From 93eacee86f3969c1a8163c2dcf430aab4349a8bc Mon Sep 17 00:00:00 2001 From: FNTwin Date: Mon, 22 Jul 2024 14:48:22 -0400 Subject: [PATCH 1/2] badges + enums --- README.md | 17 ++++++++ openqdc/datasets/potential/ani.py | 26 +++++------ .../datasets/potential/proteinfragments.py | 6 +-- openqdc/datasets/potential/vqm24.py | 4 +- openqdc/methods/enums.py | 43 +++++++++++++++++++ 5 files changed, 78 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index cd3f517d..a35b56ed 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ Open Quantum Data Commons +[![license](https://licensebuttons.net/l/by-nc/4.0/80x15.png)](https://github.com/valence-labs/openQDC/blob/main/LICENSE) + ### Installing openQDC ```bash git clone git@github.com:OpenDrugDiscovery/openQDC.git @@ -91,6 +93,21 @@ We also provide support for the following publicly available QM Noncovalent Inte | [X40](https://pubs.acs.org/doi/10.1021/ct300647k) | | [L7](https://pubs.acs.org/doi/10.1021/ct400036b) | +# CI Status + +The CI runs tests and performs code quality checks for the following combinations: + +- The three major platforms: Windows, OSX and Linux. +- The four latest Python versions. + +| | `main` | +| --------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| Lib build & Testing | [![test](https://github.com/valence-labs/openQDC/actions/workflows/test.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/test.yml) | +| Code Sanity (linting and type analysis) | [![code-check](https://github.com/valence-labs/openQDC/actions/workflows/code-check.yml/badge.svg)](https://github.com/valence-labs/openQDC//actions/workflows/code-check.yml) | +| Documentation Build | [![doc](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/doc.yml) | +| Pre-Commit | [![pre-commit](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml/badge.svg)](https://github.com/valence-labs/openQDC/actions/workflows/pre-commit-ci.yml) | + + # How to cite All data presented in the OpenQDC are already published in scientific journals, full reference to the respective paper is attached to each dataset class. When citing data obtained from OpenQDC, you should cite both the original paper(s) the data come from and our paper on OpenQDC itself. The reference is: diff --git a/openqdc/datasets/potential/ani.py b/openqdc/datasets/potential/ani.py index aac35635..42f5fd4e 100644 --- a/openqdc/datasets/potential/ani.py +++ b/openqdc/datasets/potential/ani.py @@ -60,7 +60,7 @@ class ANI1(BaseDataset): __name__ = "ani1" __energy_methods__ = [ - PotentialMethod.WB97X_6_31G_D, # "wb97x/6-31g(d)" + PotentialMethod.WB97X_6_31G_D, ] energy_target_names = [ @@ -121,14 +121,14 @@ class ANI1X(ANI1): __forces_unit__ = "hartree/ang" __energy_methods__ = [ - PotentialMethod.NONE, # "hf/cc-pvdz", - PotentialMethod.NONE, # "hf/cc-pvqz", - PotentialMethod.NONE, # "hf/cc-pvtz", - PotentialMethod.NONE, # "mp2/cc-pvdz", - PotentialMethod.NONE, # "mp2/cc-pvqz", - PotentialMethod.NONE, # "mp2/cc-pvtz", - PotentialMethod.NONE, # "wb97x/6-31g(d)", - PotentialMethod.NONE, # "wb97x/cc-pvtz", + PotentialMethod.HF_CC_PVDZ, + PotentialMethod.HF_CC_PVQZ, + PotentialMethod.HF_CC_PVTZ, + PotentialMethod.MP2_CC_PVDZ, + PotentialMethod.MP2_CC_PVQZ, + PotentialMethod.MP2_CC_PVTZ, + PotentialMethod.WB97X_6_31G_D, + PotentialMethod.WB97X_CC_PVTZ, ] energy_target_names = [ @@ -179,10 +179,10 @@ class ANI1CCX(ANI1): __forces_unit__ = "hartree/ang" __energy_methods__ = [ - PotentialMethod.NONE, # "ccsd(t)/cbs", - PotentialMethod.NONE, # "ccsd(t)/cc-pvdz", - PotentialMethod.NONE, # "ccsd(t)/cc-pvtz", - PotentialMethod.NONE, # "tccsd(t)/cc-pvdz", + PotentialMethod.CCSD_T_CBS, # "ccsd(t)/cbs", + PotentialMethod.CCSD_T_CC_PVDZ, # "ccsd(t)/cc-pvdz", + PotentialMethod.CCSD_T_CC_PVTZ, # "ccsd(t)/cc-pvtz", + PotentialMethod.TCSSD_T_CC_PVDZ, # "tccsd(t)/cc-pvdz", ] energy_target_names = [ diff --git a/openqdc/datasets/potential/proteinfragments.py b/openqdc/datasets/potential/proteinfragments.py index d6289750..337c988c 100644 --- a/openqdc/datasets/potential/proteinfragments.py +++ b/openqdc/datasets/potential/proteinfragments.py @@ -120,13 +120,13 @@ class ProteinFragments(BaseDataset): __name__ = "proteinfragments" # PBE0/def2-TZVPP+MBD __energy_methods__ = [ - PotentialMethod.WB97X_6_31G_D, # "wb97x/6-31g(d)" + PotentialMethod.PBE0_MBD_DEF2_TZVPP, ] energy_target_names = [ - "ωB97x:6-31G(d) Energy", + "PBE0+MBD/def2-TZVPP", ] - # PBE0/def2-TZVPP+MBD + __energy_unit__ = "ev" __distance_unit__ = "ang" __forces_unit__ = "ev/ang" diff --git a/openqdc/datasets/potential/vqm24.py b/openqdc/datasets/potential/vqm24.py index 1710e1dd..aca19aed 100644 --- a/openqdc/datasets/potential/vqm24.py +++ b/openqdc/datasets/potential/vqm24.py @@ -59,11 +59,11 @@ class VQM24(BaseDataset): __name__ = "vqm24" __energy_methods__ = [ - PotentialMethod.WB97X_6_31G_D, # "wb97x/6-31g(d)" + PotentialMethod.WB97X_D3_CC_PVDZ, # "wB97x-D3/cc-pVDZ." ] energy_target_names = [ - "ωB97x:6-31G(d) Energy", + "wB97x-D3/cc-pVDZ", ] # ωB97X-D3/cc-pVDZ __energy_unit__ = "hartree" diff --git a/openqdc/methods/enums.py b/openqdc/methods/enums.py index 9dff4a15..85c81549 100644 --- a/openqdc/methods/enums.py +++ b/openqdc/methods/enums.py @@ -71,6 +71,7 @@ class CORRECTION(StrEnum): D4 = "d4" # Grimmes -D4 correction (we don t have any so feel free to not add this one) GCP = "gcp" # Geometrical Counter-Poise Correction CP = "cp" # Counter-Poise Correction + MBD = "mbd" # Many-Body Dispersion Correction/vdw-TS correction VWN = "vwn" # VWN5 = "vwn5" # NONE = "" @@ -119,6 +120,7 @@ class Functional(Enum): HCTH_407 = "hcth-407" HCTH_93 = "hcth-93" HF = "hf" + HF_R2SCAN_DC4 = "hf-r2scan-dc4" KCIS_MODIFIED = "kcis-modified" KCIS_ORIGINAL = "kcis-original" KMLYP_VWN5 = "kmlyp", CORRECTION.VWN5 @@ -153,23 +155,42 @@ class Functional(Enum): PBE_D = "pbe", CORRECTION.D PBE_D3_BJ = "pbe", CORRECTION.D3BJ PBE0 = "pbe0" + PBE0_MBD = "pbe0+mbd" PBESOL = "pbesol" PKZB = "pkzb" PKZBX_KCISCOR = "pkzbx-kciscor" PM6 = "pm6" PW91 = "pw91" QCISDT = "qcisd(t)" + R2_SCAN = "r2Scan" + R2_SCAN_HF = "r2Scan@hf" + R2_SCAN_R2_SCAN50 = "r2Scan@r2Scan50" + R2_SCAN50 = "r2Scan50" + R2_SCAN100 = "r2Scan100" + R2_SCAN10 = "r2Scan10" + R2_SCAN20 = "r2Scan20" + R2_SCAN25 = "r2Scan25" + R2_SCAN30 = "r2Scan30" + R2_SCAN40 = "r2Scan40" + R2_SCAN60 = "r2Scan60" + R2_SCAN70 = "r2Scan70" + R2_SCAN80 = "r2Scan80" + R2_SCAN90 = "r2Scan90" REVPBE = "revpbe" REVPBE_D3_BJ = "revpbe", CORRECTION.D3BJ REVTPSS = "revtpss" RGE2 = "rge2" RPBE = "rpbe" SAPT0 = "sapt0" + SCAN = "scan" + SCAN_HF = "scan@hf" + SCAN_R2SCAN50 = "scan@r2scan50" SSB_D = "ssb", CORRECTION.D SVWN = "svwn" TMGGA = "t-mgga" TAU_HCTH = "tau-hcth" TAU_HCTH_HYBRID = "tau-hcth-hybrid" + TCSSD_T = "tccsd(t)" TPSS = "tpss" TPSSD = "tpss", CORRECTION.D TPSSH = "tpssh" @@ -296,8 +317,11 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 BP86_D_DZP = Functional.BP86_D, BasisSet.DZP BP86_D_SZ = Functional.BP86_D, BasisSet.SZ BP86_D_TZP = Functional.BP86_D, BasisSet.TZP + CCSD_T_CBS = Functional.CCSDT, BasisSet.CBS + CCSD_T_CC_PVTZ = Functional.CCSDT, BasisSet.CC_PVDZ CCSD_T_CC_PVDZ = Functional.CCSDT, BasisSet.CC_PVDZ CCSD_CC_PVDZ = Functional.CCSD, BasisSet.CC_PVDZ + DFT3B = Functional.DFT3B, BasisSet.NONE DSD_BLYP_D3_BJ_DEF2_TZVP = Functional.DSD_BLYP_D3_BJ, BasisSet.DEF2_TZVP FT97_DZP = Functional.FT97, BasisSet.DZP @@ -318,6 +342,18 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 HCTH_93_SZ = Functional.HCTH_93, BasisSet.SZ HCTH_93_TZP = Functional.HCTH_93, BasisSet.TZP HF_DEF2_TZVP = Functional.HF, BasisSet.DEF2_TZVP + HF_CC_PVDZ = ( + Functional.HF, + BasisSet.CC_PVDZ, + ) + HF_CC_PVQZ = ( + Functional.HF, + BasisSet.CC_PVQZ, + ) + HF_CC_PVTZ = ( + Functional.HF, + BasisSet.CC_PVTZ, + ) KCIS_MODIFIED_DZP = Functional.KCIS_MODIFIED, BasisSet.DZP KCIS_MODIFIED_SZ = Functional.KCIS_MODIFIED, BasisSet.SZ KCIS_MODIFIED_TZP = Functional.KCIS_MODIFIED, BasisSet.TZP @@ -351,6 +387,9 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 M06_DZP = Functional.M06, BasisSet.DZP M06_SZ = Functional.M06, BasisSet.SZ M06_TZP = Functional.M06, BasisSet.TZP + MP2_CC_PVDZ = Functional.MP2, BasisSet.CC_PVDZ + MP2_CC_PVQZ = Functional.MP2, BasisSet.CC_PVQZ + MP2_CC_PVTZ = Functional.MP2, BasisSet.CC_PVTZ MPBE_DZP = Functional.MPBE, BasisSet.DZP MPBE_SZ = Functional.MPBE, BasisSet.SZ MPBE_TZP = Functional.MPBE, BasisSet.TZP @@ -408,6 +447,7 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 PBE0_DEF2_TZVP = Functional.PBE0, BasisSet.DEF2_TZVP PBE0_SZ = Functional.PBE0, BasisSet.SZ PBE0_TZP = Functional.PBE0, BasisSet.TZP + PBE0_MBD_DEF2_TZVPP = Functional.PBE0_MBD, BasisSet.DEF2_TZVPPD PBESOL_DZP = Functional.PBESOL, BasisSet.DZP PBESOL_SZ = Functional.PBESOL, BasisSet.SZ PBESOL_TZP = Functional.PBESOL, BasisSet.TZP @@ -447,6 +487,7 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 TAU_HCTH_DZP = Functional.TAU_HCTH, BasisSet.DZP TAU_HCTH_SZ = Functional.TAU_HCTH, BasisSet.SZ TAU_HCTH_TZP = Functional.TAU_HCTH, BasisSet.TZP + TCSSD_T_CC_PVDZ = Functional.TCSSD_T, BasisSet.CC_PVDZ TPSSD_DZP = Functional.TPSSD, BasisSet.DZP TPSSD_SZ = Functional.TPSSD, BasisSet.SZ TPSSD_TZP = Functional.TPSSD, BasisSet.TZP @@ -470,7 +511,9 @@ class PotentialMethod(QmMethod): # SPLIT FOR INTERACTIO ENERGIES AND FIX MD1 WB97M_D3BJ_DEF2_TZVPPD = Functional.WB97M_D3BJ, BasisSet.DEF2_TZVPPD WB97X_D_DEF2_SVP = Functional.WB97X_D, BasisSet.DEF2_SVP WB97X_D3_DEF2_TZVP = Functional.WB97X_D3, BasisSet.DEF2_TZVP + WB97X_D3_CC_PVDZ = Functional.WB97X_D3, BasisSet.CC_PVDZ WB97X_6_31G_D = Functional.WB97X, BasisSet.GSTAR + WB97X_CC_PVTZ = Functional.WB97X, BasisSet.CC_PVTZ X3LYP_VWN5_DZP = Functional.X3LYP_VWN5, BasisSet.DZP X3LYP_VWN5_SZ = Functional.X3LYP_VWN5, BasisSet.SZ X3LYP_VWN5_TZP = Functional.X3LYP_VWN5, BasisSet.TZP From 3d4c7674a832d069648a718b14a135c7359c7989 Mon Sep 17 00:00:00 2001 From: FNTwin Date: Mon, 22 Jul 2024 15:05:41 -0400 Subject: [PATCH 2/2] Site description --- mkdocs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 67d7b043..4c649c00 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,8 +1,8 @@ site_name: "OpenQDC" -site_description: "I don't know... Something about data and Quantum stuff I guess :D" +site_description: "Harness the power of quantum chemistry in one line of code." repo_url: "https://github.com/valence-labs/openQDC" repo_name: "openQDC" -copyright: Copyright 2023 Valence Labs +copyright: Copyright 2024 Valence Labs site_url: "https://github.com/valence-labs/openQDC" remote_branch: "gh-pages"