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Feature/hbond #64

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merged 7 commits into from
Jan 18, 2024
Merged

Feature/hbond #64

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ee0478d
add H bond support in precalculate_gpu
ysyecust Jan 14, 2024
563c2f0
fix: add ad atom type number
ysyecust Jan 17, 2024
e96b67d
fix: donor type
ysyecust Jan 17, 2024
72668ea
format code
ysyecust Jan 18, 2024
6b3e806
fix cpu H bond eval
ysyecust Jan 18, 2024
2a4d4e1
Merge branch 'main' into feature/Hbond
ysyecust Jan 18, 2024
75c9064
fix: H atom type error
ysyecust Jan 18, 2024
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,10 @@ unidock/example/screening_test/result
unidock/example/screening_test/def_ligands.txt
unidock/example/screening_test/rundock.sh
unidock/example/screening_test/unidock
unidock/example/screening_test/fail_result
unidock/example/screening_test/receptor_grids
unidock/example/screening_test/unidock_root
unidock/example/screening_test/test_dock
unidock_tools/dist
unidock_tools/dist/*
unidock_tools/unidock_tools.egg-info
Expand Down
42 changes: 35 additions & 7 deletions unidock/src/cuda/atom_constants_gpu.cuh
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Expand Up @@ -49,7 +49,11 @@ __device__ __constant__ sz AD_TYPE_CG1 = 27;
__device__ __constant__ sz AD_TYPE_CG2 = 28;
__device__ __constant__ sz AD_TYPE_CG3 = 29;
__device__ __constant__ sz AD_TYPE_W = 30; // hydrated ligand
__device__ __constant__ sz AD_TYPE_SIZE = 31;
__device__ __constant__ sz AD_TYPE_OXA = 31; // biased protein hydrogen bond acceptor
__device__ __constant__ sz AD_TYPE_NXA = 32; // biased protein hydrogen bond acceptor
__device__ __constant__ sz AD_TYPE_OXD = 33; // biased protein hydrogen bond donor
__device__ __constant__ sz AD_TYPE_NXD = 34; // biased protein hydrogen bond donor
__device__ __constant__ sz AD_TYPE_SIZE = 35;

// X-Score
__device__ __constant__ sz XS_TYPE_C_H = 0;
Expand Down Expand Up @@ -84,7 +88,11 @@ __device__ __constant__ sz XS_TYPE_C_H_CG3 = 28;
__device__ __constant__ sz XS_TYPE_C_P_CG3 = 29;
__device__ __constant__ sz XS_TYPE_G3 = 30;
__device__ __constant__ sz XS_TYPE_W = 31; // hydrated ligand
__device__ __constant__ sz XS_TYPE_SIZE = 32;
__device__ __constant__ sz XS_TYPE_O_XA = 32;
__device__ __constant__ sz XS_TYPE_N_XA = 33;
__device__ __constant__ sz XS_TYPE_O_XD = 34;
__device__ __constant__ sz XS_TYPE_N_XD = 35;
__device__ __constant__ sz XS_TYPE_SIZE = 36;

// DrugScore-CSD
__device__ __constant__ sz SY_TYPE_C_3 = 0;
Expand Down Expand Up @@ -155,7 +163,11 @@ __device__ atom_kind_gpu atom_kind_data_gpu[] = {
{"CG1", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 27
{"CG2", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 28
{"CG3", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 29
{"W", 0.00000, 0.00000, 0.0, 0.0, 0.00000, 0.00000, 0.00} // 30
{"W", 0.00000, 0.00000, 0.0, 0.0, 0.00000, 0.00000, 0.00}, // 30
{"OXA", 1.60000, 0.20000, 0.0, 0.0, -0.00251, 17.15730, 0.73}, // 31
{"NXA", 1.75000, 0.16000, 0.0, 0.0, -0.00162, 22.44930, 0.75}, // 32
{"OXD", 1.60000, 0.20000, 0.0, 0.0, -0.00251, 17.15730, 0.73}, // 33
{"NXD", 1.75000, 0.16000, 0.0, 0.0, -0.00162, 22.44930, 0.75} // 34
};

__device__ __constant__ fl metal_solvation_parameter_gpu = -0.00110;
Expand Down Expand Up @@ -258,6 +270,14 @@ __device__ __forceinline__ sz ad_type_to_el_type_gpu(sz t) {
return EL_TYPE_Dummy;
case AD_TYPE_W:
return EL_TYPE_Dummy;
case AD_TYPE_OXA:
return EL_TYPE_O;
case AD_TYPE_NXA:
return EL_TYPE_N;
case AD_TYPE_OXD:
return EL_TYPE_O;
case AD_TYPE_NXD:
return EL_TYPE_N;
case AD_TYPE_SIZE:
return EL_TYPE_SIZE;
default:
Expand Down Expand Up @@ -299,7 +319,11 @@ __device__ __constant__ fl xs_vdw_radii_gpu[] = {
0.0, // G1
0.0, // G2
0.0, // G3
0.0 // W
0.0, // W
1.7, // O_XA
1.8, // N_XA
1.7, // O_XD
1.8 // N_XD
};

__device__ __constant__ fl xs_vinardo_vdw_radii_gpu[] = {
Expand Down Expand Up @@ -334,7 +358,11 @@ __device__ __constant__ fl xs_vinardo_vdw_radii_gpu[] = {
0.0, // G1
0.0, // G2
0.0, // G3
0.0 // W
0.0, // W
1.6, // O_XA
1.7, // N_XA
1.6, // O_XD
1.7
};

__device__ __forceinline__ fl xs_radius_gpu(sz t) {
Expand Down Expand Up @@ -366,12 +394,12 @@ __device__ __forceinline__ bool xs_is_hydrophobic_gpu(sz xs) {
}

__device__ __forceinline__ bool xs_is_acceptor_gpu(sz xs) {
return xs == XS_TYPE_N_A || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_A || xs == XS_TYPE_O_DA;
return xs == XS_TYPE_N_A || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_A || xs == XS_TYPE_O_DA||xs == XS_TYPE_O_XA ||xs == XS_TYPE_N_XA;
}

__device__ __forceinline__ bool xs_is_donor_gpu(sz xs) {
return xs == XS_TYPE_N_D || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_D || xs == XS_TYPE_O_DA
|| xs == XS_TYPE_Met_D;
|| xs == XS_TYPE_Met_D||xs == XS_TYPE_O_XD ||xs == XS_TYPE_N_XD;
}

__device__ __forceinline__ bool xs_donor_acceptor_gpu(sz t1, sz t2) {
Expand Down
2 changes: 1 addition & 1 deletion unidock/src/cuda/kernel.h
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Expand Up @@ -36,7 +36,7 @@ void check(T result, char const *const func, const char *const file, int const l
#define MAX_NUM_OF_LIG_PAIRS 4096
#define MAX_NUM_OF_BFGS_STEPS 64
#define MAX_NUM_OF_RANDOM_MAP 1000 // not too large (stack overflow!)
#define GRIDS_SIZE 34 // larger than vina1.1, max(XS_TYPE_SIZE, AD_TYPE_SIZE + 2)
#define GRIDS_SIZE 37 // larger than vina1.1, max(XS_TYPE_SIZE, AD_TYPE_SIZE + 2)

#define MAX_NUM_OF_GRID_MI 128 // 55
#define MAX_NUM_OF_GRID_MJ 128 // 55
Expand Down
7 changes: 5 additions & 2 deletions unidock/src/cuda/precalculate_gpu.cuh
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Expand Up @@ -144,8 +144,11 @@ __device__ __forceinline__ fl vina_non_dir_h_bond_cuda_eval(sz t1, sz t2, fl r,
fl cutoff) {
if (r >= cutoff) return 0.0;
if ((t1 >= XS_TYPE_SIZE) || (t2 >= XS_TYPE_SIZE)) return 0.0;
if (xs_h_bond_possible_gpu(t1, t2))
return slope_step_gpu(bad, good, r - optimal_distance_gpu(t1, t2));
if (xs_h_bond_possible_gpu(t1, t2)){
if ((t1 >= 32 && t1 <= 35) || (t2 >= 32 && t2 <= 35))
return 10.0*slope_step_gpu(bad, good, r - optimal_distance_gpu(t1, t2));
else
return slope_step_gpu(bad, good, r - optimal_distance_gpu(t1, t2));}
return 0.0;
};

Expand Down
10 changes: 5 additions & 5 deletions unidock/src/lib/ad4cache.cpp
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Expand Up @@ -412,7 +412,7 @@ void ad4cache::read(const std::string& map_prefix) {
read_ad4_map(p, gds, m_grids[t]);

} // if file exists
} // map loop
} // map loop

// elec map
filename = map_prefix + ".e.map";
Expand Down Expand Up @@ -506,9 +506,9 @@ void ad4cache::write(const std::string& out_prefix, const szv& atom_types,
VINA_FOR(y, m_grids[t].m_data.dim1()) {
VINA_FOR(x, m_grids[t].m_data.dim0()) {
out << std::setprecision(4) << m_grids[t].m_data(x, y, z) << "\n"; // slow?
} // x
} // y
} // z
} // x
} // y
} // z
} // map initialized
} // map atom type
} // map atom type
} // cache::write
8 changes: 4 additions & 4 deletions unidock/src/lib/array3d.h
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Expand Up @@ -41,10 +41,10 @@ template <typename T> class array3d {

friend class boost::serialization::access;
template <typename Archive> void serialize(Archive& ar, const unsigned version) {
ar& m_i;
ar& m_j;
ar& m_k;
ar& m_data;
ar & m_i;
ar & m_j;
ar & m_k;
ar & m_data;
}

public:
Expand Down
14 changes: 7 additions & 7 deletions unidock/src/lib/atom.h
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Expand Up @@ -34,8 +34,8 @@ struct atom_index {
private:
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) {
ar& i;
ar& in_grid;
ar & i;
ar & in_grid;
}
};

Expand All @@ -54,9 +54,9 @@ struct bond {
private:
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) {
ar& connected_atom_index;
ar& length;
ar& rotatable;
ar & connected_atom_index;
ar & length;
ar & rotatable;
}
};

Expand All @@ -70,8 +70,8 @@ struct atom : public atom_base {
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) {
ar& boost::serialization::base_object<atom_base>(*this);
ar& coords;
ar& bonds;
ar & coords;
ar & bonds;
}
};

Expand Down
2 changes: 1 addition & 1 deletion unidock/src/lib/atom_base.h
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Expand Up @@ -33,7 +33,7 @@ struct atom_base : public atom_type {
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) {
ar& boost::serialization::base_object<atom_type>(*this);
ar& charge;
ar & charge;
}
};

Expand Down
45 changes: 37 additions & 8 deletions unidock/src/lib/atom_constants.h
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Expand Up @@ -73,8 +73,12 @@ const sz AD_TYPE_CG0 = 26;
const sz AD_TYPE_CG1 = 27;
const sz AD_TYPE_CG2 = 28;
const sz AD_TYPE_CG3 = 29;
const sz AD_TYPE_W = 30; // hydrated ligand
const sz AD_TYPE_SIZE = 31;
const sz AD_TYPE_W = 30; // hydrated ligand
const sz AD_TYPE_OXA = 31; // biased protein hydrogen bond acceptor
const sz AD_TYPE_NXA = 32; // biased protein hydrogen bond acceptor
const sz AD_TYPE_OXD = 33; // biased protein hydrogen bond donor
const sz AD_TYPE_NXD = 34; // biased protein hydrogen bond donor
const sz AD_TYPE_SIZE = 35;

// X-Score
const sz XS_TYPE_C_H = 0;
Expand Down Expand Up @@ -109,7 +113,11 @@ const sz XS_TYPE_C_H_CG3 = 28;
const sz XS_TYPE_C_P_CG3 = 29;
const sz XS_TYPE_G3 = 30;
const sz XS_TYPE_W = 31; // hydrated ligand
const sz XS_TYPE_SIZE = 32;
const sz XS_TYPE_O_XA = 32;
const sz XS_TYPE_N_XA = 33;
const sz XS_TYPE_O_XD = 34;
const sz XS_TYPE_N_XD = 35;
const sz XS_TYPE_SIZE = 36;

// DrugScore-CSD
const sz SY_TYPE_C_3 = 0;
Expand Down Expand Up @@ -178,7 +186,11 @@ const atom_kind atom_kind_data[] = {
{"CG1", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 27
{"CG2", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 28
{"CG3", 2.00000, 0.15000, 0.0, 0.0, -0.00143, 33.51030, 0.77}, // 29
{"W", 0.00000, 0.00000, 0.0, 0.0, 0.00000, 0.00000, 0.00} // 30
{"W", 0.00000, 0.00000, 0.0, 0.0, 0.00000, 0.00000, 0.00}, // 30
{"OXA", 1.60000, 0.20000, 0.0, 0.0, -0.00251, 17.15730, 0.73}, // 31
{"NXA", 1.75000, 0.16000, 0.0, 0.0, -0.00162, 22.44930, 0.75}, // 32
{"OXD", 1.60000, 0.20000, 0.0, 0.0, -0.00251, 17.15730, 0.73}, // 33
{"NXD", 1.75000, 0.16000, 0.0, 0.0, -0.00162, 22.44930, 0.75} // 34
};

const fl metal_solvation_parameter = -0.00110;
Expand Down Expand Up @@ -281,6 +293,14 @@ inline sz ad_type_to_el_type(sz t) {
return EL_TYPE_Dummy;
case AD_TYPE_W:
return EL_TYPE_Dummy;
case AD_TYPE_OXA:
return EL_TYPE_O;
case AD_TYPE_NXA:
return EL_TYPE_N;
case AD_TYPE_OXD:
return EL_TYPE_O;
case AD_TYPE_NXD:
return EL_TYPE_N;
case AD_TYPE_SIZE:
return EL_TYPE_SIZE;
default:
Expand Down Expand Up @@ -322,7 +342,11 @@ const fl xs_vdw_radii[] = {
0.0, // G1
0.0, // G2
0.0, // G3
0.0 // W
0.0, // W
1.7, // O_XA
1.8, // N_XA
1.7, // O_XD
1.8 // N_XD
};

const fl xs_vinardo_vdw_radii[] = {
Expand Down Expand Up @@ -357,7 +381,11 @@ const fl xs_vinardo_vdw_radii[] = {
0.0, // G1
0.0, // G2
0.0, // G3
0.0 // W
0.0, // W
1.6, // O_XA
1.7, // N_XA
1.6, // O_XD
1.7 // N_XD
};

inline fl xs_radius(sz t) {
Expand Down Expand Up @@ -388,12 +416,13 @@ inline bool xs_is_hydrophobic(sz xs) {
}

inline bool xs_is_acceptor(sz xs) {
return xs == XS_TYPE_N_A || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_A || xs == XS_TYPE_O_DA;
return xs == XS_TYPE_N_A || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_A || xs == XS_TYPE_O_DA
|| xs == XS_TYPE_O_XA || xs == XS_TYPE_N_XA;
}

inline bool xs_is_donor(sz xs) {
return xs == XS_TYPE_N_D || xs == XS_TYPE_N_DA || xs == XS_TYPE_O_D || xs == XS_TYPE_O_DA
|| xs == XS_TYPE_Met_D;
|| xs == XS_TYPE_Met_D || xs == XS_TYPE_N_XD || xs == XS_TYPE_O_XD;
}

inline bool xs_donor_acceptor(sz t1, sz t2) { return xs_is_donor(t1) && xs_is_acceptor(t2); }
Expand Down
8 changes: 4 additions & 4 deletions unidock/src/lib/atom_type.h
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Expand Up @@ -73,10 +73,10 @@ struct atom_type {
private:
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) {
ar& el;
ar& ad;
ar& xs;
ar& sy;
ar & el;
ar & ad;
ar & xs;
ar & sy;
}
};

Expand Down
20 changes: 14 additions & 6 deletions unidock/src/lib/cache.cpp
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Expand Up @@ -68,6 +68,14 @@ std::string convert_XS_to_string(sz t) {
return "Met_D";
case XS_TYPE_W:
return "W";
case XS_TYPE_O_XA:
return "O_XA";
case XS_TYPE_N_XA:
return "N_XA";
case XS_TYPE_O_XD:
return "O_XD";
case XS_TYPE_N_XD:
return "N_XD";
default:
VINA_CHECK(false);
}
Expand Down Expand Up @@ -445,12 +453,12 @@ void cache::write(const std::string& out_prefix, const szv& atom_types,
VINA_FOR(x, m_grids[t].m_data.dim0()) {
out << std::setprecision(4) << m_grids[t].m_data(x, y, z)
<< "\n"; // slow?
} // x
} // y
} // z
} // even voxels
} // map initialized
} // map atom type
} // x
} // y
} // z
} // even voxels
} // map initialized
} // map atom type
} // cache::write

float cache::get_slope() const { return this->m_slope; }
Expand Down
2 changes: 1 addition & 1 deletion unidock/src/lib/common.h
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Expand Up @@ -115,7 +115,7 @@ struct vec {

private:
friend class boost::serialization::access;
template <class Archive> void serialize(Archive& ar, const unsigned version) { ar& data; }
template <class Archive> void serialize(Archive& ar, const unsigned version) { ar & data; }
};

inline vec operator*(fl s, const vec& v) { return vec(s * v[0], s * v[1], s * v[2]); }
Expand Down
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