cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14894963
title: tmQM-xtb dataset

description: This provides an hdf5 file for a subset of the tmQM-xtb dataset sampled at T=300K.  This  consists of 51252 systems (1,537,560 configurations total, 30 per system), considering only those systems with the following metal centers and organic elements, respectively: - Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, or Ag - C, H, P, S O, N, F Cl, or Br. This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM). The original dataset contains 108541 unique molecules.  Here each molecule, that matches the criteria above, was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 300K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 30 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic.
DOI: 10.5281/zenodo.14894964
title: tmQM-xtb dataset

description: This provides an hdf5 file for the tmQM-xtb dataset.  This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 400K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 10 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic.
DOI: 10.5281/zenodo.14919908
title: tmQM-xtb dataset

description: This provides an hdf5 file for the tmQM-xtb dataset.  This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 400K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 10 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic. 

 

Note, this version now inclues units for each entry; these were inadvertantly left out in the prior version
DOI: 10.5281/zenodo.15215124
title: tmQM-xtb dataset

description: This provides an hdf5 file for a subset of the tmQM-xtb dataset sampled at T=200K.  This  consists of 51249 systems (1,537,470 configurations total, 30 per system), considering only those systems with the following metal centers and organic elements, respectively: - Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, or Ag - C, H, P, S O, N, F Cl, or Br. This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM). The original dataset contains 108541 unique molecules.  Here each molecule, that matches the criteria above, was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 200K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 30 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic.
DOI: 10.5281/zenodo.15221008
title: tmQM-xtb dataset

description: This provides an hdf5 file for a subset of the tmQM-xtb dataset sampled at T=300K.  This  consists of 51252 systems (1,537,560 configurations total, 30 per system), considering only those systems with the following metal centers and organic elements, respectively: - Pd, Zn, Fe, Cu, Ni, Pt, Ir, Rh, Cr, or Ag - C, H, P, S O, N, F Cl, or Br. This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM). The original dataset contains 108541 unique molecules.  Here each molecule, that matches the criteria above, was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. 



The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism.

MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator 

Simulations were performed at 300K with a 1 fs timestep and 0.01 1/fs friction damping factor.  

In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset.

100 steps were taken between snapshots,  with 30 total snapshots per molecule

During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. 


Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen

Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic.
DOI: 10.15468/dl.xrzwp2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centaurea nemenyiana J.Wagner",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Human Observation, Specimen, Unknown evidence)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082146-230224095556074/datasets/export for details.
DOI: 10.15468/dl.u7fs7t
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus javanica L.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 103 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0333295-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5hpp2
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Auxopus macranthus Summerh."
 ]
}

 The dataset includes 44 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082152-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pagzn5
title: Occurrence Download

description: A dataset containing 389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus laceyi Small",
 "HasCoordinate is true"
 ]
}

 The dataset includes 389 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0359361-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g36wca
title: Occurrence Download

description: A dataset containing 30793 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crepis setosa Haller fil.",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Human Observation, Specimen, Unknown evidence)"
 ]
}

 The dataset includes 30793 records from 496 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082142-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ca4njv
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lyriothemis pachygastra (Selys, 1878)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 297 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0333313-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hjmmr5
title: Occurrence Download

description: A dataset containing 8462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Lathyrus nissolia L."
 ]
}

 The dataset includes 8462 records from 259 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082144-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4wpafe
title: Occurrence Download

description: A dataset containing 1718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus michauxii Nutt.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1718 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0359369-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5kf8z
title: Occurrence Download

description: A dataset containing 4560 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Pedicularis foliosa L."
 ]
}

 The dataset includes 4560 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082141-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tnqku
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Roppaneura beckeri Santos, 1966)"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011260-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.axj3c6
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chaetostoma alternifasciatum Fowler, 1945"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0333314-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ebbrw
title: Occurrence Download

description: A dataset containing 637 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macroclemys temminckii (Troost, 1835)"
 ]
}

 The dataset includes 637 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082161-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6273k
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dunckerocampus boylei Kuiter, 1998"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065838-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qx9yn
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Auxopus madagascariensis Schltr."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082155-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zfgjcb
title: Occurrence Download

description: A dataset containing 459 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus minima (Sarg.) Small",
 "HasCoordinate is true"
 ]
}

 The dataset includes 459 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0359377-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smayum
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Avena aemulans Nevski"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082164-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j83nfs
title: Occurrence Download

description: A dataset containing 654 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Betula schmidtii Regel",
 "HasCoordinate is true"
 ]
}

 The dataset includes 654 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065834-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmapnv
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Centrolene acanthidiocephalum (Ruiz-Carranza & Lynch, 1989)"
 ]
}

 The dataset includes 64 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082148-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dyxhx9
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.6782 -57.33087,-29.81756 -57.33087,-29.81756 13.95785,-88.6782 13.95785,-88.6782 -57.33087))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Liriomyza huidobrensis (Blanchard, 1926)"
 ]
}

 The dataset includes 155 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067420-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rnub9r
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crithopsis delileana (Schult.) Roshev.",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Human Observation, Specimen, Unknown evidence)"
 ]
}

 The dataset includes 59 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082182-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3e7k5b
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scopimera inflata A.Milne-Edwards, 1873"
 ]
}

 The dataset includes 69 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0132258-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dugguc
title: Occurrence Download

description: A dataset containing 1756 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Selaginella uncinata (Desv. ex Poir.) Spring"
 ]
}

 The dataset includes 1756 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005011-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wa8vrv
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Nepal)",
 "OccurrenceStatus is Present",
 "TaxonKey is Prunus mira Koehne"
 ]
}

 The dataset includes 143 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067401-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h8vsxf
title: Occurrence Download

description: A dataset containing 2000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is ITA",
 "TaxonKey is Gentiana lutea L."
 ]
}

 The dataset includes 2000 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082145-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58brmk
title: Occurrence Download

description: A dataset containing 263 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Similiparma lurida (Cuvier, 1830)"
 ]
}

 The dataset includes 263 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065833-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ru2yj
title: Occurrence Download

description: A dataset containing 4299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Occurrence evidence)",
 "Country is Greece",
 "OccurrenceStatus is Present",
 "TaxonKey is Passer hispaniolensis (Temminck, 1820)",
 "Year 1990-2022"
 ]
}

 The dataset includes 4299 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082201-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpkbpe
title: Occurrence Download

description: A dataset containing 10184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diospyros virginiana L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10184 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0359407-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z285tt
title: Occurrence Download

description: A dataset containing 2876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)",
 "Year 2001-2023"
 ]
}

 The dataset includes 2876 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0112520-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wm9m58
title: Occurrence Download

description: A dataset containing 24675 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Malaysia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bucerotiformes",
 "Year 2012-2022"
 ]
}

 The dataset includes 24675 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0359415-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnkkce
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hymenaster ecomari Dilman, 2013"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082208-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.