From 93c8a24894058b34844d92e53ae6fd3525120d61 Mon Sep 17 00:00:00 2001 From: lipengfei Date: Mon, 5 Aug 2024 11:10:05 +0800 Subject: [PATCH] updates on README.md --- README.md | 13 ++++++++----- abfe/md/charge_correction.py | 7 ++----- environment_abfe.yml | 4 ++-- testing/abfe_testing/dG_components_results.csv | 4 ++-- testing/abfe_testing/dG_results.csv | 4 ++-- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 45d551c..b9d9e1b 100644 --- a/README.md +++ b/README.md @@ -56,12 +56,15 @@ module load apbs/3.4.1 5. source $HOME/software/anaconda3/2024.06/bin/activate base 6. conda create --name FEP-SPell-ABFE --clone base 7. conda activate FEP-SPell-ABFE - 9. pip install rdkit -10. pip install parmed -11. pip install griddata -12. pip install alchemlyb + 8. pip install alchemlyb==2.3.1 + 9. pip install gridDataFormats==1.0.2 +10. pip install loguru==0.7.2 +11. pip install mrcfile==1.5.3 +12. pip install parmed==4.2.2 +13. pip install pymbar==4.0.3 +14. pip install rdkit==2024.3.3 or, you can also create `FEP-SPell-ABFE` environment using `environment_abfe_yml` file, like: -6-12. conda env create --name FEP-SPell-ABFE --file=environment_abfe.yml +6-14. conda env create --name FEP-SPell-ABFE --file=environment_abfe.yml ############################################################################### diff --git a/abfe/md/charge_correction.py b/abfe/md/charge_correction.py index badd6b0..ab761c2 100644 --- a/abfe/md/charge_correction.py +++ b/abfe/md/charge_correction.py @@ -18,10 +18,7 @@ import pandas as pd import sys import time -try: - import griddata # v0.1.0 -except ModuleNotFoundError: - import gridData # v1.0.2 +import gridData # pip install gridDataFormats==1.0.2 import numpy as np import parmed as pmd @@ -312,7 +309,7 @@ def compute_rip(self, dx_file, net_charge): The result is in kcal-A^3/mol-e (in AMBER units, not APBS units). """ - dxfile = griddata.Grid(dx_file) + dxfile = gridData.Grid(dx_file) dV = dxfile.delta.prod() V = dxfile.grid.size*dV # Label this as B for box integral, X because it refers to the system X. diff --git a/environment_abfe.yml b/environment_abfe.yml index d93ee70..e31246f 100644 --- a/environment_abfe.yml +++ b/environment_abfe.yml @@ -502,9 +502,9 @@ dependencies: - zstandard=0.22.0=py312h2c38b39_0 - zstd=1.5.5=hc292b87_2 - pip: - - griddata==0.1.0 + - griddataformats==1.0.2 - loguru==0.7.2 + - mrcfile==1.5.3 - parmed==4.2.2 - pymbar==4.0.3 - rdkit==2024.3.3 - - alchemlyb==2.3.1 \ No newline at end of file diff --git a/testing/abfe_testing/dG_components_results.csv b/testing/abfe_testing/dG_components_results.csv index dc86c34..bd19c65 100644 --- a/testing/abfe_testing/dG_components_results.csv +++ b/testing/abfe_testing/dG_components_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic -phn,5.27,0.00,5.22,0.00,4.60,0.00,-8.37,9.58,4.58,0.00,-8.77,9.58 +phn,5.20,0.00,5.16,0.00,9.72,0.00,-5.57,9.64,9.70,0.00,-6.27,9.64 ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic -bnz,1.13,0.00,1.06,0.00,6.25,0.00,-7.06,9.60,6.25,0.00,-7.62,9.60 +bnz,1.19,0.00,1.14,0.00,7.15,0.00,-6.72,9.58,7.06,0.00,-7.33,9.58 diff --git a/testing/abfe_testing/dG_results.csv b/testing/abfe_testing/dG_results.csv index e34444d..968083a 100644 --- a/testing/abfe_testing/dG_results.csv +++ b/testing/abfe_testing/dG_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -phn,1.88,0.07,1.46,0.08 +phn,-0.45,0.06,-1.16,0.09 ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -bnz,-2.59,0.06,-3.21,0.07 +bnz,-3.11,0.06,-3.67,0.07