eqc-bio 0.1.2__tar.gz

eqc_bio-0.1.2/LICENSE.txt

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eqc_bio-0.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: eqc-bio
+Version: 0.1.2
+Summary: Biological modeling package targeting EQC devices
+Author-email: "Quantum Computing Inc." <support@quantumcomputinginc.com>
+Project-URL: Homepage, https://quantumcomputinginc.com
+Project-URL: Documentation, https://quantumcomputinginc.com/learn/support/software-packages/
+Project-URL: Issues, https://support.quantumcomputinginc.com/
+Requires-Python: <3.14,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy<3,>=1.22.1
+Requires-Dist: networkx<3,>=2.6.3
+Requires-Dist: pandas<3,>=2.1.0
+Requires-Dist: eqc-models>=0.22.2
+Requires-Dist: pyyaml<7,>=6.0
+Requires-Dist: pymetis>=2023.1
+Provides-Extra: dev
+Requires-Dist: pytest<8,>=7.1.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: sphinx_rtd_theme<2,>=1.3.0; extra == "dev"
+Provides-Extra: viewer
+Requires-Dist: py3Dmol<3,>=2.0; extra == "viewer"
+Requires-Dist: nglview<5,>=3.0; extra == "viewer"
+Dynamic: license-file
+
+# eqc_bio.protein_design
+
+The `eqc_bio.protein_design` module provides tools for fixed-backbone protein design using quantum-inspired optimization on Dirac-3 solvers.
+
+## Overview
+
+Fixed-backbone protein design (also known as rotamer optimization or side-chain packing) involves selecting optimal side-chain conformations (rotamers) for a given protein backbone structure to minimize the total energy of the system. The `eqc_bio.protein_design` package formulates this combinatorial problem as a quadratic binary optimization (QUBO) model that can be solved efficiently using Quantum Computing Inc.'s Dirac-3 solvers.
+
+## Key Components
+
+### ProteinDesignFixed
+
+The main class `ProteinDesignFixed` (in `fixed_backbone.py`) handles:
+- Loading problem configurations from YAML files
+- Reading precomputed energy matrices (interaction energies between rotamers)
+- Constructing the QUBO Hamiltonian with linear and quadratic terms
+- Running optimization on Dirac-3 (cloud or direct) solvers
+- Iterative batch solving for larger problems using METIS graph partitioning
+- Post-processing solutions into rotamer selections and PDB structures
+
+Configuration parameters include:
+- `n_samples`, relaxation schedule, photon number, quantum fluctuation coefficient
+- Energy thresholds and scaling factors (alpha, beta)
+- Support for integer vs. continuous variables and iterative refinement
+
+### Supporting Modules
+
+- `base.py`: Core `ProteinDesign` class with Dirac-3 execution logic and iterative batching
+- `rotamers.py`: Rotamer library handling (Dunbrack, OSPREY formats), chi angle extraction, library parsing and validation
+- `sidechains.py`: Side-chain heavy-atom construction from χ angles using ideal geometry
+- `viewer.py`: PDB building (`build_designed_pdb`), visualization (`view_pdb`), backbone dihedrals and rotamer angle utilities
+
+## Usage
+
+Typical workflow:
+1. Prepare a config YAML pointing to an energy matrix CSV and expected solution
+2. Instantiate `ProteinDesignFixed(config_file, solver)`
+3. Call `run()` to solve and obtain design DataFrame
+4. Use `get_rotamer_angles()` and `build_pdb()` to generate output structures
+
+Example scripts are provided in `scripts/protein_design_fixed_backbone.py` and `scripts/protein_design_expected_pdb.py`.
+
+## Building and Viewing Designed Structures
+
+A solution assigns a rotamer such as `MET-3` (the third MET rotamer) to each designed position. The structure tools turn that into a PDB in three steps:
+
+1. **Rotamer angles**: look up the χ angles of each selected rotamer in the rotamer library the energy matrix was generated with.
+2. **PDB building**: keep the template's backbone atoms (N, CA, C, O, OXT) at each designed position, rename the residue, and build its side-chain heavy atoms from the χ angles. Other residues are copied unchanged.
+3. **Viewing**: show the PDB in Jupyter with py3Dmol or nglview.
+
+### Configuration
+
+The structure tools read these optional keys from the config YAML:
+
+```yaml
+template_pdb: data/1MJC/1MJC.pdb   # backbone the energy matrix was built on
+rotamer_library: null              # null = OSPREY Lovell default, or a path to a library file
+rotamer_library_format: osprey     # osprey (OSPREY .dat, e.g. Lovell) or dunbrack (Dunbrack bbdep file)
+position_numbering: index          # index (1-based residue order in the file) or resseq (PDB residue number)
+```
+
+- `template_pdb` is needed to build or view a PDB, and also for a Dunbrack library.
+- `rotamer_library` must be the library the energy matrix was generated with, because rotamer numbers index into it. The rotamer names in the matrix are checked against the library's rotamer counts. A name that exceeds the library's count raises an error, and a residue type that uses fewer rotamers than the library has gives a warning.
+- `position_numbering: index` matches how OSPREY energy matrices number positions. Use `resseq` when positions are PDB residue numbers.
+
+### Rotamer Libraries
+
+- **Lovell (default)**: the Lovell "Penultimate" library as distributed with OSPREY (`LovellRotamer.dat`). It is downloaded from a pinned OSPREY commit on first use and cached in `~/.eqc_bio/rotamers` (set `EQC_BIO_CACHE` to use another directory).
+- **Dunbrack (backbone-dependent)**: set `rotamer_library_format: dunbrack` and give a local copy of the Dunbrack bbdep file by path, since the library is not redistributable. It is read the way OSPREY reads it (10° φ/ψ bins, 0.001 probability cutoff, no PRO rotamers), so rotamer numbers match OSPREY matrices. Each position's φ/ψ is measured from `template_pdb`. The energy matrix must use position-prefixed rotamer names such as `4-MET-3`.
+
+### With ProteinDesignFixed
+
+```python
+from eqc_bio.protein_design import ProteinDesignFixed
+
+obj = ProteinDesignFixed(config_file="config_files/config_file_1MJC.yml", solver=solver)
+obj.run()
+
+angles = obj.get_rotamer_angles()                    # position, residue, rotamer, chi_angles
+pdb_str = obj.build_pdb(output_path="output/designed_1MJC.pdb")
+obj.view()                                           # in Jupyter; designed side chains drawn as sticks
+```
+
+Each method uses the design from the last `run()`, or a design DataFrame (columns `position` and `selected_rotamer`) passed as `design_df`. `load_expected_design()` returns the expected solution in that form, so its structure can be built without running a solver:
+
+```bash
+cd scripts
+python protein_design_expected_pdb.py config_files/config_file_1MJC.yml   # writes output/expected_1MJC.pdb
+```
+
+`view(viewer="nglview")` uses nglview instead of py3Dmol. Neither viewer is a required dependency. Install both with the `viewer` extra (`pip install "eqc-bio[viewer]"`), or install the one you need (`pip install py3Dmol` or `pip install nglview`).
+
+### Standalone Functions
+
+The same steps are available as functions that take plain data, so angles or structures from other sources can be used at any step:
+
+```python
+from eqc_bio.protein_design import get_rotamer_angles, build_designed_pdb, view_pdb
+
+angles = get_rotamer_angles(design_df)               # default Lovell library
+pdb_str = build_designed_pdb("data/1MJC/1MJC.pdb", angles, output_path="out.pdb")
+view_pdb(pdb_str, highlight=[4, 6])                  # PDB residue numbers to draw as sticks
+```
+
+- `get_rotamer_angles(design, rotamer_library=None, template_pdb=None, position_numbering="index", library_format="osprey")`: χ angles for each selected rotamer. A Dunbrack library also needs `template_pdb`.
+- `build_designed_pdb(template_pdb, rotamer_angles, output_path=None, position_numbering="index")`: returns the PDB as a string and writes it if `output_path` is given. A position missing from the template raises `ValueError`.
+- `view_pdb(pdb_str, viewer="py3Dmol", highlight=None)`: returns a py3Dmol or nglview widget.
+- `get_backbone_dihedrals(template_pdb, position_numbering="index")`: `{position: (phi, psi)}` in degrees, with NaN where an atom is missing, such as at chain ends.
+- `resolve_rotamer_library`, `load_rotamer_library`, `download_rotamer_library`, `parse_dunbrack_library`, `check_rotamer_counts` and `get_chi_angles` give lower-level access to the rotamer libraries.
+
+## Applications
+
+- Computational protein engineering
+- Designing stable mutants or novel sequences on fixed backbones
+- Benchmarking quantum-inspired solvers on NP-hard bioinformatics problems
+
+(C) Quantum Computing Inc., 2026.

eqc_bio-0.1.2/README.md

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+# eqc_bio.protein_design
+
+The `eqc_bio.protein_design` module provides tools for fixed-backbone protein design using quantum-inspired optimization on Dirac-3 solvers.
+
+## Overview
+
+Fixed-backbone protein design (also known as rotamer optimization or side-chain packing) involves selecting optimal side-chain conformations (rotamers) for a given protein backbone structure to minimize the total energy of the system. The `eqc_bio.protein_design` package formulates this combinatorial problem as a quadratic binary optimization (QUBO) model that can be solved efficiently using Quantum Computing Inc.'s Dirac-3 solvers.
+
+## Key Components
+
+### ProteinDesignFixed
+
+The main class `ProteinDesignFixed` (in `fixed_backbone.py`) handles:
+- Loading problem configurations from YAML files
+- Reading precomputed energy matrices (interaction energies between rotamers)
+- Constructing the QUBO Hamiltonian with linear and quadratic terms
+- Running optimization on Dirac-3 (cloud or direct) solvers
+- Iterative batch solving for larger problems using METIS graph partitioning
+- Post-processing solutions into rotamer selections and PDB structures
+
+Configuration parameters include:
+- `n_samples`, relaxation schedule, photon number, quantum fluctuation coefficient
+- Energy thresholds and scaling factors (alpha, beta)
+- Support for integer vs. continuous variables and iterative refinement
+
+### Supporting Modules
+
+- `base.py`: Core `ProteinDesign` class with Dirac-3 execution logic and iterative batching
+- `rotamers.py`: Rotamer library handling (Dunbrack, OSPREY formats), chi angle extraction, library parsing and validation
+- `sidechains.py`: Side-chain heavy-atom construction from χ angles using ideal geometry
+- `viewer.py`: PDB building (`build_designed_pdb`), visualization (`view_pdb`), backbone dihedrals and rotamer angle utilities
+
+## Usage
+
+Typical workflow:
+1. Prepare a config YAML pointing to an energy matrix CSV and expected solution
+2. Instantiate `ProteinDesignFixed(config_file, solver)`
+3. Call `run()` to solve and obtain design DataFrame
+4. Use `get_rotamer_angles()` and `build_pdb()` to generate output structures
+
+Example scripts are provided in `scripts/protein_design_fixed_backbone.py` and `scripts/protein_design_expected_pdb.py`.
+
+## Building and Viewing Designed Structures
+
+A solution assigns a rotamer such as `MET-3` (the third MET rotamer) to each designed position. The structure tools turn that into a PDB in three steps:
+
+1. **Rotamer angles**: look up the χ angles of each selected rotamer in the rotamer library the energy matrix was generated with.
+2. **PDB building**: keep the template's backbone atoms (N, CA, C, O, OXT) at each designed position, rename the residue, and build its side-chain heavy atoms from the χ angles. Other residues are copied unchanged.
+3. **Viewing**: show the PDB in Jupyter with py3Dmol or nglview.
+
+### Configuration
+
+The structure tools read these optional keys from the config YAML:
+
+```yaml
+template_pdb: data/1MJC/1MJC.pdb   # backbone the energy matrix was built on
+rotamer_library: null              # null = OSPREY Lovell default, or a path to a library file
+rotamer_library_format: osprey     # osprey (OSPREY .dat, e.g. Lovell) or dunbrack (Dunbrack bbdep file)
+position_numbering: index          # index (1-based residue order in the file) or resseq (PDB residue number)
+```
+
+- `template_pdb` is needed to build or view a PDB, and also for a Dunbrack library.
+- `rotamer_library` must be the library the energy matrix was generated with, because rotamer numbers index into it. The rotamer names in the matrix are checked against the library's rotamer counts. A name that exceeds the library's count raises an error, and a residue type that uses fewer rotamers than the library has gives a warning.
+- `position_numbering: index` matches how OSPREY energy matrices number positions. Use `resseq` when positions are PDB residue numbers.
+
+### Rotamer Libraries
+
+- **Lovell (default)**: the Lovell "Penultimate" library as distributed with OSPREY (`LovellRotamer.dat`). It is downloaded from a pinned OSPREY commit on first use and cached in `~/.eqc_bio/rotamers` (set `EQC_BIO_CACHE` to use another directory).
+- **Dunbrack (backbone-dependent)**: set `rotamer_library_format: dunbrack` and give a local copy of the Dunbrack bbdep file by path, since the library is not redistributable. It is read the way OSPREY reads it (10° φ/ψ bins, 0.001 probability cutoff, no PRO rotamers), so rotamer numbers match OSPREY matrices. Each position's φ/ψ is measured from `template_pdb`. The energy matrix must use position-prefixed rotamer names such as `4-MET-3`.
+
+### With ProteinDesignFixed
+
+```python
+from eqc_bio.protein_design import ProteinDesignFixed
+
+obj = ProteinDesignFixed(config_file="config_files/config_file_1MJC.yml", solver=solver)
+obj.run()
+
+angles = obj.get_rotamer_angles()                    # position, residue, rotamer, chi_angles
+pdb_str = obj.build_pdb(output_path="output/designed_1MJC.pdb")
+obj.view()                                           # in Jupyter; designed side chains drawn as sticks
+```
+
+Each method uses the design from the last `run()`, or a design DataFrame (columns `position` and `selected_rotamer`) passed as `design_df`. `load_expected_design()` returns the expected solution in that form, so its structure can be built without running a solver:
+
+```bash
+cd scripts
+python protein_design_expected_pdb.py config_files/config_file_1MJC.yml   # writes output/expected_1MJC.pdb
+```
+
+`view(viewer="nglview")` uses nglview instead of py3Dmol. Neither viewer is a required dependency. Install both with the `viewer` extra (`pip install "eqc-bio[viewer]"`), or install the one you need (`pip install py3Dmol` or `pip install nglview`).
+
+### Standalone Functions
+
+The same steps are available as functions that take plain data, so angles or structures from other sources can be used at any step:
+
+```python
+from eqc_bio.protein_design import get_rotamer_angles, build_designed_pdb, view_pdb
+
+angles = get_rotamer_angles(design_df)               # default Lovell library
+pdb_str = build_designed_pdb("data/1MJC/1MJC.pdb", angles, output_path="out.pdb")
+view_pdb(pdb_str, highlight=[4, 6])                  # PDB residue numbers to draw as sticks
+```
+
+- `get_rotamer_angles(design, rotamer_library=None, template_pdb=None, position_numbering="index", library_format="osprey")`: χ angles for each selected rotamer. A Dunbrack library also needs `template_pdb`.
+- `build_designed_pdb(template_pdb, rotamer_angles, output_path=None, position_numbering="index")`: returns the PDB as a string and writes it if `output_path` is given. A position missing from the template raises `ValueError`.
+- `view_pdb(pdb_str, viewer="py3Dmol", highlight=None)`: returns a py3Dmol or nglview widget.
+- `get_backbone_dihedrals(template_pdb, position_numbering="index")`: `{position: (phi, psi)}` in degrees, with NaN where an atom is missing, such as at chain ends.
+- `resolve_rotamer_library`, `load_rotamer_library`, `download_rotamer_library`, `parse_dunbrack_library`, `check_rotamer_counts` and `get_chi_angles` give lower-level access to the rotamer libraries.
+
+## Applications
+
+- Computational protein engineering
+- Designing stable mutants or novel sequences on fixed backbones
+- Benchmarking quantum-inspired solvers on NP-hard bioinformatics problems
+
+(C) Quantum Computing Inc., 2026.

eqc_bio-0.1.2/eqc_bio/protein_design/__init__.py

@@ -0,0 +1,30 @@
+# (C) Quantum Computing Inc., 2024.
+from .fixed_backbone import ProteinDesignFixed
+from .viewer import (
+    build_designed_pdb,
+    get_backbone_dihedrals,
+    get_rotamer_angles,
+    view_pdb,
+)
+from .rotamers import (
+    download_rotamer_library,
+    load_rotamer_library,
+    parse_dunbrack_library,
+    resolve_rotamer_library,
+    check_rotamer_counts,
+    get_chi_angles,
+)
+
+__all__ = [
+    "ProteinDesignFixed",
+    "build_designed_pdb",
+    "get_backbone_dihedrals",
+    "get_rotamer_angles",
+    "view_pdb",
+    "download_rotamer_library",
+    "load_rotamer_library",
+    "parse_dunbrack_library",
+    "resolve_rotamer_library",
+    "check_rotamer_counts",
+    "get_chi_angles",
+]

eqc_bio-0.1.2/eqc_bio/protein_design/base.py

@@ -0,0 +1,168 @@
+import os
+import sys
+import warnings
+import logging
+import numpy as np
+import pandas as pd
+
+from eqc_models.base import ModelSolver, SolutionResults
+from eqc_models.solvers.qciclient import Dirac3CloudSolver
+from eqc_models import QuadraticModel
+from eqc_bio.utils import timer
+from eqc_bio.utils import metis_partition
+
+warnings.filterwarnings("ignore")
+log = logging.getLogger(name=__name__)
+
+# Seconds per unit for SolutionResults.time_units
+TIME_UNIT_SECONDS = {"ns": 1e-9, "s": 1.0}
+
+
+class ProteinDesign:
+    def __init__(self, solver: ModelSolver = None):
+        # Defaults to a cloud solver configured from QCI_API_URL/QCI_TOKEN
+        self.solver = solver
+
+    def get_dirac3_time(self, results: SolutionResults):
+        """Return the device time of a solve in seconds."""
+        device_time = results.device_time
+        if device_time is None:
+            log.warning("Device timing not available for this solve")
+            return 0.0
+
+        return np.sum(device_time) * TIME_UNIT_SECONDS[results.time_units]
+
+    def run_dirac3(self, J, C, sum_constraint, n_vars, num_samples):
+        model = QuadraticModel(C, J)
+        model.upper_bound = np.array([1] * n_vars)
+
+        solver = self.solver
+        if solver is None:
+            solver = Dirac3CloudSolver()
+
+        results = solver.solve(
+            model,
+            sum_constraint=sum_constraint,
+            relaxation_schedule=self.relaxation_schedule,
+            num_samples=num_samples,
+            mean_photon_number=self.mean_photon_number,
+            quantum_fluctuation_coefficient=self.quantum_fluctuation_coefficient,
+        )
+        log.info(results)
+
+        dirac3_time = self.get_dirac3_time(results)
+
+        return results, dirac3_time
+
+    def run_dirac3_iterative(
+        self,
+        J,
+        C,
+        sum_constraint,
+        n_vars,
+        positions,
+        position_graph,
+        position_index_hash,
+    ):
+        batch_count = int(round(n_vars / self.batch_size))
+
+        X = np.random.rand(n_vars)
+
+        if sum_constraint is not None:
+            X = X * (sum_constraint / np.sum(X))
+
+        tmp_group_list = metis_partition(position_graph, k=batch_count)
+        tmp_hash = dict(enumerate(positions))
+        position_groups = []
+        for tmp_group in tmp_group_list:
+            position_groups.append([tmp_hash[item] for item in tmp_group])
+
+        groups = []
+        for position_group in position_groups:
+            tmp_list = []
+            for position in position_group:
+                tmp_list += position_index_hash[position]
+            groups.append(tmp_list)
+
+        sols = []
+        energies = []
+        dirac3_time = 0.0
+        for epoch in range(self.n_epochs):
+            order = np.random.permutation(batch_count)
+            for i in order:
+                idx_p = groups[i]
+                idx_q = np.setdiff1d(np.arange(n_vars), idx_p)
+                Cp = C[idx_p]
+                Cq = C[idx_q]
+                Xq = X[idx_q]
+                Jpp = J[np.ix_(idx_p, idx_p)]
+                Jpq = J[np.ix_(idx_p, idx_q)]
+                Jqp = J[np.ix_(idx_q, idx_p)]
+                Jqq = J[np.ix_(idx_q, idx_q)]
+
+                tmp_v = 2 * Jpq @ Xq
+                tmp_v = tmp_v.reshape((tmp_v.shape[0], 1))
+                tmp_C = Cp + tmp_v
+                tmp_J = Jpp
+
+                if sum_constraint is not None:
+                    tmp_sum_constraint = sum_constraint - np.sum(Xq)
+                else:
+                    tmp_sum_constraint = None
+
+                sub_response, sub_dirac3_time = self.run_dirac3(
+                    tmp_J,
+                    tmp_C,
+                    max(1.0, tmp_sum_constraint),
+                    tmp_C.shape[0],
+                    self.n_samples,
+                )
+                dirac3_time += sub_dirac3_time
+
+                sub_sols = sub_response.solutions
+
+                glob_loc_hash = {}
+                for loc_k, glob_k in enumerate(idx_p):
+                    glob_loc_hash[glob_k] = loc_k
+
+                for sub_sol in sub_sols:
+                    sub_sol = np.array(sub_sol)
+                    feasible_flag = True
+                    for position in position_groups[i]:
+                        glob_indexes = position_index_hash[position]
+                        loc_indexes = [
+                            glob_loc_hash[item] for item in glob_indexes
+                        ]
+                        if np.sum(sub_sol[loc_indexes]) == 0:
+                            feasible_flag = False
+                            break
+
+                    if feasible_flag:
+                        break
+
+                Xp = sub_sol
+                fct = np.sum(Xp)
+                if fct != 0:
+                    fct = tmp_sum_constraint / fct
+                Xp = fct * np.array(Xp)
+                X[idx_p] = Xp
+
+                sol = np.array(X)
+                energy = sol.T @ J @ sol + sol.T @ C
+                energy = energy[0]
+
+                sols.append(sol)
+                energies.append(energy)
+
+        # Device time is summed over the sub-solves and returned separately
+        results = SolutionResults(
+            solutions=np.array(sols),
+            energies=np.array(energies),
+            counts=np.ones(len(sols)),
+            objectives=None,
+            run_time=None,
+            preprocessing_time=None,
+            postprocessing_time=None,
+        )
+
+        return results, dirac3_time