From 2eff9a322489bb40e6d3243108d583879c5503f4 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 16 Nov 2022 09:24:49 +0100
Subject: [PATCH] default stereo parameters from CCP4 MON_LIB
---
modules/mol/alg/pymod/CMakeLists.txt | 5 ++
modules/mol/alg/pymod/stereo_data.json | 1 +
modules/mol/alg/pymod/stereochemistry.py | 62 ++++++++++++++++++++----
3 files changed, 59 insertions(+), 9 deletions(-)
create mode 100644 modules/mol/alg/pymod/stereo_data.json
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 06f2b3427..23ad53e3b 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -33,3 +33,8 @@ if (NOT ENABLE_STATIC)
pymod(NAME mol_alg OUTPUT_DIR ost/mol/alg CPP ${OST_MOL_ALG_PYMOD_SOURCES}
PY ${OST_MOL_ALG_PYMOD_MODULES})
endif()
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure"
+ "stereo_data.json" "STEREO_DATA"
+ "ost_mol_alg_pymod")
+install(FILES "stereo_data.json" DESTINATION "share/openstructure/")
diff --git a/modules/mol/alg/pymod/stereo_data.json b/modules/mol/alg/pymod/stereo_data.json
new file mode 100644
index 000000000..797411344
--- /dev/null
+++ b/modules/mol/alg/pymod/stereo_data.json
@@ -0,0 +1 @@
+{"bond_data": {"ALA": {"N_CA": [1.482, 0.0101], "CA_C": [1.533, 0.01], "CA_CB": [1.509, 0.0143], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.986, 0.02], "CB_HB3": [0.972, 0.0152], "CB_HB2": [0.972, 0.0152], "CB_HB1": [0.972, 0.0152]}, "ARG": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.532, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.522, 0.01], "CG_CD": [1.517, 0.0143], "CD_NE": [1.456, 0.0136], "NE_CZ": [1.328, 0.0112], "CZ_NH1": [1.321, 0.01], "CZ_NH2": [1.322, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.98, 0.016], "CB_HB2": [0.98, 0.016], "CG_HG3": [0.981, 0.016], "CG_HG2": [0.981, 0.016], "CD_HD3": [0.981, 0.0152], "CD_HD2": [0.981, 0.0152], "NE_HE": [0.872, 0.02], "NH1_HH11": [0.881, 0.02], "NH1_HH12": [0.881, 0.02], "NH2_HH21": [0.879, 0.02], "NH2_HH22": [0.879, 0.02]}, "ASN": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.531, 0.0107], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.514, 0.01], "CG_OD1": [1.229, 0.0102], "CG_ND2": [1.323, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.986, 0.02], "CB_HB3": [0.979, 0.0159], "CB_HB2": [0.979, 0.0159], "ND2_HD21": [0.884, 0.02], "ND2_HD22": [0.884, 0.02]}, "ASP": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.531, 0.0107], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.519, 0.0109], "CG_OD1": [1.247, 0.0187], "CG_OD2": [1.247, 0.0187], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.986, 0.02], "CB_HB3": [0.979, 0.0159], "CB_HB2": [0.979, 0.0159]}, "CYS": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.524, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_SG": [1.812, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.979, 0.0172], "CB_HB2": [0.979, 0.0172], "SG_HG": [1.203, 0.02]}, "GLN": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.53, 0.0105], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.522, 0.0131], "CG_CD": [1.509, 0.01], "CD_OE1": [1.229, 0.0102], "CD_NE2": [1.323, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.98, 0.0178], "CB_HB2": [0.98, 0.0178], "CG_HG3": [0.981, 0.0185], "CG_HG2": [0.981, 0.0185], "NE2_HE21": [0.884, 0.02], "NE2_HE22": [0.884, 0.02]}, "GLU": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.53, 0.0105], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.518, 0.0153], "CG_CD": [1.519, 0.0109], "CD_OE1": [1.247, 0.0187], "CD_OE2": [1.247, 0.0187], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.98, 0.0178], "CB_HB2": [0.98, 0.0178], "CG_HG3": [0.981, 0.0185], "CG_HG2": [0.981, 0.0185]}, "GLY": {"N_CA": [1.476, 0.01], "CA_C": [1.519, 0.0106], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA3": [0.99, 0.02], "CA_HA2": [0.99, 0.02]}, "HIS": {"N_CA": [1.489, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.533, 0.0104], "C_O": [1.251, 0.0183], "C_OXT": [1.251, 0.0183], "CB_CG": [1.493, 0.0146], "CG_ND1": [1.378, 0.01], "CG_CD2": [1.338, 0.0174], "ND1_CE1": [1.326, 0.0133], "CD2_NE2": [1.371, 0.0154], "CE1_NE2": [1.316, 0.0157], "N_H": [0.902, 0.0102], "N_H2": [0.902, 0.0102], "N_H3": [0.902, 0.0102], "CA_HA": [0.989, 0.02], "CB_HB3": [0.982, 0.0176], "CB_HB2": [0.982, 0.0176], "ND1_HD1": [0.881, 0.02], "CD2_HD2": [0.937, 0.0104], "CE1_HE1": [0.942, 0.02], "NE2_HE2": [0.877, 0.02]}, "ILE": {"N_CA": [1.494, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.542, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG1": [1.531, 0.01], "CB_CG2": [1.521, 0.0135], "CG1_CD1": [1.511, 0.02], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.974, 0.02], "CB_HB": [0.989, 0.0175], "CG1_HG12": [0.981, 0.016], "CG1_HG13": [0.981, 0.016], "CG2_HG21": [0.973, 0.0146], "CG2_HG22": [0.973, 0.0146], "CG2_HG23": [0.973, 0.0146], "CD1_HD11": [0.973, 0.0157], "CD1_HD12": [0.973, 0.0157], "CD1_HD13": [0.973, 0.0157]}, "LEU": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.532, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.528, 0.0105], "CG_CD1": [1.521, 0.0151], "CG_CD2": [1.521, 0.0151], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.978, 0.0119], "CB_HB2": [0.978, 0.0119], "CG_HG": [0.989, 0.0162], "CD1_HD11": [0.973, 0.0146], "CD1_HD12": [0.973, 0.0146], "CD1_HD13": [0.973, 0.0146], "CD2_HD21": [0.973, 0.0146], "CD2_HD22": [0.973, 0.0146], "CD2_HD23": [0.973, 0.0146]}, "LYS": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.532, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.523, 0.0114], "CG_CD": [1.514, 0.02], "CD_CE": [1.514, 0.0111], "CE_NZ": [1.482, 0.0123], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.98, 0.016], "CB_HB2": [0.98, 0.016], "CG_HG3": [0.981, 0.0163], "CG_HG2": [0.981, 0.0163], "CD_HD3": [0.981, 0.016], "CD_HD2": [0.981, 0.016], "CE_HE3": [0.976, 0.0165], "CE_HE2": [0.976, 0.0165], "NZ_HZ1": [0.907, 0.02], "NZ_HZ2": [0.907, 0.02], "NZ_HZ3": [0.907, 0.02]}, "MET": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.532, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.517, 0.02], "CG_SD": [1.811, 0.02], "SD_CE": [1.792, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB3": [0.978, 0.02], "CB_HB2": [0.978, 0.02], "CG_HG3": [0.981, 0.0122], "CG_HG2": [0.981, 0.0122], "CE_HE3": [0.965, 0.017], "CE_HE2": [0.965, 0.017], "CE_HE1": [0.965, 0.017]}, "MSE": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.532, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.514, 0.02], "CG_SE": [1.963, 0.02], "SE_CE": [1.963, 0.02], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB2": [0.954, 0.02], "CB_HB3": [0.954, 0.02], "CG_HG2": [0.981, 0.0167], "CG_HG3": [0.981, 0.0167], "CE_HE1": [0.97, 0.0162], "CE_HE2": [0.97, 0.0162], "CE_HE3": [0.97, 0.0162]}, "PHE": {"N_CA": [1.487, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.531, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.508, 0.01], "CG_CD1": [1.385, 0.0111], "CG_CD2": [1.385, 0.0111], "CD1_CE1": [1.386, 0.01], "CD2_CE2": [1.386, 0.01], "CE1_CZ": [1.376, 0.0124], "CE2_CZ": [1.376, 0.0124], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.991, 0.02], "CB_HB3": [0.98, 0.0164], "CB_HB2": [0.98, 0.0164], "CD1_HD1": [0.944, 0.0174], "CD2_HD2": [0.944, 0.0174], "CE1_HE1": [0.944, 0.0175], "CE2_HE2": [0.944, 0.0175], "CZ_HZ": [0.944, 0.0161]}, "PRO": {"N_CA": [1.468, 0.0148], "N_CD": [1.468, 0.0152], "CA_C": [1.536, 0.01], "CA_CB": [1.534, 0.0126], "C_O": [1.218, 0.02], "C_OXT": [1.218, 0.02], "CB_CG": [1.508, 0.02], "CG_CD": [1.515, 0.0118], "N_H": [0.887, 0.02], "CA_HA": [0.99, 0.0121], "CB_HB3": [0.981, 0.0193], "CB_HB2": [0.981, 0.0193], "CG_HG3": [0.979, 0.0132], "CG_HG2": [0.979, 0.0132], "CD_HD3": [0.975, 0.01], "CD_HD2": [0.975, 0.01]}, "SER": {"N_CA": [1.487, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.507, 0.0177], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_OG": [1.42, 0.014], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.995, 0.02], "CB_HB3": [0.984, 0.02], "CB_HB2": [0.984, 0.02], "OG_HG": [0.846, 0.02]}, "THR": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.534, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_OG1": [1.428, 0.01], "CB_CG2": [1.513, 0.01], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.985, 0.02], "CB_HB": [0.987, 0.02], "OG1_HG1": [0.848, 0.02], "CG2_HG21": [0.974, 0.0145], "CG2_HG22": [0.974, 0.0145], "CG2_HG23": [0.974, 0.0145]}, "TRP": {"N_CA": [1.488, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.534, 0.0118], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.498, 0.01], "CG_CD1": [1.365, 0.01], "CG_CD2": [1.439, 0.01], "CD1_NE1": [1.369, 0.01], "CD2_CE2": [1.411, 0.01], "CD2_CE3": [1.399, 0.01], "NE1_CE2": [1.37, 0.01], "CE2_CZ2": [1.394, 0.01], "CE3_CZ3": [1.377, 0.01], "CZ2_CH2": [1.376, 0.01], "CZ3_CH2": [1.395, 0.0112], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.986, 0.02], "CB_HB3": [0.979, 0.0197], "CB_HB2": [0.979, 0.0197], "CD1_HD1": [0.945, 0.0191], "NE1_HE1": [0.877, 0.02], "CE3_HE3": [0.944, 0.02], "CZ2_HZ2": [0.942, 0.0188], "CZ3_HZ3": [0.944, 0.0181], "CH2_HH2": [0.941, 0.0181]}, "TYR": {"N_CA": [1.487, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.531, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG": [1.508, 0.01], "CG_CD1": [1.385, 0.011], "CG_CD2": [1.385, 0.011], "CD1_CE1": [1.385, 0.01], "CD2_CE2": [1.385, 0.01], "CE1_CZ": [1.383, 0.01], "CE2_CZ": [1.383, 0.01], "CZ_OH": [1.374, 0.0155], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.991, 0.02], "CB_HB3": [0.98, 0.0164], "CB_HB2": [0.98, 0.0164], "CD1_HD1": [0.943, 0.0173], "CD2_HD2": [0.943, 0.0173], "CE1_HE1": [0.943, 0.0169], "CE2_HE2": [0.943, 0.0169], "OH_HH": [0.861, 0.02]}, "VAL": {"N_CA": [1.494, 0.01], "CA_C": [1.533, 0.01], "CA_CB": [1.541, 0.01], "C_O": [1.247, 0.0187], "C_OXT": [1.247, 0.0187], "CB_CG1": [1.521, 0.0135], "CB_CG2": [1.521, 0.0135], "N_H": [0.911, 0.02], "N_H2": [0.911, 0.02], "N_H3": [0.911, 0.02], "CA_HA": [0.974, 0.02], "CB_HB": [0.989, 0.0175], "CG1_HG11": [0.973, 0.0146], "CG1_HG12": [0.973, 0.0146], "CG1_HG13": [0.973, 0.0146], "CG2_HG21": [0.973, 0.0146], "CG2_HG22": [0.973, 0.0146], "CG2_HG23": [0.973, 0.0146]}, "DA": {"OP3_P": [1.517, 0.0192], "P_OP1": [1.517, 0.0192], "P_OP2": [1.517, 0.0192], "P_\"O5'\"": [1.614, 0.0178], "\"O5'\"_\"C5'\"": [1.45, 0.0166], "\"C5'\"_\"C4'\"": [1.509, 0.01], "\"C4'\"_\"O4'\"": [1.442, 0.01], "\"C4'\"_\"C3'\"": [1.526, 0.0115], "\"O4'\"_\"C1'\"": [1.425, 0.01], "\"C3'\"_\"O3'\"": [1.424, 0.01], "\"C3'\"_\"C2'\"": [1.526, 0.0101], "\"C2'\"_\"C1'\"": [1.521, 0.0118], "\"C1'\"_N9": [1.462, 0.0111], "N9_C8": [1.373, 0.01], "N9_C4": [1.377, 0.01], "C8_N7": [1.31, 0.01], "N7_C5": [1.388, 0.01], "C5_C6": [1.408, 0.01], "C5_C4": [1.381, 0.01], "C6_N6": [1.33, 0.01], "C6_N1": [1.354, 0.01], "N1_C2": [1.339, 0.01], "C2_N3": [1.33, 0.01], "N3_C4": [1.343, 0.01], "\"C5'\"_\"H5'\"": [0.989, 0.02], "\"C5'\"_\"H5''\"": [0.989, 0.02], "\"C4'\"_\"H4'\"": [0.987, 0.017], "\"C3'\"_\"H3'\"": [0.988, 0.0189], "\"O3'\"_\"HO3'\"": [0.849, 0.02], "\"C2'\"_\"H2'\"": [0.977, 0.0113], "\"C2'\"_\"H2''\"": [0.977, 0.0113], "\"C1'\"_\"H1'\"": [0.993, 0.0101], "C8_H8": [0.942, 0.017], "N6_H61": [0.877, 0.02], "N6_H62": [0.877, 0.02], "C2_H2": [0.945, 0.02]}, "A": {"OP3_P": [1.517, 0.0192], "P_OP1": [1.517, 0.0192], "P_OP2": [1.517, 0.0192], "P_\"O5'\"": [1.614, 0.0178], "\"O5'\"_\"C5'\"": [1.45, 0.0166], "\"C5'\"_\"C4'\"": [1.509, 0.01], "\"C4'\"_\"O4'\"": [1.451, 0.01], "\"C4'\"_\"C3'\"": [1.535, 0.01], "\"O4'\"_\"C1'\"": [1.409, 0.01], "\"C3'\"_\"O3'\"": [1.422, 0.01], "\"C3'\"_\"C2'\"": [1.531, 0.01], "\"C2'\"_\"O2'\"": [1.411, 0.01], "\"C2'\"_\"C1'\"": [1.525, 0.01], "\"C1'\"_N9": [1.458, 0.01], "N9_C8": [1.372, 0.01], "N9_C4": [1.374, 0.0101], "C8_N7": [1.31, 0.01], "N7_C5": [1.388, 0.01], "C5_C6": [1.408, 0.01], "C5_C4": [1.381, 0.01], "C6_N6": [1.33, 0.01], "C6_N1": [1.354, 0.01], "N1_C2": [1.339, 0.01], "C2_N3": [1.33, 0.01], "N3_C4": [1.343, 0.01], "\"C5'\"_\"H5'\"": [0.989, 0.02], "\"C5'\"_\"H5''\"": [0.989, 0.02], "\"C4'\"_\"H4'\"": [0.981, 0.02], "\"C3'\"_\"H3'\"": [0.992, 0.02], "\"O3'\"_\"HO3'\"": [0.849, 0.02], "\"C2'\"_\"H2'\"": [0.994, 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"O_C_OXT": [125.683, 1.5], "CA_CB_HB3": [109.546, 1.5], "CA_CB_HB2": [109.546, 1.5], "CA_CB_HB1": [109.546, 1.5], "HB3_CB_HB2": [109.386, 1.5], "HB3_CB_HB1": [109.386, 1.5], "HB2_CB_HB1": [109.386, 1.5]}, "ARG": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.374, 1.62], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.037, 2.4], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [108.967, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [114.117, 1.5], "CA_CB_HB3": [108.549, 1.5], "CA_CB_HB2": [108.549, 1.5], "CG_CB_HB3": [108.775, 1.5], "CG_CB_HB2": [108.775, 1.5], "HB3_CB_HB2": [107.844, 1.5], "CB_CG_CD": [112.387, 3.0], "CB_CG_HG3": [109.262, 1.5], "CB_CG_HG2": [109.262, 1.5], "CD_CG_HG3": [108.956, 1.5], "CD_CG_HG2": [108.956, 1.5], "HG3_CG_HG2": [107.927, 1.57], "CG_CD_NE": [112.382, 2.9], "CG_CD_HD3": [109.197, 1.51], "CG_CD_HD2": [109.197, 1.51], "NE_CD_HD3": [109.183, 1.5], "NE_CD_HD2": [109.183, 1.5], "HD3_CD_HD2": [107.877, 1.5], "CD_NE_CZ": [124.51, 1.5], "CD_NE_HE": [117.883, 1.5], "CZ_NE_HE": [117.606, 1.5], "NE_CZ_NH1": [120.052, 1.5], "NE_CZ_NH2": [120.052, 1.5], "NH1_CZ_NH2": [119.896, 1.5], "CZ_NH1_HH11": [119.855, 2.01], "CZ_NH1_HH12": [119.855, 2.01], "HH11_NH1_HH12": [120.29, 2.09], "CZ_NH2_HH21": [119.855, 2.01], "CZ_NH2_HH22": [119.855, 2.01], "HH21_NH2_HH22": [120.29, 2.09]}, "ASN": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [111.766, 1.5], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.54, 2.6], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [107.983, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [112.981, 1.5], "CA_CB_HB3": [108.904, 1.5], "CA_CB_HB2": [108.904, 1.5], "CG_CB_HB3": [109.076, 1.5], "CG_CB_HB2": [109.076, 1.5], "HB3_CB_HB2": [108.069, 1.5], "CB_CG_OD1": [120.613, 1.5], "CB_CG_ND2": [116.821, 1.5], "OD1_CG_ND2": [122.566, 1.5], "CG_ND2_HD21": [120.022, 1.65], "CG_ND2_HD22": [120.022, 1.65], "HD21_ND2_HD22": [119.956, 2.38]}, "ASP": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [111.338, 1.5], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.804, 2.58], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [108.666, 1.69], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [113.398, 1.64], "CA_CB_HB3": [108.488, 2.17], "CA_CB_HB2": [108.488, 2.17], "CG_CB_HB3": [107.84, 2.14], "CG_CB_HB2": [107.84, 2.14], "HB3_CB_HB2": [107.891, 1.66], "CB_CG_OD1": [117.986, 1.5], "CB_CG_OD2": [117.986, 1.5], "OD1_CG_OD2": [124.027, 1.5]}, "CYS": {"CA_N_H": [109.671, 1.5], "CA_N_H2": [109.671, 1.5], "CA_N_H3": [109.671, 1.5], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.494, 1.5], "N_CA_CB": [110.827, 1.5], "N_CA_HA": [107.983, 1.5], "C_CA_CB": [109.612, 2.06], "C_CA_HA": [108.606, 1.5], "CB_CA_HA": [108.443, 1.5], "CA_C_O": [117.134, 1.5], "CA_C_OXT": [117.134, 1.5], "O_C_OXT": [125.732, 1.5], "CA_CB_SG": [113.455, 1.5], "CA_CB_HB3": [109.118, 1.5], "CA_CB_HB2": [109.118, 1.5], "SG_CB_HB3": [108.544, 1.5], "SG_CB_HB2": [108.544, 1.5], "HB3_CB_HB2": [107.93, 1.5], "CB_SG_HG": [97.249, 3.0]}, "GLN": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.374, 1.62], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.037, 2.4], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [108.967, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [113.607, 1.5], "CA_CB_HB3": [108.549, 1.5], "CA_CB_HB2": [108.549, 1.5], "CG_CB_HB3": [109.107, 1.5], "CG_CB_HB2": [109.107, 1.5], "HB3_CB_HB2": [107.844, 1.5], "CB_CG_CD": [112.22, 2.15], "CB_CG_HG3": [109.204, 1.5], "CB_CG_HG2": [109.204, 1.5], "CD_CG_HG3": [109.082, 1.5], "CD_CG_HG2": [109.082, 1.5], "HG3_CG_HG2": [107.846, 1.5], "CG_CD_OE1": [121.405, 1.5], "CG_CD_NE2": [116.125, 1.5], "OE1_CD_NE2": [122.47, 1.5], "CD_NE2_HE21": [120.022, 1.65], "CD_NE2_HE22": [120.022, 1.65], "HE21_NE2_HE22": [119.956, 2.38]}, "GLU": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.374, 1.62], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.037, 2.4], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [108.967, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [113.445, 1.5], "CA_CB_HB3": [108.549, 1.5], "CA_CB_HB2": [108.549, 1.5], "CG_CB_HB3": [108.89, 1.5], "CG_CB_HB2": [108.89, 1.5], "HB3_CB_HB2": [107.844, 1.5], "CB_CG_CD": [114.629, 2.24], "CB_CG_HG3": [108.906, 1.5], "CB_CG_HG2": [108.906, 1.5], "CD_CG_HG3": [108.404, 1.5], "CD_CG_HG2": [108.404, 1.5], "HG3_CG_HG2": [107.521, 1.5], "CG_CD_OE1": [118.214, 1.64], "CG_CD_OE2": [118.214, 1.64], "OE1_CD_OE2": [123.571, 1.5]}, "GLY": {"CA_N_H": [110.311, 2.11], "CA_N_H2": [110.311, 2.11], "CA_N_H3": [110.311, 2.11], "H_N_H2": [109.021, 2.83], "H_N_H3": [109.021, 2.83], "H2_N_H3": [109.021, 2.83], "N_CA_C": [111.723, 1.5], "N_CA_HA3": [109.054, 1.5], "N_CA_HA2": [109.054, 1.5], "C_CA_HA3": [109.424, 1.5], "C_CA_HA2": [109.424, 1.5], "HA3_CA_HA2": [108.229, 1.89], "CA_C_O": [117.073, 1.5], "CA_C_OXT": [117.073, 1.5], "O_C_OXT": [125.855, 1.5]}, "HIS": {"CA_N_H": [109.992, 2.14], "CA_N_H2": [109.992, 2.14], "CA_N_H3": [109.992, 2.14], "H_N_H2": [109.032, 3.0], "H_N_H3": [109.032, 3.0], "H2_N_H3": [109.032, 3.0], "N_CA_C": [109.292, 1.55], "N_CA_CB": [110.573, 1.5], "N_CA_HA": [108.019, 2.27], "C_CA_CB": [111.874, 3.0], "C_CA_HA": [108.29, 1.5], "CB_CA_HA": [108.89, 2.34], "CA_C_O": [117.058, 3.0], "CA_C_OXT": [117.058, 3.0], "O_C_OXT": [125.883, 1.5], "CA_CB_CG": [113.931, 1.83], "CA_CB_HB3": [108.697, 1.5], "CA_CB_HB2": [108.697, 1.5], "CG_CB_HB3": [108.948, 1.5], "CG_CB_HB2": [108.948, 1.5], "HB3_CB_HB2": [107.846, 2.68], "CB_CG_ND1": [122.94, 3.0], "CB_CG_CD2": [131.173, 3.0], "ND1_CG_CD2": [105.887, 1.5], "CG_ND1_CE1": [109.313, 1.5], "CG_ND1_HD1": [125.337, 2.6], "CE1_ND1_HD1": [125.35, 3.0], "CG_CD2_NE2": [107.589, 1.5], "CG_CD2_HD2": [126.688, 3.0], "NE2_CD2_HD2": [125.723, 3.0], "ND1_CE1_NE2": [108.287, 1.5], "ND1_CE1_HE1": [125.729, 2.42], "NE2_CE1_HE1": [125.984, 1.51], "CD2_NE2_CE1": [108.93, 1.5], "CD2_NE2_HE2": [125.575, 3.0], "CE1_NE2_HE2": [125.489, 3.0]}, "ILE": {"CA_N_H": [110.089, 1.83], "CA_N_H2": [110.089, 1.83], "CA_N_H3": [110.089, 1.83], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [108.763, 1.5], "N_CA_CB": [110.82, 1.5], "N_CA_HA": [108.396, 1.5], "C_CA_CB": [111.764, 1.5], "C_CA_HA": [108.542, 1.5], "CB_CA_HA": [108.383, 1.5], "CA_C_O": [117.133, 1.5], "CA_C_OXT": [117.133, 1.5], "O_C_OXT": [125.734, 1.5], "CA_CB_CG1": [111.759, 1.5], "CA_CB_CG2": [110.782, 1.5], "CA_CB_HB": [107.412, 1.5], "CG1_CB_CG2": [111.775, 1.5], "CG1_CB_HB": [107.402, 1.5], "CG2_CB_HB": [107.601, 1.5], "CB_CG1_CD1": [113.965, 1.5], "CB_CG1_HG12": [108.703, 1.5], "CB_CG1_HG13": [108.703, 1.5], "CD1_CG1_HG12": [108.717, 1.5], "CD1_CG1_HG13": [108.717, 1.5], "HG12_CG1_HG13": [107.862, 1.5], "CB_CG2_HG21": [109.662, 1.5], "CB_CG2_HG22": [109.662, 1.5], "CB_CG2_HG23": [109.662, 1.5], "HG21_CG2_HG22": [109.411, 1.5], "HG21_CG2_HG23": [109.411, 1.5], "HG22_CG2_HG23": [109.411, 1.5], "CG1_CD1_HD11": [109.566, 1.5], "CG1_CD1_HD12": [109.566, 1.5], "CG1_CD1_HD13": [109.566, 1.5], "HD11_CD1_HD12": [109.38, 1.5], "HD11_CD1_HD13": [109.38, 1.5], "HD12_CD1_HD13": [109.38, 1.5]}, "LEU": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [108.955, 1.5], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.075, 1.5], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [109.549, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [115.442, 1.5], "CA_CB_HB3": [108.332, 1.5], "CA_CB_HB2": [108.332, 1.5], "CG_CB_HB3": [108.478, 1.5], "CG_CB_HB2": [108.478, 1.5], "HB3_CB_HB2": [107.542, 1.5], "CB_CG_CD1": [110.88, 1.5], "CB_CG_CD2": [110.88, 1.5], "CB_CG_HG": [108.053, 1.5], "CD1_CG_CD2": [110.507, 1.5], "CD1_CG_HG": [108.052, 1.5], "CD2_CG_HG": [108.052, 1.5], "CG_CD1_HD11": [109.488, 1.5], "CG_CD1_HD12": [109.488, 1.5], "CG_CD1_HD13": [109.488, 1.5], "HD11_CD1_HD12": [109.411, 1.5], "HD11_CD1_HD13": [109.411, 1.5], "HD12_CD1_HD13": [109.411, 1.5], "CG_CD2_HD21": [109.488, 1.5], "CG_CD2_HD22": [109.488, 1.5], "CG_CD2_HD23": [109.488, 1.5], "HD21_CD2_HD22": [109.411, 1.5], "HD21_CD2_HD23": [109.411, 1.5], "HD22_CD2_HD23": [109.411, 1.5]}, "LYS": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.374, 1.62], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [111.037, 2.4], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [108.967, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [115.311, 1.56], "CA_CB_HB3": [108.549, 1.5], "CA_CB_HB2": [108.549, 1.5], "CG_CB_HB3": [108.65, 1.5], "CG_CB_HB2": [108.65, 1.5], "HB3_CB_HB2": [107.844, 1.5], "CB_CG_CD": [113.328, 2.0], "CB_CG_HG3": [108.601, 1.5], "CB_CG_HG2": [108.601, 1.5], "CD_CG_HG3": [108.806, 1.5], "CD_CG_HG2": [108.806, 1.5], "HG3_CG_HG2": [107.646, 1.5], "CG_CD_CE": [113.073, 1.98], "CG_CD_HD3": [109.041, 1.5], "CG_CD_HD2": [109.041, 1.5], "CE_CD_HD3": [108.889, 1.5], "CE_CD_HD2": [108.889, 1.5], "HD3_CD_HD2": [107.927, 1.57], "CD_CE_NZ": [111.734, 1.84], "CD_CE_HE3": [109.576, 1.5], "CD_CE_HE2": [109.576, 1.5], "NZ_CE_HE3": [108.989, 1.5], "NZ_CE_HE2": [108.989, 1.5], "HE3_CE_HE2": [108.067, 1.5], "CE_NZ_HZ1": [109.775, 1.81], "CE_NZ_HZ2": [109.775, 1.81], "CE_NZ_HZ3": [109.775, 1.81], "HZ1_NZ_HZ2": [109.021, 2.83], "HZ1_NZ_HZ3": [109.021, 2.83], "HZ2_NZ_HZ3": [109.021, 2.83]}, "MET": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.906, 1.5], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [109.344, 1.5], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [109.67, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [113.476, 1.5], "CA_CB_HB3": [108.666, 1.5], "CA_CB_HB2": [108.666, 1.5], "CG_CB_HB3": [108.955, 1.5], "CG_CB_HB2": [108.955, 1.5], "HB3_CB_HB2": [107.698, 1.5], "CB_CG_SD": [112.576, 2.44], "CB_CG_HG3": [109.206, 1.5], "CB_CG_HG2": [109.206, 1.5], "SD_CG_HG3": [108.861, 1.5], "SD_CG_HG2": [108.861, 1.5], "HG3_CG_HG2": [107.939, 1.5], "CG_SD_CE": [100.595, 1.5], "SD_CE_HE3": [109.425, 1.5], "SD_CE_HE2": [109.425, 1.5], "SD_CE_HE1": [109.425, 1.5], "HE3_CE_HE2": [109.509, 1.5], "HE3_CE_HE1": [109.509, 1.5], "HE2_CE_HE1": [109.509, 1.5]}, "MSE": {"CA_N_H": [110.062, 1.93], "CA_N_H2": [110.062, 1.93], "CA_N_H3": [110.062, 1.93], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.241, 1.5], "N_CA_CB": [110.245, 1.51], "N_CA_HA": [108.487, 1.5], "C_CA_CB": [110.728, 2.07], "C_CA_HA": [108.824, 1.5], "CB_CA_HA": [109.207, 1.5], "CA_C_O": [117.124, 1.5], "CA_C_OXT": [117.124, 1.5], "O_C_OXT": [125.752, 1.5], "CA_CB_CG": [113.897, 1.5], "CA_CB_HB2": [108.567, 1.5], "CA_CB_HB3": [108.567, 1.5], "CG_CB_HB2": [108.056, 1.5], "CG_CB_HB3": [108.056, 1.5], "HB2_CB_HB3": [107.715, 1.5], "CB_CG_SE": [111.593, 3.0], "CB_CG_HG2": [109.535, 1.63], "CB_CG_HG3": [109.535, 1.63], "SE_CG_HG2": [109.134, 1.5], "SE_CG_HG3": [109.134, 1.5], "HG2_CG_HG3": [108.011, 1.5], "CG_SE_CE": [98.689, 1.5], "SE_CE_HE1": [109.134, 1.5], "SE_CE_HE2": [109.134, 1.5], "SE_CE_HE3": [109.134, 1.5], "HE1_CE_HE2": [109.29, 1.5], "HE1_CE_HE3": [109.29, 1.5], "HE2_CE_HE3": [109.29, 1.5]}, "PHE": {"CA_N_H": [109.646, 1.54], "CA_N_H2": [109.646, 1.54], "CA_N_H3": [109.646, 1.54], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.448, 1.5], "N_CA_CB": [110.494, 1.5], "N_CA_HA": [108.601, 1.5], "C_CA_CB": [111.331, 2.53], "C_CA_HA": [108.45, 1.5], "CB_CA_HA": [108.69, 1.5], "CA_C_O": [117.228, 2.13], "CA_C_OXT": [117.228, 2.13], "O_C_OXT": [125.543, 1.5], "CA_CB_CG": [114.745, 1.55], "CA_CB_HB3": [108.434, 1.5], "CA_CB_HB2": [108.434, 1.5], "CG_CB_HB3": [108.862, 1.5], "CG_CB_HB2": [108.862, 1.5], "HB3_CB_HB2": [107.782, 1.5], "CB_CG_CD1": [120.97, 1.5], "CB_CG_CD2": [120.97, 1.5], "CD1_CG_CD2": [118.06, 1.5], "CG_CD1_CE1": [120.624, 1.5], "CG_CD1_HD1": [119.591, 1.5], "CE1_CD1_HD1": [119.786, 1.5], "CG_CD2_CE2": [120.624, 1.5], "CG_CD2_HD2": [119.591, 1.5], "CE2_CD2_HD2": [119.786, 1.5], "CD1_CE1_CZ": [120.325, 1.5], "CD1_CE1_HE1": [119.792, 1.5], "CZ_CE1_HE1": [119.883, 1.5], "CD2_CE2_CZ": [120.325, 1.5], "CD2_CE2_HE2": [119.792, 1.5], "CZ_CE2_HE2": [119.883, 1.5], "CE1_CZ_CE2": [120.043, 1.5], "CE1_CZ_HZ": [119.979, 1.5], "CE2_CZ_HZ": [119.979, 1.5]}, "PRO": {"CA_N_CD": [109.056, 3.0], "CA_N_H": [109.307, 3.0], "CD_N_H": [106.136, 2.25], "N_CA_C": [111.42, 2.45], "N_CA_CB": [103.43, 2.23], "N_CA_HA": [109.296, 1.5], "C_CA_CB": [110.031, 2.42], "C_CA_HA": [110.011, 1.5], "CB_CA_HA": [109.388, 1.5], "CA_C_O": [117.013, 1.95], "CA_C_OXT": [117.013, 1.95], "O_C_OXT": [125.975, 1.5], "CA_CB_CG": [103.507, 1.5], "CA_CB_HB3": [111.018, 1.5], "CA_CB_HB2": [111.018, 1.5], "CG_CB_HB3": [110.886, 1.5], "CG_CB_HB2": [110.886, 1.5], "HB3_CB_HB2": [108.922, 1.5], "CB_CG_CD": [104.503, 1.95], "CB_CG_HG3": [110.864, 1.5], "CB_CG_HG2": [110.864, 1.5], "CD_CG_HG3": [110.804, 1.5], "CD_CG_HG2": [110.804, 1.5], "HG3_CG_HG2": [108.899, 1.5], "N_CD_CG": [105.071, 2.33], "N_CD_HD3": [110.738, 1.5], "N_CD_HD2": [110.738, 1.5], "CG_CD_HD3": [110.867, 1.5], "CG_CD_HD2": [110.867, 1.5], "HD3_CD_HD2": [108.731, 1.5]}, "SER": {"CA_N_H": [109.619, 1.5], "CA_N_H2": [109.619, 1.5], "CA_N_H3": [109.619, 1.5], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.829, 1.5], "N_CA_CB": [110.99, 1.5], "N_CA_HA": [108.049, 1.5], "C_CA_CB": [111.379, 1.5], "C_CA_HA": [108.255, 1.5], "CB_CA_HA": [108.518, 1.5], "CA_C_O": [117.181, 1.5], "CA_C_OXT": [117.181, 1.5], "O_C_OXT": [125.637, 1.5], "CA_CB_OG": [110.825, 1.5], "CA_CB_HB3": [109.305, 1.5], "CA_CB_HB2": [109.305, 1.5], "OG_CB_HB3": [109.411, 1.5], "OG_CB_HB2": [109.411, 1.5], "HB3_CB_HB2": [108.07, 1.5], "CB_OG_HG": [108.529, 2.94]}, "THR": {"CA_N_H": [109.889, 1.5], "CA_N_H2": [109.889, 1.5], "CA_N_H3": [109.889, 1.5], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.414, 1.5], "N_CA_CB": [111.125, 1.5], "N_CA_HA": [108.031, 1.5], "C_CA_CB": [111.511, 2.91], "C_CA_HA": [108.6, 1.5], "CB_CA_HA": [108.62, 1.5], "CA_C_O": [117.003, 1.5], "CA_C_OXT": [117.003, 1.5], "O_C_OXT": [125.994, 1.5], "CA_CB_OG1": [108.093, 2.62], "CA_CB_CG2": [112.909, 1.5], "CA_CB_HB": [108.271, 1.5], "OG1_CB_CG2": [109.779, 2.11], "OG1_CB_HB": [108.878, 1.5], "CG2_CB_HB": [108.799, 1.5], "CB_OG1_HG1": [109.608, 2.55], "CB_CG2_HG21": [109.564, 1.5], "CB_CG2_HG22": [109.564, 1.5], "CB_CG2_HG23": [109.564, 1.5], "HG21_CG2_HG22": [109.425, 1.5], "HG21_CG2_HG23": [109.425, 1.5], "HG22_CG2_HG23": [109.425, 1.5]}, "TRP": {"CA_N_H": [109.321, 1.91], "CA_N_H2": [109.321, 1.91], "CA_N_H3": [109.321, 1.91], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.666, 1.5], "N_CA_CB": [110.562, 1.5], "N_CA_HA": [108.03, 1.5], "C_CA_CB": [111.644, 1.5], "C_CA_HA": [108.922, 1.5], "CB_CA_HA": [108.128, 1.5], "CA_C_O": [117.134, 1.5], "CA_C_OXT": [117.134, 1.5], "O_C_OXT": [125.731, 1.5], "CA_CB_CG": [113.843, 1.64], "CA_CB_HB3": [108.266, 1.5], "CA_CB_HB2": [108.266, 1.5], "CG_CB_HB3": [109.029, 1.5], "CG_CB_HB2": [109.029, 1.5], "HB3_CB_HB2": [107.759, 1.5], "CB_CG_CD1": [127.068, 1.62], "CB_CG_CD2": [126.82, 1.5], "CD1_CG_CD2": [106.112, 1.5], "CG_CD1_NE1": [110.404, 1.5], "CG_CD1_HD1": [125.159, 1.59], "NE1_CD1_HD1": [124.437, 1.5], "CG_CD2_CE2": [106.987, 1.5], "CG_CD2_CE3": [134.307, 1.5], "CE2_CD2_CE3": [118.706, 1.5], "CD1_NE1_CE2": [109.042, 1.5], "CD1_NE1_HE1": [125.328, 1.77], "CE2_NE1_HE1": [125.63, 1.6], "CD2_CE2_NE1": [107.455, 1.5], "CD2_CE2_CZ2": [122.25, 1.5], "NE1_CE2_CZ2": [130.294, 1.5], "CD2_CE3_CZ3": [118.817, 1.5], "CD2_CE3_HE3": [120.505, 1.5], "CZ3_CE3_HE3": [120.678, 1.5], "CE2_CZ2_CH2": [117.385, 1.5], "CE2_CZ2_HZ2": [121.137, 1.5], "CH2_CZ2_HZ2": [121.477, 1.5], "CE3_CZ3_CH2": [121.212, 1.5], "CE3_CZ3_HZ3": [119.471, 1.5], "CH2_CZ3_HZ3": [119.316, 1.5], "CZ2_CH2_CZ3": [121.628, 1.5], "CZ2_CH2_HH2": [119.132, 1.5], "CZ3_CH2_HH2": [119.24, 1.5]}, "TYR": {"CA_N_H": [109.646, 1.54], "CA_N_H2": [109.646, 1.54], "CA_N_H3": [109.646, 1.54], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [109.448, 1.5], "N_CA_CB": [110.494, 1.5], "N_CA_HA": [108.601, 1.5], "C_CA_CB": [111.331, 2.53], "C_CA_HA": [108.45, 1.5], "CB_CA_HA": [108.69, 1.5], "CA_C_O": [117.228, 2.13], "CA_C_OXT": [117.228, 2.13], "O_C_OXT": [125.543, 1.5], "CA_CB_CG": [114.745, 1.55], "CA_CB_HB3": [108.434, 1.5], "CA_CB_HB2": [108.434, 1.5], "CG_CB_HB3": [108.862, 1.5], "CG_CB_HB2": [108.862, 1.5], "HB3_CB_HB2": [107.782, 1.5], "CB_CG_CD1": [121.083, 1.5], "CB_CG_CD2": [121.083, 1.5], "CD1_CG_CD2": [117.834, 1.5], "CG_CD1_CE1": [121.472, 1.5], "CG_CD1_HD1": [119.317, 1.5], "CE1_CD1_HD1": [119.21, 1.5], "CG_CD2_CE2": [121.472, 1.5], "CG_CD2_HD2": [119.317, 1.5], "CE2_CD2_HD2": [119.21, 1.5], "CD1_CE1_CZ": [119.825, 1.5], "CD1_CE1_HE1": [120.168, 1.5], "CZ_CE1_HE1": [120.006, 1.5], "CD2_CE2_CZ": [119.825, 1.5], "CD2_CE2_HE2": [120.168, 1.5], "CZ_CE2_HE2": [120.006, 1.5], "CE1_CZ_CE2": [119.571, 1.5], "CE1_CZ_OH": [120.215, 3.0], "CE2_CZ_OH": [120.215, 3.0], "CZ_OH_HH": [120.0, 3.0]}, "VAL": {"CA_N_H": [110.089, 1.83], "CA_N_H2": [110.089, 1.83], "CA_N_H3": [110.089, 1.83], "H_N_H2": [109.028, 2.41], "H_N_H3": [109.028, 2.41], "H2_N_H3": [109.028, 2.41], "N_CA_C": [108.763, 1.5], "N_CA_CB": [111.441, 1.5], "N_CA_HA": [108.396, 1.5], "C_CA_CB": [111.388, 1.5], "C_CA_HA": [108.542, 1.5], "CB_CA_HA": [108.631, 1.5], "CA_C_O": [117.133, 1.5], "CA_C_OXT": [117.133, 1.5], "O_C_OXT": [125.734, 1.5], "CA_CB_CG1": [111.772, 1.5], "CA_CB_CG2": [111.772, 1.5], "CA_CB_HB": [107.252, 1.5], "CG1_CB_CG2": [110.676, 1.5], "CG1_CB_HB": [107.603, 1.5], "CG2_CB_HB": [107.603, 1.5], "CB_CG1_HG11": [109.507, 1.5], "CB_CG1_HG12": [109.507, 1.5], "CB_CG1_HG13": [109.507, 1.5], "HG11_CG1_HG12": [109.411, 1.5], "HG11_CG1_HG13": [109.411, 1.5], "HG12_CG1_HG13": [109.411, 1.5], "CB_CG2_HG21": [109.507, 1.5], "CB_CG2_HG22": [109.507, 1.5], "CB_CG2_HG23": [109.507, 1.5], "HG21_CG2_HG22": [109.411, 1.5], "HG21_CG2_HG23": [109.411, 1.5], "HG22_CG2_HG23": [109.411, 1.5]}, "DA": {"OP3_P_OP1": [112.864, 1.69], "OP3_P_OP2": [112.864, 1.69], "OP3_P_\"O5'\"": [105.808, 2.07], "OP1_P_OP2": [112.864, 1.69], "OP1_P_\"O5'\"": [105.808, 2.07], "OP2_P_\"O5'\"": [105.808, 2.07], "P_\"O5'\"_\"C5'\"": [118.783, 1.5], "\"O5'\"_\"C5'\"_\"C4'\"": [109.342, 1.5], "\"O5'\"_\"C5'\"_\"H5'\"": [109.845, 1.5], "\"O5'\"_\"C5'\"_\"H5''\"": [109.845, 1.5], "\"C4'\"_\"C5'\"_\"H5'\"": [109.624, 1.5], "\"C4'\"_\"C5'\"_\"H5''\"": [109.624, 1.5], "\"H5'\"_\"C5'\"_\"H5''\"": [108.472, 1.5], "\"C5'\"_\"C4'\"_\"O4'\"": [109.123, 1.5], "\"C5'\"_\"C4'\"_\"C3'\"": [114.866, 1.63], "\"C5'\"_\"C4'\"_\"H4'\"": [108.268, 1.5], "\"O4'\"_\"C4'\"_\"C3'\"": [105.506, 1.5], "\"O4'\"_\"C4'\"_\"H4'\"": [108.947, 1.5], "\"C3'\"_\"C4'\"_\"H4'\"": [109.069, 1.5], "\"C4'\"_\"O4'\"_\"C1'\"": [108.795, 1.5], "\"C4'\"_\"C3'\"_\"O3'\"": [110.527, 2.37], "\"C4'\"_\"C3'\"_\"C2'\"": [102.433, 1.5], "\"C4'\"_\"C3'\"_\"H3'\"": [110.775, 1.5], "\"O3'\"_\"C3'\"_\"C2'\"": [111.424, 1.96], "\"O3'\"_\"C3'\"_\"H3'\"": [110.713, 1.5], "\"C2'\"_\"C3'\"_\"H3'\"": [110.846, 1.5], "\"C3'\"_\"O3'\"_\"HO3'\"": [109.026, 2.38], "\"C3'\"_\"C2'\"_\"C1'\"": [102.663, 1.5], "\"C3'\"_\"C2'\"_\"H2'\"": [111.194, 1.5], "\"C3'\"_\"C2'\"_\"H2''\"": [111.194, 1.5], "\"C1'\"_\"C2'\"_\"H2'\"": [111.213, 1.5], "\"C1'\"_\"C2'\"_\"H2''\"": [111.213, 1.5], "\"H2'\"_\"C2'\"_\"H2''\"": [109.148, 1.5], "\"O4'\"_\"C1'\"_\"C2'\"": [106.035, 1.5], "\"O4'\"_\"C1'\"_N9": [108.236, 1.5], "\"O4'\"_\"C1'\"_\"H1'\"": [109.059, 1.5], "\"C2'\"_\"C1'\"_N9": [114.19, 1.67], "\"C2'\"_\"C1'\"_\"H1'\"": [109.272, 1.5], "N9_\"C1'\"_\"H1'\"": [109.282, 1.5], "\"C1'\"_N9_C8": [127.636, 2.81], "\"C1'\"_N9_C4": [126.671, 2.93], "C8_N9_C4": [105.693, 1.5], "N9_C8_N7": [113.469, 1.5], "N9_C8_H8": [123.206, 1.5], "N7_C8_H8": [123.326, 1.5], "C8_N7_C5": [104.739, 1.5], "N7_C5_C6": [132.25, 1.5], "N7_C5_C4": [110.483, 1.5], "C6_C5_C4": [117.267, 1.5], "C5_C6_N6": [123.792, 1.5], "C5_C6_N1": [117.409, 1.5], "N6_C6_N1": [118.799, 1.5], "C6_N6_H61": [119.723, 1.5], "C6_N6_H62": [119.723, 1.5], "H61_N6_H62": [120.554, 1.88], "C6_N1_C2": [118.521, 1.5], "N1_C2_N3": [129.332, 1.5], "N1_C2_H2": [115.313, 1.5], "N3_C2_H2": [115.355, 1.5], "C2_N3_C4": [110.982, 1.5], "N9_C4_C5": [105.616, 1.5], "N9_C4_N3": [127.895, 1.5], "C5_C4_N3": [126.489, 1.5]}, "A": {"OP3_P_OP1": [112.864, 1.69], "OP3_P_OP2": [112.864, 1.69], "OP3_P_\"O5'\"": [105.808, 2.07], "OP1_P_OP2": [112.864, 1.69], "OP1_P_\"O5'\"": [105.808, 2.07], "OP2_P_\"O5'\"": [105.808, 2.07], "P_\"O5'\"_\"C5'\"": [118.783, 1.5], "\"O5'\"_\"C5'\"_\"C4'\"": 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"OP1_P_\"O5'\"": [105.808, 2.07], "OP2_P_\"O5'\"": [105.808, 2.07], "P_\"O5'\"_\"C5'\"": [118.783, 1.5], "\"O5'\"_\"C5'\"_\"C4'\"": [109.342, 1.5], "\"O5'\"_\"C5'\"_\"H5'\"": [109.845, 1.5], "\"O5'\"_\"C5'\"_\"H5''\"": [109.845, 1.5], "\"C4'\"_\"C5'\"_\"H5'\"": [109.624, 1.5], "\"C4'\"_\"C5'\"_\"H5''\"": [109.624, 1.5], "\"H5'\"_\"C5'\"_\"H5''\"": [108.472, 1.5], "\"C5'\"_\"C4'\"_\"O4'\"": [109.123, 1.5], "\"C5'\"_\"C4'\"_\"C3'\"": [114.866, 1.63], "\"C5'\"_\"C4'\"_\"H4'\"": [108.268, 1.5], "\"O4'\"_\"C4'\"_\"C3'\"": [105.506, 1.5], "\"O4'\"_\"C4'\"_\"H4'\"": [108.947, 1.5], "\"C3'\"_\"C4'\"_\"H4'\"": [109.069, 1.5], "\"C4'\"_\"O4'\"_\"C1'\"": [108.795, 1.5], "\"C4'\"_\"C3'\"_\"O3'\"": [110.527, 2.37], "\"C4'\"_\"C3'\"_\"C2'\"": [102.433, 1.5], "\"C4'\"_\"C3'\"_\"H3'\"": [110.775, 1.5], "\"O3'\"_\"C3'\"_\"C2'\"": [111.424, 1.96], "\"O3'\"_\"C3'\"_\"H3'\"": [110.713, 1.5], "\"C2'\"_\"C3'\"_\"H3'\"": [110.846, 1.5], "\"C3'\"_\"O3'\"_\"HO3'\"": [109.026, 2.38], "\"C3'\"_\"C2'\"_\"C1'\"": [102.663, 1.5], "\"C3'\"_\"C2'\"_\"H2'\"": [111.194, 1.5], "\"C3'\"_\"C2'\"_\"H2''\"": [111.194, 1.5], "\"C1'\"_\"C2'\"_\"H2'\"": [111.213, 1.5], "\"C1'\"_\"C2'\"_\"H2''\"": [111.213, 1.5], "\"H2'\"_\"C2'\"_\"H2''\"": [109.148, 1.5], "\"O4'\"_\"C1'\"_\"C2'\"": [106.035, 1.5], "\"O4'\"_\"C1'\"_N9": [108.236, 1.5], "\"O4'\"_\"C1'\"_\"H1'\"": [109.059, 1.5], "\"C2'\"_\"C1'\"_N9": [114.19, 1.67], "\"C2'\"_\"C1'\"_\"H1'\"": [109.272, 1.5], "N9_\"C1'\"_\"H1'\"": [109.282, 1.5], "\"C1'\"_N9_C8": [127.617, 2.81], "\"C1'\"_N9_C4": [126.652, 2.93], "C8_N9_C4": [105.731, 1.5], "N9_C8_N7": [113.507, 1.5], "N9_C8_H8": [123.187, 1.5], "N7_C8_H8": [123.307, 1.5], "C8_N7_C5": [104.778, 1.5], "N7_C5_C6": [130.391, 1.5], "N7_C5_C4": [110.574, 1.5], "C6_C5_C4": [119.035, 1.5], "C5_C6_O6": [128.572, 1.5], "C5_C6_N1": [109.765, 1.5], "O6_C6_N1": [121.664, 1.5], "C6_N1_C2": [125.186, 1.5], "C6_N1_H1": [117.309, 1.5], "C2_N1_H1": [117.505, 1.5], "N1_C2_N3": [125.293, 1.5], "N1_C2_H2": [117.332, 1.5], "N3_C2_H2": [117.375, 1.5], "C2_N3_C4": [113.45, 1.5], "N9_C4_C5": [105.411, 1.5], "N9_C4_N3": [127.317, 1.5], "C5_C4_N3": [127.272, 1.5]}, "I": {"OP3_P_OP1": [112.864, 1.69], "OP3_P_OP2": [112.864, 1.69], "OP3_P_\"O5'\"": [105.808, 2.07], "OP1_P_OP2": [112.864, 1.69], "OP1_P_\"O5'\"": [105.808, 2.07], "OP2_P_\"O5'\"": [105.808, 2.07], "P_\"O5'\"_\"C5'\"": [118.783, 1.5], "\"O5'\"_\"C5'\"_\"C4'\"": [109.342, 1.5], "\"O5'\"_\"C5'\"_\"H5'\"": [109.845, 1.5], "\"O5'\"_\"C5'\"_\"H5''\"": [109.845, 1.5], "\"C4'\"_\"C5'\"_\"H5'\"": [109.624, 1.5], "\"C4'\"_\"C5'\"_\"H5''\"": [109.624, 1.5], "\"H5'\"_\"C5'\"_\"H5''\"": [108.472, 1.5], "\"C5'\"_\"C4'\"_\"O4'\"": [109.123, 1.5], "\"C5'\"_\"C4'\"_\"C3'\"": [116.008, 1.52], "\"C5'\"_\"C4'\"_\"H4'\"": [108.268, 1.5], "\"O4'\"_\"C4'\"_\"C3'\"": [105.388, 1.5], "\"O4'\"_\"C4'\"_\"H4'\"": [108.947, 1.5], "\"C3'\"_\"C4'\"_\"H4'\"": [109.363, 1.86], "\"C4'\"_\"O4'\"_\"C1'\"": [109.903, 1.5], "\"C4'\"_\"C3'\"_\"O3'\"": [111.281, 2.46], "\"C4'\"_\"C3'\"_\"C2'\"": [102.602, 1.5], "\"C4'\"_\"C3'\"_\"H3'\"": [110.452, 2.54], "\"O3'\"_\"C3'\"_\"C2'\"": [111.581, 2.83], "\"O3'\"_\"C3'\"_\"H3'\"": [110.38, 1.67], "\"C2'\"_\"C3'\"_\"H3'\"": [110.504, 1.75], "\"C3'\"_\"O3'\"_\"HO3'\"": [108.744, 3.0], "\"C3'\"_\"C2'\"_\"O2'\"": [112.782, 2.45], "\"C3'\"_\"C2'\"_\"C1'\"": [101.239, 1.5], "\"C3'\"_\"C2'\"_\"H2'\"": [110.596, 1.51], "\"O2'\"_\"C2'\"_\"C1'\"": [111.715, 2.69], "\"O2'\"_\"C2'\"_\"H2'\"": [110.448, 1.97], "\"C1'\"_\"C2'\"_\"H2'\"": [110.636, 1.7], "\"C2'\"_\"O2'\"_\"HO2'\"": [109.103, 2.13], "\"O4'\"_\"C1'\"_\"C2'\"": [106.047, 1.5], "\"O4'\"_\"C1'\"_N9": [108.477, 1.5], "\"O4'\"_\"C1'\"_\"H1'\"": [109.807, 1.5], "\"C2'\"_\"C1'\"_N9": [113.824, 1.5], "\"C2'\"_\"C1'\"_\"H1'\"": [109.015, 1.5], "N9_\"C1'\"_\"H1'\"": [109.561, 1.5], "\"C1'\"_N9_C8": [126.829, 1.91], "\"C1'\"_N9_C4": [127.44, 1.8], "C8_N9_C4": [105.731, 1.5], "N9_C8_N7": [113.507, 1.5], "N9_C8_H8": [123.187, 1.5], "N7_C8_H8": [123.307, 1.5], "C8_N7_C5": [104.778, 1.5], "N7_C5_C6": [130.391, 1.5], "N7_C5_C4": [110.574, 1.5], "C6_C5_C4": [119.035, 1.5], "C5_C6_O6": [128.572, 1.5], "C5_C6_N1": [109.765, 1.5], "O6_C6_N1": [121.664, 1.5], "C6_N1_C2": [125.186, 1.5], "C6_N1_H1": [117.309, 1.5], "C2_N1_H1": [117.505, 1.5], "N1_C2_N3": [125.293, 1.5], "N1_C2_H2": [117.332, 1.5], "N3_C2_H2": [117.375, 1.5], "C2_N3_C4": [113.45, 1.5], "N9_C4_C5": [105.411, 1.5], "N9_C4_N3": [127.317, 1.5], "C5_C4_N3": [127.272, 1.5]}}, "COPYING": "This data has been derived from the CCP4 MON_LIB on 2022-11-16 09:21:06.524751. MON_LIB is licensed under GNU LESSER GENERAL PUBLIC LICENSE Version 3. Consult the latest CCP4 for the full license text."}
\ No newline at end of file
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index f04f71406..39c8217c1 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -1,8 +1,10 @@
import os
import json
+import datetime
import numpy as np
+import ost
from ost import geom
from ost import mol
@@ -163,21 +165,34 @@ def StereoDataFromMON_LIB(mon_lib_path, compounds=None):
angle_data = _ParseAngleData(doc)
data["bond_data"].update(bond_data)
data["angle_data"].update(angle_data)
+
+ # add license info
+ copying_str = f"This data has been derived from the CCP4 MON_LIB on "
+ copying_str += f"{datetime.datetime.now()}. MON_LIB is licensed under "
+ copying_str += f"GNU LESSER GENERAL PUBLIC LICENSE Version 3. Consult the "
+ copying_str += f"latest CCP4 for the full license text."
+ data["COPYING"] = copying_str
+
return data
-def GetBondParam(a1, a2, stereo_data):
+def GetBondParam(a1, a2, stereo_data = None):
""" Returns mean and standard deviation for bond
:param a1: First atom that defines bond
:type a1: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param a2: Second atom that defines bond
:type a2: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
- :param stereo_data: Stereochemistry data
+ :param stereo_data: Stereochemistry data, use return value of
+ :func:`GetDefaultStereoData` if not given.
+ If you call this function repeatedly, you
+ really should provide *stereo_data*!
:type stereo_data: :class:`dict`
:returns: :class:`tuple` with mean and standard deviation. Values are None
if respective bond is not found in *stereo_data*
"""
+ if stereo_data is None:
+ stereo_data = GetDefaultStereoData()
if a1.GetResidue().GetHashCode() == a2.GetResidue().GetHashCode():
# intra residue case, inter-residue case not yet implemented
rname = a1.GetResidue().GetName()
@@ -197,7 +212,7 @@ def GetBondParam(a1, a2, stereo_data):
return (None, None)
-def GetAngleParam(a1, a2, a3, stereo_data):
+def GetAngleParam(a1, a2, a3, stereo_data = None):
""" Returns mean and standard deviation for angle
:param a1: First atom that defines angle
@@ -206,11 +221,16 @@ def GetAngleParam(a1, a2, a3, stereo_data):
:type a2: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
:param a3: Third atom that defines angle
:type a3: :class:`ost.mol.AtomView`/:class:`ost.mol.AtomHandle`
- :param stereo_data: Stereochemistry data
+ :param stereo_data: Stereochemistry data, use return value of
+ :func:`GetDefaultStereoData` if not given.
+ If you call this function repeatedly, you
+ really should provide *stereo_data*!
:type stereo_data: :class:`dict`
:returns: :class:`tuple` with mean and standard deviation. Values are None
if respective angle is not found in *stereo_data*
"""
+ if stereo_data is None:
+ stereo_data = GetDefaultStereoData()
h1 = a1.GetResidue().handle.GetHashCode()
h2 = a2.GetResidue().handle.GetHashCode()
h3 = a3.GetResidue().handle.GetHashCode()
@@ -313,7 +333,8 @@ def GetBadBonds(ent, stereo_data = None, tolerance=12):
:param ent: Entity for which you want to identify unrealistic bonds
:type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
- :param stereo_data: Stereochemistry data
+ :param stereo_data: Stereochemistry data, use return value of
+ :func:`GetDefaultStereoData` if not given.
:type stereo_data: :class:`dict`
:param tolerance: Bonds that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
@@ -322,12 +343,14 @@ def GetBadBonds(ent, stereo_data = None, tolerance=12):
:class:`ost.mol.AtomHandle` from *ent* that represent bad bonds.
"""
+ if stereo_data is None:
+ stereo_data = GetDefaultStereoData()
assert("bond_data" in stereo_data)
return_list = list()
for b in ent.bonds:
a1 = b.first
a2 = b.second
- mean, std = GetBondParam(a1, a2, stereo_data)
+ mean, std = GetBondParam(a1, a2, stereo_data = stereo_data)
if None not in [mean, std]:
diff = abs(mean-b.length)
if diff > tolerance*std:
@@ -340,7 +363,8 @@ def GetBadAngles(ent, stereo_data = None, tolerance=12):
:param ent: Entity for which you want to identify unrealistic angles
:type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
- :param stereo_data: Stereochemistry data
+ :param stereo_data: Stereochemistry data, use return value of
+ :func:`GetDefaultStereoData` if not given.
:type stereo_data: :class:`dict`
:param tolerance: Angles that devaiate more than *tolerance* times standard
deviation from expected mean are considered bad
@@ -348,10 +372,12 @@ def GetBadAngles(ent, stereo_data = None, tolerance=12):
:returns: :class:`list` of tuples. Each tuple consists of three
:class:`ost.mol.AtomHandle` from *ent* that represent bad angles.
"""
+ if stereo_data is None:
+ stereo_data = GetDefaultStereoData()
assert("angle_data" in stereo_data)
return_list = list()
for a in _GetAngles(ent.bonds):
- mean, std = GetAngleParam(a[0], a[1], a[2], stereo_data)
+ mean, std = GetAngleParam(a[0], a[1], a[2], stereo_data = stereo_data)
if None not in [mean, std]:
angle = geom.Angle(a[0].GetPos() - a[1].GetPos(),
a[2].GetPos() - a[1].GetPos())
@@ -378,13 +404,18 @@ def StereoCheck(ent, stereo_data = None):
:param ent: Entity to be stereochecked
:type ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
- :param stereo_data: Stereochemistry data
+ :param stereo_data: Stereochemistry data, use return value of
+ :func:`GetDefaultStereoData` if not given.
:type stereo_data: :class:`dict`
:returns: Tuple with four elements: 1) :class:`ost.mol.EntityView` of
*ent* processed as described above 2) Return value of
:func:`GetClashes` 3) return value of :func:`GetBadBonds`
4) return value of :func:`GetBadAngles`
"""
+
+ if stereo_data is None:
+ stereo_data = GetDefaultStereoData()
+
sel = ent.Select("peptide=true or nucleotide=true")
clashes = GetClashes(sel)
bad_bonds = GetBadBonds(sel, stereo_data = stereo_data)
@@ -437,3 +468,16 @@ def StereoCheck(ent, stereo_data = None):
return_view = sel
return return_view, clashes, bad_bonds, bad_angles
+
+def GetDefaultStereoData():
+ """ Get default stereo data derived from CCP4 MON_LIB
+
+ Used as default if not provided in :func:`GetBadBonds`, :func:`GetBadAngles`
+ and :func:`StereoCheck`.
+
+ MON_LIB is licensed under GNU LESSER GENERAL PUBLIC LICENSE Version 3.
+ Consult the latest CCP4 for the full license text.
+ """
+ data_path = os.path.join(ost.GetSharedDataPath(), "stereo_data.json")
+ with open(data_path, 'r') as fh:
+ return json.load(fh)
--
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