.Topology.from_ex"]], "from_top_gro() (htpolynet.topocoord.topocoord class method)": [[0, "HTPolyNet.topocoord.TopoCoord.from_top_gro"]], "from_yaml() (htpolynet.checkpoint.checkpoint class method)": [[0, "HTPolyNet.checkpoint.Checkpoint.from_yaml"]], "from_yaml() (htpolynet.curecontroller.curestate class method)": [[0, "HTPolyNet.curecontroller.CureState.from_yaml"]], "generate() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate"]], "generate_conformers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate_conformers"]], "generate_molecules() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.generate_molecules"]], "generate_product_name() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.generate_product_name"]], "generate_stereo_reactions() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.generate_stereo_reactions"]], "generate_stereoisomers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate_stereoisomers"]], "generate_symmetry_reactions() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.generate_symmetry_reactions"]], "geometric_center() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.geometric_center"]], "getversions() (htpolynet.software.software method)": [[0, "HTPolyNet.software.Software.getVersions"]], "get_r() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_R"]], "get_r() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_R"]], "get_angles_dihedrals() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_angles_dihedrals"]], "get_atom_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_atom_attribute"]], "get_atom_attribute() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_atom_attribute"]], "get_atoms_w_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_atoms_w_attribute"]], "get_atomtype() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_atomtype"]], "get_bond_parameters() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_bond_parameters"]], "get_bystanders() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_bystanders"]], "get_energy_menu() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.get_energy_menu"]], "get_example_depot_location() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.get_example_depot_location"]], "get_example_names() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.get_example_names"]], "get_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_gro_attribute_by_attributes"]], "get_gro_attributelist_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_gro_attributelist_by_attributes"]], "get_idx() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_idx"]], "get_molecular_weight() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_molecular_weight"]], "get_oneaways() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_oneaways"]], "get_origin() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_origin"]], "get_r() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.get_r"]], "get_resid_sets() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_resid_sets"]], "get_resname() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_resname"]], "get_row() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row"]], "get_row_as_string() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row_as_string"]], "get_row_attribute() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row_attribute"]], "get_rows_w_attribute() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_rows_w_attribute"]], "global_trace() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.global_trace"]], "gmx_command() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_command"]], "gmx_energy_trace() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_energy_trace"]], "gmx_traj_info() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_traj_info"]], "go_proj() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_proj"]], "go_root() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_root"]], "go_to() (htpolynet.projectfilesystem.projectfilesystem method)": [[0, "HTPolyNet.projectfilesystem.ProjectFileSystem.go_to"]], "go_to() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_to"]], "grab_files() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.grab_files"]], "graph() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.graph"]], "graph_from_bondsfile() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.graph_from_bondsfile"]], "gro_dataframe() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.gro_DataFrame"]], "gro_attributes (htpolynet.coordinates.coordinates attribute)": [[0, "HTPolyNet.coordinates.Coordinates.gro_attributes"]], "gro_from_trr() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gro_from_trr"]], "gromacs": [[0, "module-gromacs"]], "gromacs_distance() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gromacs_distance"]], "grompp_and_mdrun() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.grompp_and_mdrun"]], "grompp_and_mdrun() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.grompp_and_mdrun"]], "half_as_list() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.half_as_list"]], "has_atom_attributes() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.has_atom_attributes"]], "homog_trans() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.homog_trans"]], "idx_mappers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.idx_mappers"]], "idxorder() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.idxorder"]], "increment_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.increment_gro_attribute_by_attributes"]], "info() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.info"]], "info() (htpolynet.software.software method)": [[0, "HTPolyNet.software.Software.info"]], "info() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.info"]], "info() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.info"]], "info() (in module htpolynet.software)": [[0, "HTPolyNet.software.info"]], "inherit_grx_attributes_from_molecules() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.inherit_grx_attributes_from_molecules"]], "init_molecule_graph() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.init_molecule_graph"]], "initial_composition (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.initial_composition"]], "initialize_molecule_rings() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.initialize_molecule_rings"]], 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(htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.make_resid_graph"]], "make_resid_graph() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.make_resid_graph"]], "makes_bondcycle() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.makes_bondcycle"]], "makes_shortcircuit() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.makes_shortcircuit"]], "map_from_templates() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.map_from_templates"]], "maxspan() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.maxspan"]], "maxspan() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.maxspan"]], "mdp_get() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.mdp_get"]], "mdp_modify() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.mdp_modify"]], "mdp_to_dict() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.mdp_to_dict"]], "merge() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.merge"]], "merge() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.merge"]], "merge() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.merge"]], "merge() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.merge"]], "merge_ex() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.merge_ex"]], "merge_types() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.merge_types"]], "mic() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.mic"]], "minimize() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.minimize"]], "minimum_distance() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.minimum_distance"]], "minimum_distance() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.minimum_distance"]], "minmax() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.minmax"]], "minmax() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.minmax"]], "module": [[0, "module-HTPolyNet.ambertools"], [0, "module-HTPolyNet.analyze"], [0, "module-HTPolyNet.banner"], [0, "module-HTPolyNet.bondlist"], [0, "module-HTPolyNet.bondtemplate"], [0, "module-HTPolyNet.checkpoint"], [0, "module-HTPolyNet.command"], [0, "module-HTPolyNet.configuration"], [0, "module-HTPolyNet.coordinates"], [0, "module-HTPolyNet.countTime"], [0, "module-HTPolyNet.curecontroller"], [0, "module-HTPolyNet.dataframetools"], [0, "module-HTPolyNet.driver"], [0, "module-HTPolyNet.expandreactions"], [0, "module-HTPolyNet.gromacs"], [0, "module-HTPolyNet.inputcheck"], [0, "module-HTPolyNet.linkcell"], [0, "module-HTPolyNet.matrix4"], [0, "module-HTPolyNet.molecule"], [0, "module-HTPolyNet.plot"], [0, 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"module-software"], [0, "module-stringthings"], [0, "module-topocoords"], [0, "module-topology"], [0, "module-unused_symmetry_stuff"], [0, "module-utils"]], "mol2_atom_attributes (htpolynet.coordinates.coordinates attribute)": [[0, "HTPolyNet.coordinates.Coordinates.mol2_atom_attributes"]], "mol2_bond_attributes (htpolynet.coordinates.coordinates attribute)": [[0, "HTPolyNet.coordinates.Coordinates.mol2_bond_attributes"]], "mol2_bond_types (htpolynet.coordinates.coordinates attribute)": [[0, "HTPolyNet.coordinates.Coordinates.mol2_bond_types"]], "molecule": [[0, "module-molecule"]], "molecules (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.molecules"]], "molname_sequence_resnames() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.molname_sequence_resnames"]], "multi_trace() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.multi_trace"]], "mwbxl() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.mwbxl"]], "my_logger() (in module htpolynet.stringthings)": [[0, "HTPolyNet.stringthings.my_logger"]], "neighbors_of_cellndx() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.neighbors_of_cellndx"]], "network_graph() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.network_graph"]], "next_iter() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.next_iter"]], "null_check() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.null_check"]], "overwrite_coords() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.overwrite_coords"]], "pack_example() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.pack_example"]], "param (htpolynet.reaction.reaction_stage attribute)": [[0, "HTPolyNet.reaction.reaction_stage.param"]], "parameterize() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.parameterize"]], "parameterize() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.parameterize"]], "parse() (htpolynet.analyze.analyzeconfiguration method)": [[0, "HTPolyNet.analyze.AnalyzeConfiguration.parse"]], "parse() (htpolynet.configuration.configuration method)": [[0, "HTPolyNet.configuration.Configuration.parse"]], "parse() (htpolynet.postsim.postsimconfiguration method)": [[0, "HTPolyNet.postsim.PostsimConfiguration.parse"]], "parse_console_output() (htpolynet.analyze.analyze method)": [[0, "HTPolyNet.analyze.Analyze.parse_console_output"]], "parse_reaction_list() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.parse_reaction_list"]], "partners_of() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.partners_of"]], "partners_of() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.partners_of"]], "passed (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.passed"]], "pfs_setup() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.pfs_setup"]], "pierced_by() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.pierced_by"]], "pierces() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.pierces"]], "pierces_ring() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.pierces_ring"]], "plot": [[0, "module-plot"]], "plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.plots"]], "point_in_cellndx() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.point_in_cellndx"]], "populate() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.populate"]], "populate_par() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.populate_par"]], "post_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.post_plots"]], "postsim": [[0, "module-postsim"]], "postsim() (in module htpolynet.postsim)": [[0, "HTPolyNet.postsim.postsim"]], "postsim_density_evolution() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.postsim_density_evolution"]], "predefined_classes (htpolynet.analyze.analyzeconfiguration attribute)": [[0, "HTPolyNet.analyze.AnalyzeConfiguration.predefined_classes"]], "prepare_new_bonds() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.prepare_new_bonds"]], "previously_parameterized() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.previously_parameterized"]], "product_sequence_resnames() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.product_sequence_resnames"]], "proj() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.proj"]], "proj_abspath() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.proj_abspath"]], "projectfilesystem": [[0, "module-projectfilesystem"]], "reactant_resid_to_presid() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.reactant_resid_to_presid"]], "reaction": [[0, "module-reaction"]], "reaction_stage (class in htpolynet.reaction)": [[0, "HTPolyNet.reaction.reaction_stage"]], "reactions (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.reactions"]], "read() (htpolynet.analyze.analyzeconfiguration class method)": [[0, "HTPolyNet.analyze.AnalyzeConfiguration.read"]], "read() (htpolynet.configuration.configuration class method)": [[0, "HTPolyNet.configuration.Configuration.read"]], "read() (htpolynet.postsim.postsimconfiguration class method)": [[0, "HTPolyNet.postsim.PostsimConfiguration.read"]], "read_atomset_attributes() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.read_atomset_attributes"]], "read_checkpoint() (in module htpolynet.checkpoint)": [[0, "HTPolyNet.checkpoint.read_checkpoint"]], "read_gro() (htpolynet.coordinates.coordinates class method)": [[0, "HTPolyNet.coordinates.Coordinates.read_gro"]], "read_gro() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_gro"]], "read_gro_attributes() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.read_gro_attributes"]], "read_gro_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_gro_attributes"]], "read_mol2() (htpolynet.coordinates.coordinates class method)": [[0, "HTPolyNet.coordinates.Coordinates.read_mol2"]], "read_mol2() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_mol2"]], "read_top() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_top"]], "read_top() (htpolynet.topology.topology class method)": [[0, "HTPolyNet.topology.Topology.read_top"]], "read_top_gro() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_top_gro"]], "read_tpx() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.read_tpx"]], "read_tpx() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.read_tpx"]], "reconcile_subcoords() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.reconcile_subcoords"]], "relax() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.relax"]], "remap() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.remap"]], "remap() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.remap"]], "remove_restraints() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.remove_restraints"]], "remove_restraints() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.remove_restraints"]], "rep_ex() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.rep_ex"]], "repeat_check() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.repeat_check"]], "report_duplicate_types() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.report_duplicate_types"]], "report_type() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.report_type"]], "required_keys (htpolynet.analyze.analyze attribute)": [[0, "HTPolyNet.analyze.Analyze.required_keys"]], "reset() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.reset"]], "reset() (htpolynet.curecontroller.curestate method)": [[0, "HTPolyNet.curecontroller.CureState.reset"]], "reset_grx_attributes_from_idx_list() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.reset_grx_attributes_from_idx_list"]], "reset_idx_list_from_grx_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.reset_idx_list_from_grx_attributes"]], "reset_override_from_type() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.reset_override_from_type"]], "reset_type() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.reset_type"]], "resid_partners_of() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.resid_partners_of"]], "restore_bond_parameters() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.restore_bond_parameters"]], "restore_bond_parameters() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.restore_bond_parameters"]], "return_bond_lengths() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.return_bond_lengths"]], "return_bond_lengths() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.return_bond_lengths"]], "reverse() (htpolynet.bondtemplate.bondtemplate method)": [[0, "HTPolyNet.bondtemplate.BondTemplate.reverse"]], "reverse() (htpolynet.bondtemplate.reactionbond method)": [[0, "HTPolyNet.bondtemplate.ReactionBond.reverse"]], "rij() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.rij"]], "ring": [[0, "module-ring"]], "root() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.root"]], "rot() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.rot"]], "rotate() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.rotate"]], "rotate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.rotate"]], "rotate_axis() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.rotate_axis"]], "rotate_bond() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.rotate_bond"]], "run() (htpolynet.command.command method)": [[0, "HTPolyNet.command.Command.run"]], "run() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.run"]], "runtime": [[0, "module-runtime"]], "runtime_defaults (htpolynet.runtime.runtime attribute)": [[0, "HTPolyNet.runtime.Runtime.runtime_defaults"]], "sach() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.sacH"]], "save_data() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.save_data"]], "scatter() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.scatter"]], "searchlist_of_ldx() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.searchlist_of_ldx"]], "select_topology_type_option() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.select_topology_type_option"]], "set_atom_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.set_atom_attribute"]], "set_atomset_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.set_atomset_attribute"]], "set_box() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.set_box"]], "set_gmx_preferences() (htpolynet.software.software method)": [[0, "HTPolyNet.software.Software.set_gmx_preferences"]], "set_gmx_preferences() (in module htpolynet.software)": [[0, "HTPolyNet.software.set_gmx_preferences"]], "set_gro_attribute() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.set_gro_attribute"]], "set_gro_attribute() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.set_gro_attribute"]], "set_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.set_gro_attribute_by_attributes"]], "set_grx_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.set_grx_attributes"]], "set_origin() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.set_origin"]], "set_row_attribute() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.set_row_attribute"]], "set_rows_attributes_from_dict() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.set_rows_attributes_from_dict"]], "set_sequence_from_coordinates() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.set_sequence_from_coordinates"]], "set_sequence_from_moldict() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.set_sequence_from_moldict"]], "setup() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.setup"]], "shift() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.shift"]], "shift() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.shift"]], "shiftatomsidx() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.shiftatomsidx"]], "show_z_report() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.show_z_report"]], "software": [[0, "module-software"]], "spew_atom() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.spew_atom"]], "stringthings": [[0, "module-stringthings"]], "subcoords() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.subcoords"]], "subpath() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.subpath"]], "sw_setup() (in module htpolynet.software)": [[0, "HTPolyNet.software.sw_setup"]], "swap_atom_names() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.swap_atom_names"]], "symm() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.symm"]], "system() (htpolynet.projectfilesystem.runtimelibrary class method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.system"]], "system() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.system"]], "to_string() (in module htpolynet.software)": [[0, "HTPolyNet.software.to_string"]], "to_yaml() (htpolynet.checkpoint.checkpoint method)": [[0, "HTPolyNet.checkpoint.Checkpoint.to_yaml"]], "topocoords": [[0, "module-topocoords"]], "topology": [[0, "module-topology"]], "total_charge() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.total_charge"]], "total_mass() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.total_mass"]], "total_mass() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.total_mass"]], "total_volume() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.total_volume"]], "total_volume() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.total_volume"]], "trace() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.trace"]], "transform() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.transform"]], "transinvec() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.transinvec"]], "translate() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.translate"]], "translate() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.translate"]], "translate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.translate"]], "transrot() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.transrot"]], "transvec() (htpolynet.matrix4.matrix4 method)": [[0, "HTPolyNet.matrix4.Matrix4.transvec"]], "treadmill() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.treadmill"]], "typedata() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.typedata"]], "typeorder() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.typeorder"]], "unknown (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.unknown"]], "unset (htpolynet.reaction.reaction_stage attribute)": [[0, "HTPolyNet.reaction.reaction_stage.unset"]], "unset (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.unset"]], "unused_symmetry_stuff": [[0, "module-unused_symmetry_stuff"]], "unwrap() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.unwrap"]], "unwrap() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.unwrap"]], "update() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.update"]], "update_topology_and_coordinates() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.update_topology_and_coordinates"]], "update_zrecs() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.update_zrecs"]], "user() (htpolynet.projectfilesystem.runtimelibrary class method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.user"]], "utils": [[0, "module-utils"]], "vacuum_minimize() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.vacuum_minimize"]], "vacuum_simulate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.vacuum_simulate"]], "wrap_coords() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.wrap_coords"]], "wrap_coords() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.wrap_coords"]], "wrap_point() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.wrap_point"]], "write_atomset_attributes() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_atomset_attributes"]], "write_gro() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_gro"]], "write_gro() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_gro"]], "write_gro_attributes() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.write_gro_attributes"]], "write_gro_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_gro_attributes"]], "write_grx_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_grx_attributes"]], "write_mol2() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_mol2"]], "write_mol2() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_mol2"]], "write_top() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_top"]], "write_top() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.write_top"]], "write_tpx() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_tpx"]], "write_tpx() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.write_tpx"]], "yield_bonds() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.yield_bonds"]], "yield_bonds_as_df() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.yield_bonds_as_df"]]}})
\ No newline at end of file
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"Monomer: 4-methylstyrene": [[6, "monomer-4-methylstyrene"]], "Reactions": [[7, "reactions"], [14, "reactions"], [20, "reactions"]], "Results": [[8, "results"], [15, "results"], [21, "results"]], "Overall behavior": [[8, "overall-behavior"]], "Details": [[8, "details"]], "proj-0/systems": [[8, "proj-0-systems"]], "proj-0/plots": [[8, "proj-0-plots"]], "Running the Build": [[9, "running-the-build"], [16, "running-the-build"], [22, "running-the-build"]], "Console output": [[9, "console-output"]], "A Note About FutureWarnings": [[9, "a-note-about-futurewarnings"]], "DGEBA-PACM Thermoset": [[11, "dgeba-pacm-thermoset"]], "Monomers": [[13, "monomers"]], "DGEBA": [[13, "dgeba"]], "PACM": [[13, "pacm"]], "BisGMA-Styrene Thermoset": [[18, "bisgma-styrene-thermoset"]], "Building bisGMA": [[20, "building-bisgma"]], "Cure reactions": [[20, "cure-reactions"]], "Monomer-monomer reactions in the bisGMA/styrene system": [[20, "id4"]], "Examples Using htpolynet run": [[23, "examples-using-htpolynet-run"]], "HTPolyNet": [[24, "htpolynet"]], "Citation": [[24, "citation"]], "Indices and tables": [[24, "indices-and-tables"]], "Installation and Prerequisites": [[25, "installation-and-prerequisites"]], "Software Prequisites": [[25, "software-prequisites"]], "Installation": [[25, "installation"]], "Notes": [[25, "notes"]], "Compilation of AmberTools": [[25, "compilation-of-ambertools"]], "Compilation of Gromacs": [[25, "compilation-of-gromacs"]], "Compilation of obabel": [[25, "compilation-of-obabel"]], "Other Prequisites": [[25, "other-prequisites"]], "References": [[26, "references"]], "Cited Works": [[26, "cited-works"]], "Other Reference Material": [[26, "other-reference-material"]], "Configuration Files for htpolynet analyze": [[27, "configuration-files-for-htpolynet-analyze"]], "Simple examples": [[27, "simple-examples"]], "Shortcut analyses": [[27, "shortcut-analyses"]], "Configuration Files for htpolynet postsim": [[28, 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"HTPolyNet.linkcell.Linkcell.create"]], "create_new_stereoisomers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.create_new_stereoisomers"]], "cure (htpolynet.reaction.reaction_stage attribute)": [[0, "HTPolyNet.reaction.reaction_stage.cure"]], "cure_bondsearch (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_bondsearch"]], "cure_drag (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_drag"]], "cure_equilibrate (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_equilibrate"]], "cure_relax (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_relax"]], "cure_step (class in htpolynet.curecontroller)": [[0, "HTPolyNet.curecontroller.cure_step"]], "cure_update (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.cure_update"]], "curecontroller": [[0, "module-curecontroller"]], "curedict_defaults (htpolynet.curecontroller.curecontroller attribute)": [[0, "HTPolyNet.curecontroller.CureController.curedict_defaults"]], "cwd() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.cwd"]], "dataframetools": [[0, "module-dataframetools"]], "decrement_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.decrement_gro_attribute_by_attributes"]], "decrement_z() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.decrement_z"]], "default_class (htpolynet.analyze.analyzeconfiguration attribute)": [[0, "HTPolyNet.analyze.AnalyzeConfiguration.default_class"]], "default_classes (htpolynet.postsim.postsimconfiguration attribute)": [[0, "HTPolyNet.postsim.PostsimConfiguration.default_classes"]], "default_directives (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.default_directives"]], "default_directives (htpolynet.reaction.reaction attribute)": [[0, "HTPolyNet.reaction.Reaction.default_directives"]], "default_edict (htpolynet.runtime.runtime attribute)": [[0, "HTPolyNet.runtime.Runtime.default_edict"]], "default_equilibration_sequence (htpolynet.curecontroller.curecontroller attribute)": [[0, "HTPolyNet.curecontroller.CureController.default_equilibration_sequence"]], "default_filename (htpolynet.checkpoint.checkpoint attribute)": [[0, "HTPolyNet.checkpoint.Checkpoint.default_filename"]], "default_params (htpolynet.analyze.analyze attribute)": [[0, "HTPolyNet.analyze.Analyze.default_params"]], "default_params (htpolynet.analyze.analyzedensity attribute)": [[0, "HTPolyNet.analyze.AnalyzeDensity.default_params"]], "default_params (htpolynet.analyze.analyzeffv attribute)": [[0, "HTPolyNet.analyze.AnalyzeFFV.default_params"]], "default_params (htpolynet.postsim.postsimanneal attribute)": [[0, "HTPolyNet.postsim.PostSimAnneal.default_params"]], "default_params (htpolynet.postsim.postsimdeform attribute)": [[0, "HTPolyNet.postsim.PostSimDeform.default_params"]], "default_params (htpolynet.postsim.postsimladder attribute)": [[0, "HTPolyNet.postsim.PostSimLadder.default_params"]], "default_params (htpolynet.postsim.postsimmd attribute)": [[0, "HTPolyNet.postsim.PostSimMD.default_params"]], "delete_atoms() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.delete_atoms"]], "delete_atoms() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.delete_atoms"]], "delete_atoms() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.delete_atoms"]], "delete_atoms() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.delete_atoms"]], "density() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.density"]], "density_evolution() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.density_evolution"]], "density_from_gro() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.density_from_gro"]], "detect_rings() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.detect_rings"]], "determine_sequence() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.determine_sequence"]], "df_typeorder() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.df_typeorder"]], "dfrotate() (in module htpolynet.coordinates)": [[0, "HTPolyNet.coordinates.dfrotate"]], "diag_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.diag_plots"]], "diagnostics_graphs() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.diagnostics_graphs"]], "do() (htpolynet.analyze.analyze method)": [[0, "HTPolyNet.analyze.Analyze.do"]], "do() (htpolynet.postsim.postsimmd method)": [[0, "HTPolyNet.postsim.PostSimMD.do"]], "do_e_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.do_E_plots"]], "do_capping() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.do_capping"]], "do_cure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_cure"]], "do_densification() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_densification"]], "do_initialization() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_initialization"]], "do_iter() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.do_iter"]], "do_postcure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_postcure"]], "do_precure() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_precure"]], "do_tg_plots() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.do_tg_plots"]], "do_workflow() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.do_workflow"]], "driver": [[0, "module-driver"]], "dup_check() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.dup_check"]], "enablecheckpoint() (in module htpolynet.checkpoint)": [[0, "HTPolyNet.checkpoint.enableCheckpoint"]], "encluster() (in module htpolynet.unused_symmetry_stuff)": [[0, "HTPolyNet.unused_symmetry_stuff.encluster"]], "enumerate_1_4_pairs() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.enumerate_1_4_pairs"]], "equilibrate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.equilibrate"]], "exists() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.exists"]], "exists() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.exists"]], "expandreactions": [[0, "module-expandreactions"]], "extract_molecule_reactions() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.extract_molecule_reactions"]], "failed_pierced_ring (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.failed_pierced_ring"]], "failed_shortcircuit (htpolynet.topocoord.btrc attribute)": [[0, "HTPolyNet.topocoord.BTRC.failed_shortcircuit"]], "fcc() (htpolynet.coordinates.coordinates class method)": [[0, "HTPolyNet.coordinates.Coordinates.fcc"]], "fetch_example() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.fetch_example"]], "fetch_molecule_files() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.fetch_molecule_files"]], "filter() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.filter"]], "find_sacrificial_h() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.find_sacrificial_H"]], "find_template() (in module htpolynet.topocoord)": [[0, "HTPolyNet.topocoord.find_template"]], "finished (htpolynet.curecontroller.cure_step attribute)": [[0, "HTPolyNet.curecontroller.cure_step.finished"]], "flip_stereocenters() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.flip_stereocenters"]], "flip_stereocenters() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.flip_stereocenters"]], "fromdataframe() (htpolynet.bondlist.bondlist class method)": [[0, "HTPolyNet.bondlist.Bondlist.fromDataFrame"]], "from_ex() (htpolynet.topology.topology class method)": [[0, "HTPolyNet.topology.Topology.from_ex"]], "from_top_gro() (htpolynet.topocoord.topocoord class method)": [[0, "HTPolyNet.topocoord.TopoCoord.from_top_gro"]], "from_yaml() (htpolynet.checkpoint.checkpoint class method)": [[0, "HTPolyNet.checkpoint.Checkpoint.from_yaml"]], "from_yaml() (htpolynet.curecontroller.curestate class method)": [[0, "HTPolyNet.curecontroller.CureState.from_yaml"]], "generate() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate"]], "generate_conformers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate_conformers"]], "generate_molecules() (htpolynet.runtime.runtime method)": [[0, "HTPolyNet.runtime.Runtime.generate_molecules"]], "generate_product_name() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.generate_product_name"]], "generate_stereo_reactions() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.generate_stereo_reactions"]], "generate_stereoisomers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.generate_stereoisomers"]], "generate_symmetry_reactions() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.generate_symmetry_reactions"]], "geometric_center() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.geometric_center"]], "getversions() (htpolynet.software.software method)": [[0, "HTPolyNet.software.Software.getVersions"]], "get_r() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_R"]], "get_r() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_R"]], "get_angles_dihedrals() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_angles_dihedrals"]], "get_atom_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_atom_attribute"]], "get_atom_attribute() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_atom_attribute"]], "get_atoms_w_attribute() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_atoms_w_attribute"]], "get_atomtype() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_atomtype"]], "get_bond_parameters() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.get_bond_parameters"]], "get_bystanders() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_bystanders"]], "get_energy_menu() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.get_energy_menu"]], "get_example_depot_location() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.get_example_depot_location"]], "get_example_names() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.get_example_names"]], "get_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_gro_attribute_by_attributes"]], "get_gro_attributelist_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_gro_attributelist_by_attributes"]], "get_idx() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.get_idx"]], "get_molecular_weight() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_molecular_weight"]], "get_oneaways() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_oneaways"]], "get_origin() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_origin"]], "get_r() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.get_r"]], "get_resid_sets() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.get_resid_sets"]], "get_resname() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.get_resname"]], "get_row() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row"]], "get_row_as_string() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row_as_string"]], "get_row_attribute() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_row_attribute"]], "get_rows_w_attribute() (in module htpolynet.dataframetools)": [[0, "HTPolyNet.dataframetools.get_rows_w_attribute"]], "global_trace() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.global_trace"]], "gmx_command() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_command"]], "gmx_energy_trace() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_energy_trace"]], "gmx_traj_info() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gmx_traj_info"]], "go_proj() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_proj"]], "go_root() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_root"]], "go_to() (htpolynet.projectfilesystem.projectfilesystem method)": [[0, "HTPolyNet.projectfilesystem.ProjectFileSystem.go_to"]], "go_to() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.go_to"]], "grab_files() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.grab_files"]], "graph() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.graph"]], "graph_from_bondsfile() (in module htpolynet.utils)": [[0, "HTPolyNet.utils.graph_from_bondsfile"]], "gro_dataframe() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.gro_DataFrame"]], "gro_attributes (htpolynet.coordinates.coordinates attribute)": [[0, "HTPolyNet.coordinates.Coordinates.gro_attributes"]], "gro_from_trr() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gro_from_trr"]], "gromacs": [[0, "module-gromacs"]], "gromacs_distance() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.gromacs_distance"]], "grompp_and_mdrun() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.grompp_and_mdrun"]], "grompp_and_mdrun() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.grompp_and_mdrun"]], "half_as_list() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.half_as_list"]], "has_atom_attributes() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.has_atom_attributes"]], "homog_trans() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.homog_trans"]], "idx_mappers() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.idx_mappers"]], "idxorder() (in module htpolynet.topology)": [[0, "HTPolyNet.topology.idxorder"]], "increment_gro_attribute_by_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.increment_gro_attribute_by_attributes"]], "info() (htpolynet.projectfilesystem.runtimelibrary method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.info"]], "info() (htpolynet.software.software method)": [[0, "HTPolyNet.software.Software.info"]], "info() (in module htpolynet.driver)": [[0, "HTPolyNet.driver.info"]], "info() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.info"]], "info() (in module htpolynet.software)": [[0, "HTPolyNet.software.info"]], "inherit_grx_attributes_from_molecules() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.inherit_grx_attributes_from_molecules"]], "init_molecule_graph() (in module htpolynet.plot)": [[0, "HTPolyNet.plot.init_molecule_graph"]], "initial_composition (htpolynet.configuration.configuration attribute)": [[0, "HTPolyNet.configuration.Configuration.initial_composition"]], "initialize_molecule_rings() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.initialize_molecule_rings"]], "initialize_monomer_grx_attributes() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.initialize_monomer_grx_attributes"]], "injest_coordinates() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.injest_coordinates"]], "injest_coordinates() (htpolynet.ring.ringlist method)": [[0, "HTPolyNet.ring.RingList.injest_coordinates"]], "input_check() (in module htpolynet.inputcheck)": [[0, "HTPolyNet.inputcheck.input_check"]], "inputcheck": [[0, "module-inputcheck"]], "insert_molecules() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.insert_molecules"]], "interresidue_partners_of() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.interresidue_partners_of"]], "is_cured() (htpolynet.curecontroller.curecontroller method)": [[0, "HTPolyNet.curecontroller.CureController.is_cured"]], "is_reactant() (in module htpolynet.reaction)": [[0, "HTPolyNet.reaction.is_reactant"]], "is_reverse_of() (htpolynet.bondtemplate.bondtemplate method)": [[0, "HTPolyNet.bondtemplate.BondTemplate.is_reverse_of"]], "lawofcos() (in module htpolynet.ring)": [[0, "HTPolyNet.ring.lawofcos"]], "ldx_of_cellndx() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.ldx_of_cellndx"]], "lib_setup() (in module htpolynet.projectfilesystem)": [[0, "HTPolyNet.projectfilesystem.lib_setup"]], "linelen (htpolynet.command.command attribute)": [[0, "HTPolyNet.command.Command.linelen"]], "linkcell": [[0, "module-linkcell"]], "linkcell_cleanup() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.linkcell_cleanup"]], "linkcell_initialize() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.linkcell_initialize"]], "linkcell_initialize() (htpolynet.topocoord.topocoord method)": 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"HTPolyNet.linkcell.Linkcell.make_memberlists"]], "make_neighborlists() (htpolynet.linkcell.linkcell method)": [[0, "HTPolyNet.linkcell.Linkcell.make_neighborlists"]], "make_resid_graph() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.make_resid_graph"]], "make_resid_graph() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.make_resid_graph"]], "makes_shortcircuit() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.makes_shortcircuit"]], "map_from_templates() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.map_from_templates"]], "maxspan() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.maxspan"]], "maxspan() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.maxspan"]], "mdp_get() (in module htpolynet.gromacs)": [[0, "HTPolyNet.gromacs.mdp_get"]], "mdp_modify() (in module htpolynet.gromacs)": [[0, 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"HTPolyNet.coordinates.Coordinates.unwrap"]], "unwrap() (htpolynet.ring.ring method)": [[0, "HTPolyNet.ring.Ring.unwrap"]], "update() (htpolynet.bondlist.bondlist method)": [[0, "HTPolyNet.bondlist.Bondlist.update"]], "update_topology_and_coordinates() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.update_topology_and_coordinates"]], "update_zrecs() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.update_zrecs"]], "user() (htpolynet.projectfilesystem.runtimelibrary class method)": [[0, "HTPolyNet.projectfilesystem.RuntimeLibrary.user"]], "utils": [[0, "module-utils"]], "vacuum_minimize() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.vacuum_minimize"]], "vacuum_simulate() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.vacuum_simulate"]], "wrap_coords() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.wrap_coords"]], "wrap_coords() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.wrap_coords"]], "wrap_point() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.wrap_point"]], "write_atomset_attributes() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_atomset_attributes"]], "write_gro() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_gro"]], "write_gro() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_gro"]], "write_gro_attributes() (htpolynet.molecule.molecule method)": [[0, "HTPolyNet.molecule.Molecule.write_gro_attributes"]], "write_gro_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_gro_attributes"]], "write_grx_attributes() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_grx_attributes"]], "write_mol2() (htpolynet.coordinates.coordinates method)": [[0, "HTPolyNet.coordinates.Coordinates.write_mol2"]], "write_mol2() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_mol2"]], "write_top() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_top"]], "write_top() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.write_top"]], "write_tpx() (htpolynet.topocoord.topocoord method)": [[0, "HTPolyNet.topocoord.TopoCoord.write_tpx"]], "write_tpx() (htpolynet.topology.topology method)": [[0, "HTPolyNet.topology.Topology.write_tpx"]], "yield_bonds() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.yield_bonds"]], "yield_bonds_as_df() (in module htpolynet.molecule)": [[0, "HTPolyNet.molecule.yield_bonds_as_df"]]}})
\ No newline at end of file