Merge pull request #106 from valence-labs/improvs

Read me badges + new enums
valence-labs · Jul 22, 2024 · 7730577 · 7730577
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diff --git 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/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"

diff --git 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
@@ -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
@@ -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
@@ -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