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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| """ | ||
| .. module:: chain | ||
| :synopsis: Manages data structure that keeps track of polymerized chains | ||
| .. moduleauthor: Cameron F. Abrams, <[email protected]> | ||
| """ | ||
| import logging | ||
| logger=logging.getLogger(__name__) | ||
|
|
||
| class Chain: | ||
| def __init__(self,head=-1,tail=-1,idx=-1): | ||
| self.idx_list=[] | ||
| if head!=-1: | ||
| self.idx_list.append(head) | ||
| if tail!=-1: | ||
| self.idx_list.append(tail) | ||
| self.is_cyclic=False | ||
| self.idx=idx | ||
| def is_head(self,a): | ||
| return not self.is_cyclic and a==self.idx_list[0] | ||
| def is_tail(self,a): | ||
| return not self.is_cyclic and a==self.idx_list[-1] | ||
| def merge(self,other): | ||
| # tail of self bonds to head of other | ||
| self.idx_list.extend(other.idx_list) | ||
|
|
||
| def remap_idx(self,idx_mapper): | ||
| self.idx_list=[idx_mapper[x] for x in self.idx_list] | ||
| def shift(self,shift): | ||
| self.idx_list=[x+shift for x in self.idx_list] | ||
|
|
||
| class ChainManager: | ||
| def __init__(self,**kwargs): | ||
| self.chains=[] | ||
| self.create_if_missing=kwargs.get('create_if_missing',False) | ||
|
|
||
| def chain_of(self,a): | ||
| for c in self.chains: | ||
| if a in c.idx_list: | ||
| return c | ||
| return None | ||
|
|
||
| def new_chain(self,head,tail): | ||
| self.chains.append(Chain(head=head,tail=tail,idx=len(self.chains))) | ||
|
|
||
| def mergechains(self,dst,src): | ||
| dst.merge(src) | ||
| self.chains.remove(src) | ||
| self.reindex() | ||
|
|
||
| def injest_other(self,other): | ||
| self.chains.extend(other.chains) | ||
| self.reindex() | ||
|
|
||
| def reindex(self): | ||
| for i,c in enumerate(self.chains): | ||
| c.idx=i | ||
|
|
||
| def shift(self,shift): | ||
| for c in self.chains: | ||
| c.shift(shift) | ||
|
|
||
| def remap(self,idx_mapper): | ||
| for c in self.chains: | ||
| c.remap_idx(idx_mapper) | ||
|
|
||
| def injest_bond(self,ai,aj): | ||
| ic=self.chain_of(ai) | ||
| jc=self.chain_of(aj) | ||
| if not ic and not jc: | ||
| if self.create_if_missing: | ||
| logger.debug(f'New chain with head {ai} and tail {aj}') | ||
| self.new_chain(ai,aj) | ||
| else: | ||
| pass | ||
| elif not ic: | ||
| logger.debug(f'j-Atom {aj} (chain {jc.idx}) bonds to atom {ai}, but {ai} is not yet in a chain.') | ||
| logger.debug(f'This should never happen in a C=C polymerizing system; all reactive Cs are in chains from the very beginning!') | ||
| raise Exception('This is a bug - no i-chain!') | ||
| elif not jc: | ||
| logger.debug(f'i-Atom {ai} (chain {ic.idx}) bonds to atom {aj}, but {aj} is not yet in a chain.') | ||
| logger.debug(f'This should never happen in a C=C polymerizing system; all reactive Cs are in chains from the very beginning!') | ||
| raise Exception('This is a bug - no j-chain!') | ||
| elif ic==jc: | ||
| assert (ic.is_head(ai) and ic.is_tail(aj)) or (ic.is_head(aj) and ic.is_tail(ai)) | ||
| ic.is_cyclic=True | ||
| logger.debug(f'New bond between {ai} and {aj} creates a cyclic chain of length ({len(ic.idx_list)})') | ||
| elif ic.is_head(ai) and jc.is_tail(aj): | ||
| assert not ic.is_cyclic and not jc.is_cyclic | ||
| self.mergechains(jc,ic) | ||
| elif jc.is_head(aj) and ic.is_tail(ai): | ||
| assert not ic.is_cyclic and not jc.is_cyclic | ||
| self.mergechains(ic,jc) | ||
|
|
||
| def injest_bonds(self,bondlist): | ||
| for b in bondlist: | ||
| self.injest_bond(b[0],b[1]) | ||
|
|
||
| def to_dataframe(self,D,lidx_col='bondchain_idx',gidx_col='bondchain'): | ||
| assert lidx_col in D and gidx_col in D,f'Dataframe missing column {lidx_col} or {gidx_col}' | ||
| # wipe out df | ||
| D[lidx_col]=[-1]*D.shape[0] | ||
| D[gidx_col]=[-1]*D.shape[0] | ||
| for gidx,c in enumerate(self.chains): | ||
| for lidx,atidx in enumerate(c.idx_list): | ||
| df_idx=atidx-1 # should be true always | ||
| D.loc[df_idx,lidx_col]=lidx | ||
| D.loc[df_idx,gidx_col]=gidx | ||
|
|
||
| def from_dataframe(self,D,lidx_col='bondchain_idx',gidx_col='bondchain'): | ||
| # overwrites whole thing | ||
| self.chains=[] | ||
| heads=D[D[lidx_col]==0].index+1 # always! | ||
| headchains=D[D[lidx_col]==0][gidx_col] | ||
| for h,hc in zip(heads,headchains): | ||
| self.chains.append(Chain(head=h,idx=hc)) | ||
| self.chains.sort(key=lambda x: x.idx) | ||
| old_idx=[x.idx for x in self.chains] | ||
| self.reindex() | ||
| assert all([(x==y) for x,y in zip([x.idx for x in self.chains],list(range(len(self.chains))))]) | ||
| next_idx=1 | ||
| while next_idx<D.shape[0]: | ||
| if D[D[lidx_col]==next_idx].shape[0]==0: | ||
| break | ||
| next_ats=D[D[lidx_col]==next_idx].index+1 # always | ||
| next_atchains=D[D[lidx_col]==next_idx][gidx_col] | ||
| for a,ac in zip(next_ats,next_atchains): | ||
| acidx=old_idx.index(ac) | ||
| self.chains[acidx].idx_list.append(a) | ||
| next_idx+=1 | ||
|
|
||
|
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||
|
|
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