Models Reference

Python API reference for Models Reference

Data classes used throughout PrimerLab.

Module

from primerlab.core.models import (
    Primer,
    PrimerPair,
    Amplicon,
    QCResult
)
from primerlab.core.models.blast import BlastResult, BlastHit
from primerlab.core.insilico import BindingSite, InsilicoPCRResult

---

Primer

Single primer representation.

Attributes

Attribute	Type	Description
sequence	str	Primer sequence (5’→3’)
length	int	Primer length
tm	float	Melting temperature (°C)
gc_content	float	GC percentage
name	str	Primer name/ID
direction	str	”forward” or “reverse”

Example

from primerlab.core.models import Primer

primer = Primer(
    sequence="ATGGTGAGCAAGGGCGAGGAG",
    name="GFP_F1",
    direction="forward"
)

print(f"Sequence: {primer.sequence}")
print(f"Length: {primer.length} bp")
print(f"Tm: {primer.tm:.1f}°C")
print(f"GC: {primer.gc_content:.1f}%")

---

PrimerPair

Forward + Reverse primer pair.

Attributes

Attribute	Type	Description
forward	Primer	Forward primer
reverse	Primer	Reverse primer
amplicon_size	int	Product size (bp)
tm_diff	float	Tm difference
score	float	Overall QC score
probe	Primer	TaqMan probe (qPCR only)

Example

pair = result.primers[0]

print(f"Forward: {pair.forward.sequence}")
print(f"Reverse: {pair.reverse.sequence}")
print(f"Amplicon: {pair.amplicon_size} bp")
print(f"Tm difference: {pair.tm_diff:.1f}°C")
print(f"Score: {pair.score:.1f}")

---

Amplicon

Predicted PCR product.

Attributes

Attribute	Type	Description
sequence	str	Amplicon sequence
size	int	Length in bp
start	int	Start position on template
end	int	End position on template
gc_content	float	GC percentage

Example

amplicon = insilico_result.products[0]

print(f"Size: {amplicon.size} bp")
print(f"Position: {amplicon.start}-{amplicon.end}")
print(f"Sequence: {amplicon.sequence[:50]}...")

---

BindingSite

Primer binding site analysis result.

Attributes

Attribute	Type	Description
position	int	Binding position
mismatches	int	Number of mismatches
mismatch_positions	List[int]	Positions of mismatches
three_prime_dg	float	3’ end ΔG (kcal/mol)
estimated_tm	float	Corrected Tm
is_valid	bool	Passes binding criteria
validation_notes	List[str]	Warnings/notes

Example

from primerlab.core.insilico import analyze_binding

binding = analyze_binding(primer_seq, target_seq)

print(f"Position: {binding.position}")
print(f"Mismatches: {binding.mismatches}")
print(f"3' ΔG: {binding.three_prime_dg:.2f} kcal/mol")
print(f"Valid: {binding.is_valid}")

if binding.validation_notes:
    for note in binding.validation_notes:
        print(f"  Warning: {note}")

---

BlastResult

Off-target detection result.

Attributes

Attribute	Type	Description
primer_id	str	Primer identifier
hits	List[BlastHit]	List of BLAST hits
score	float	Specificity score (0-100)
grade	str	Letter grade (A-F)
offtarget_count	int	Number of off-targets
is_specific	bool	Passes specificity threshold

BlastHit Attributes

Attribute	Type	Description
subject_id	str	Hit sequence ID
identity	float	Percent identity
alignment_length	int	Alignment length
mismatches	int	Number of mismatches
evalue	float	E-value

Example

blast_result = offtarget_check(primer, database)

print(f"Specificity Score: {blast_result.score:.1f}")
print(f"Grade: {blast_result.grade}")
print(f"Off-targets: {blast_result.offtarget_count}")

for hit in blast_result.hits[:5]:
    print(f"  {hit.subject_id}: {hit.identity:.1f}% identity")

---

QCResult

Quality control assessment.

Attributes

Attribute	Type	Description
passed	bool	Overall QC pass
hairpin_dg	float	Hairpin ΔG
homodimer_dg	float	Self-dimer ΔG
heterodimer_dg	float	Cross-dimer ΔG
gc_clamp	bool	Has GC clamp
warnings	List[str]	QC warnings

Example

qc = primer_pair.qc_result

print(f"QC Passed: {qc.passed}")
print(f"Hairpin ΔG: {qc.hairpin_dg:.2f} kcal/mol")
print(f"Homodimer ΔG: {qc.homodimer_dg:.2f} kcal/mol")
print(f"GC Clamp: {'Yes' if qc.gc_clamp else 'No'}")

for warning in qc.warnings:
    print(f"  ⚠ {warning}")

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See Also

• Public API
• In-silico API
• Report API