Add information on ProteoScribe instructions

README.md

@@ -269,19 +269,82 @@ The facilitated embeddings are saved to the specified output_data_path for furth
 
 ## Stage 3: ProteoScribe
 
-🚧 **Coming Soon** 🚧
+[Previous sections remain the same...]
+
+### Expected Output
+
+The script generates multiple sequence variants for each input embedding. Here's the sample output showing different replicas:
+[Previous sections remain the same...]
+
+## Stage 3: ProteoScribe
+
+### Overview
+
+In this stage, the **ProteoScribe model** takes the facilitated embeddings (z_c) from Stage 2 and generates novel protein sequences that match the desired functional description. The model outputs multiple sequence variants (replicas) for each input embedding.
+
+### Model Weights
+
+Before running the model, ensure you have:
+- Configuration file: `stage3_config.json`
+- Pre-trained weights: `BioM3_ProteoScribe_pfam_epoch20_v1.bin`
+
+### Running ProteoScribe
+
+Run the sequence generation:
+```bash
+python run_ProteoScribe_sample.py \
+    --json_path "./stage3_config.json" \
+    --model_path "./weights/ProteoScribe/BioM3_ProteoScribe_pfam_epoch20_v1.bin" \
+    --input_path "test_Facilitator_embeddings.pt" \
+    --output_path "test_ProteoScribe_samples.pt"
+```
+
+### Expected Output
+
+The script generates multiple sequence variants for each input embedding. Here's a sample output showing different replicas:
+
+**Replica 0:**
+
+Prompt 1 (Translation initiation factor):
+- <span style="color:purple">TAKEDWLEMQNTVLETLPNTMFRVELENGHVITAAISGGMRKNYIRILTGDKAKVELTPYDLSKGRICFRAK</span>
+
+Prompt 2 (Peptidyl-tRNA hydrolase):
+- <span style="color:purple">MSLIIGLLGNEKKYEFTRHRGVVFISDIANPFYDEFKETIGSVKTGHGFVEDGNYVIKFLVLTIPNRFSIERSARAVQDFYPDLDKVIIYIDDLPFKGGVRLSLHGGDHGNDNLVNGIADKSIGMGIDRRVIRVPEPMVVEVLWHPVFYVFDRFALEIKEIPKLMDILVEKAKELLFDVNKAYFEVL</span>
+
+Prompt 3 (tRNA-ribosyltransferase):
+- <span style="color:purple">MSKGPVHFVNVQEEAHTGRLLGAIVETEHGTPPVMYNPSLYSYTNPEPAMQDRLQDASNILLYNTYLWHGPDRCVILQSRGHLNKMNDKPYLILDSGGFMQIMLLSRRIGEFYVHETFHPHKTLSFLSPERVANIQMDLDTTVFDIMDNCPEKPYKYIEESVRLSDRWTTALSDRPDYGRRDQALFGIVGEAQFEDLRERSIEFGLDWAFDGYAIGGLSVGQPPEEMENVINYTKQVPEKLPRTLYNVSGTQLSDDIIGIARVGDMFDCVLPTRIARNGTFLTGQRNVKFAKASRDFNPPIDCKTCDCYTCQNYIRHVLHSGERLGFDGTIIHTIYLFDNLMALMKEAIQKDRKPYFEQHFAEDLSR</span>
+
+Prompt 4 (Chaperonin GroEL):
+- <span style="color:purple">MAAKDVKFGNEARVRMLRGVNTLADAVKTTLGPKGRNVVLEKSFGSPTITKDGVSVAREIELDDKFETMGAQMVKEVASKANDKAGDGTTTATVLAQSIITEGLKAVASGMNPMDLKRGIDKAVAAAVENLKTMKVPASDSKAIAQVGTISANSDETIGKLEADAMDKVGKDGVITVEEGQGLKDELDVVEGMQFDRGYLSPYFINKPDSGAVELESPFILLVDKKISNIRELMPVLEAVAKSSKPLLIIAEDVEGEALATLVVNTMRGIIKIAAVKAPGFTHRRKEMLQDIATLTAGTVISEQIDIELEKATLNDLGQAKRIVINKDTATIVDGAGDVADISSRVHQIRANVEEATSDYDREKLQERLAKLSGGVAVIKVGAGTEVEMKEKKARVEDALHQTRAATEEGVVAGGGVALIRAASKLAAVRPNSANDALEGIERVLAKELLPQQIALDGVGVSPNKATAIIANGVGGYAAANYEYGLVDKLEQVGDAPTKVVRAIVSDAMGSAMGAETIVVDAMGEAQA</span>
+
+Prompt 5 (Chaperone DnaK):
+- <span style="color:purple">MSTLKTVPLGCFNFQYTWNELNKIDTTISACFEEATSREIKETATDKQVLYEMRKHLCCTTDAHIGPPSVKGIHSPNKVTFGQRYCAQSGVEAFAGKEDIGKLKLVDVAGEGKPHALQLGSYAVIRVINQQALDDWLPVQEFDRVGKKIAGETNIMFDDLDFALNDWKVTENTQLRGGREGRNEITSLPLGLQWNLIEDQFFKHECDADNTILDEARLSAGWTKIAVFGIGASGVAHIIRVMSGAGLEMKSARLVGPRLCARIRQIVEEAKKNGILNARNISCAYEFAVCPFLCSISLDSKTRLDVEDLQPPLLKKFEEEIVKILEGAGKTLDKLDSVELIGFGMRVPIIRELIKFIFEAPTAAPNLFGDETIAKPKIALTHILIIKHYLKPRSRHKVKLYDNVSFWAELDVQGEDDIIVVNHAKSTVKVVLDDVKGVSFLENAKGINPSILILKLRNGEPKYDTTSDIVFRGFADDDTVPEEGLPDDCAKLKCLGLESPTYRVAEKTIDEGLKPEENEAKELIIKENKGSSSGESGVTNSSDVTEPDQLALDPANPSMDKTGSEERQNGVDEQMKNALTSNTGVSSGNGKLQELVELTEAAYTKRQIIEEEDGRSLLIQCTVICLEAKKKDRTLYDDEYGEGPYGEWPAVLAQRKAMSYQDECEAEFLEWFPSKSIKIKVVDRKMGADKDLKALSVEDAVSAEQATGQPLIESVLRKDDEKESE</span>
+
+**Replica 4:**
+
+Prompt 1 (Translation initiation factor):
+- <span style="color:purple">MAKEDCLEMQGTVLETLPNTMFRVELENGHVILAAISGKMRKNYIRILTGDKVKVDMTPYDLSKGRIVFRAK</span>
+
+Prompt 2 (Peptidyl-tRNA hydrolase):
+- <span style="color:purple">MKLIVGLGTNSDKNRPTRNTNVGFFYLDDLKSITPVQIKAKFNGLTRCGPKADEHVLIVDVKTPMNKNGNEQSMKFTDYFGPVDYISLVVIHDDVQIIDGKDKPFKVGKYRGPHLGIANILALIKSGRVRIVVSNLPKKGNHVINGVVGIDMDDWLNLVQDFKENNGLIFICGGSARHGVINRLKKKDGLFEAPDCFSEKLEEKMRKCDGDPAITLDPFEAVQF</span>
+
+Prompt 3 (tRNA-ribosyltransferase):
+- <span style="color:purple">MVNKPVRAVKIKTTKPVGKYIGSIVVPAGTFPMPPFMVPEITPTCKEKTPALIQLATSIGDIYTLHSWIRQAGNMIDHGELHMKKFMNWKALVTDSGGFFMVLSLRYHVDYGFHFQTNGSHFPLSSMFMSDSIIASIQAGMDNFGADIVFDWPYPAQTYEYMMNSLEWTDRCRRALGELIKATDKPHLKNFGYVQIGGIHVLRSEQSLRVLTLRDDSLFGVGVMGESKPYQNDFLWQVIPKTLPYNPLRYGRPMQAIERSIDAGIRMFDCIDPTLPPRLIATTGCHMTSREGRSVVSNRDYDRSFSPLDPKCDCYHCRGYIRCYVNHLFKAKEILGLPLWSDNTVYSLRDMIDRVQHFTVDGLKMEDLHNLFKGFVSEFRHHSAEKKGSE</span>
+
+Prompt 4 (Chaperonin GroEL):
+- <span style="color:purple">MAAKEVKFGNDARVKMLRGVNTLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAKEIELKDKFENMGAQMVKEIANKANDLAGDGTTTATVLAQSIINEGLKAVAAGMNPMDLKRGIDKAVIAAVANLKTLSVPCSDSKAIAQVATISANSVETVGKLKAEAMDKVGKEGVITVEEGSGLQDELDVVEGMQFDRGYLSPYFINKPDSGALELESPFILLVDKKISNIRELLAVLEAVAKSGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLSELGQAKRVVINKDTTTIIDGGGEEAQIRLRVAQIQAQIEDASSDYDKEKLQERVAKLSGGVAVIKVGAATEVEMKEKKARVEDALHATRACIEEGVVAGGGVALIRVAKKFADLQGSNEDQNVGVKVALRAMEAPLRQIVLNMGEEPSVVANTVKAGEGNYGYNAASGEYGDMIEYGILDPTKVTRSTLQYAASVAGLMITTEAMVAEMEPKD</span>
+
+Prompt 5 (Chaperone DnaK):
+- <span style="color:purple">MMNGTKKLNSWQIGAPGAFKDSGILPVVINRYQNTPTSAIVQAYRTERGIAAKSRNALKNPSSCFDIFRYDLKKVGRFNGEKNLVDYDTLPFVIAICYTKIKAEAEDYLGREIDEILVIPPMYFVSYKGRVVKKIKDKADVDVNRIIAEPSAAAIAYGLDSSNNAEMIVYDYGGGSIDVSIVEATENNDKYRAVEFDMGKSGLNNVLRKDARVRGKRDRDSSDPTYIALYNSGLALQEKVEEGVEIDEVNQDSLPLNNKNAIGMRKEKIELRRTTFSSLAKDLLEKTKEPMKKAFKEAGLTHEEVGEIVLVGGDMKIPAVVARVQETFQKTLLNLALDPEVVSLGSAIQGLVLYGNQIYINEDRLKPYVIPDGLNFNPDPDLSENLFIPRKSTILEGVFMGNLTAPIVHSFEPYSKEFPLGPNNGLLNLKLKSFIEFSTINENSVPPTTKDKFIGLCNDLSMSNARYKDAEPTDEKKHEENIVVEDEHSDSQAQLLQGREKIQKKCILNEEKKEKVKTELKKLESLVNPELRSKMTADEISGCLAKSKNALEKFQRKMTPKPEDGDEKRDFLKTKNSDNTEYFTFES</span>
+
+Each replica represents a different possible sequence design that maintains the desired functional properties specified in the input text description. The different replicas allow for exploration of sequence diversity while preserving the intended functionality.
 
-This stage will contain scripts and models for the ProteoScribe process. Check back for:
-- Configuration files
-- Model weights
-- Running instructions
-- Output examples
 
 ## Support
 
 For questions or issues:
 - Open an issue in this repository
-- Contact: [Your contact information]
+- Contact: [email protected]
 
 ---
 Repository maintained by the BioM3 Team