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qcscine/chemoton: Release 2.0.0

Authors: Bensberg, Moritz; Grimmel, Stephanie A.; Simm, Gregor N.; Sobez, Jan-Grimo; Steiner, Miguel; Türtscher, Paul L.; Unsleber, Jan P.; +2 Authors

qcscine/chemoton: Release 2.0.0

Abstract

Python rewrite, and open source release with the following initial features: Scriptable framework including a base set of features for the automated exploration of chemical reaction networks Initial chemical reaction networks consisting of Structures aggregated into Compounds Elementary Steps aggregated into Reactions Properties tagged to Structures Calculations that generated the network Definitions of Engines with perpetually running Gears to continuously perform tasks with chemical reaction networks (see list below) Storage and expansion of chemical reaction networks in a SCINE Database Automated job set up and execution via SCINE Puffin Definitions of basic filters to reduce number of Elementary Step trials (see list below) Initial Engines/Gears: Basic bookkeeping jobs: Sorting Structures into Compounds (BasicCompoundHousekeeping) Sorting Elementary Steps into Reactions (BasicReactionHousekeeping) Basic Scheduling and prioritization of Calculations (Scheduler) Data completion jobs: Conformer generation per compound (BruteForceConformers) Hessian generation per transition state and minimum energy Structure (BasicThermoDataCompletion) Elementary Step exploration based on existing Compounds: For one Structure per Compound (MinimalElementarySteps): Based on atoms/fragments (AFIR, NT1) Based on bonds (NT2) For all combinations of Structures per Compounds (BruteForceElementarySteps): Based on atoms/fragments (AFIR, NT1) Based on bonds (NT2) Steering of network growth via simple kinetic analyses: Based on connectivity to user input (MinimalConnectivityKinetics) Based on barrier heights of Elementary Steps (BasicBarrierHeightKinetics) Initial set of filters: Compound filtering possible: Base class, allows all compounds (CompoundFilter) By element counts (ElementCountFilter, ElementSumCountFilter) By atom counts or molecular weights (MolecularWeightFilter, AtomNumberFilter) By database IDs (IDFilter, OneCompoundIDFilter, SelectedCompoundIDFilter) By context (SelfReactionFilter) By Hessian evaluation (TrueMinimumFilter) By composition (CatalystFilter) Reactive site filtering possible: Base class, allows all reactive sites (ReactiveSiteFilter) By fixed, simple rankings (SimpleRankingFilter, MasmChemicalRankingFilter) By custom user rules (AtomRuleBasedFilter, FunctionalGroupRule) By atom types (ElementWiseReactionCoordinateFilter) All filters of the same type can be chained with logical operations to tailor the behaviour

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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3